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Reptile responses to anthropogenic habitat modification: A global meta-analysis
Abstract
Aim
The aim was to determine how reptile populations respond to anthropogenic habitat modification and determine whether species traits and environmental factors influence such responses.
Location
Global.
Time period
1981–2018.
Major taxa studied
Squamata.
Methods
We compiled a database of 56 studies reporting how habitat modification affects reptile abundance and calculated standardized mean differences in abundance (Hedges’ g ). We used Bayesian meta‐analytical models to test whether responses to habitat modification depended on body size, clutch size, reproductive mode, habitat specialization, range size, disturbance type, vegetation type, temperature and precipitation.
Results
Based on 815 effect sizes from 376 species, we found an overall negative effect of habitat modification on reptile abundance (mean Hedges’ g = −0.43, 95% credible intervals = −0.61 to −0.26). Reptile abundance was, on average, one‐third lower in modified compared with unmodified habitats. Small range sizes and small clutch sizes were associated with more negative responses to habitat modification, although the responses were weak and the credible intervals overlapped zero. We detected no effects of body size, habitat specialization, reproductive mode (egg‐laying or live‐bearing), temperature or precipitation. Some families exhibited more negative responses than others, although overall there was no phylogenetic signal in the data. Mining had the most negative impacts on reptile abundance, followed by agriculture, grazing, plantations and patch size reduction, whereas the mean effect of logging was neutral.
Main conclusions
Habitat modification is a key cause of reptile population declines, although there is variability in responses both within and between species, families and vegetation types. The effect of disturbance type appeared to be related to the intensity of habitat modification. Ongoing development of environmentally sustainable practices that ameliorate anthropogenic impacts is urgently needed to prevent declines in reptile populations.
... This implies that the urban environment introduces novel and intricate selective pressures and consequently has a significant effect on animal populations. While many reptiles experience the negative effects of human-induced environmental changes, they are underrepresented in urban ecology research (Doherty et al. 2020). Ectothermic creatures demonstrate heightened sensitivity to their thermal environment, and the limited dispersal ability of reptiles makes them more vulnerable to habitat changes (Inman et al. 2023). ...
... The majority of research investigating the impact of urbanization on reptile populations suggests a decline in population size or species richness with urbanization. For instance, a worldwide meta-analysis, incorporating 56 studies on reptiles, revealed that the average reptile abundance is one-third lower in modified habitats compared to unmodified ones (Doherty et al. 2020). Besides this, Ackley et al. (2015a) discovered that the proportion of building cover within a 200-m diameter buffer had a significantly adverse effect on both lizard diversity and abundance. ...
... Given that previous findings indicated a negative correlation between urbanization and reptile abundance (Doherty et al. 2020) and developmental stability (Mészáros et al. 2023), attributed to the higher pollution rates (Tombesi et al. 2014), our first prediction was that at the landscape scale (i) urban land use cover would negatively, while; (ii) natural or semi-natural land cover would positively affect the abundance of dice snakes. We also predicted that; (iii) populations residing in larger settlements might experience heightened human disturbance due to a larger number of inhabitants and tourists resulting in decreased snake abundance. ...
Context
Human-induced landscape modification, such as urbanization, creates new environments that can have adverse effects on flora and fauna, posing threats to biodiversity. Understanding how reptiles respond to urbanization is crucial, especially in light of their ongoing population declines.
Objectives
We examined the influence of landscape-scale and local-scale urbanization features on the abundance of an aquatic snake species. Our investigation focused on dice snakes (Natrix tessellata) inhabiting a lake with a heavily urbanized shoreline.
Methods
We conducted visual encounter surveys at 25 study sites during the activity period of dice snakes around Lake Balaton in Hungary. We measured both landscape-scale and local-scale variables, including urban land use cover, vegetation cover, road cover, distance of main roads and city size, emergent vegetation cover and the area of artificial rock and concrete shoreline protection structures. We analysed snake survey data using N-mixture models to estimate abundance and examine relationships with landscape-scale and local-scale variables.
Results
Urban land use cover, road cover, the proximity of main roads and the extent of artificial rock and concrete shoreline protection structures positively affected the abundance of snakes. These findings imply that urban habitats may offer new ecological opportunities for dice snakes.
Conclusions
The findings of this study indicate that both landscape-scale and local-scale human-induced landscape modifications may have a positive impact on the abundance of urban snakes. Taken together, our findings suggest that urbanization is a complex phenomenon, affecting species at different levels and with subtle effects.
... It is essential to expand studies on urban cognition beyond mammals and birds, given that different taxonomic groups perceive and obtain information from their surroundings differently, and therefore, may respond in various ways to anthropogenic disturbance (Ficetola et al. 2007;French et al. 2018). Reptiles, for example, are in global decline directly due to anthropogenic pressures, which can impact them in different ways than birds or mammals, due to drastic differences in ecology and behavior (French et al. 2018;Doherty et al. 2020). Nonetheless, little research has been conducted toward understanding how reptiles might cope with anthropogenic disturbance and urban challenges (e.g., reviewed in French et al. 2018;Doherty et al. 2020), and even less has been done on exploring if and how cognitive performance can play a role for urban reptiles. ...
... Reptiles, for example, are in global decline directly due to anthropogenic pressures, which can impact them in different ways than birds or mammals, due to drastic differences in ecology and behavior (French et al. 2018;Doherty et al. 2020). Nonetheless, little research has been conducted toward understanding how reptiles might cope with anthropogenic disturbance and urban challenges (e.g., reviewed in French et al. 2018;Doherty et al. 2020), and even less has been done on exploring if and how cognitive performance can play a role for urban reptiles. In fact, to the best of our knowledge, only 2 studies have addressed the impact of urbanization on reptile cognition (Kang et al. 2018;Batabyal & Thaker 2019), although by now we acknowledge that reptiles have better cognitive abilities than previously believed. ...
... Lacertidae, the most common lizard family in Europe, is among the reptile families that globally suffer the most due to anthropogenic habitat modification (Doherty et al. 2020). However, different lacertid species can vary in their tolerance to anthropogenic environments, even when living in sympatry (Speybroeck et al. 2016). ...
Urbanization occurs at a global scale, imposing dramatic and abrupt environmental changes that lead to biodiversity loss. Yet, some animal species can handle these changes, and thrive in such artificial environments. One possible explanation is that urban individuals are equipped with better cognitive abilities, but most studies have focussed on birds and mammals and yielded varied results. Reptiles have received much less attention, despite some lizard species being common city dwellers. The Italian wall lizard, Podarcis siculus, and the common wall lizard, Podarcis muralis, are two successful lizards in anthropogenic habitats that thrive in urban locations.
To test for differences in a cognitive skill between urban and semi-natural environments, we investigated inhibitory control through a detour task in syntopic populations of the two species, across 249 lizards that were tested in partially artificial field settings. Sophisticated inhibitory control is considered essential for higher degrees of cognitive flexibility and other higher-level cognitive abilities. In this task, we confronted lizards with a transparent barrier, separating them from a desired shelter area which they could only reach by controlling their impulse of going straight and instead detour the barrier. We found no differences between lizards in urban and semi-natural environments, nor between species, but females overall performed better than males. Moreover, 48% of the lizards in our study did not perform a correct trial in any of the five trials, hinting at the difficulty of the task for these species. This study is among the first in addressing lizard cognition, through their inhibitory control, as a potential explanation for success in cities and highlights one should be careful with assuming that urban animals generally have enhanced cognitive performance, as it might be taxa, task or condition dependent.
... In reptiles, habitat loss is a leading cause of population declines globally (Gibbons et al. 2000;Böhm et al. 2013;Doherty et al. 2020), and Australia has one of the worst track records for threatened species (Ritchie et al. 2013). Of Australia's most threatened reptile taxa, invasive species (exotic weeds and predators) and agriculture are leading threats to the persistence of these taxa (Geyle et al. 2021). ...
... For example, the endangered swamp skink (Lissolepis coventryi) has suffered declines in population size and genetic diversity associated with fragmentation of its preferred dense wetland vegetation (Senior et al. 2022). Small ectotherms such as lizards generally have poor dispersal abilities, and thus make excellent models for evaluating the effects of habitat loss on populations at fine scales (Olsson and Shine 2003;Dubey and Shine 2010;Ackley et al. 2015;Doherty et al. 2020). ...
... Understanding population fragmentation and dispersal characteristics can assist with predicting the impact of habitat loss on vegetation-specialised fauna (Sato et al. 2014a;Doherty et al. 2020). The glossy grass skink (Pseudemoia rawlinsoni) is a small (adult snout-vent length up to ~65 mm) lizard that appears to specialise on densely vegetated wetland habitats, with a disjunct distribution across south-eastern Australia, including Tasmania and alpine regions of New South Wales and the Australian Capital Territory (Hutchinson and Donnellan 1988;Wilson and Swan 2021;Farquhar et al. 2023). ...
Context
Habitat loss and degradation are major drivers of biodiversity loss worldwide. In particular, wetland environments are being removed and degraded faster than any other terrestrial habitat on earth. The loss and degradation of wetlands has been particularly pronounced in south-eastern Australia.
Aims
Here we investigated the impact of habitat loss and degradation on the Data Deficient glossy grass skink (Pseudemoia rawlinsoni), a species that predominantly favours wetland vegetation in south-eastern Australia.
Methods
We established artificial cover-object (roofing tiles) survey grids in paired remnant and disturbed sites at six locations across Victoria, Australia, and surveyed for skinks between November 2021 and April 2022.
Key results
Sites at which glossy grass skinks occur are characterised by tall dense vegetation, with a high cover of matted biomass. Thermal profiles within these complex vegetation structures remain much cooler during hot days, and warmer during cold nights, than external temperatures. Nearby disturbed sites (i.e. grazed or mowed areas within dispersal distance of remnant sites) are generally devoid of skinks, have very low and structurally simple (open) vegetation, and have thermal regimes that offer lizards no respite from high summer temperatures. We found that roofing tiles are an effective way to survey for glossy grass skinks; even on cool cloudy days, the temperature of tiles, and the lizards sheltering beneath them, are often much higher than ambient temperatures.
Conclusions
These findings implicate habitat loss and degradation as having a substantial negative impact on glossy grass skink presence and abundance; skinks largely avoid disturbed areas, even at sites immediately adjacent to remnant habitat. This may be driven not simply by the removal of tall and dense vegetation structures, but the consequent loss of the optimal thermal buffer afforded by such structures.
Implications
Our study emphasises the threat that habitat loss and degradation pose to wetland species in Australia, and throughout the world.
... Consequently, the need for more land, whether residential, industrial, or agricultural, leads to the disturbance, transformation, and even destruction of habitats. How reptiles respond to changes in their habitats is dependent on several factors: disturbance type, microhabitat availability, and the ecology and physiology of a species (Masterson et al., 2009;Sasaki et al., 2016;Doherty et al., 2020). Consequently, habitat transformation can cause a decrease in species richness and abundances of persisting species (Santelmann et al., 2006;Masterson et al., 2009;De Solan et al., 2019). ...
... The effects of grazing on grassland reptile species varies with grazing intensity Howland et al., 2014;Neilly et al., 2018;Doherty et al., 2020). A relation of reptile assemblages to different livestock stocking strategies, and therefore grazing intensity, found that when stocking rates are managed sustainably, reptile communities may be unaffected, but the converse was true when stocking rates were high (Neilly et al., 2018). ...
... Although habitat transformation is known to generally have a negative impact on reptile populations, the impact caused by mine-altered habitats appears to be particularly severe (Doherty et al., 2020). Mining is known to cause changes to habitat structure, not only through the physical alteration (destruction) of habitats, but also through contaminants in the soil and water (Sasaki et al., 2015). ...
Climate change and habitat transformation are some of the primary threats that reptiles face as a consequence of persisting in their selected habitats. Some species, such as habitat specialists, may be particularly vulnerable to these threats given their restricted geographic ranges, strict habitat requirements, and limited dispersal abilities. Knowledge of the factors that drive habitat and microhabitat selection by a species, the impact that habitat transformation may have on that species, and how the species is expected to respond to climate change is necessary for informing conservation management strategies.
Smaug giganteus (the sungazer) is a threatened (Vulnerable), habitat specialist lizard that is endemic to the Highveld grasslands of South Africa. Unfortunately, suitable habitat exists in a landscape where anthropogenic activities (e.g., agriculture and mining) are prevalent, and a major threat that sungazers face is habitat transformation and fragmentation. Sungazers are unique within their family (Cordylidae) in that they rely on self-constructed burrows in specific microhabitats within the grassland matrix as long-term, often permanent, shelter and refuge sites. Because of this, aspects of their life history, and the current threats that they face, sungazers may be particularly vulnerable to the combined effects of climate change and habitat transformation. The primary aim of this thesis was to assess the consequences of habitat selection and use by sungazers by investigating the potential impact of climate change
on habitat suitability for the species, the fine-scale impacts of habitat transformation, and to identify the microhabitat requirements by sungazers such that recommendations for future conservation management of the species could be made.
The potential impact of climate change on habitat suitability for sungazers was assessed by projecting their current ecological niche envelope into the future, under different climate change scenarios. The models predicted that sungazers may experience minor range contractions under the moderate case scenario, but vulnerability to climate change increased under the worst-case scenario. At the broadscale level, the models predicted that sungazers would shift their geographic range to the southwest. However, given the species life history traits, limited dispersal capacity, and the fragmented habitat in which subpopulations exist, climate tracking is unlikely, and sungazers may be more vulnerable to the effects of climate change than predicted by niche models.
An assessment of the demographics and dynamics of four sungazer subpopulations existing at sites with different habitat conditions revealed that the impact of habitat transformation on sungazers may be more devasting than what was previously reported. In this study, the sungazer subpopulations existing in habitats transformed by mining activities, and severe overgrazing have declined by more than 50% over a 16-year period. This assessment at the subpopulation level (colony level) suggests that the current size of the sungazer population is probably an overestimate.
A comparison between the microhabitat characteristics surrounding sungazer burrows and random sites in the landscape revealed that sungazers use microhabitats comprised of low vegetation cover and short grasses in which to construct their burrows. Burrow construction in these microhabitats generally occurs on northerly facing slopes. When constructing their burrows, sungazers tend to orientate burrow entrances in the same direction as the aspect of the slope but northerly directions are preferred.
This thesis provides the first insights into the potential effects that climate change may have on sungazers in the future and highlights the severity of impact that habitat transformation has on sungazers at fine spatial scales. The findings not only justify the importance of conservation management for sungazers but provide critical information to assist with future conservation protocols.
... Despite this diversity, there is limited knowledge of the ecology, distributions, and population trends for most species (Tingley et al., 2019;Chapple et al., 2021;Senior et al., 2021), and few studies have explicitly focused on heathy woodland communities (but see Friend, 1993;Lindenmayer et al., 2008;Ensbey et al., 2023). As ectotherms, reptiles have fundamentally different traits and life history strategies from other vertebrates, and therefore may also be expected to respond differently to disturbances (Doherty et al., 2020;Van Dyke et al., 2021). Reptiles are expected to be vulnerable to both fire and landscape structure due to their relatively low dispersal ability, small home ranges, energy use, and thermoregulatory strategies (Böhm et al., 2013;Tingley et al., 2019;Doherty et al., 2020;Mulhall et al., 2022). ...
... As ectotherms, reptiles have fundamentally different traits and life history strategies from other vertebrates, and therefore may also be expected to respond differently to disturbances (Doherty et al., 2020;Van Dyke et al., 2021). Reptiles are expected to be vulnerable to both fire and landscape structure due to their relatively low dispersal ability, small home ranges, energy use, and thermoregulatory strategies (Böhm et al., 2013;Tingley et al., 2019;Doherty et al., 2020;Mulhall et al., 2022). Furthermore, many reptiles are closely associated with elements of habitat structure that may be affected by fire, such as leaf litter, canopy cover, and understorey cover (Caughley, 1985;Driscoll and Henderson, 2008;Elzer et al., 2013;Infante et al., 2021). ...
... Indeed, a recent review found that fire is a threat to 43% of Australian squamates of conservation concern (Santos et al., 2022). Habitat loss and modification has been found to have a primarily negative effect on reptile abundance (Doherty et al., 2020), with agriculture amongst the most common sources of threat in Australia (Tingley et al., 2019) and worldwide (Böhm et al., 2013;Cox et al., 2022). Selective loss of habitats in southeastern Australia, including native woodlands and grasslands, has disproportionately impacted certain taxa, including fossorial reptiles (Brown et al., 2008). ...
Land use changes, such as the development of agriculture and plantation forestry, and altered fire regimes, are major drivers of biodiversity loss worldwide, influencing the availability of suitable habitat for species. Reptiles are sensitive to both these processes as they are influenced by native vegetation extent and habitat structure. While much is known about the independent effects of fire and land use change on species distributions, few studies have investigated potential interactive effects; specifically, whether the influence of site-scale variables on reptiles depends on the properties of the surrounding landscape. We sampled reptiles at 107 sites in fire-prone heathy woodland, interspersed with plantation forestry and agriculture in south-west Victoria, Australia. We investigated the responses of seven reptile species to both site-scale variables (time since fire and several measures of habitat structure) and landscape-scale variables (extent of native vegetation and plantations and the presence of pasture within a 3.14 square km area) to 1) identify whether species’ responses to fire and habitat depended on landscape structure, and 2) examine the relative influence of time since fire, habitat structure and landscape structure on reptile abundance. We predicted that responses to site-scale variables would vary with a key landscape structure variable: the amount of native vegetation cover. Further, we predicted that site-scale variables would be stronger predictors of species abundance than landscape-scale variables. Generalised linear models, accounting for imperfect detection, were used to estimate species responses to site and landscape-scale predictors. For two species (Amphibolurus muricatus and Liopholis whitii) there was evidence that their responses to site-scale variables depended on landscape structure. However, contrary to our first prediction, native vegetation cover was not the only landscape structure variable that influenced species’ responses to site-scale variables. Three species (Acritoscincus duperreyi, A. muricatus, and Lerista bougainvillii) responded to both habitat structure and landscape structure variables, though the relative influence of the variables at the different scales was varied among the species. One species (Lampropholis guichenoti) responded to fire and habitat structure variables at the site-scale but did not respond to landscape structure. One species (Aprasia striolata) responded to landscape structure variables but not to site-scale variables. Our second prediction, that site-scale variables would be the strongest predictors of abundance, was true for two species, but overall, our results were varied, with species responding at both scales. Examining species' responses to drivers at multiple spatial scales is essential for conservation management, as even species with low dispersal capacity such as reptiles can respond to processes occurring at large spatial scales.
