Project

Hierarchical Models in Herpetological Studies

Goal: Evaluate the effectiveness of hierarchical models (Occupancy and N-mixture) in herpetology:
- To study the ecology of amphibians and reptiles
- To estimate population abundance
- To inform practitioners and drive conservation plans


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Andrea Costa
added 2 research items
Reptile populations are relevant components of biodiversity in both temperate and tropical forests. However, in forest habitats reptiles are secretive and the complex structure of the environment makes it difficult to assess with confidence their abundance and density. In general, capture-mark-recapture (CMR) or distance sampling (DS) are used to estimate demographic parameters of reptiles in these complex habitats. CMR may be expensive in terms of time, materials and sampling effort, while DS is strongly biased when animals lying on the transect line are overlooked. In this study, we applied a combination of CMR and hierarchical distance sampling (HDS) to estimate the density of the Common Wall Lizard (Podarcis muralis), a widespread Mediterranean terrestrial reptile. We randomly placed linear transects in a deciduous woodland (i.e Castanea sativa), in a coniferous plantation forest (Pinus nigra) and in a dry prairie habitat, and we applied a hierarchical mark-recapture distance sampling (HMRDS) protocol. Density estimates were similar between the deciduous woodland (47 individuals/ha) and the dry prairie habitat (44 individuals/ha), while markedly lower in the coniferous plantation forest (13 individuals/ha). HMRDS data, analyzed in a Bayesian framework, showed the importance of correcting for the assumption of complete detection on the transect line, in all the three habitat types. Therefore, our approach should be useful when assessing the density of small and cryptic terrestrial animals, not only in forest but also in habitat with an apparently less complex vegetation structure.
Spatial distribution of animals is affected by environmental and social factors, acting both at inter- and intraspecific levels, and generating patterns of segregation or aggregation. Several studies investigated age-class segregation of the European Cave Salamander Speleomantes strinatii, in underground environments, showing a clear spatial segregation. We investigated the spatial distribution of S. strinatii on the forest floor, on 111 plots surveyed three times/season for two consecutive seasons, in northern Italy during autumn 2017 and spring 2018. We analyzed count data to model co-abundance of adults and juveniles, using a conditional two-species N-mixture model, incorporating environmental covariates. In contrast with what was observed in underground environments, we recorded no spatial segregation between juvenile and adult of S. strinatii on the forest floor. Instead, we found that adults and juveniles showed different responses to environmental features.
Andrea Costa
added a research item
Monitoring wild populations is an essential tool to assess the conservation status and the ecological requirements of a species. Capture–mark–recapture (CMR), based on individual recognition, is the most commonly used and most effective technique. However, in cases of species with no individual color pattern, tracing the encounter history of individuals without invasive marking methods is impossible. In this study we aimed to (1) estimate population abundance and density using a less effort-intensive and nonstressful technique, (2) test a long-term monitoring protocol, and (3) assess the fine-scale ecological requirements of a black-colored amphibian, Salamandra atra, in the Italian Alps. For three populations we applied an N-mixture model on data collected using a dependent double-observer approach. To understand ecological requirements, we assessed the relative importance of a set of environmental and topographical variables. The double-observer approach was a cost-effective technique that provided reliable demographic estimates of population density. Our results suggest that the most important fine-scale ecological variables positively associated with salamander abundance were canopy cover and terrain ruggedness, which are strictly related to shelter availability and soil moisture.
Marco Basile
added a research item
N-mixture models usually rely on a meta-population design, in which repeated counts of individuals in multiple sampling locations are obtained over time. The time-for-space substitution (TSS) in N-mixture models allows to estimate population abundance and trend of a single population, without spatial replication. This application could be of great interest in ecological studies and conservation programs; however, its reliability has only been evaluated on a single case study. Here we perform a simulation-based evaluation of this particular application of N-mixture modelling. We generated count data, under 144 simulated scenarios, from a single population surveyed several times per year and subject to different dynamics. We compared simulated abundance and trend values with TSS estimates. TSS estimates are overall in good agreement with real abundance. Trend and abundance estimation is mainly affected by detection probability and population size. After evaluating the reliability of TSS, both against real world data, and simulations, we suggest that this particular application of N-mixture model could be reliable for monitoring abundance in single populations of rare or difficult to study species, in particular in cases of species with very narrow geographic ranges, or known only for few localities.
