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Nlme: Linear and Nonlinear Mixed Effects Models

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... To better deal with heterogeneous data resulting from sporadic GPS collar failures, animal response variables were analyzed using mixed linear models that considered both the occurrence of mixed effects and repeated measures over time (Pinheiro et al., 2013). Models considered the fixed effect for year, season and breed (and their possible two-and three-way interactions) and the random effect of animal and day, and selecting for best fitting models. ...
... An autoregressive correlation structure was used as the main model for repeated measures data. Comparisons and selection of adjusted models and their significance were conducted using the maximum likelihood ratio test (Pinheiro et al., 2013). Multiple comparisons for significant effects were made using protected pairwise contrasts, with a significance level declared at P = 0.05. ...
... All statistical analyses were carried out in R (R Core Team 2017) using the RStudio interface software (Version 0.99.903). Mixed model analyses were conducted using the nlme package for R (Pinheiro et al., 2013). ...
Article
We monitored grazing behavior and habitat selection of Argentine Criollo (AC), South American heritage cattle breed, and Angus (AA) cows during summer and winter of 2016 (wetter year) and 2017 (drier year) at a site in La Rioja, Argentina. In each year and season, five AC and five AA cows were fitted with GPS collars configured to log animal position at 10-min intervals for 40 days. Movement, activity, and vegetation use patterns of each breed were derived from the GPS data. In summer, AC cows traveled similar daily distances, explored smaller (wetter year) or slightly larger (drier year) areas of the pasture, tended to move along more sinuous path trajectories, and showed stronger selection of the vegetation unit with higher forage quality and lowest woody cover compared to AA counterparts. AC cows allocated similar (wetter year) or more time to graze (drier year), allocated roughly the same amount of time to travel, and spent similar (wetter year) or less time resting (drier year) than AA cows. In winter, foraging behavior differences between breeds were only observed in the drier year. AC cows traveled farther and spent less time resting than AA counterparts that year. When comparing summer vs. winter movement patterns of each breed, AC cows showed an apparent greater ability to adapt to changing forage conditions (foraging plasticity) compared to AA counterparts which appeared to exhibit more rigid foraging patterns. Criollo cattle could be a tool to increase the resilience of Arid Chaco beef systems in the face of climate change. The rangeland conservation implications of raising Criollo vs. British beef cattle require further investigation.
... Variation of diversity, composition, and structure over time To assess the variation of diversity, composition, and structure over time and evaluate restoration success for the restoration plantings, we fitted separate mixed-effects models for small, medium, and large trees with richness, evenness, Shannon-Wiener diversity, compositional similarity, stem density, basal area, height, and crown width as response variables (Pinheiro et al., 2014). For each response, the model included sampling year as an eightlevel factor variable (2003, 2008, 2011, 2014, 2017, R2003, R2011, and R2017) as the explanatory variable. ...
... The proportion of elephant grass was highly correlated with the proportion of shrubs (r = À0.7, Figure S2) and moderately correlated with the proportion of short grass (r = À0.5, Figure S3), so elephant grass was not included in further analyses (Crawley, 2013). To assess the influence of initial site conditions on recovery under active restoration, we fitted generalized linear models with richness, evenness, Shannon-Wiener diversity, crown width, basal area, height, and stem density each pooled for all tree size classes as response variables (Pinheiro et al., 2014). For compositional similarity (Bray-Curtis index), we fitted beta regression models with a logit link function. ...
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Several studies evaluate active (i.e., seeding/planting) and passive (i.e., protecting forest regrowth) restoration, but few studies examine successional patterns for different plant sizes. By using biodiversity and structure, we examined whether restoration communities approach old‐growth forests over time, and whether restoration success varies for different tree sizes in both active and passive interventions. We examined how initial site conditions affect active restoration. Small (dbh ≥ 5 cm), medium (≥15 cm), and large trees (≥30 cm) were measured in 2003–2017 in permanent sample plots in restoration plantings (initially 3–8 years old) and in an old‐growth forest in Kibale National Park, Uganda. Trees were also measured in regrowth forests (initially 16 years old) in 2011–2017. We collated information about site conditions from restoration reports. Biodiversity and structure increased over time towards the old‐growth forest. Restoration plantings and regrowth forests recovered diversity and structure of small and medium trees except for large trees. Forest recovery increased with proportions of remnant banana plants and shrubs, while isolation from the old‐growth forest slowed recovery. Disaggregating vegetation inventory data by tree size may be useful in achieving a holistic measure of restoration. Restorationists could prioritize sites with remnant banana plants and shrubs, and sites closer to old‐growth forests in order to achieve better results. Our article examined whether restoration communities approach reference forests over time, assessed the influence of tree size on restoration success in restoration plantings and regrowth forests, and how landscape conditions affect active restoration. We show that restoration success is faster for smaller than larger trees. Forest recovery increases with the proportion of banana plants and remnant shrubs, while isolation from the old‐growth forest slows recovery.