... The decline in reptiles increased sharply after the 1970s (Alroy 2015) due to habitat loss derived from agricultural expansion (Böhm et al. 2013). However, they are the most underrepresented vertebrates in studies analyzing the effects of landscape changes on community diversity, especially in non-forest ecoregions such as the Cerrado (Doherty et al. 2020;Teixido et al. 2020Teixido et al. , 2021López-Bedoya et al. 2022;Tan et al. 2023). The Brazilian Cerrado ecoregion is one of the world's hotspots of biodiversity (Myers et al. 2000), with more than 290 species of Squamata reptiles (Nogueira et al. 2011Azevedo et al. 2016). ...
... We found that lizards showed lower abundance and observed species richness in landscapes with higher percentages of agricultural cover. The conversion of natural vegetation into agricultural areas (e.g., crop and pasturelands) is a limiting factor of lizards' population size and species richness in several countries worldwide (Ribeiro et al. 2009;Ghosh and Basu 2020;López-Bedoya et al. 2022;Băncilă Fig (Jenkins et al. 2014;Palmeirim et al. 2017a;Falaschi et al. 2019;Doherty et al. 2020;Teixeira et al. 2022). This pattern is associated with reptiles' limited dispersal abilities (Jellinek et al. 2014;Guiller et al. 2022), sensibility to vegetation type and structure (Santos et al. 2016;Rotem and Ziv 2016;Rotem et al. 2020;Iglesias-Carrasco et al. 2022), and shape and size of remaining habitats (Jellinek et al. 2014;Ramírez et al. 2023). ...
Context
Changes in landscapes due to the conversion of natural vegetation into agroecosystems are causing an alarming and rapid loss of biodiversity on a global scale.
Objectives
We assess how local environmental factors and landscape structure influence Squamata reptiles’ abundance, and alpha and beta diversities in agricultural landscapes in the Brazilian Cerrado.
Methods
We sampled 20 sites using active visual search and pitfall traps to record Squamata reptiles’ abundance and richness. For each sampling site, we measured seven variables of vegetation structure at local scale and calculated four landscape metrics at five spatial scales.
Results
We recorded 145 individuals of 30 Squamata species comprising 15 lizards, 12 snakes, and three amphisbaenians. Agriculture cover had a negative effect on lizards’ abundance and richness. No effect was found on the abundance and richness of snakes. Species turnover was the major process responsible for Squamata reptile dissimilarity among sites. Reptile total beta diversity and species turnover were influenced by variations in the number of trees at the local scale.
Conclusions
Our results highlight the negative effects of agriculture expansion on species abundance and richness in lizard communities. Moreover, vegetation structure may act as an environmental filter and predict the variation in Squamata reptiles’ species turnover between sites. Our findings show that maintaining well-preserved patches of natural vegetation in agricultural landscapes is of utmost importance for Squamata reptiles’ conservation and should be considered in landscape conservation and management design.
... The habitat where the new species was found appears to be intact and stable, but the threat of future habitat fragmentation within the region looms, which could have negative effects on the range-restricted gecko species. This is well illustrated by the global meta-analysis on the response of reptiles to anthropogenic habitat modification, which showed that on average, reptile abundance was one-third lower in modified habitat compared with unmodified habitats (Doherty et al. 2020). Additionally, mining was shown to have the most negative impacts on reptile abundance, followed by agriculture, grazing, plantations and patch size reduction (Doherty et al. 2020). ...
... This is well illustrated by the global meta-analysis on the response of reptiles to anthropogenic habitat modification, which showed that on average, reptile abundance was one-third lower in modified habitat compared with unmodified habitats (Doherty et al. 2020). Additionally, mining was shown to have the most negative impacts on reptile abundance, followed by agriculture, grazing, plantations and patch size reduction (Doherty et al. 2020). Current mining activity within the area and the prospect of more mining operations in the future (Smit 2024), thus poses the biggest threat to the species moving forward. ...
The genus Goggia is composed of ten small bodied leaf-toed gecko species endemic to South Africa and adjacent Namibia. Using a combination of phylogenetic and morphological analyses we assessed the taxonomic status of an isolated rupicolous population discovered south of Klein Pella in the Northern Cape Province of South Africa. The newly collected material was recovered as a well supported clade by two independent phylogenetic algorithms (maximum likelihood and Bayesian inference), with little intraspecies structuring. While the particular interspecific relationships among closely related Goggia remain unresolved, the phylogenetic results suggest the novel material is related to G. rupicola, G. gemmula, G. incognita and G. matzikamaensis. This is supported by the similar ecologies (rupicolous lifestyle), geographies (arid western extent of South Africa) and morphologies (prominent dorsal chevrons and yellow-centred pale dorsal spots), which are shared among these closely related species. Despite their similarity, the novel population from Klein Pella remains geographically separate, differs from congeners by an uncorrected ND2 p-distance of 11.03-22.91%, and is morphologically diagnosable. Based on these findings we describe the Klein Pella population as a new species.
... While a recent meta-analysis demonstrated that native reptile abundance was lower in monoculture plantations in the tropics (López-Bedoyaa et al. 2022), another did not find any effect of plantations on squamate abundance (Doherty et al. 2020). Most studies included in the meta-analysis were from the Americas, with poor representation from the Asian tropics, which harbour distinct reptilian lineages. ...
... Previous meta-analyses have reported neutral or negative impacts of plantations on reptilian abundances in the tropics (Doherty et al. 2020;López-Bedoya et al. 2022). Our study found significantly lower densities in cashew plantations compared to low-elevation forests, but densities in rubber plantations were not significantly different from those in forests. ...
Low-elevation wet tropical forests support herpetofaunal diversity but are increasingly replaced by monoculture tree plantations and have poor Protected Area coverage, leaving herpetofauna vulnerable. Research on how monoculture plantations affect reptile populations remains inconclusive, and the ecology of endemic species in these changing landscapes is poorly understood. We compared densities and roosting ecology of Monilesaurus rouxii, an endemic agamid lizard, across low- and high-elevation forests and cashew and rubber plantations in the Western Ghats Biodiversity Hotspot using nocturnal transects. We found that low-elevation forests, despite poor Protected Area coverage, had significantly higher densities of Monilesaurus rouxii than high-elevation forests and cashew plantations. Roost site use did not differ significantly across the different land-use, indicating roost fidelity. However, Monilesaurus rouxii exhibited ontogenetic shifts in roosting substrate and height. Our findings highlight the conservation importance of unprotected low-elevation forests, which are rapidly being converted to monoculture tree plantations. We show that plantation types may differ in their impacts on reptile populations. We also show the utility of nocturnal transects for population estimation of diurnal lizards.
... Generally, landscape changes are associated negatively with amphibians and reptiles since deforestation alters the structure and functions of forest, resulting in less species of these two groups (Cordier et al. 2021). Fragmentation negatively affects amphibians and reptiles (Teixido et al. 2021), and landscapes changes reduce amphibians diversity (Doherty et al. 2020;Oro et al. 2024). This may explain the decrease in roadkill for these groups in sections with more Farming. ...
... The Urban area was identified in all models, with a negative relation with amphibians and a positive relation with the other three groups. This is expected for amphibians because the group commonly reduces with landscape change (Doherty et al. 2020;Oro et al. 2024). Since birds, mammals, and reptiles are not associated with Forest areas, according to our results, it is necessary to understand how cities can influence roadkill. ...
Roadkill poses a critical threat to wildlife and can cause the extinction of local populations. In this context, analyzing roadkill patterns could provide valuable insight into the severity of the threat, particularly in protected areas. We collected roadkill data for 16 months around the Chapada Diamantina National Park (PNCD) in Bahia, Brazil, to study the spatiotemporal distribution of roadkill across different tourist and climatic seasons. Moreover, the influence of landscape and highway characteristics on roadkill hotspots was analyzed, as well as their association with the protected area. In all, 580 roadkill consisting of 182 amphibians (31.4%), 185 reptiles (32.0%), 143 birds (24.6%), and 70 mammals (12.0%) were recorded. Of the sample, five species of amphibians, 20 species of reptiles, 36 species of birds, and 14 species of mammals were identified. The abundance and richness of roadkill were not statistically different between seasons. However, only herpetofauna richness and abundance for the amphibians (richness: p = 0.0053; W = 826, abundance: p = 0.000956; W = 754) and reptiles (richness: p = 0.0000259; W = 595, abundance: p = 0.00000165; W = 512) were statistically different and greater in the rainy season. The aggregation and number of roadkill hotspots change for each taxonomic group, which reveals that different variables are influencing this process. Most roadkill hotspots were outside the PNCD, and less than 30% of all roadkill hotspots were inside the PNCD. We emphasize the importance of analyzing the taxonomic groups separately to obtain better estimates and results and better understand the influence of roadkill on protected areas.
... Similarly, Perumal et al. (2021) also found that roads within protected areas are no different in their level of protection to species than areas outside of protection. However, regardless of body size category or location, roads are still considered to be a significant and continually growing threat to the safety of both humans and wildlife (Forman and Alexander, 1998;Van der Ree et al., 2015;Collinson et al., 2019), with anthropogenic driven habitat change in general being one of the greatest threats to biodiversity globally (Almeida-Rocha et al., 2020;Doherty et al., 2020;Prakash and Verma, 2022). However, despite this, of the 106 species identified in our study, only 26 had habitat change or road-related issues listed as threats to species at an international level and only 22 listed these issues as threats locally ( Supplementary Information Table S5). ...
... This drastic increase in recorded mortalities is likely because of two factors: the taxa included and the survey length. As is the case with most road ecology studies (Gardner et al., 2007;Tingley et al., 2016;Doherty et al., 2020;Tipton et al., 2023), studies from the African continent did not include all terrestrial vertebrate taxa, either excluding amphibians (Drews, 1995;Lala et al., 2021;Mulualem et al., 2023), only focusing on birds and mammals (Lyamuya et al., 2021), large mammals (Gandiwa et al., 2020) or single species (Naciri et al., 2023). Additionally, our study had 240 surveys conducted over 120 days across two consecutive years, with 12 surveys per month. ...
Anthropogenic change is a global threat to wildlife and the biosphere’s health. Wildlife faces growing threats from anthropogenic activities, especially infrastructure. Protected areas (PAs) are not exempt, particularly those that experience high traffic volumes on public road passages both within and on their peripheries. Globally, studies have found that public roads in PAs cause large numbers of wildlife-vehicle collisions (WVCs), threatening the stability of these wildlife refugia. As vehicle traffic density is increasing globally, particularly in Africa, where little research on the ecological impact of linear infrastructure has been done, the impact of roads on wildlife in protected areas must be determined. We determined the effect of public roads on vertebrate mortalities in the protected areas of Hluhluwe-iMfolozi Park (HiP) and iSimangaliso Wetland Park (ISWP), KwaZulu-Natal Province, South Africa, collected monthly in 2022 and 2023. Species composition of vertebrate mortalities, and heat maps of mortalities, combined with a suite of ecological factors, were used to identify drivers of wildlife-vehicle collisions. A total of 1606 road
mortalities were recorded, with small-bodied vertebrates (< 5 kg) comprising most of the identified species. Amphibians experienced the highest number of mortalities, 1066 individuals, while birds had the highest species diversity in the mortality record with 31 identified species. High mortality levels were concentrated in areas with unsloped road surfaces and increased vehicle traffic within HiP, while the surrounding habitat had a larger influence on mortalities within ISWP. Our results showed that intervention is needed along portions of the two public roads in both protected areas, particularly during the wet season, with mortality rates as high as 13 carcasses per km. Mitigation measures should be implemented to reduce the number of wildlife
mortalities along the roads in both locations, with specific measures to mitigate small vertebrate road mortalities. All planned mitigation measures should focus on the sections identified as high mortalities zones.
... For example, some studies have identified broad-scale commonalities in trait responses to anthropogenic impacts, such as shifts to smallerbodied birds (Richards, Cooke, and Bates 2021) and mammals (McCain and King 2014). However, many other studies show no consistent broad-scale trait responses, such as in fishes (Brumm, Infante, and Cooper 2023), reptiles (Doherty et al. 2020), freshwater invertebrates (Hamilton et al. 2020;Statzner and Bêche 2010) and terrestrial invertebrates (Bartomeus et al. 2018;Tordoff et al. 2022). This variability may reflect limitations in analysed traits. ...
... 'Biological traits' sensu Usseglio-Polatera et al. (2000) are measures representing inherent taxon-specific attributes (e.g., body size, life history or feeding morphology), which can have clearer links to ecosystem processes (Verberk, van Noordwijk, and Hildrew 2013), such as feeding traits influencing energy transfer (Hébert, Beisner, and Maranger 2017). Both ecological and biological traits are often hypothesised to respond consistently to anthropogenic impacts (Statzner and Bêche 2010;Doherty et al. 2020), given that they reflect preferences for and adaptations to prevailing environmental conditions, respectively. However, differences in how these two trait groups are measured could influence their response consistency. ...
Aim
To determine which riverine invertebrate traits respond consistently to anthropogenic impacts across multiple biogeographic regions.
Location
Europe.
Time Period
1981–2021.
Major Taxa Studied
Riverine invertebrates.
Methods
We compiled a database of riverine invertebrate community time series for 673 sites across six European countries spanning six freshwater ecoregions. We compared trait responses to anthropogenic impacts (quantified as changes in ‘ecological quality’) among regions for seven ‘ecological’ traits, which reflect habitat preferences, and nine ‘biological’ traits (e.g., morphology or life history), which represent taxon‐specific attributes that can influence ecosystem processes.
Results
Four ecological traits (current, microhabitat, salinity and trophic preferences) and one biological trait (dispersal mode) responded consistently across regions. These responses were primarily driven by spatial differences among poorer to better quality sites. Responses to temporal changes in quality were comparable but less pronounced.
Main Conclusions
Consistent responses to anthropogenic impacts across multiple ecological traits indicate these traits may improve broader scale measurements, comparisons and predictions of community responses. However, we could not use ecological traits to identify the actions of specific stressors because multiple traits always responded as a group. Inconsistent responses across almost all biological traits indicated that these traits may be less predictive of impacts across regions. Predictions of how biological traits, and associated ecosystem processes, respond to anthropogenic impacts may be most effective at regional scales where responses are more consistent.
... Hillman et al., 2014), have uncovered varied patterns. For instance, urban areas and roads negatively affect connectivity between populations, reducing the distribution range, abundance and dispersal of lizards, whereas agricultural areas can exert both negative and positive effects (Beninde et al., 2016(Beninde et al., , 2018Doherty et al., 2020Doherty et al., , 2021. Lizards of the genus Sceloporus have been frequently used as study models; for example, Orton et al. (2020) found that dispersal and connectivity of S. woodi populations were facilitated by human-created sand corridors, while Trumbo et al. (2021) established that connectivity between populations of S. occidentalis becki increased after the eradication of livestock and the recovery of native vegetation, facilitated by tree canopy and shrubland cover. ...
... grammicus is not significantly affected by the anthropized landscapes we assessed, this is not the case for many lizards, which are susceptible to land use changes and habitat loss (Doherty et al., 2020;Paterson et al., 2021;Wolf et al., 2013). Besides, climate change, because of various anthropogenic activities, is another factor that puts lizards at risk. ...
Functional connectivity, the extent to which a landscape facilitates or impedes the dispersal of individuals across the landscape, is a key factor for the survival of species. Anthropogenic activities, such as urbanization, agriculture and roads, negatively impact functional connectivity of most species, particularly low-vagility species like lizards. Here, we examine how a landscape modified by anthropogenic activities affects the functional connectivity, at both broad and fine scales, of a widely distributed generalist lizard Sceloporus grammicus in the eastern Trans-Mexican Volcanic Belt, Mexico. We estimated for the first time the species' genetic structure, gene flow and functional connectivity in agricultural and forest zones using genomic data, a comprehensive landscape characterization and novel methods including gravity models. Our results showed not only marked genetic differentiation across the study region but also that functional connectivity is maintained for tens of kilometres despite S. gram-micus low vagility. Specifically, we found that substrate and air temperature facilitated connectivity over broad and fine scales, respectively, while agricultural cover, relative humidity and slope were important for connectivity and gene flow. Contrastingly, forest cover and roads favoured (broad-scale) and limited (fine-scale) connectivity, likely associated with movement facilitated by small forest patches and with thermoregula-tion. Altogether, these results support that S. grammicus alternates its thermoregula-tory behaviour depending on the distance travelled and the habitat environmental conditions, and that it can disperse through relatively modified landscapes, mainly using agricultural zones. The information obtained is crucial to understanding the response of lizards to current anthropogenic pressures and their potential to adapt. K E Y W O R D S functional connectivity,
... W hereas many reptile populations have been monitored in order to analyse their demography (e.g. Guiller et al., 2022;Kusrini et al., 2022), quantitative data on reptiles living in anthropised landscapes, especially at the level of the individual, are still limited (French et al., 2018;Doherty et al., 2020). For example, since reptiles have a limited ability for dispersal and relatively small home ranges, they are more likely to be exposed to increased risk of population decline and collapse due to habitat modifications (Doherty et al., 2020;Guiller et al., 2022). ...