Andrea Costa
added a research item
Information on population abundance is important to correctly plan conservation and management of animal populations. In general, capture-mark-recapture (CMR) is considered the most robust technique to estimate population abundance, but it is costly in terms of time and effort. Recently, binomial N-mixture models, based on counts of unmarked individuals, have been widely employed to estimate abundance. These models have limits and their reliability has been criticized. In the majority of cases, multinomial N-mixture models based on multiple observer protocols, that are hierarchical extensions of simple CMR, are applied in estimating abundance of animals with large body size, conspicuous behavior or high detection probabilities. We applied and evaluated the reliability of a multinomial N-mixture modelling approach with multiple observer data to a small and cryptic terrestrial salamander, found in different habitats where populations possess different level of detectability. Estimates obtained with multinomial N-mixture models were compared to estimates obtained with classical methods, such as removal sampling, and their reliability has also been evaluated by simulations scenarios. Our results show that multinomial N-mixture models, applied within a multiple observer framework, give reliable and robust estimates of population abundance even when detection and density are relatively low. Therefore, multinomial N-mixture models appear efficient and cost-effective when planning and identifying management actions and conservation programs of small terrestrial animals such as amphibians and reptiles.
Sebastiano Salvidio
added a research item
The Stripeless tree-frog Hyla meridionalis reaches its eastern-most European distributional limit in NW Ita-ly, and specifically in the Cinque Terre National Park. Here for two consecutive years, we estimated tree-frog population abundance by call surveys at 24 sites. Data were analysed in the framework of N-mixture open population models based on repeated counts of calling males. The results obtained by this statistical approach were effective in estimating population size together with annual recruitment and survival. The tree-frog male population size remained constant between years and site abundance was inversely related with altitude. On the bases of these findings, our application of N-mixture models to tree-frog calling males was successful and is a promising cost-effective method to obtain long-term monitoring data on this species over large geographic areas.
Andrea Costa
added 17 research items
Many small terrestrial vertebrates exhibit limited spatial movement and are considerably exposed to changes in local environmental variables. Among such vertebrates, amphibians at present experience a dramatic decline due to their limited resilience to environmental change. Since the local survival and abundance of amphibians is intrinsically related to the availability of shelters, conservation plans need to take microhabitat requirements into account. In order to gain insight into the terrestrial ecology of the spectacled salamander Salamandrina perspicillata and to identify appropriate forest management strategies, we investigated the salamander’s seasonal variability in habitat use of trees as shelters in relation to tree features (size, buttresses, basal holes) and environmental variables in a beech forest in Italy. We used the occupancy approach to assess tree suitability on a non-conventional spatial scale. Our approach provides fine-grained parameters of microhabitat suitability and elucidates many aspects of the salamander’s terrestrial ecology. Occupancy changed with the annual life cycle and was higher in autumn than in spring, when females were found closer to the stream in the study area. Salamanders showed a seasonal pattern regarding the trees they occupied and a clear preference for trees with a larger diameter and more burrows. With respect to forest management, we suggest maintaining a suitable number of trees with a trunk diameter exceeding 30 cm. A practice of selective logging along the banks of streams could help maintain an adequate quantity of the appropriate microhabitat. Furthermore, in areas with a presence of salamanders, a good forest management plan requires leaving an adequate buffer zone around streams, which should be wider in autumn than in spring.
!e aim of this study, which is part of the Life project ManFor CBD, was to estimate the abundance of a population of Salamandrina perspicillata and assessing the influence of fine-scale habitat features on the abundance of this salamander. Our study area is a one hectare plot located in a beech forest within “Montedimezzo” Nature Reserve (Molise region) and at the study site salamanders use holes near buttress roots at the basis of trees as shelters. In the survey site we individually numbered all trees with diameter at breast height (DBH) > 10 cm obtaining a total of 385 trees that we employed as sites for our spatially replicated survey. In addition we measured some habitat features (number of holes and of buttresses, DBH value). In autumn 2013 all sites were visited 6 times and we analysed the count data of Salamandrina using the N-mixture models to estimate abundance, which we modelled as a function of site covariates with detectability considered either constant or time- dependent. !e best model accounted for time-dependent detectability, and abundance of salamanders to be positively influenced by DBH and number of buttresses, estimating an abundance of 1635 salamanders (95% C.I. 574 - 1656). Influence of number of buttresses and DBH on salamander’s abundance is relevant in relation to forest management policies and we believe that the knowledge of fine-scale habitat features, that influences local abundances of salamanders, can help to properly address forest management plans, taking into account amphibians conservation.