... Guiller et al., 2022;Kusrini et al., 2022), quantitative data on reptiles living in anthropised landscapes, especially at the level of the individual, are still limited (French et al., 2018;Doherty et al., 2020). For example, since reptiles have a limited ability for dispersal and relatively small home ranges, they are more likely to be exposed to increased risk of population decline and collapse due to habitat modifications (Doherty et al., 2020;Guiller et al., 2022). One species that thrives in urban areas is the European wall lizard Podarcis muralis (e.g. ...
Urbanisation impacts on both abiotic and biotic characteristics of the environment and is likely to bring new selective pressures on animal species living within these areas. The common European wall lizard Podarcis muralis adapts well to urbanisation and indeed may be described as the archetypical urban lizard. In this paper we investigated some aspects of the demography of two populations of P. muralis from western France, one living in a hedgerow system situated in an agricultural area on the edge of a village and a second in an urban garden. The active year in both populations was from February-March until October-December, the latter in the urban garden where temperatures were higher. Numbers decreased from around June then increased again during September but this varied annually and between populations. Diversity and equality indexes for both populations were high, especially in females, indicating a range of individuals and their frequency of presence. Both populations were therefore stable despite only limited numbers of lizards being present for more than one year. Male lizards with high presence were more frequently seen in the company of females than males that were seen less frequently. Hatchling lizards were seen from June after the spring mating period with a second period of hatchlings appearing during autumn. This supports the notion that females annually deposit two clutches of eggs in the area.
... For example, the Amur tiger (Panthera tigris altaica), whose habitat has been severely fragmented by human activities, must cross busy roads and populated areas to reach favoured habitat patches, increasing their energy expenditure and risking human-wildlife conflict [28]. Disturbance can also introduce sublethal effects for animals, disrupting or altering other processes such as predator-prey interactions, genetic connectivity, and disease transmission [9,29,30]. Changes in movement patterns due to disturbance can also negatively affect fitness or breeding success, sometimes requiring more energy than in natural habitats to avoid increased threats or to search for scarce resources [10,31,32]. The presence of habitats which are attractive (e.g., offer shelter), but do not offer all required resources-or increase other threats to the animal-may lead to an ecological trap [33][34][35]. ...
... Selection above or below this line reflects the relative selection strength being higher or lower than the median or mean energy requirements during this time. Anthropogenic landscape disturbances, like mining, can reduce the abundance of potential prey species such as reptiles [30,138,139], mammals [140,141], birds [142], invertebrates [143,144], and vegetation [145], meaning that disturbed mining habitats may not satisfy the high resource requirements of quolls during breeding season [31]. ...
Background
Efficient movement and energy expenditure are vital for animal survival. Human disturbance can alter animal movement due to changes in resource availability and threats. Some animals can exploit anthropogenic disturbances for more efficient movement, while others face restricted or inefficient movement due to fragmentation of high-resource habitats, and risks associated with disturbed habitats. Mining, a major anthropogenic disturbance, removes natural habitats, introduces new landscape features, and alters resource distribution in the landscape. This study investigates the effect of mining on the movement of an endangered mesopredator, the northern quoll (Dasyurus hallucatus). Using GPS collars and accelerometers, we investigate their habitat selection and energy expenditure in an active mining landscape, to determine the effects of this disturbance on northern quolls.
Methods
We fit northern quolls with GPS collars and accelerometers during breeding and non-breeding season at an active mine site in the Pilbara region of Western Australia. We investigated broad-scale movement by calculating the movement ranges of quolls using utilisation distributions at the 95% isopleth, and compared habitat types and environmental characteristics within observed movement ranges to the available landscape. We investigated fine-scale movement by quolls with integrated step selection functions, assessing the relative selection strength for each habitat covariate. Finally, we used piecewise structural equation modelling to analyse the influence of each habitat covariate on northern quoll energy expenditure.
Results
At the broad scale, northern quolls predominantly used rugged, rocky habitats, and used mining habitats in proportion to their availability. However, at the fine scale, habitat use varied between breeding and non-breeding seasons. During the breeding season, quolls notably avoided mining habitats, whereas in the non-breeding season, they frequented mining habitats equally to rocky and riparian habitats, albeit at a higher energetic cost.
Conclusion
Mining impacts northern quolls by fragmenting favoured rocky habitats, increasing energy expenditure, and potentially impacting breeding dispersal. While mining habitats might offer limited resource opportunities in the non-breeding season, conservation efforts during active mining, including the creation of movement corridors and progressive habitat restoration would likely be useful. However, prioritising the preservation of natural rocky and riparian habitats in mining landscapes is vital for northern quoll conservation.
... Urbanization has been shown to reduce wildlife presence and cause habitat fragmentation, while snakebite incidence is higher in rural and isolated communities. [28][29][30] Snakebite was shown to be influenced by land use and change factors. Changes in the natural land cover can increase snakebite in areas without the health infrastructure to deal with it. ...
Objetivo: este estudo teve como objetivo identificar fatores de uso e cobertura de terra que afetam a incidência e a ocorrência de acidentes ofídicos. Métodos: foi realizada uma revisão sistemática utilizando estudos publicados nas bases ScienceDirect, Scopus, PubMed e Web of Science entre 2012 e 2022. Resultados: um total de 883 estudos foi obtido; desses, cinco publicações foram selecionadas após a leitura completa, todas realizadas no Brasil. Foram encontradas 13 variáveis diferentes, e a maioria relacionada à cobertura natural da terra. A cobertura vegetal foi a variável mais estudada, com seus efeitos dependendo das características ecológicas da serpente envolvida na picada. Variáveis relacionadas à urbanização e à densidade populacional foram identificadas como negativamente relacionadas com as picadas de cobra, enquanto a agricultura demonstrou ter uma associação positiva, assim como todas as variáveis relacionadas à atividade agrícola. Conclusão: alterações no uso e cobertura da terra têm impactos no ofidismo, no entanto, estudos retrospectivos sobre o assunto são escassos.
... Reptiles are among the most threatened groups of vertebrates globally, with habitat loss and fragmentation being major drivers of their current decline [24]. Agricultural intensification, which often involves the removal of natural vegetation, the use of pesticides added to the indirect loss of prey, and the simplification of landscape structure, has been shown to negatively impact biodiversity as a whole [25] and reptiles in particular [26]. However, low-intensity farming systems, which mimic natural habitats and maintain structural complexity, can provide suitable conditions for reptiles, indicating that semi-natural patches of traditional cultural landscape can support diverse reptile communities, particularly when they are embedded in a heterogeneous landscape with patches of natural vegetation (e.g., [11]). ...
Agricultural expansion and intensification are major drivers of biodiversity loss, particularly through habitat fragmentation. In the Mediterranean region, traditional farming systems like olive groves have historically supported biodiversity by creating heterogeneous landscapes. This study evaluates the role of olive groves in maintaining ecological connectivity for reptiles in Liguria, Italy. Using a dataset of 5211 georeferenced reptile records and habitat suitability models, we constructed taxon-specific resistance maps and applied circuit theory to model landscape-scale connectivity. We addressed three key questions: (1) Do olive groves act as barriers to reptile movement? (2) Do olive groves provide connectivity levels comparable to those of natural habitats? (3) Do olive groves serve as corridors connecting protected areas? Our results indicate that olive groves do not impede reptile movement, with normalized current flow (NCF) values close to 1, similar to those of natural habitats. Additionally, olive groves frequently intersect with least-cost paths between protected areas, highlighting their role as connectivity corridors. These findings underscore the conservation value of traditional olive groves in fragmented landscapes. By integrating these agroecosystems into regional conservation strategies, we can enhance biodiversity while supporting sustainable agriculture. This study provides critical insights for land management practices that balance ecological and agricultural priorities.
... Reptiles and amphibians are among the most threatened vertebrates globally (Araújo et al., 2006;Cox et al., 2022;Gibbons et al., 2000;Luedtke et al., 2023). In the tropics, these ectotherms often have small distributions and low dispersal capacities, and are particularly vulnerable to habitat fragmentation and change in microclimate conditions due to climate change (Araújo et al., 2006;Cox et al., 2022;Doherty et al., 2020;Gibbons et al., 2000;Moore et al., 2018;Nowakowski et al., 2018). Rapid changes in climate in the next decades are notably expected to adversely affect amphibians and reptiles in South-East Asia, with high predicted impact in Cambodia (Bickford et al., 2010). ...
Suggested citation:
Van Berkel, T., Dezetter, M., Hamer, M., Merckx, J., Suanjak, M., Sao, S., Tranchant, J., van Noppen,M., Eam, S.U., Jocque, M. (2024). The Mekong Project: a biological assessment of two wildlifesanctuaries in Kratie Province, Cambodia. BES Report 12.1 (26 January 2025). Biodiversity Inventoryfor Conservation. Glabbeek, Belgium pp. 102.
... Studies on certain reptiles suggest that positive anthropogenic influences may influence size, as urban lizards may be larger than their non-urban counterparts [35]. Other studies show that anthropogenic influences may have a neutral effect [36]. Another parameter to consider is food availability. ...
Stressors such as injuries, embryonic instability during development, and higher levels of stress hormones such as testosterone can result in increases in fluctuating asymmetry in reptiles and other vertebrates. Digit asymmetry, digit ratio variability, and skull trait asymmetry such as eye and jaw size have been correlated with stress level in both snakes and lizards. Teeth asymmetry has also been used as a biomarker for stress and brain laterality. Body size is correlated with many potential stressors, yet there has been little research on how body size in reptiles relates to asymmetry. We investigate teeth asymmetry within the lizard family Varanidae, a clade with a diverse range of sizes consisting of the largest living lizard, Varanus komodoensis. Using a landmark/semi-landmark analysis, we derived Centroid Size for 671 pairs of teeth from 13 varanid species, and asymmetry was derived for each pair. Right-biased asymmetry was significantly greater in the upper tooth row, but breaking up tooth positions into further sections did not yield a significant difference. We found a significant positive linear correlation between body size and right-biased teeth directional asymmetry within Varanus, but only when excluding V. komodoensis. This significant correlation may result from fewer potential predators and more potential food items, thus resulting in less overall stress. When analyzed separately, V. komodoensis individuals with <180 mm head length demonstrated a positive, yet non-significant, trend along a similar trajectory to their congenerics with a high goodness of fit. On the other hand, individuals > 180 mm showed a high degree of scatter, with several specimens having pronounced left-biased asymmetry. We suspect that this dramatic change was due to a combination of ontogenetic niche shift, bigger home ranges, a greater susceptibility to negative anthropogenic influences, and/or a male bias in the bigger specimens sampled, but a larger sample size is required to determine if there is statistical significance in these intra-specific trends. Body asymmetry can reflect brain laterality, which may be a potential driver for the teeth asymmetry seen here.
... Although not statistically significant, a recent meta-analysis of reptile responses to anthropogenic disturbance found that the greatest negative effect size was in forest and the least was in grassland (Doherty et al. 2020). Results of meta-analyses are typically confounded by a high level of uncontrolled variation in the type and intensity of disturbance, which can mask predictable patterns of response (Andersen 2021). ...
Disturbance is fundamental to the state and dynamics of biological communities, and understanding biotic responses to disturbance is critical to effective biodiversity conservation. However, a predictive understanding of how faunal communities respond to habitat disturbance remains elusive. Recently, a conceptual framework centred on habitat openness was developed for understanding ant responses to disturbance. It proposes that habitat openness is a fundamental driver of variation among ant communities, and that the primary impacts of disturbance are mediated through ant functional responses to changes in openness. Like ants, terrestrial reptiles are ectotherms and are therefore especially sensitive to disturbance‐induced increases in habitat openness because of changes in the thermal environment. Therefore, reptiles might also be expected to conform to a disturbance framework based on habitat openness. Here we assess the extent to which this occurs by combining a quantitative analysis of recent publications with a broader synthesis of the literature. We found strong support for the framework applying to terrestrial reptiles. We suggest that the framework can be strengthened by a mechanistic understanding of functional traits in relation to habitat openness. For ectotherms, ecophysiological traits could be particularly important for responding to disturbance‐mediated changes in microclimate, but habitat openness also influences other important factors such as food availability and predation. Finally, the framework appears to be highly applicable to a wider range of faunal groups beyond ants and reptiles.
... We did not explicitly examine between-study variations in design and sample size but attempted to account for this heterogeneity in the random-effects structure of our model. We also included random effects for taxonomic family to account for the non-independence of measures due to phylogenetic relatedness [38]. We fit univariate models using a means parameterization, i.e., we excluded the intercept, to test for the effect of study type on weighted dispersal rates. ...
Gaps in dispersal data limit habitat protection efforts. We sought to characterize such gaps and compare the utility of dispersal data from demographic and genetic methods in making habitat protection decisions. Here, we used a search string to retrieve dispersal studies for amphibians, reptiles, birds, and mammals. We included studies based on a set of selection criteria. We used this sample of selected studies to assess for persistence of taxonomic and geographic biases. We extracted non-effective (i.e., demographic) and effective (i.e., genetic) dispersal rates. We weighted these dispersal rates by associated sample size and standard deviation to indicate the ability to capture population-level dispersal. We then tested for variation in weighted dispersal by study type using Bayesian mixed-effects models. Amphibians were the most under-represented taxonomic group in our sample. Dispersal studies were mostly retrieved from developed nations indicating the distribution of dispersal research reflected GDP rather than the number of threatened species. The magnitude of dispersal from genetic methods exceeded demographic methods in all vertebrate groups considered in our study. Further, genetic studies consistently sampled a larger number of individuals. Thus, genetic methods may be better suited to characterize population-level dispersal. However, demographic and genetic approaches enable examination of the dispersal process at varying spatial and temporal scales and a combination of these approaches can be used to address persistent gaps in dispersal and enable land-management decisions.
... Ectotherms are bioindicators of the environmental quality because of their tight dependence on environmental conditions, and several studies have demonstrated that human activities, habitat modification and global change are the main causes of their decline (e.g., Gibbons et al. 2000;Huey et al. 2012;Lara-Reséndiz et al. 2015;Wang et al. 2016;Doherty et al. 2020). Nowadays many ectotherms' populations are living on (or close to) the edge of their thermal tolerance. ...
Ectotherms are particularly threatened by climate change because they are strictly reliant on environmental conditions for homeostasis. Increasing environmental temperatures may approach the species' critical thermal maximum, with deleterious effects on individual thermoregulation capacities. This study tests the hypothesis developed in a recent work that under ongoing global warming populations living in sites at the warm edge of the species' thermal niche will suffer a disruption of the thermoregulation process, with detrimental effects at the individual and population level. We collected individual measurements and temperature data for Mediterranean endemic rock lizards, across the entire distribution range of the species and during two different sampling periods ~20 years apart to compare thermoregulation coefficient (C), body condition index (BCI) and population size under different climatic conditions. We found that C and BCI vary across space and time following a linear pattern along the thermal niche gradient (Niche Margin Effect, NME) until a threshold temperature, beyond which the NME is disrupted. This threshold temperature indicates the warm edge of the species' thermal niche. A slightly higher temperature marks the threshold at which we observed significant population declines over the 20‐year study period in the warmest sites. This suggests a lagged response of population trends to climate warming. This study suggests a mechanism of disruption of homeostatic processes when the warm margin of the thermal niche is reached and indicates that individual parameters such as thermoregulation coefficient and body condition, rather than demographic trends, are key indicators for an early detection of population extinction risk. The multipopulation approach implemented in our study allows to identify the niche edge that underlies species' vulnerability to global warming, and to identify populations suffering negative effects of climate change before demographic collapse. This might allow to plan appropriate mitigation measures and management strategies to avoid local extinctions.
... Reptiles, especially snakes, are particularly vulnerable to climate change due to their ectothermic nature and temperature-dependent life processes (Lourenço-de-Moraes et al., 2019;Martinez et al., 2024). Climate change disrupts their habitat, body temperature regulation, and food sources, leading to population declines and potential extinction (Winter et al., 2016;Doherty et al., 2020). This study focuses on the genus Zamenis (Reptilia, Squamata, Colubridae), which encompasses six snake species distributed widely across the western Palearctic region (Salvi et al., 2018). ...
Climate change poses a significant threat to ectothermic, dispersal-limited reptiles such as Zamenis snakes in the western Palearctic. This study used ensemble ecological models to assess the potential distribution of six Zamenis species under climate change scenarios (SSP1-2.6 and SSP5-8.5). In addition, we examined niche dynamics through overlap, equivalency, and similarity analyses. Results reveal distinct ecological niches for each species, primarily influenced by temperature and precipitation. Projected distribution shifts vary across species, with some species like Z. persicus and Z. situla showing potential for range expansion, while others such as Z. lineatus and Z. scalaris face significant habitat loss. Z. hohenackeri and Z. longissimus exhibit complex patterns of both expansion and contraction. Niche analyses indicate varying degrees of overlap among species, with a trend toward niche conservatism. This study underscores the importance of niche ecology in understanding climate change impacts and highlights the need for species-specific conservation strategies.
... Reptiles, especially snakes, are particularly vulnerable to climate change due to their ectothermic nature and temperature-dependent life processes (Lourenço-de-Moraes et al., 2019;Martinez et al., 2024). Climate change disrupts their habitat, body temperature regulation, and food sources, leading to population declines and potential extinction (Winter et al., 2016;Doherty et al., 2020). This study focuses on the genus Zamenis (Reptilia, Squamata, Colubridae), which encompasses six snake species distributed widely across the western Palearctic region (Salvi et al., 2018). ...
Climate change poses a significant threat to ectothermic, dispersal-limited reptiles such as Zamenis snakes in the western Palearctic. This study used ensemble ecological models to assess the potential distribution of six Zamenis species under climate change scenarios (SSP1-2.6 and SSP5-8.5). In addition, we examined niche dynamics through overlap, equivalency, and similarity analyses. Results reveal distinct ecological niches for each species, primarily influenced by temperature and precipitation. Projected distribution shifts vary across species, with some species like Z. persicus and Z. situla showing potential for range expansion, while others such as Z. lineatus and Z. scalaris face significant habitat loss. Z. hohenackeri and Z. longissimus exhibit complex patterns of both expansion and contraction. Niche analyses indicate varying degrees of overlap among species, with a trend toward niche conservatism. This study underscores the importance of niche ecology in understanding climate change impacts and highlights the need for species-specific conservation strategies.
... Activity patterns, microhabitat preferences and feeding guilds, related to spatial and dietary demands, are also influenced by climatic factors and can vary with habitat changes Barnagaud et al. 2021). Additionally, clutch size and reproduction type, although more studied in amphibians, may vary with climate and habitat alterations Doherty et al. 2020). Trait information was obtained by reviewing several bibliographic references and trait databases (Appendix S1 and Table S4). ...
Aim
Mountainous regions are rich in reptile biodiversity but face threats from climate and land use changes. Understanding how these factors affect reptile diversity in these regions can highlight key conservation hotspots that require effective conservation actions. Here, we explored reptile taxonomic and functional diversity patterns along the Sierra Madre del Sur region in southeast Mexico, and potential changes in future years caused by different climate and land use change scenarios.
Location
Sierra Madre del Sur, México.
Taxon
Reptiles.
Methods
We used species distribution models and information on species traits to estimate taxonomic and functional diversity throughout the Sierra Madre del Sur (SMS) region under current and future climate and land use change scenarios.
Results
Greater taxonomic and functional diversity was observed in both temperate and tropical forests. Taxonomic diversity was higher in more drier areas at high elevations while higher functional diversity was observed in wetter areas at intermediate‐to‐high elevations. Lower diversity for both dimensions was associated with anthropic land uses. In future scenarios, both dimensions of diversity are expected to increase in temperate forest in highlands of central Oaxaca and decrease in the southcentral portion of the SMS, particularly for the worst scenarios due to increased deforestation rates.
Main Conclusions
Higher taxonomic diversity in more drier areas at high elevations could be due to historical and evolutionary factors, while higher functional diversity in wetter areas at intermediate‐to‐high elevations may be explained by a higher environmental heterogeneity in forests within these conditions. Larger diversity losses in the southcentral portion of the SMS are probably due to larger predicted deforestation rates in those areas. Our results are valuable not just for informing conservation actions, such as the creation of protected natural areas but also to understand the underlying processes behind the patterns of reptile diversity.
... Among vertebrates, birds and mammals have received more attention, leaving a significant gap in our understanding of the impact of habitat conversion on reptiles (Davison et al., 2021). Reptiles, despite having more described species than mammals and amphibians, have been remarkably understudied concerning land-use change (Doherty et al., 2020). ...
Change in land-use patterns affects a landscape by changing the composition of local flora and fauna. The lateritic plateaus in Konkan are one such example of this rapid land-use change. Although these plateaus are rich in endemic flora and fauna, they are considered as “wastelands” due to lack of woody vegetation and thus, are subjected to various land-uses. Mango cultivation in this region has become a major source of income due to its Alphonso variety of mangoes. Hence, over the last few decades, many plateaus have been converted into mango orchards. However, how the conversion of plateaus to mango orchards has affected species composition of different groups of organisms remains unclear. In the present study, we sampled the lateritic plateaus and plateaus converted into mango orchards in Ratnagiri, Maharashtra, to investigate the response of the reptile communities. We observed more species heterogeneity in the orchards compared to the unaltered sites. Moreover, it appeared that there was a species turnover when the plateaus were converted into orchards. The generalist and widespread species such as agamids and skinks and very few specialist species were comparatively more abundant in the orchards. On the contrary, the plateaus without orchards harbored more specialist species such as Hemidactylus albofasciatus (n = 62, in unaltered sites vs. n = 5 in the orchards), Echis carinatus (n = 15 in unaltered sites and none in the orchards) and Ophisops jerdonii (n = 45 in unaltered site vs. n = 12 in the orchards) compared to the generalist species.
... The accelerated rate in land use change (LUC), a consequence of macroeconomic demands reflected as the increase in the extraction of natural resources -i.e., mining, agricultural and fishing activities-, drastically damages natural environments and causes fragmentation processes of primary vegetation and, therefore, loss of habitat (Chase et al., 2020;Foley et al., n.d.;Monsarrat et al., 2019). This LUC has delimited fragments of habitat without full connectivity, which is why it is considered one of the main aspects that affect biological diversity (Capinha et al., 2020;Chase et al., 2020;Doherty et al., 2020;Tan et al., 2023). As a consequence, that is, areas of a certain habitat become isolated (or relatively isolated) from other areas of the same habitat or habitats with similar characteristics due to roads, highways, crops and even human settlements, preventing the movement of species and re-sources (Foley et al., 2005). ...
... Univariate models, excluding the intercept, were fitted for each moderator to evaluate how the type of drying, the severity of drying, experimental setting (type of study and study object), or climate zone (table 1) influenced the overall effect of drying on river metabolism and GHG emissions (see section below). Intercepts were excluded because models for categorical predictors with more than two levels use the intercept as a reference against all others, and we aimed to compare between different levels of each moderator (Doherty et al 2020). The assessment of interactions between fixed effects was not conducted due to the poor replication of some moderator combinations. ...
More than half of the world’s rivers experience occasional, seasonal, or permanent drying, and this may increase because of climate change. Drying, i.e. severe reduction in water flow even leading to streambed desiccation, can have a profound impact on the available aquatic habitat, biodiversity, and functions of rivers. Yet, to date, it is unclear whether similar drying events in comparable climate zones result in similar changes in ecosystem processes, such as river metabolism or greenhouse gas (GHG) emissions. Here, we synthesise the detected effects of drying on gross primary production (GPP) and ecosystem respiration (ER), as well as on the emissions of GHGs (CO2, CH4, and N2O) in rivers and streams. We examined the current available scientific literature detailing the impact of drying on these variables when measured either in the field or in the laboratory. We extracted data from 30 studies analysing GPP and ER responses, and data on GHG emissions from another 35 studies. Then, we conducted a meta-analysis to determine whether the magnitude and direction of the effects varied across the systems and climate zones studied, or according to the type (natural or human-induced) and severity of drying. In general, drying enhanced GPP (under low flows) and CH4 emissions, and decreased CO2 and N2O emissions. The hydrological phases throughout streambed drying (low water flow, isolated pools, or desiccation) had differential effects on metabolism and GHG emissions. The effects of drying were generally more severe when it induced desiccation, rather than just periods of low flow. Desiccation strongly reduced GPP, likely because of the die-off of algae, while its negative effect on ER was smaller. Greater decrease in GPP than in ER under desiccation would lead to increase in CO2 emissions; our results showed accordingly that desiccation increased CO2 emissions. Furthermore, the magnitude and direction of the effects varied depending on the study type. Experimental studies conducted in micro- and mesocosms demonstrated greater effects than field studies, thus the extrapolation of results from these to real conditions should be done with caution. Overall, the effects’ direction was inconsistent across climate zones, except for the Mediterranean climate zone, where drying was showing a negative effect on both metabolism and GHG emissions. Our synthesis may contribute to identifying the worldwide trends and patterns of drying on riverine functions associated to global change impacts on river and stream ecosystems.
... Algumas espécies são predadoras de topo de cadeia (jacarés, sucuris) e desempenham funções importantes no ecossistema, sendo que a exclusão dessas espécies acarretaria efeitos catastróficos para ou-tras ao longo da cadeia trófica e em processos ecossistêmicos. Em decorrência, esses animais são considerados excelentes bioindicadores ambientais, principalmente como organismos modelo em pesquisas com foco na alteração ambiental, como as mudanças climáticas e o desmatamento (DOHERTY et al., 2020;SINERVO et al., 2010; VITT e CALDWELL, 2013), ou estudos ecotoxicológicos, como agrotóxicos, metais pesados e outros poluentes (CAMPBELL e CAMPBELL, 2000HOPKINS, 2000). Muitas espécies de répteis e anfíbios produzem veneno, tendo, portanto, importância médica, seja pelos acidentes causados por envenenamento, seja para pesquisa de fármacos a partir da composição dos venenos. ...
O presente estudo apresenta informações relacionadas às espécies da herpetofauna encontradas na RPPN Canguçu e entorno a partir de uma base de dados construída nos últimos 20 anos, durante atividades de pesquisa e docência nesta área de ecótono. Foram encontradas 31 espécies de anfíbios, todas pertencentes à ordem Anura, e 44 espécies de répteis, sendo 35 Squamata, três Crocodylia e cinco Testudines. Os resultados evidenciam uma expressiva biodiversidade da herpetofauna na área estudada, uma vez que foram registradas, aproximadamente, 15% do total de espécies compiladas para o Cerrado. Ressalta-se que a diversidade de espécies para alguns grupos de anfíbios e répteis pode aumentar, especialmente devido à vasta dimensão territorial da região e com parte ainda não estudada, bem como em razão da área ser caracterizada pela transição Amazônia-Cerrado. Apesar de esta área estar localizada dentro e no entorno de importantes Unidades de Conservação (UCs), são preocupantes, no âmbito da conservação, fatores como o avanço agrícola na região; a forte pressão da caça sobre algumas espécies, principalmente do grupo de quelônios e crocodilianos; os barramentos para uso na irrigação e também para hidrelétricas; e a introdução de espécies exóticas. Nesse sentido, reforça-se a necessidade de fortalecimento dos recursos humanos e financeiros para as UCs da região, além das pesquisas científicas e dos programas de conservação da biodiversidade.
https://docs.uft.edu.br/s/4RYir52UQ46wnF1g8aGmMg
... A recent meta-analysis suggests that lizards in the family Phrynosomatidae are less negatively affected by human-modified habitat than other groups of lizards, possibly because many of them live in arid habitats with sparse vegetation that may mimic disturbed sites (Doherty et al., 2020). Consistent with this pattern, Texas horned lizards have remained a wildlife component of some small towns (<10,000 people) in Texas, although they have disappeared from larger urban areas. ...
There is a general expectation that urban populations will be fragmented and the movement of individuals will be restricted leading to low effective population sizes, low genetic diversity, higher inbreeding, and higher differentiation than populations living in more continuous habitat. In this study, we compare the genetic diversity and differentiation of Texas horned lizards that are found in four small towns (Kenedy, Karnes City, Rockdale, and Smithville) in Texas and at Tinker Air Force Base, Oklahoma to populations that occur in 16 natural areas and to an introduced population in South Carolina. We also present more detailed spatial genetic data and home range data for several of the towns. Texas horned lizards (Phrynosoma cornutum) living in small towns have lower genetic diversity, higher differentiation, and smaller effective population sizes than populations located in more natural areas. There was evidence for human‐mediated movement of lizards into town; however, it has not been enough to counteract the effects of drift. Home range size is smaller in town than in more natural areas. Genetic patterns suggest dispersal occurs over short distances and is inhibited across areas with a high percent of impervious surface and major roads. These data suggest that effective planning to maintain suitable habitat and corridors to facilitate movement is critical to maintaining small terrestrial species like the Texas horned lizard and must be integrated into the early stages of urban development.
... Moreover, previous studies associated HB directly with extinction risk (ER, Owens & Bennett 2000;González-Suárez et al. 2013;Tingley et al. 2013;Ducatez et al. 2014;Senior et al. 2021;Zhong et al. 2021), while other studies found an association between narrow HB and reduction of geographic range size and abundance related to habitat perturbation and climatic change; in birds, reptiles, mammals, and insects (Warren et al. 2001;Gehring and Swihart 2003;Fisher et al. 2003;Le Viol et al. 2012;Gonçalves et al. 2021). Taken together, the results of these studies suggest that species with narrow HB have an increased probability of becoming extinct due to human perturbation activities (but see Collen et al. 2011;Doherty et al. 2020). The majority of those studies focus on a sizeable taxonomic scale (e.g., class or phylum; e.g., Pagel et al. 1991;Collen et al. 2011;González-Suárez et al. 2013;Ducatez et al. 2014;Martinossi-Allibert et al. 2017), which generalizes results and conclusions. ...
The tight relationship of niche breadth (i.e., environmental tolerance and resource use) with ecomorphological traits and extinction risk makes the study of habitat niche breadth (i.e., habitat heterogeneity; HB) crucial to understanding the species’ ecological niche and macroecological aspects. Additionally, HB has been associated with the species extinction risk (ER) due to human activity. Bats can be ideal for understanding HB’s ecological and conservation relevance due to their diverse diet and other traits, as well as the high number of threatened species. Here, we studied the association between HB, trophic guild (TG), body mass (BoM), and extinction risk (ER) in phyllostomid bat species using a phylogenetic comparative approach. Our results showed that the TG, not BoM, is significantly associated with HB in phyllostomid bats. Omnivorous and sanguinivorous bats have a wider HB than plant-eating and insectivorous bats. Regarding the ER of bats, our results showed that species without risk have wider HB than species at risk. The HB of species without conservation status does not differ from at-risk species, which suggests that at least some species should be considered at risk. In conclusion, our study suggests that diet is a relevant trait that influences the macroecological dynamic of phyllostomid bats due to its relation with HB. Additionally, we provided evidence supporting HB’s use as an ER predictor. Finally, we discussed the necessity of finding alternative and quicker ways to assess the ER of the species.
... Ecological traits influence a species' response to fragmentation, where some species are better equipped to withstand disturbance compared to others (Henle et al. 2004;Keinath et al. 2017;Doherty et al. 2020). We found three traits-diet, habitat breadth and habit-affect species abundance between fragments and pseudo-fragments. ...
Context
Human disturbance has transformed ecosystems globally, yet studies of the ecological impact of landscape modification are often confounded. Non-random patterns of land clearing cause differing vegetation types and soil productivity between fragments in modified landscapes and reference areas—like national parks—with which they are compared.
Objectives
We sought to explore the influence of land modification on herpetofauna and small mammal communities using multiple biodiversity measures—species richness and diversity, individual species abundance, and community composition. We also aimed to investigate the role of traits such as diet, habitat breadth, and litter size in moderating species responses to land modification.
Methods
We established 100 sampling sites to survey herpetofauna and small mammals in 11 fragments in an agricultural landscape compared to 11 ecologically equivalent ‘pseudo-fragments’ in a nearby national park in south-eastern Australia. We selected pairs of fragments and pseudo-fragments of the same size and vegetation type, and used identical survey methods to sample pairs simultaneously, thereby controlling for numerous confounding factors, such as differing vegetation type, weather, and survey effort.
Results
Species richness and diversity were similar between fragments and pseudo-fragments. Despite this, we found community composition differed markedly—driven by the varying responses of individual species—indicating a shift in fauna communities associated with land modification. Fossorial habit, omnivorous diet, and broad habitat requirements led to higher abundance in fragments whilst arboreality, carnivorous diet, and narrow habitat requirements led to higher abundance in pseudo-fragments.
Conclusions
Although fragments hold similar numbers of species to continuous areas, they contain distinct and novel communities, and sustain high abundances of some species. These diverse communities are dominated by native species, including threatened species, and their distinctive composition is shaped by traits conducive to persistence amidst land modification. These novel communities may provide a reservoir of resilience in the face of environmental change and should be viewed as complementary to conservation areas.
... Snakes play an important role in balancing ecosystems as both prey and predators (Mullin & Seigel, 2009) and also serve as bioindicators (Bonnet, 2012;Haskins et al., 2021;Rasmussen et al., 2021). Unfortunately, anthropogenic activities, most importantly habitat destruction and snake persecution, are responsible for the decline and extinction of snake populations worldwide (Gibbon et al., 2000;Doherty et al., 2020). Therefore, the development of policies and strategies for the conservation of snake populations is both urgent and critical (Mir et al., 2015;Castillo-Huitrón et al., 2020;Musah et al., 2022). ...
Habitat destruction and snake persecution are the leading causes of the decline of snake populations worldwide, highlighting the need to formulate scientifically robust conservation management plans that incorporate an understanding of local public attitudes toward snakes. We conducted an in-person survey of 968 residents of Maguindanao Provinces, Mindanao Island, Philippines, to investigate attitudes toward snakes and assess the effects of knowledge about snakes, worldviews, and demographic characteristics on the support for snake conservation. Survey participants were primarily intolerant of and aversive to snakes but generally supported their conservation. Additionally, they were knowledgeable about the behavior of snakes, and shared either highly moralistic or dominionistic worldviews of nature, while most did not believe in folklore traditions. High levels of knowledge about the behavior of snakes, positive folkloric beliefs, high tolerance and low aversion to the presence of snakes, and moralistic worldviews positively affected support for snake conservation. Female participants were less tolerant and more averse to snakes than males. Participants with higher levels of education were more tolerant and supportive of snake conservation than those with little or no education. Farmers were less supportive of snake conservation than non-farmers. Our survey results provide important information to understand how cognitions, folklore, and demographics influence snake conservation on an island in the Philippines. This information may be valuable to government agencies and various stakeholders that could use it to design effective strategies for promoting snake conservation in the country, or other countries with similar societal systems and cultures.