Herpetofauna includes both amphibians and reptiles. Despite the fact that these two vertebrate groups are often considered together in the study of herpetology, they are quite different. They come from independent lineages since 300 million years ago (Zug et al., 2001) and have quite different reproductive systems, behav-ioural traits and ecological requirements. Despite their biological and ecological differences, amphibians and reptiles may be considered together regarding their conservation status. Both groups, in the last decades, generated a lot of interest among researchers and wildlife managers because of their worldwide decline (Stuart et al., 2004; Gibbons et al., 2000). As a consequence of their different biology and ecology, causes of amphibians and reptiles decline should be studied separately: for example they are both ectotherm, but while reptiles have integument covered with scales, amphibians have a permeable skin that makes them more vulnerable to pollutants and desiccation. The major part of amphibians have a biphasic life cycle with an aquatic life stage (Wells, 2010) and are exposed both to terrestrial and aquatic habitat disturbances. Both groups are threatened in the same way by habitat disturbance and fragmentation. In the present chapter a brief overview on the main effects of forest management practices in relation to herpetofauna conservation is reported. The suitability of different approaches and indicators used in literature to study the effect of forest harvesting on herpetofauna is also discussed. Finally, the effects at multiple scales, identifying at the same time the best forestry practice for optimal conservation, are reported at three levels: i) at landscape scale, ii) at forest level and iii) at microsite level, related to deadwood retention. Indicators of herpetofauna response to forest management-their suitability Forests with many water bodies have generally higher amphibian species diversity compared to reptiles. In the last years, amphibians and reptiles conservation received an increased interest within groups of researchers and wildlife managers focused on a multitude of different approaches and indices to identify and understand the causes of this decline. A large literature on this topic, mainly focusing on papers related to forest management, was reviewed as well as the state of the art of the methodologies currently employed in quantitative ecology and population biology, that may be considered suitable for assessing and monitoring the effects of forest management on herpetofauna. Although the major part of the literature on this topic is referred to North-American species and habitats nevertheless indices/approach selection and application, field methodologies, data analysis and observed effects (see following paragraphs) are fully transposable, as a main guideline, to the European context. One of the main concerns planning to estimate the effect of forestry practices is the temporal scale of the study, and in particular the adoption of temporally and spatially stratified samplings. In the major part of the examined literature the effects of forest management is estimated comparing different indices between unharvested and harvested sites. The best option is to conduct forest experiments, including different treatment levels, along with control treatments, and to compare the selected metrics between different treatments and between pre-and post-treatment (Todd and Rothermel, 2006; Todd and Andrews, 2008; Todd et al., 2009); such approach allows to discriminate variations due to forest management options, taking into account pre-existent discrepancies between different sites. Even if the aforementioned option is the most preferable, practically it is really expensive in terms of time and sampling effort; then another suitable approach is to compare sites with different management histories (Welsh et al., 2008), if possible selecting sites with in-depth knowledge of pre-existent herpetofauna assemblages. Even if the second option is not preferable to compare the effects of different treatments, due to the absence of pre-existent information on study sites, it allows comparing long term effects of different forest practices on her-petofauna (Welsh et al., 2008; Sung et al., 2012). As regards sampling techniques and metrics commonly employed to study her-petofauna responses to forest management a main distinction concerns the target of the study: major part of the examined literature focuses at population or community level, while at a lesser extent some studies focus on individual metrics. As regards the individual level approach, a lot of metrics can be employed and compared between harvested and unharvested sites: for example measurement of body mass (Chazal and Niewiarowski, 1998), body length and juvenile growth (Chazal and Niewiarowski, 1998; Todd and
Andrea Costa
added a project goal
Evaluate the effectiveness of hierarchical models (Occupancy and N-mixture) in herpetology:
- To study the ecology of amphibians and reptiles
- To estimate population abundance
- To inform practitioners and drive conservation plans