... We found that postfire afforested habitats were poorer ecosystems for reptiles than postfire forests that had been less managed. This result supports the general decline observed in reptile communities after anthropogenic habitat changes (Cordier et al., 2021;Doherty et al., 2020). The reptile decline caused by afforestation practices occurred in all fire age classes. ...
Effects of anthropogenic activities, including climate change, are modifying fire regimes, and the dynamic nature of these modifications requires identification of general patterns of organisms’ responses to fire. This is a challenging task because of the high complexity of factors involved (including climate, geography, land use, and species‐specific ecology). We aimed to describe the responses of the reptile community to fire across a range of environmental and fire‐history conditions in the western Mediterranean Basin. We sampled 8 sites that spanned 4 Mediterranean countries. We recorded 6064 reptile sightings of 36 species in 1620 transects and modeled 3 community metrics (total number of individuals, species richness, and Shannon diversity) as responses to environmental and fire‐history variables. Reptile community composition was also analyzed. Habitat type (natural vs. afforestation), fire age class (time since the last fire), rainfall, and temperature were important factors in explaining these metrics. The total number of individuals varied according to fire age class, reaching a peak at 15–40 years after the last fire. Species richness and Shannon diversity were more stable during postfire years. The 3 community metrics were higher under postfire conditions than in unburned forest plots. This pattern was particularly prevalent in afforested plots, indicating that the negative effect of fire on reptiles was lower than the negative effect of afforestation. Community composition varied by fire age class, indicating the existence of early‐ and late‐successional species (xeric and saxicolous vs. mesic reptiles, respectively). Species richness was 46% higher in areas with a single fire age class relative to those with a mixture of fire age classes, which indicates pyrodiverse landscapes promoted reptile diversity. An expected shift to more frequent fires will bias fire age distribution toward a predominance of early stages, and this will be harmful to reptile communities.
... Thе cumulativе еffеct of habitat loss and fragmеntation is particularly obvious for spеciеs with spеcific habitat rеquirеmеnts or limitеd dispеrsion ability (Gibbons et al. 2000). For еxamplе, thе dеstruction of tropical rainforеsts providеs a sеrious thrеat to various rеptilе spеciеs, such as arborеal snakеs and lizards, which dеpеnd on thе vеrtical structurе of thick vеgеtation for rеfugе and foraging (Doherty et al. 2020). As habitats dеcrеasе and grow isolatеd, rеptilе populations confront difficulty in obtaining partnеrs, food rеsourcеs, and adеquatе microhabitats, ultimatеly lеading to dеclinеs. ...
This chapter examines the crucial role of reptiles as environmental indicators, highlighting their importance in influencing current methods of environmental management. The fundamental principle of indicator species is the basis for understanding how reptiles function as tangible indicators of the overall health of ecosystems. They exhibit dynamic responses to changes in habitat, variations in climate, and disturbances caused by human activities. The incorporation of reptile monitoring into conservation efforts is increasingly recognized as a pragmatic and adaptable approach, providing significant contributions to the fields of biodiversity conservation, habitat management, and the alleviation of environmental risks. The discourse revolves around the examination of forthcoming challenges and opportunities, emphasizing the imperative for innovation, interdisciplinary collaboration, and community engagement. This paper emphasizes the necessity of adopting a comprehensive conservation approach, which emphasizes the importance of acknowledging and safeguarding the complicated interrelationships between reptiles and larger ecological processes. It examines the significant contribution of reptiles in serving as early indicators of ecosystem disruptions, facilitating informed habitat management strategies, and evaluating the effects of urbanization, pollution, and climate change. Upon the culmination of the exploration, a compelling appeal is made to advocate for the allocation of resources toward research, education, technological advancements, and global cooperation. These endeavors are crucial for fostering a sustainable future wherein reptiles assume a pivotal position in bolstering environmental resilience. Proposal for the integration of reptile monitoring findings into environmental management methods, with the aim to establishing a symbiotic relationship with the natural environment, and achieving equilibrium between human activities and the complex ecosystems represented by reptiles is also made.
... In extreme environments, however, they can slow down metabolism by entering into hibernation, which limits energy expenditure and enhances survival (Holden et al., 2021). Nevertheless, major and rapid environmental changes following anthropization are responsible for their decline worldwide (Gibbons et al., 2000;Todd et al., 2010;Weir et al., 2010;Doherty et al., 2020). Accordingly, environmental pollutions can affect animal survival (Trakimas and Sidaravičius, 2008;Owen-Jones et al., 2016) and population stability (Gibbons et al., 2000;Irwin and Irwin, 2006;Boissinot et al., 2015). ...
Human activities affect terrestrial and aquatic habitats leading to changes at both individual and population levels in wild animal species. In this study, we investigated the phenotype and demographics of the Mediterranean pond turtle Mauremys leprosa (Schweigger, 1812) in contrasted environments of Southern France: two peri-urban rivers receiving effluents from wastewater treatment plants (WWTP), and another one without sewage treatment plant. Our findings revealed the presence of pesticides and pharmaceuticals in the three rivers of investigation, the highest diversities and concentrations of pollutants being found in the river subsections impacted by WWTP effluents. Principal component analysis and hierarchical clustering identified three levels of habitat quality, with different pollutant concentrations, thermal conditions, nutrient, and organic matter levels. The highest turtle densities, growth rates, and body sizes were estimated in the most disturbed habitats, suggesting potential adult benefits derived from harsh environmental conditions induced by pollution and eutrophication. Conversely, juveniles were the most abundant in the least polluted habitats, suggesting adverse effects of pollution on juvenile survival or adult reproduction. This study suggests that turtles living in polluted habitats may benefit from enhanced growth and body size, at the expense of reproductive success.
... The effects of habitat changes on snake diversity are still poorly known (Gardner et al. 2007;Doherty et al. 2020), especially in relation to processes that act at the landscape level. Such effects on snakes are frequently investigated at the species level to understand how a species moves and/or selects habitats in fragmented landscapes (Heard et al. 2004;Wisler et al. 2008;Miller et al. 2012;Nordberg et al. 2021). ...
Snake response to habitat changes is frequently investigated at the species level, but it is still poorly known how snakes respond to habitat changes at the community level and at which spatial scale. Here, we used a multi-model inference approach to evaluate the effects of local and landscape composition (percentage of forest cover and silviculture) and habitat fragmentation (number of forest patches and total edge) on species, functional, and phylogenetic diversity of snake communities in tropical fragmented landscapes. Additionally, we tested whether silviculture acted as an environmental filter for snakes. Species and functional diversity responded primarily to landscape elements: species richness, abundance, and functional diversity decreased with deforestation. In addition, species richness and abundance increased with the proportion of forest and the number of patches in the landscape. In contrast, phylogenetic diversity was driven by the local habitat composition. Although habitat types did not filter entire clades and functional groups, each species tended to have a co-occurring species with similar traits (at landscape level) and a close relative (at both levels) in impacted habitats. In contrast, the co-occurrence of close relatives and functionally similar species was avoided in the native forest. Our findings indicate that snake responses to habitat changes occur on multiple scales and highlight the importance of conserving native forests to maintain multiple components of biodiversity. Strategies for conserving snake diversity in tropical fragmented landscapes should therefore consider management practices at both the local and landscape scales.
... Unfortunately, the TMVB has experienced substantial disturbance, with a staggering 73.4 % of the region dedicated to anthropogenic activities (Sunny et al., 2017). The high levels of disturbance and habitat fragmentation pose a greater threat to reptiles than to other vertebrates, as reptiles have limited ability to move between fragmented habitats or to escape degraded areas compared to more mobile taxa like birds and larger mammals (Carthew et al., 2009;Qian, 2009;Garland and Albuquerque, 2017;Keinath et al., 2017;Doherty et al., 2020;Balouch et al., 2022). The geographic distributions of reptiles in Mexico have significantly contracted due primarily to these anthropogenic activities (Ochoa-Ochoa and Flores-Villela, 2006). ...
Anthropogenic changes pose a significant threat to global biodiversity, especially in reptiles. Mexico, renowned for its diverse reptile population, is experiencing habitat disturbance and fragmentation, endangering rattlesnakes in particular due to their specific habitat requirements and limited mobility. The loss of structural connectivity further increases the risk of extinction for reptiles. Our study focuses on predicting the distribution and connectivity of nine Crotalus species in the Trans-Mexican Volcanic Belt (TMVB), using environmental modeling. We used climate models (CNRM-CM5 and MPI-ESM-LR) for the year 2050 and Representative Concentration Pathways (RCP 85) alongside changes in vegetation cover and land use. The Maxent modeling method in ENMeval helped assess distribution patterns and to identify key environmental variables influencing these species’ distributions and niche overlap. We also conducted an analysis of the structural connectivity of the different Crotalus species. Our findings indicate reductions in suitable habitats due to changes in agriculture, urbanization, and forest cover. The Maxent models showed high accuracy in predicting species distributions. The most influential variables varied among species and included forest types and climatic factors. We observed limited connectivity among small Crotalus species, although some species exhibited greater connectivity than others. Future models suggest potential distribution reductions for all species, with C. armstrongi facing the greatest reduction (78%) according to the cn85 global climate model. Protected areas do not encompass the majority of potential distribution for these small rattlesnake species. These findings highlight the urgency of conservation efforts and the need to mitigate the impacts of future environmental changes on reptile populations.
... The loss and modification of natural habitats pose one of the greatest threats to the decline of amphibian and reptile species worldwide. In disturbed habitats, there is a limitation in the availability of food resources and shelters (Bishop et al., 2012;Doherty et al., 2020). Additionally, many species of amphibians and reptiles present limited dispersal capacity and high specialization in the use of microhabitats; characteristics that make them highly vulnerable to environmental changes (Bishop et al., 2012;Gibbons et al., 2010;Todd et al., 2010). ...
Global herpetofauna faces threats by habitat loss and degradation, with amphibian and reptile species maintenance in human-modified landscapes not only depending on forest remnants, but also on biodiversity-friendly matrices, such as agroforestry systems. Nevertheless, herpetological studies in agroforests are limited, hindering conservation decisions. To fill this gap, we conducted a global meta-analysis to assess the ability of agroforestry systems to maintain abundance and richness of amphibian and reptile species when compared to native forests. We analyze how community parameters (richness or abundance) and agroforest types based on the vegetation characteristics described by the studies (simplified or complex) impact the variation of overall effect size. We also used meta-regression models to examine how the amount of forest cover around agroforests affects the effect size. Finally, we calculated Sorensen's Index based on incidence data to investigate the degree of similarity in species composition of amphibians and reptiles between agroforestry systems and native forests. Our results showed that amphibian diversity in agroforests is lower than in native forests, regardless of the parameter and agroforestry type. For reptiles, agroforests showed higher abundance and similar species richness to forests. Simplified agroforestry systems support less reptile diversity than complex systems, which are more similar to forests. Interestingly, landscape forest amount modulates the ability of agroforests in maintain reptile richness. In fact, agroforests inserted in highly forested landscapes can harbor higher richness of reptiles than forests. We also found that half of the amphibian and reptile species observed in agroforests are different from those observed in native forests. Our findings highlights that agroforests cannot replace native forests because such systems harbor reduced abundance and species richness, especially amphibians, and a distinct species composition. However, when inserted in forested landscapes these agricultural systems can host rich reptile communities. Thus, preserving native forests and restoring deforested regions are crucial for herpetofauna conservation in human-modified landscapes.
... Information about species living in such environments is important information for organizations in developing mitigation programs for conservation. One reptile group commonly found in anthropogenically modified landscapes are the lizards, which are usually small species with a rapid population turnover [1,[3][4][5]. Hedgerows are key wildlife habitats and the most commonly found in agricultural landscapes [5]. They can be defined as ecotones, as they are often present in a mix of natural and anthropized habitats, mostly farmland [6]. ...
The expansion of human activities across natural environments is now well known. This includes agricultural activities that effectively render many former natural environments sterile habitats for animals. Very often, what remains of the natural habitat are hedgerows that serve as habitat or pathways for movement between habitats for many species, including reptiles. In this study, we describe population changes in the western green lizard, Lacerta bilineata, in a hedgerow system in western France. The results are derived from a univariate diversity analysis of photographic data to identify individual lizards over a 4-year study period. Lizards were sighted from March April to October early November but there was a midsummer gap in sightings during July-August. The annual presence of individual lizards was low, both between and within years, but based on the diversity analysis, the overall stability of the population was high. Female numbers varied and were highest in 2020, but juveniles were highest in 2023; the numbers of males present each year were approximately the same. Individual lizards that were present before the midsummer gap were mostly absent after the midsummer gap and were replaced by new individuals. Incidences of autotomy were low in males and juveniles and were not recorded in females. In general, the results suggest that the lizards move through hedgerow systems but remain in a specific section for reproduction from March to July. Through this study, we also highlight the importance of univariate diversity formulas to obtain robust results in investigations of the demographic aspects of animal populations that are easy to monitor.
... The Intergovernmental Panel on Climate Change (IPCC) has stated that endangered species are at risk under projected climate change during and beyond the 21 st century, especially as climate change interacts with other factors, such as habitat modification (Doherty et al. 2020), over-exploitation (Auliya et al. 2016), environmental pollution (Gibbons et al. 2000), and invasive species (Dueñas et al. 2021). Specifically, a considerably larger percentage of amphibians and reptiles are at risk compared to birds or mammals (Cordier et al. 2021;IUCN 2023). ...
Eremias argus , known as the Mongolian racerunner, is a reptile that has been designated as a level II endangered species in South Korea since 2005 despite being listed as “Least Concern” by the International Union for Conservation of Nature. Particular vegetation and soil characteristics are critical components of the habitat of E. argus , which is an ectotherm. However, research on the environmental characteristics of E. argus living on a fluvial island is lacking. This study sought to characterize the soil environmental factors and vegetation composition of E. argus habitats on Doriseom Island, South Korea by dividing the island into an area in which E. argus occurred frequently (F zone) and an area in which E. argus occurred rarely (R zone). Both soil hardness and cobble cover were significantly higher in the R zone (soil hardness: 1.6 ± 0.2 kg‧cm ⁻² , mean ± standard error; cobble cover: 40 ± 5%) than in the F zone (soil hardness: 0.9 ± 0.1 kg‧cm ⁻² ; cobble cover: 18 ± 3%). Plant litter cover did not differ significantly based on E. argus occurrence. The vegetation composition within F and R zones appeared distinct, though Coreopsis lanceolata dominated both zones. A sand dune sedge, Carex pumila , thrived in F zone sites, where soil hardness was low, while the endemic Aster danyangensis , which prefers cobble areas, was found largely in the R zone. In conclusion, E. argus was most commonly found in areas with low soil hardness dominated by dune vegetation. Understanding endangered species’ habitat requirements can provide important clues for establishing conservation plans and restoration measures.
... The low number of reptiles recorded in this study contradicts the finding of Razzetti and Msuya 25 who reported that reptiles' abundance and activity pattern increase in early rain as they respond to the abundance of their food. Doherty et al. 26 found an overall negative effect of anthropogenic activities on squamate abundance. ...
... However, we also found that primates and all amphibian and reptile guilds but one (venomous snakes) are decreasing in the studied reserves. This is unsurprising as all the former guilds comprise highly threatened forest-dependent species (40)(41)(42). Forest loss is known to eliminate tree species and associated plants (epiphytes) that constitute the structural and functional basis of old-growth forests (43,44). Logically, removing trees, especially the largest ones, negatively impacts arboreal mammals, including primates and birds of prey (44). ...
Protected areas are of paramount relevance to conserving wildlife and ecosystem contributions to people. Yet, their conservation success is increasingly threatened by human activities including habitat loss, climate change, pollution, and species overexploitation. Thus, understanding the underlying and proximate drivers of anthropogenic threats is urgently needed to improve protected areas’ effectiveness, especially in the biodiversity-rich tropics. We addressed this issue by analyzing expert-provided data on long-term biodiversity change (last three decades) over 14 biosphere reserves from the Mesoamerican Biodiversity Hotspot. Using multivariate analyses and structural equation modeling, we tested the influence of major socioeconomic drivers (demo- graphic, economic, and political factors), spatial indicators of human activities (agriculture expansion and road extension), and forest landscape modifications (forest loss and isolation) as drivers of biodiversity change. We uncovered a significant proliferation of disturbance-tolerant guilds and the loss or decline of disturbance-sensitive guilds within reserves causing a “winner and loser” species replacement over time. Guild change was directly related to forest spatial changes promoted by the expansion of agriculture and roads within reserves. High human population density and low nonfarming occupation were identified as the main underlying drivers of biodiversity change. Our findings suggest that to mitigate anthropogenic threats to biodiversity within biosphere reserves, fostering human population well-being via sustainable, nonfarming livelihood opportunities around reserves is imperative.
... Species' pools within anthropogenically modified habitats are often constrained -taxonomically, functionally, and phylogenetically -when compared with unmodified habitats (Aronson et al. 2014, Nowakowski et al. 2018. The consequences of anthropogenic modification are apparent across taxa (Piano et al. 2020), negatively impacting abundance (Doherty et al. 2020), movement (Tucker et al. 2018), and phylogenetic and functional diversity (Sol et al. 2020). As urban and agricultural areas continue to expand (Liu et al. 2020) concomitantly with production landscapes such as forestry and mining (Curtis et al. 2018), mitigation of such negative consequences necessarily relies on quantifying the components underlying biodiversity that are most heavily impacted by anthropogenic modification. ...
Anthropogenic habitat modification is a leading contributor to biodiversity change, but it is unclear what factors, including scale, influence the magnitude of change. Changes in species richness and its scaling relationship across an anthropogenic gradient can be influenced by changes in the total number of individuals in each sample, the species abundance distribution, and/or the spatial arrangement of conspecific individuals. Here, we integrated continental‐scale citizen science data on bird occurrences across the contiguous United States – from eBird – with an analytical framework capable of dissecting the aforementioned biodiversity components to quantify bird diversity changes along an anthropogenic landscape habitat modification gradient. We found an overall decline in bird diversity along an anthropogenic modification gradient, with peak levels of bird diversity at low to moderate levels of modification. The magnitude of biodiversity change was greater at gamma than at alpha scales and was most strongly associated with a declining number of individuals along the anthropogenic gradient. Spatial species turnover was lower at higher impacted sites, but this was also due to the sampling of fewer individuals rather than changes in spatial species patchiness. Our results suggest that local‐scale management can promote bird diversity, especially at the natural–rural–suburban interface. Management efforts (e.g. managing natural habitat or preserving urban greenspaces against development) should be focused on creating, restoring, and preserving resources (e.g. nesting habitat, foraging resources) necessary for a large number of individuals, as this is the primary influence of diversity change along an anthropogenic gradient.
Species distribution modelling is a valuable tool for understanding and managing protected areas globally. This study used MaxEnt modelling with high-resolution environmental data and extensive in-situ observations to create habitat suitability maps for 16 reptile species in the highly biodiverse Souss-Massa National Park (SMNP), Morocco. The study examined the influence of environmental variables on species distribution and identified ecologically significant areas (species-rich areas). The results indicated that 94% of the models exhibited excellent predictive performance (AUC >0.9). Habitat types emerged as the most influential environmental variable for 75% of species, while the remaining taxa were primarily affected by soil type, vegetation density, and ocean proximity. Habitat suitability maps revealed distinct habitat preferences among species. The potential species richness map revealed variations within SMNP. Fenced reserves and undisturbed habitats both had a greater composition of highly diverse areas compared to unfenced and disturbed areas, respectively. The substantial proportion of disturbed areas with low species richness further supports the findings from a recent study conducted in the same area, which indicated that habitat disturbance can lead to the loss or decline of reptile populations. Priority for conservation should shift towards less protected areas to better safeguard reptile biodiversity, as most areas needing attention are outside wellprotected reserves.
Plateau Spot-tailed Earless Lizards Holbrookia lacerata are a species of ground lizard in central Texas that are under review for listing as endangered under the U.S. Endangered Species Act, but heretofore no predictive models of population dynamics or viability have been developed. We used limited available data and published demographic rates in a population viability analysis model to predict the future status of these lizards under parametric and ecological uncertainty and temporal variability. Even in cases where data are sparse and life history information are limited, viability models can help clarify the consequences of management choices given the uncertainty. Our model predicted that on average populations will decline in the future. Quasi-extinction probability was low 20 years into the future but up to 0.60 by 50 years. Extinction risk was highly dependent on the road mortality effect and the proportion of the population exposed to roadways, both of which are currently uncertain quantities. Despite these unknowns, our model enables managers to consider the future abundance and extinction risk for the species and make decisions about management to project population viability and also identifies key uncertainties for future research and monitoring.
Rock lizards of the genus Darevskia have long been an important model object for study of reptile evolution. To understand the overall picture, it is important to know how bisexual and parthenogenetic species are distributed within this genus. The ranges of Caucasian species of rock lizards have been studied for a long time and in detail. However, recent attention to the species inhabiting the territory of Iran has been attracted after the description of several new species in 2013. As part of the continuation of these studies, we studied the distribution and genetic diversity of five species of lizards of the Darevskia genus along the Alborz mountain range in Iran: D. chlorogaster, D. caspica, D. defilippii, D. schaekeli and D. raddei. In the course of this, we discovered new localities of D. defilippii that are outside their known range. We assessed the phylogenetic relationships between the studied species according to the ND4 – Leu tRNA region of mitochondrial DNA and found a relatively high level of genetic variability in D. defilippii and D. chlorogaster, while D. raddei, despite its wide distribution, has low variability. In general, the phylogenetic position of the studied species is somewhat different from that described by Ahmadzadeh et al. (2013).
It is generally assumed that deforestation affects a species consistently across space, however populations near their geographic range edge may exist at their niche limits and therefore be more sensitive to disturbance. We found that both within and across Atlantic Forest bird species, populations are more sensitive to deforestation when near their range edge. In fact, the negative effects of deforestation on bird occurrences switched to positive in the range core (>829 km), in line with Ellenberg’s rule. We show that the proportion of populations at their range core and edge varies across Brazil, suggesting deforestation effects on communities, and hence the most appropriate conservation action, also vary geographically.
Macroclimate warming is often assumed to occur within forests despite the potential for tree cover to modify microclimates. Here, using paired measurements, we compared the temperatures under the canopy versus in the open at 98 sites across 5 continents. We show that forests function as a thermal insulator, cooling the understory when ambient temperatures are hot and warming the understory when ambient temperatures are cold. The understory versus open temperature offset is magnified as temperatures become more extreme and is of greater magnitude than the warming of land temperatures over the past century. Tree canopies may thus reduce the severity of warming impacts on forest biodiversity and functioning.
Human impacts, especially land-use change, are precipitating biodiversity loss. Yet anthropogenic drivers are layered atop natural biogeographic gradients. We ask whether the effects of anthropogenic habitat conversion depend on climatic context. We studied the structure of Anolis lizard communities in intact and human-modified habitats across natural climate gradients in the northern Dominican Republic. Using community-wide mark–resight methods to control for detection bias, we show that the effects of habitat conversion reverse with elevation (and thus macroclimate temperature). Deforestation reduces abundance and biomass in lowland communities but has no such effect at high elevations. In contrast, forest loss results in no compositional change in the lowlands, but complete community turnover between habitats in the highlands. These contrasting community-level patterns emerge from consistent responses of individual species based on their thermal niches. Community reorganization in the highlands stems from thermal niche tracking and habitat switching by abundant lowland species. We find no support for the hypothesis that climate generalists outperform specialists to succeed in anthropogenic habitats. Instead, warm-climate specialists dominate anthropogenic habitats, even in cool macroclimates. Human impacts interact with pre-existing environmental gradients to reorganize biodiversity. Leveraging a biogeographic perspective will provide insight into the future communities of life on Earth. © 2019, The Author(s), under exclusive licence to Springer Nature Limited.
The brms package allows R users to easily specify a wide range of Bayesian single-level and multilevel models which are fit with the probabilistic programming language Stan behind the scenes. Several response distributions are supported, of which all parameters (e.g., location, scale, and shape) can be predicted. Non-linear relationships may be specified using non-linear predictor terms or semi-parametric approaches such as splines or Gaussian processes. Multivariate models can be fit as well. To make all of these modeling options possible in a multilevel framework, brms provides an intuitive and powerful formula syntax, which extends the well known formula syntax of lme4. The purpose of the present paper is to introduce this syntax in detail and to demonstrate its usefulness with four examples, each showing relevant aspects of the syntax.
Mapping global deforestation patterns
Forest loss is being driven by various factors, including commodity production, forestry, agriculture, wildfire, and urbanization. Curtis et al. used high-resolution Google Earth imagery to map and classify global forest loss since 2001. Just over a quarter of global forest loss is due to deforestation through permanent land use change for the production of commodities, including beef, soy, palm oil, and wood fiber. Despite regional differences and efforts by governments, conservationists, and corporations to stem the losses, the overall rate of commodity-driven deforestation has not declined since 2001.
Science , this issue p. 1108
Preventing biodiversity loss in fragmented agricultural landscapes is a global problem. The persistence of biodiversity within remnant vegetation can be influenced by an animal's ability to move through the farmland matrix between habitat patches. Yet, many of the mechanisms driving species occurrence within these landscapes are poorly understood, particularly for reptiles.
We used scented and unscented plasticine lizard models and wildlife cameras to (a) estimate predation risk of reptiles in four farmland types (crop field, pasture paddock, restoration tree planting and areas with applied woody mulch) relative to the patch edge and remnant vegetation, and (b) examine how predation risk was influenced by temporal change in the matrix (crop harvesting).
Birds (55.1%), mammals (41.1%), reptiles (3.4%), and invertebrates (0.5%) attacked models, of which 87% were native species. Mammalian predators were 60.2% more likely to attack scented models then unscented models. Bird predators were not influenced by scent.
We found predator attacks on models were highest at edges (49%, irrespective of adjacent farmland type, with a reduced risk within farmland (29%) and remnant patches (33%) (p < 0.01). Both mammal and bird predators contributed to high numbers of predation attempts at edges.
Removal of crops did not increase predation attempts in crop fields or other farmland types, although predation attempts were significantly lower along the crop transect after harvesting, compared to the woody debris transect. However, numbers of predation attempts were higher in edge habitats, particularly prior to harvesting.
Synthesis and applications. Reptiles are at risk of predation by birds and mammals in both remnant patches and the farmland matrix, particularly in edge habitat. Our results demonstrate that edge habitats are potentially riskier for lizards than the farmland. Vulnerability to predation may be increased by a lack of shelter within edge habitats such as by increasing visibility of reptiles to predators. Therefore, to benefit reptiles, land managers could provide shelter (rocks, logs, and grasses), particularly between remnants and linear plantings which could improve landscape connectivity.
Motivation
over the last 12 years I have been collecting trait and geographic data on lizards. These data could be useful for scientists studying this remarkable reptilian radiation. Furthermore, as published data for some of the less well known species are scarce, I hope this study can initiate a community effort to fill in data gaps. I present geographical, morphological, ecological, physiological and life history data for the 6,657 known species of lizards. I further indicate whether there are phylogenetic data associated with them, and their threat assessment, if they have one. I present descriptive statistics regarding these traits and point to avenues for future research using the dataset.
Main types of variable contained
body size, ecological, thermal biology, geographic, phylogenetic and life history data.
Spatial location
Global.
Time period
data are for species known from living, or recently extinct species. Most underlying data were collected during the 20th and 21st centuries.
Major taxa
Reptilia, Sauria (Squamata, including Amphisbaenia but excluding Serpentes).
Level of measurement
species.
Software format
csv.
Human activities often replace native forests with warmer, modified habitats that represent novel thermal environments for biodiversity. Reducing biodiversity loss hinges upon identifying which species are most sensitive to the environmental conditions that result from habitat modification. Drawing on case studies and a meta-analysis, we examined whether observed and modelled thermal traits, including heat tolerances, variation in body temperatures, and evaporative water loss, explained variation in sensitivity of ectotherms to habitat modification. Low heat tolerances of lizards and amphibians and high evaporative water loss of amphibians were associated with increased sensitivity to habitat modification, often explaining more variation than non-thermal traits. Heat tolerances alone explained 24–66% (mean = 38%) of the variation in species responses, and these trends were largely consistent across geographic locations and spatial scales. As habitat modification alters local microclimates, the thermal biology of species will likely play a key role in the reassembly of terrestrial communities.
The distributions of amphibians, birds and mammals have underpinned global and local conservation priorities, and have been fundamental to our understanding of the determinants of global biodiversity. In contrast, the global distributions of reptiles, representing a third of terrestrial vertebrate diversity, have been unavailable. This prevented the incorporation of reptiles into conservation planning and biased our understanding of the underlying processes governing global vertebrate biodiversity. Here, we present and analyse the global distribution of 10,064 reptile species (99% of extant terrestrial species). We show that richness patterns of the other three tetrapod classes are good spatial surrogates for species richness of all reptiles combined and of snakes, but characterize diversity patterns of lizards and turtles poorly. Hotspots of total and endemic lizard richness overlap very little with those of other taxa. Moreover, existing protected areas, sites of biodiversity significance and global conservation schemes represent birds and mammals better than reptiles. We show that additional conservation actions are needed to effectively protect reptiles, particularly lizards and turtles. Adding reptile knowledge to a global complementarity conservation priority scheme identifies many locations that consequently become important. Notably, investing resources in some of the world’s arid, grassland and savannah habitats might be necessary to represent all terrestrial vertebrates efficiently.
The brms package implements Bayesian multilevel models in R using the probabilistic programming language Stan. A wide range of distributions and link functions are supported, allowing users to fit – among others – linear, robust linear, binomial, Poisson, survival, ordinal, zero-inflated, hurdle, and even non-linear models all in a multilevel context. Further modeling options include autocorrelation of the response variable, user defined covariance structures, censored data, as well as meta-analytic standard errors. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their beliefs. In addition, model fit can easily be assessed and compared with the Watanabe-Akaike information criterion and leave-one-out cross-validation.
Domestic livestock grazing directly alters ground‐level habitat but its effects on arboreal habitat are poorly known. Similarly, the response to grazing of ground‐dwelling fauna has been examined, but there are few studies of arboreal fauna. Globally, grazing has been implicated in the decline of vertebrate fauna species, but some species appear resistant to the effects of grazing, either benefiting from the structural changes at ground level or avoiding them, as may be the case with arboreal species. Here, we examine arboreal and terrestrial habitat responses and reptile community responses to grazing, to determine whether arboreal reptile species are more resistant than terrestrial reptile species.
We conducted arboreal and terrestrial reptile surveys on four different grazing treatments, at a 19‐year experimental grazing trial in northern Australia. To compare the grazing response of arboreal and terrestrial reptile assemblages, we used community, functional group and individual species‐level analyses. Species responses were modelled in relation to landscape‐scale and microhabitat variables.
Arboreal reptile species were resistant to the impact of grazing, whereas terrestrial reptiles were negatively affected by heavy grazing. Terrestrial reptiles were positively associated with complex ground structures, which were greatly reduced in heavily grazed areas. Arboreal lizards responded positively to microhabitat features such as tree hollows.
Synthesis and applications . Arboreal and terrestrial reptiles have different responses to the impact of livestock grazing. This has implications for rangeland management, particularly if management objectives include goals relating to conserving certain species or functional groups. Arboreal reptiles showed resistance in a landscape that is grazed, but where trees have not been cleared. We highlight the importance of retaining trees in rangelands for both terrestrial and arboreal microhabitats.
Assessments of risk to biodiversity often rely on spatial distributions of species and ecosystems. Range‐size metrics used extensively in these assessments, such as area of occupancy (AOO), are sensitive to measurement scale, prompting proposals to measure them at finer scales or at different scales based on the shape of the distribution or ecological characteristics of the biota. Despite its dominant role in red‐list assessments for decades, appropriate spatial scales of AOO for predicting risks of species’ extinction or ecosystem collapse remain untested and contentious. There are no quantitative evaluations of the scale‐sensitivity of AOO as a predictor of risks, the relationship between optimal AOO scale and threat scale, or the effect of grid uncertainty. We used stochastic simulation models to explore risks to ecosystems and species with clustered, dispersed, and linear distribution patterns subject to regimes of threat events with different frequency and spatial extent. Area of occupancy was an accurate predictor of risk (0.81<|r|<0.98) and performed optimally when measured with grid cells 0.1–1.0 times the largest plausible area threatened by an event. Contrary to previous assertions, estimates of AOO at these relatively coarse scales were better predictors of risk than finer‐scale estimates of AOO (e.g., when measurement cells are <1% of the area of the largest threat). The optimal scale depended on the spatial scales of threats more than the shape or size of biotic distributions. Although we found appreciable potential for grid‐measurement errors, current IUCN guidelines for estimating AOO neutralize geometric uncertainty and incorporate effective scaling procedures for assessing risks posed by landscape‐scale threats to species and ecosystems.
Logging to “salvage” economic returns from forests affected by natural disturbances has become increasingly prevalent globally. Despite potential negative effects on biodiversity, salvage logging is often conducted, even in areas otherwise excluded from logging and reserved for nature conservation, inter alia because strategic priorities for post‐disturbance management are widely lacking.
A review of the existing literature revealed that most studies investigating the effects of salvage logging on biodiversity have been conducted less than 5 years following natural disturbances, and focused on non‐saproxylic organisms.
A meta‐analysis across 24 species groups revealed that salvage logging significantly decreases numbers of species of eight taxonomic groups. Richness of dead wood dependent taxa (i.e. saproxylic organisms) decreased more strongly than richness of non‐saproxylic taxa. In contrast, taxonomic groups typically associated with open habitats increased in the number of species after salvage logging.
By analysing 134 original species abundance matrices, we demonstrate that salvage logging significantly alters community composition in 7 of 17 species groups, particularly affecting saproxylic assemblages.
Synthesis and applications . Our results suggest that salvage logging is not consistent with the management objectives of protected areas. Substantial changes, such as the retention of dead wood in naturally disturbed forests, are needed to support biodiversity. Future research should investigate the amount and spatio‐temporal distribution of retained dead wood needed to maintain all components of biodiversity.
Landscape fragmentation alters biotic and abiotic characteristics of landscapes, variously affecting the size and demographic structure of species' populations. Fragmentation is predicted to negatively impact habitat specialists because of perturbations to their habitat, whereas generalists should be less sensitive to fragmentation. Differences in life history among the lizards in this community should partly explain some of the variation in generalist species' responses to fragmentation. During five seasons (2009–2013), we captured eight species of lizards on 27 independent trapping grids located in unfrag-mented (N = 18) and fragmented (N = 9) grids in the Mescalero-Monahans Sandhills ecosystem in southeastern New Mexico. Using a two-way ANOVA, we tested for effects of fragmentation and year on capture rates for each species. To test for effects of fragmentation on demographic structure, we used contingency tables with expected frequencies computed from the demographic structure on unfragmented grids. Capture rates of the endemic habitat specialist Sceloporus arenicolus (dunes sagebrush lizard) decreased to zero in fragmented sites. The demographic structure of S. arenicolus and Holbrookia maculata (common lesser ear-less lizard) was severely disrupted at fragmented sites, with proportions of juveniles, adult males, or adult females being over-or underrepresented during sample months. Variable responses of five generalist species could be attributed to life history patterns, habitat affinity, and breeding phenology. This is the first empirical study we are aware of that describes and quantifies the demographic effects of fragmentation on populations of multiple lizard species in a replicated study. Our findings lend important insights into how habitat specialization and differences in life history influence the susceptibility of species to the impacts of fragmentation.
Aim
Habitat modification is causing widespread declines in biodiversity and the homogenization of biotas. Amphibians are especially threatened by habitat modification, yet we know little about why some species persist or thrive in the face of this threat whereas others decline. Our aim was to identify intrinsic factors that explain variation among amphibians in their sensitivity to habitat modification (SHM), factors that could help target groups of species for conservation.
Location
Global.
Time period
1986–2015
Major taxon studied
Amphibians.
Methods
We quantified SHM using species abundances in natural and altered habitats as reported in published field surveys. We first examined associations between local SHM and range‐wide threatened status, population trends and invasiveness. We then evaluated the importance of intrinsic and extrinsic variables in explaining species SHM using multiple comparative methods. Our analyses included over 200 species that could be ranked with confidence from 47 studies across five continents.
Results
Amphibians species varied considerably in local SHM. High SHM was associated with elevated range‐wide extinction risk and declining population trends. Species that were tolerant of habitat modification were most likely to be invasive outside their native range. Geographical range size was the most important intrinsic predictor and was negatively associated with SHM. Larval habitat was also an important predictor, but was tightly coupled with phylogenetic position.
Main conclusions
Narrowly distributed species whose larvae develop on land or in lotic habitats are most sensitive to habitat modification. However, other unmeasured, phylogenetically constrained traits could underlie the effect of larval habitat. Species range size is frequently correlated with global extinction risk in vertebrates, and our analysis extends this macroecological pattern to the sensitivity of amphibians to local habitat loss, a proximate driver of extinction. These general patterns of SHM should help identify those groups of amphibians most at risk in an era of rapid habitat loss and scarce conservation resources.
The Blue Mountains water skink Eulamprus leuraensis is an Endangered swamp specialist known from < 60 sites and restricted to the rare, threatened and fragmented habitat of Temperate Highland Peat Swamps on Sandstone. Understanding the species? ecology, notably its vulnerability to threatening processes such as hydrological disturbance, is essential if we are to retain viable populations of this Endangered reptile. We examined the impact of anthropogenic disturbance (longwall mining practices, development (industrial, urban, infrastructural) and damage by recreational vehicles) on this species, other herpetofauna and the swamp by surveying six paired undisturbed and disturbed sites in south-eastern Australia. The abundance of E. leuraensis was severely affected by disturbance. The species was absent from disturbed swamps, where it was replaced by its congener E. heatwolei and other woodland reptile species. Disturbance was associated with a halving of soil moisture content and a loss of surface water; the dense, live understorey was replaced by a sparser, drier habitat with dead vegetation, logs, rocks and bare ground. In effect, disturbance eliminated the distinctive features of the swamp habitat, transforming it into an area that resembled the surrounding habitat in terms of fauna, flora and physical characteristics. Our surveys suggest that hydrological disturbance (groundwater loss or alterations in surface water chemistry) extirpates E. leuraensis . This species' dependence on groundwater renders it sensitive to habitat degradation through hydrological disturbance. The conservation message for management authorities is clear: to protect the skink, protect the habitat.
Leave-one-out cross-validation (LOO) and the widely applicable information criterion (WAIC) are methods for estimating pointwise out-of-sample prediction accuracy from a fitted Bayesian model using the log-likelihood evaluated at the posterior simulations of the parameter values. LOO and WAIC have various advantages over simpler estimates of predictive error such as AIC and DIC but are less used in practice because they involve additional computational steps. Here we lay out fast and stable computations for LOO and WAIC that can be performed using existing simulation draws. We introduce an efficient computation of LOO using Pareto-smoothed importance sampling (PSIS), a new procedure for regularizing importance weights. Although WAIC is asymptotically equal to LOO, we demonstrate that PSIS-LOO is more robust in the finite case with weak priors or influential observations. As a byproduct of our calculations, we also obtain approximate standard errors for estimated predictive errors and for comparison of predictive errors between two models. We implement the computations in an R package called loo and demonstrate using models fit with the Bayesian inference package Stan.
Cattle grazing is being used increasingly by landowners and statutory conservation bodies to manage heathlands in parts of mainland Europe and in the UK, where it is called ‘conservation grazing’. Between 2010 and 2013, cattle were excluded from six hectares of lowland heath, in southern England, that had been subject to annual summer cattle grazing between May 1997 and autumn 2009. Changes in grass snake Natrix natrix, common lizard Zootoca vivipara, slow worm Anguis fragilis and sand lizard Lacerta agilis numbers were recorded annually in the ungrazed area and in a four hectare area of heathland adjacent to it that continued to be grazed. The number of grass snake, common lizard and slow worm sightings were significantly higher in the ungrazed heath than the grazed heath and were associated with increased habitat structure, resulting principally from increased height and cover of grasses, particularly Molinia caerulea. Conversely, there was no significant difference in the number of adult sand lizard sightings between the grazed and ungrazed heath though sighting frequency was inversely correlated with both grass and grass litter cover. Our results suggest that the use of cattle grazing as a management tool on lowland heath is detrimental to grass snake, slow worm and common lizard populations but may be less so to adult sand lizards. Although newborn slow worms and common lizards were observed throughout the study area, significantly fewer were found in the grazed areas than the ungrazed areas. The absence of newborn grass snakes and sand lizards in the grazed areas suggests that successful breeding had not occurred in these areas.
Restoration can be important in slowing, or reducing, rates of biodiversity loss, but needs to consider the factors influencing fauna recolonization as part of the recovery process. Although many studies of factors influencing faunal recolonization have examined the influence of in situ site factors, fewer have examined the influence of neighborhood landscape factors, especially in landscapes with permeable matrices. To assess the relative influence of landscape and site factors on reptile recolonization in a production landscape with a permeable matrix, we surveyed reptiles at intact reference sites and post-mining restoration sites (3–20 years post-mining [YPM]) in a forest ecosystem in southwestern Australia. Reptile assemblages in restoration sites never converged on those in reference habitat. Reptile species composition and individual species abundances (>20 detections) in restoration sites were primarily influenced by site factors such as canopy height, litter cover, and coarse woody debris volume, and not by landscape factors. We suggest that the most common reptile species in our study area are primarily influenced by site factors, not landscape factors, and most reptiles detected in restoration sites were present by 3–4 YPM. Therefore, it is likely that habitat suitability is the main barrier to most species' recolonization of restoration sites in landscapes with permeable matrices. Management should continue to focus on restoring microhabitats and vegetation structure, which is similar to reference habitat to promote recolonization of restoration sites by reptiles.
Land use has large effects on the diversity of ecological assemblages. Differences among land uses in the diversity of local assemblages (alpha diversity) have been quantified at a global scale. Effects on the turnover of species composition between locations (beta diversity) are less clear, with previous studies focusing on particular regions or groups of species. Using a global database on the composition of ecological assemblages in different land uses, we test for differences in the between–site turnover of species composition, within and among land–use types. Overall, we show a strong impact of land use on assemblage composition. While we find that compositional turnover within land uses does not differ strongly among land uses, human land uses and secondary vegetation in an early stage of recovery are poor at retaining the species that characterise primary vegetation. The dissimilarity of assemblages in human–impacted habitats compared with primary vegetation was more pronounced in the tropical than temperate realm. An exploratory analysis suggests that this geographic difference might be caused primarily by differences in climate seasonality and in the numbers of species sampled. Taken together the results suggest that, while small–scale beta diversity within land uses is not strongly impacted by land–use type, compositional turnover between land uses is substantial. Therefore, land–use change will lead to profound changes in the structure of ecological assemblages. This article is protected by copyright. All rights reserved.
Habitat loss and degradation are primary threats to amphibians and reptiles, but the relative effects of common anthropogenic habitats on assemblages and the mechanisms that underlie faunal responses are poorly studied. Here we reviewed the effects of four prevalent types of habitat alteration (urbanization, agriculture, grazing, and silviculture) on amphibian and reptile species richness and abundance by summarizing reported responses in the literature and by estimating effect sizes across studies for species richness in each land-use type. We then used a multinomial model to classify species as natural habitat specialists, generalists, and disturbed habitat specialists and examined variation in effect sizes for each land-use type according to habitat specialization categories. There were mixed conclusions from individual studies, some reporting negative, neutral, or positive effects of land use on species richness and total abundance; a large proportion of studies reported species-specific effects of individual species abundance. However, in our analysis of effect sizes, we found a general trend of negative effects of land use on species richness. We also illustrate that habitat associations of common species and species turnover can explain variation in the effect of land use on herpetofauna. Our review highlights the pervasive negative effects of common land uses on amphibians and reptiles, the importance of identifying groups vulnerable to land-use change (e.g., forest-associated species) in conservation studies, and the potential influence of disturbance-associated species on whole assemblage analyses. This article is protected by copyright. All rights reserved.
Heathland in the UK, and parts of mainland Europe, is being managed increasingly by landowners and statutory conservation bodies e.g., Natural England, using cattle grazing which is often referred to as 'conservation grazing' in an attempt to justify its use in the absence of any detailed prior research into its actual benefits for wildlife species whose individual habitat requirements are likely to vary. Over four years, between 2010 and 2013, cattle were excluded from six hectares of lowland heath that had been subject to annual summer cattle grazing between May 1997 and autumn 2009 and in which reptile numbers had been monitored annually since 1997. Changes in smooth snake (Coronella austriaca) numbers were recorded annually in the ungrazed area and in a four hectare area of heathland adjacent to it that continued to be grazed. The number of individual smooth snakes, and the total number of smooth snake captures, were significantly higher in the ungrazed heath than the grazed heath and were associated with increased habitat structure, resulting principally from tall heathers and grasses. The results of the study suggest that the use of cattle grazing as a management tool on lowland heath is detrimental to smooth snake populations and that their recovery, following the cessation of grazing, may take many years.
One of the fundamental concepts in meta-analysis is that of the effect size. An effect size is a statistical parameter that can be used to compare, on the same scale, the results of different studies in which a common effect of interest has been measured. This chapter describes the conventional effect sizes most commonly encountered in ecology and evolutionary biology, and the types of data associated with them. While choice of a specific measure of effect size may influence the interpretation of results, it does not influence the actual inference methods of meta-analysis. One critical point to remember is that one cannot combine different measures of effect size in a single meta-analysis: once you have chosen how you are going to estimate effect size, you need to use it for all of the studies to be analyzed.
Phylogeny is a potentially powerful tool for conserving biodiversity. This book explores how it can be used to tackle questions of great practical importance and urgency for conservation. Using case studies from many different taxa and regions of the world, the volume evaluates how useful phylogeny is in understanding the processes that have generated today's diversity and the processes that now threaten it. The novelty of many of the applications, the increasing ease with which phylogenies can be generated, the urgency with which conservation decisions have to be made and the need to make decisions that are as good as possible together make this volume a timely and important synthesis which will be of great value to researchers, practitioners and policy-makers alike.
1. Testing the extent to which traits act alone or in combination with other traits to influence responses to fire informs the trade‐off between increased generalisation using single traits and increased predictive power using interactions. This study investigated the following question: do four traits (body size, trophic group, dispersal ability, and stratum of the ecosystem), alone or in combination, best explain changes in beetle occurrence with time since fire?
2. The data from 4 years and 15 independent fires in southern Australia were analysed using generalised linear mixed models. The study also assessed whether detectability depends on time since fire using multi‐year detection models, because detectability has the potential to confound occurrence patterns.
3. The best model included the three‐way combination of size, flight, and trophic level interacting with time since fire and with year. The relationship between detectability and time since fire was similar to the occurrence relationship in six of the 10 trait–combination groups, with flightless species generally showing reduced detection probability as time since fire increased. Detectability did not confound occurrence responses for four trait groups, with three increasing with time since fire and one decreasing.
4. Generalisation using main effects of traits risks oversimplifying animal responses to fire, because combinations of traits influence the direction and magnitude of the response. Also, taking detectability into account is critical to correctly interpretating occupancy data. Three‐way trait combinations that differ by just one trait, particularly dispersal ability, can result in either negligible effects of disturbance on detectability or strong effects that influence observed occurrence.
Nesting success is critical for oviparous species to maintain viable populations. Many species often do not provide parental care (e.g. oviparous reptiles), so embryos are left to develop in the prevailing conditions of the nest. For species that occupy diverse habitats, embryos must be able to complete development across a broad range of environmental conditions. Although much research has investigated how environmental conditions influence embryo development, we know little about how nest conditions differ between diverse habitats. Anolis lizards are commonly found in various habitats including those heavily modified by humans (e.g. cities). We describe nest sites of anoles in two different habitat types: a suburban area and a nearby forest. The suburban area had less total nesting habitat but a greater variety of microenvironment conditions for females to use for nesting, compared to the forest. Suburban nests were warmer and drier with greater thermal variance compared to forest nests. Finally, we use data from the literature to predict how nest conditions may influence development. Our study provides the first quantitative assessment of anole nest sites in human-modified environments and shows how suburban habitats may generate variation in developmental rate.
Socioeconomic factors (e.g. rural abandonment, monoculture plantations) and global warming are changing fire
regimes (fire intensity, extent, and frequency) in fire-prone regions such as the Mediterranean Basin. Understanding
the factors that shape responses of animal communities to fire is a key objective for biodiversity conservation.
Given the substitution of native forests to pine plantations in many regions of the world, we studied whether forest
type influences the responses to fire of reptile communities, in the African rim of the Western Mediterranean.
Reptiles were sampled and vegetation structure measured in 2015 and 2016. We used generalized linear mixed
models to examine the influence of fire, forest type (cork oak and pine), habitat structure and climate factors
on two reptile-community metrics (abundance, species richness). Given possible differences in reptile detectability
between unburnt and burnt transects, we used distance sampling models to estimate the density of the five
commonest reptile species. The response of reptiles to fire varied between the two forest types: reptile abundance
did not change with fire in cork oak forest, and increased with fire in pine plantation. Species richness
was higher in cork oak forests, and increased from unburnt to burnt areas. Two out of five commonest lizards in
the region, Acanthodactylus erythrurus and Podarcis vaucheri, responded positively to fire in pine plantation and
remained similar in cork oak forest. Reptile communities were more similar between burnt and unburnt cork oak
forests than between burnt and unburnt pine plantations, due to the reduced effect of fire on the former tree (a
resprouter species) than on the latter (a seeder species). This work is the first field-based study examining the
effects of fire on animal communities from north-western Africa. Overall, our results show that the response of
reptiles to fire is shaped by forest type, and this conclusion has to be considered in fire-prone regions.
Developing meta-analytic methods is an important goal for psychological science. When there are few studies in particular, commonly used methods have several limitations, most notably of which is underestimating between-study variability. Although Bayesian methods are often recommended for small sample situations, their performance has not been thoroughly examined in the context of meta-analysis. Here, we characterize and apply weakly informativepriors for estimating meta-analytic models and demonstrate with extensive simulations that fully Bayesian methods overcome boundary estimates of exactly zero between-study variance, better maintain error rates, and have lower frequentist risk according toKullback-Leibler divergence. While our results show that combining evidence with few studiesis non-trivial, we argue that this is an important goal that deserves further considerationin psychology. Further, we suggest that frequentist properties can provide importantinformation for Bayesian modeling. We conclude with meta-analytic guidelines for appliedresearchers that can be implemented with the provided computer code.
Species’ traits have been widely championed as the key to predicting which species are most threatened by habitat loss, yet previous work has failed to detect trends that are consistent enough to guide large-scale conservation and management. Here we explore whether traits and environmental variables predict species sensitivity to habitat loss across two datasets generated by independent avifaunal studies in the Atlantic Forest of Brazil, both of which detected a similar assemblage of species, and similar species-specific responses to habitat change, across an overlapping sample of sites. Specifically, we tested whether 25 distributional, climatic, ecological, behavioral and morphological variables predict sensitivity to habitat loss among 196 bird species, both within and across studies, and when data were analysed as occurrence or abundance. We found that 4-9 variables showed high explanatory power within a single study or dataset, but none performed as strong predictors across all datasets. Our results demonstrate that the use of species traits to predict sensitivity to anthropogenic habitat loss can produce predictions that are species- and site-specific and not scalable to whole regions or biomes, and thus should be used with caution. This article is protected by copyright. All rights reserved.
In arid environments, grazing by exotic herbivores, including domestic livestock, can greatly influence native, small vertebrate assemblages. Whether the removal of livestock facilitates passive recovery of these assemblages depends on habitat condition and the species present. We explore changes in small mammal and reptile species richness, abundance, and composition in a degraded chenopod shrubland dominated by Acacia victoriae ssp. and open Acacia aneura (mulga) woodland destocked in 1976 and 1984, respectively. Data were obtained between 1997 and 2007, from two grazed and two ungrazed sites in each community. Species richness increased at a faster rate in ungrazed open A. aneura woodland, but did not differ significantly between ungrazed and grazed degraded chenopod shrubland. Subsequent analyses at a finer-scale detected disparate responses in richness and abundance for microhabitat. At this scale, a greater number of species-specific responses were also detected, including increased abundance of generalist species and decreased abundance of species requiring low cover. These results reiterate the potential for species-specific responses to livestock that are more apparent in particular microhabitats. Furthermore, this investigation provides evidence for the gradual passive recovery of small mammal and reptile assemblages in both communities, which is facilitated by the removal of livestock in open A. aneura woodland in fair condition, but not degraded chenopod shrubland in poor condition.
The response and effect trait framework, if supported empirically, would provide for powerful and general predictions about how biodiversity loss leads to loss in ecosystem function. This framework proposes that species traits will explain how different species respond to disturbance (i.e. response traits) as well as their contribution to ecosystem function (i.e. effect traits). However, predictive response and effect traits remain elusive for most systems. Here, we use data on crop pollination services provided by native, wild bees to explore the role of six commonly used species traits in determining both species' response to land-use change and the subsequent effect on crop pollination. Analyses were conducted in parallel for three crop systems (watermelon, cranberry, and blueberry) located within the same geographical region (mid-Atlantic USA). Bee species traits did not strongly predict species' response to land-use change, and the few traits that were weakly predictive were not consistent across crops. Similarly, no trait predicted species' overall functional contribution in any of the three crop systems, although body size was a good predictor of per capita efficiency in two systems. Overall we were unable to make generalizable predictions regarding species responses to land-use change and its effect on the delivery of crop pollination services. Pollinator traits may be useful for understanding ecological processes in some systems, but thus far the promise of traits-based ecology has yet to be fulfilled for pollination ecology. This article is protected by copyright. All rights reserved.
Managing agricultural landscapes for biodiversity conservation is increasingly difficult as land use is modified or intensified for production. Finding ways to mitigate the negative effects of agriculture on biodiversity is therefore critical. We asked the question: How do remnant patches, paddock types and grazing regimes influence reptile assemblages in a grazing landscape?
At 12 sites, we surveyed reptiles and environmental covariates in remnant woodland patches and in four paddock types: (i) grazed pasture, (ii) linear plantings, (iii) coarse woody debris (CWD) added to grazed pasture and (iv) fences between grazed pasture. Each site was either continuously or rotationally grazed.
Remnant vegetation and other vegetation attributes such as tree cover and leaf litter greatly influenced reptiles. We recorded higher reptile abundance and species richness in areas with more tree cover and leaf litter. For rare species (captured in ≤4 sites <70 captures), there were 5·7 more animals and 2·6 more species in sites with 50% woody cover within 3 km compared to 5% woody cover.
The abundance and richness of rare species, and one common species differed between paddock types and were higher in linear plantings and fence transects compared to CWD and pasture transects.
Synthesis and applications . Grazed paddocks, particularly those with key features such as fences and plantings can provide habitat for reptiles. This suggests that discrete differentiation between patch and matrix does not apply for reptiles in these systems. Management to promote reptile conservation in agricultural landscapes should involve protecting existing remnant vegetation, regardless of amount; and promote key habitat features of trees, leaf litter and shrubs. Establishing plantings and fences is important as they support high numbers of less common reptiles and may facilitate reptiles to move through and use greater amounts of the landscape.
Aim
Dietary niche breadth has long been hypothesized to decrease towards lower latitudes as the numbers of competitors increase. Geographical variation in niche breadth is also hypothesized to be linked to high ambient energy levels, water availability, productivity and climate stability – reflecting an increased number of available prey taxa. Range size and body size are also hypothesized to be strongly and positively associated with niche breadth. We sought to determine which of these factors is associated with geographical variation in niche breadth across broad spatial scales and thus potentially drive the latitudinal diversity gradient.
Location
Global.
Methods
We collated volumetric dietary data for 308 lizard species. For each species, we gathered data on number of sympatric lizard species (a proxy for the number of competitors), annual temperature and precipitation, net primary productivity, seasonality, range size and body size. We examined the relationship between dietary niche breadth and focal parameters using both ordinary and phylogenetic generalized least squares regressions.
Results
Niche breadth was positively related to annual precipitation, temperature seasonality and range size, and negatively related to body size. Lizard species richness increased towards lower latitudes. Dietary niche breadth, however, was unrelated to parameters reflecting diversity gradients, such as primary productivity, annual temperature, precipitation seasonality and, crucially, the number of potential competitors.
Main conclusions
Contrary to prevailing ecological theory, competition is unrelated to dietary niche breadth. We found no support for interspecific competition driving the latitudinal diversity gradient. Rather, we found variation in niche breadth to be associated with water availability, climate stability, range size and body size. Our study casts doubt on the common assumption that tropical species are specialists, promoting greater alpha diversity, and on the assumption that the number of sympatric species is reflected in the intensity of interspecific competition.
Understanding how traits affect species responses to threats like habitat loss may help prevent extinctions. This may be especially true for understudied taxa for which we have little data to identify declines before it is too late to intervene. We used a metric derived from citizen science data on snake occurrences to determine which traits were most correlated with species' sensitivity to human land use. We found that snake species that feed primarily on vertebrates, that use a high proportion of aquatic habitats, and that have small geographic ranges occurred in more natural and less human-dominated landscapes. In contrast, body size, clutch (or litter) size, the degree of exposure to human-dominated landscapes, reproductive mode, habitat specialization, and whether a species was venomous or not had less effect on their sensitivity to human land use. Our results extend previous findings that higher trophic position is correlated with extinction risk in many vertebrates by showing that snake species that feed primarily on vertebrates are more sensitive to human land use – a primary driver of extinction. It is likely that conversion of natural landscapes for human land use alters biotic communities, causing losses of important trophic groups, especially in aquatic and riparian communities. Practitioners should therefore prioritize preserving aquatic habitat and natural landscapes with intact biotic communities that can support species at higher trophic levels, as well as focus monitoring on populations of range-restricted species.
Aim
Elucidating patterns in species responses to habitat fragmentation is an important focus of ecology and conservation, but studies are often geographically restricted, taxonomically narrow or use indirect measures of species vulnerability. We investigated predictors of species presence after fragmentation using data from studies around the world that included all four terrestrial vertebrate classes, thus allowing direct inter-taxonomic comparison.
Location
World-wide.
Methods
We used generalized linear mixed-effect models in an information theoretic framework to assess the factors that explained species presence in remnant habitat patches (3342 patches; 1559 species, mostly birds; and 65,695 records of patch-specific presence–absence). We developed a novel metric of fragmentation sensitivity, defined as the maximum rate of change in probability of presence with changing patch size (‘Peak Change’), to distinguish between general rarity on the landscape and sensitivity to fragmentation per se.
Results
Size of remnant habitat patches was the most important driver of species presence. Across all classes, habitat specialists, carnivores and larger species had a lower probability of presence, and those effects were substantially modified by interactions. Sensitivity to fragmentation (measured by Peak Change) was influenced primarily by habitat type and specialization, but also by fecundity, life span and body mass. Reptiles were more sensitive than other classes. Grassland species had a lower probability of presence, though sample size was relatively small, but forest and shrubland species were more sensitive.
Main conclusions
Habitat relationships were more important than life-history characteristics in predicting the effects of fragmentation. Habitat specialization increased sensitivity to fragmentation and interacted with class and habitat type; forest specialists and habitat-specific reptiles were particularly sensitive to fragmentation. Our results suggest that when conservationists are faced with disturbances that could fragment habitat they should pay particular attention to specialists, particularly reptiles. Further, our results highlight that the probability of presence in fragmented landscapes and true sensitivity to fragmentation are predicted by different factors.
Imperfect detection of individuals within an animal population can bias estimates of abundance and other population metrics. However, detectability may be improved by timing surveys with conditions that increase detection among individuals of the population. We explored the weather conditions that promote surface activity in a burrowing desert lizard, Slater's skink Liopholis slateri, with the aim of increasing detectability in observational surveys for this endangered species. We matched repeated count data (n = 126) of individuals within a population of Slater's skink sampled across four survey years with corresponding weather observations. We used classification and regression tree (CART) models to determine the environmental conditions that promoted high skink counts, and by inference high levels of surface activity. We also investigated how individual activity patterns varied over a day–night cycle through the course of a survey year using remote infrared cameras at burrow entrances set to capture images every 30 min. We found that two weather variables, air temperature and humidity, influenced activity levels, but there was no consistent single covariate, or set of covariates that explained surface activity. Variation in results of analysis between morning and evening datasets suggests that lizards respond to different weather conditions at different times of the day. We also found evidence of previously unreported nocturnal activity during the hottest months of the year.
Sustainable forest management is vital in today's human-dominated landscapes. An important part of sustainable management is protecting biodiversity, including herpetofauna (reptiles and amphibians). To examine the effects of landscape-scale forest management on a diverse herpetofauna community in oak-dominated forests in the Missouri Ozarks, we experimentally assessed differences in herpetofaunal diversity among 3 treatments (i.e., forest management systems) over 2 decades through the Missouri Ozark Forest Ecosystem Project. We assigned 9 forest compartments to 1 of 3 blocks, such that each block contained 3 compartments, and then randomly assigned 1 compartment within each block to a treatment: even-aged; uneven-aged; or no-harvest management. Management entries occurred in 1996 and 2011. We installed 12 herpetofauna trap arrays per compartment; 6 on north and east slopes and 6 on south and west slopes. We conducted trapping for 14 years during the 23 year study period, and used a variety of metrics to assess diversity, including species richness, Shannon Diversity, Jaccard's and Morisita's Indices of Similarity, and species-list occupancy. Results indicated minimal difference in herpetofaunal diversity among treatments at the landscape-scale after 23 years of management. Notable year-to-year variations in diversity were observed through time across treatments, likely due to changes in detectability. However, detection did not differ among treatments in species-list occupancy models, indicating that species richness and similarity metrics assessing differences between forest management strategies without accounting for detection are reliable for this study. We found no evidence that overall herpetofaunal diversity was negatively impacted by even-aged, uneven-aged, or no-harvest forest management in the Missouri Ozarks at the scale of forest compartments over this time period.
Habitat disturbance poses a major threat to biodiversity worldwide. The broad-headed snake (Hoplocephalus bungaroides) has become Australia's most endangered snake due to a dependence on rock habitats that are subject to high rates of human-induced degradation. The permanence of degradation can only be reversed by outcrop restoration. We constructed experimental outcrops near (<150 m) and far (>500 m) from roads and walking trails (access points). We tested two hypotheses over a 14-year period: that outcrop restoration can restore habitat quality, and that the frequency of outcrop degradation is influenced by distance from access points. We confirmed that habitat value was restored: lizard prey of the broad-headed snake was more abundant in constructed compared to natural outcrops; broad-headed snakes were detected equally in constructed and natural outcrops. Disturbance to constructed outcrops occurred more often and was more severe at near compared to far outcrops. The probability of occupancy by broad-headed snakes was 0.75 ± 0.13 in 29 far outcrops compared to 0.41 ± 0.11 in 35 near outcrops, suggesting a response to disturbance and more frequent poaching at near outcrops. Habitat restoration for the broad-headed snake should have its greatest value at locations far from access points. Restricting access should be a principal strategy to manage rock outcrop ecosystems. Outcrop disturbance is not unique to Australia. These findings have relevance to management of rock outcrops worldwide. Habitat restoration is an expensive conservation tool for endangered species, particularly if unsuccessful. Small-scale restoration experiments that aim to refine procedures should precede large-scale restoration.
1. The concept of biodiversity conservation relies primarily on protected areas. Yet, protected
areas are influenced by the surrounding anthropogenic matrix as degradation of landscapes
used by humans also has negative consequences on species within the adjacent protected, nondegraded
ecosystems. Increasing the heterogeneity of the anthropogenic landscape has the
potential to promote biodiversity conservation in protected and non-protected sites.
2. To find options for reconciling land use and biodiversity conservation, we evaluated reptile
diversity of two areas. Both areas contained three types of habitat: cultivated areas,
degraded forest and undegraded forest. In one area (Tsim), a network of hedges surrounding
fields provided a variety of possible resources for reptile species. Another area (Andremba)
lacked such landscape elements.
3. In 480 survey walks on 48 transects evenly distributed over two areas, we recorded a total
of 24 reptile species, of which 18 occurred in both areas.
4. Perennial plant cover explained the variation in local (per transect) species richness best.
Species richness was low along field margins in the cultivated area that lacked hedges and
had a perennial plant cover below 20%. It was high in undegraded and degraded forest and
along hedges in the cultivated area where perennial plant cover was above 40%.
5. Similarities of reptile assemblages were higher between habitat types in the area structurally
enriched with hedges, than in the area lacking such enrichment. In the latter area, beta diversity was
largely the result of species losses which could result from impeded movement between habitats.
6. Synthesis and applications. A continuous network of hedges and associated trees and
shrubs contribute to the maintenance of reptile biodiversity in dry south-western Madagascar.
When present, these interconnected landscape elements enhance habitat suitability of the agriculturally
used matrix. They also provide habitat for species of conservation concern. High
similarity between assemblages in the area with hedges indicated that movement between
habitats was facilitated. We conclude that incorporating hedges in pastures contributes not
just to the suitability of the matrix, but also enhances landscape connectivity and thus
improves biodiversity conservation in the human-used landscape.
Conventional logging (CL) in Amazonia is usually done without planning, resulting in a marked increase in canopy gaps, while reduced-impact logging (RIL) techniques can reduce the number of gaps by 50%. The lizard Kentropyx calcarata is known to be relatively common in those canopy gaps. We made a comparative evaluation of how the structural damage caused by CL and RIL affects K. calcarata. The study was carried out at Cauaxi Ranch, Paragominas district, Pará state, and used data from monthly samples between August and December 2000. We compared ecological and behavioral aspects of lizard populations in RIL (100 ha) and CL (100 ha), with unlogged forest (UF = 100 ha). For each area and sampling period the lizards were observed within five replicate 500-m transects, and time of day, behavior, macrohabitat (forest, gap, border), microhabitat (litter, fallen trunks, branches, leaves) and microclimate (sun, filtered sun, shade) recorded. Forest structure variables (canopy openness, understory density, and litter depth) were recorded at 50-m intervals along each transect. More lizards were observed in CL than in UF or RIL; 88 lizards were collected to record cloacal temperature and perform stomach content analyses. CL contained the largest gaps, exhibited a higher understory density, and a lower litter depth. RIL exhibited intermediate values between UF and CL. Lizards showed longer activity periods in CL, while thermoregulatory and foraging behaviors were similar in UF and RIL, and both were different from CL. The diversity of prey items taken by the lizards captured in RIL and CL were similar, but were distinct from UF, although Orthoptera, Blattodea, and Araneae were the most common prey items in all areas. Lizards captured in CL took significantly more prey items than those captured in UF and RIL. These results suggest that reduced-impact logging maintains a physical structure more similar to intact forests than conventional logging techniques.
Ecologists have used a variety of comparative mensurative and manipulative experimental approaches to study the biological consequences of habitat fragmentation. In this paper, we evaluate the merits of the two major approaches and offer guidelines for selecting a design. Manipulative experiments rigorously assess fragmentation effects by comparing pre- and post-treatment conditions. Yet they are often constrained by a number of practical limitations, such as the difficulty in implementing large-scale treatments and the impracticality of measuring the long-term (decades to centuries) responses to the imposed treatments. Comparative mensurative studies generally involve substituting space for time, and without pre-treatment control, can be constrained by variability in ecological characteristics among different landscapes. These confounding effects can seriously limit the strength of inferences. Depending on the scale of the study system and how "landscape" is defined, both approaches may be limited by the difficulty of replicating at the landscape scale. Overall, both mensurative and manipulative approaches have merit and can contribute to the body of knowledge on fragmentation. However, from our review of 134 fragmentation studies published recently in three major ecological journals, it is evident that most manipulative and mensurative fragmentation experiments have not provided clear insights into the ecological mechanisms and effects of habitat fragmentation. We discuss the reasons for this and conclude with recommendations for improving the design and implementation of fragmentation, experiments.
Aim
Size is one of the most important and obvious traits of an organism. Both small and large sizes have adaptive advantages and disadvantages. Body size–frequency distributions of most large clades are unimodal and right skewed. Species larger than the mean or range midpoint of body sizes are relatively scarce. Theoretical models suggest evolutionary rates are higher in small organisms with short generation times. Therefore diversification rates are usually thought to be maximal at relatively small body sizes. Empirical studies of the rates of molecular evolution and clade diversification, however, have usually indicated that both are unrelated to body size. Furthermore, it has been claimed that because snakes are longer than lizards, the size–frequency distribution of all squamate species is bimodal overall. We examined the shape of the size–frequency distribution of nearly all Squamata and Rhynchocephalia species, and investigated how size affected diversification rates.
Location
Global.
Methods
We collected data on maximum body length for 9805 lepidosaur (squamates and the tuatara) species (99.7% of all species) and converted them to mass using clade‐specific allometric equations. Using methods that test for relationships between continuous traits and speciation and extinction rates on a large, dated phylogeny (4155 species), we investigated the relationship between diversification rates and body size.
Results
Living squamates span six orders of magnitude in body size, eight when giant extinct snakes and mosasaurs are included. The body size–frequency distributions of snakes and lizards separately, and of all lepidosaur species combined, are unimodal and right skewed. Nonetheless, we find neither linear nor hump‐shaped relationships between size and diversification rates, except in snakes, where speciation and diversification are hump shaped.
Main conclusions
Despite a clear modality and skew in the body sizes of lepidosaurs, we find little evidence for faster diversification of modal‐sized taxa, perhaps implying that larger‐sized clades are relatively young.
Leave-one-out cross-validation (LOO) and the widely applicable information
criterion (WAIC) are methods for estimating pointwise out-of-sample prediction
accuracy from a fitted Bayesian model using the log-likelihood evaluated at the
posterior simulations of the parameter values. LOO and WAIC have various
advantages over simpler estimates of predictive error such as AIC and DIC but
are less used in practice because they involve additional computational steps.
Here we lay out fast and stable computations for LOO and WAIC that can be
performed using existing simulation draws. We compute LOO using Pareto smoothed
importance sampling (PSIS), a new procedure for regularizing importance
weights. As a byproduct of our calculations, we also obtain approximate
standard errors for estimated predictive errors and for comparing of predictive
errors between two models. We implement the computations in an R package called
'loo' and demonstrate using models fit with the Bayesian inference package
Stan.