... We modelled the effect of landscape features on population generic parameters using generalized linear mixed effects models (GLMMs) as implemented in the lme package (Pinheiro et al., 2015) in R statistical software (version 3.6.1). In the final analyses, we included population genetic estimates from patches with five or more adults and juveniles, each. ...
Article
Forest conversion and habitat loss are major threats to biological diversity. Forest regeneration can mitigate the negative effects of old growth forest loss on species diversity, but less is known about the extent to which forest loss reduces genetic diversity in remnant populations and whether secondary forests play a role in the maintenance of genetic diversity. We quantified genetic diversity in a tropical hummingbird‐pollinated understory herb, Heliconia tortuosa, across a landscape mosaic of primary and secondary forest regrowth. Using microsatellite genotypes from >850 adult and juvenile plants within 33 forest patches and extensive bird surveys, we examined the effect of contemporary and historical landscape features including forest age (primary vs. secondary forest), stand isolation, and pollinator assemblages on genetic diversity and levels of inbreeding in H. tortuosa. We found that inbreeding was up to 3x higher in secondary forest, and this effect was amplified with reductions in primary forest in the surrounding landscape through reduced observed heterozygosity in isolated fragments. Inbreeding in forest patches was negatively correlated with the local frequency of specialist long‐distance foraging traplining hummingbirds. Traplining hummingbirds therefore appear to facilitate mating among unrelated plants ‐ an inference we tested using empirically parameterized simulations. Higher levels of inbreeding in H. tortuosa are therefore associated with reduced functional diversity of hummingbirds in secondary forests and forest patches isolated from primary forests. Our findings suggest a cryptic consequence of primary forest loss and secondary forest regeneration through the disruption of mutualistic interactions resulting in the erosion of genetic diversity in a common understory plant.
... This was accounted for by including a first-order autoregressive correlation structure to describe the within-group correlation (Xu et al., 2014;Huy et al., 2020). Weighted nonlinear models were fitted by maximum likelihood (Timilsina and Staudhammer, 2013;Pinheiro et al., 2014) using nlme package in R (R Core Team, 2020). ...
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We developed a system for modeling the growth and yield of planted teak (Tectona grandis L.f.) for small diameter products under varying management regimes in the tropical Central Highlands of Viet Nam. We compared an independent and simultaneous system of models to predict dominant height (Ho), quadratic mean diameter (Dg),averaged tree height (Hg) with Dg, and mean tree volume (V) versus stand age (A). In addition, the model system performance with and without site index (SI) and stand density (N) as covariates were compared using K-fold cross-validation. The best modeling system was obtained with the simultaneously fit models that included SI and N and were in the form of: Dg=Dm/(1 + a × exp(-b × A)) × exp[e1 × (SI– 15) + e2/1000 × (N – 722)]; Hg=Hm ×exp(-a × exp(-b × A)) × exp[e1 × (SI– 15) + e2/1000 × (N – 722)]; and V = π/4 ×10-4 x Dg2 × Hg × 0.45; where Dm, Hm, a, b, e1and e2 were the parameters to be estimated. These models will help predict the growth and yield of teak planted for different planting schemes, including monoculture, agroforestry, and forest enrichment planting in this region.
... We also conducted separate linear mixed effects models for each individual variety. Here we assessed fruit mass, developmental period, and adjusted fruit mass separately as functions of pollination treatment (fixed effect) (packages nlme (Pinheiro et al., 2017), multcomp (Hothorn et al., 2008), ggplot2 (Wickham, 2009) and MuMIn (Barton, 2017)). To account for repeated measures and variation between individual plants, plant ID was used as a random effect. ...
Article
Agricultural crops are often dependent on insect pollination for commercially viable yields. Blueberries are an example of such a crop and owing to their proposed health benefits they are grown around the world, including locations where their native bumble bee pollinators do not occur. In the absence of bumble bees, blueberry pollination in South Africa and many other parts of the non-native, commercial range is performed primarily by honey bees. Despite this, the effectiveness of honey bee pollination on blueberries remains understudied. This study determined the effect of honey bee pollination on components of fruit yield (fruit set and mass) of five blueberry varieties that are extensively planted in South Africa. For each variety, two metrics were calculated: 1) the benefit of bees — a comparison of fruit yields after exposure to honey bees and fruit yields after honey bee exclusion, 2) the pollination deficit — the difference in yield between hand pollination (maximum yield potential) and yields after exposure to honey bee pollinators. Honey bee pollination consistently resulted in improved yields, although the magnitude of this improvement (i.e., the benefit of bees) was dependent on the variety considered. Similarly, the pollination deficit also varied considerably across varieties and while some varieties appeared to perform close to maximum potential (small pollination deficit), others yielded well below their maximum potential under honey bee pollination. This study demonstrates that honey bees are functional pollinators of blueberries in areas where native blueberry pollinators are absent. However, in such areas, it is important that special focus is given to selecting blueberry varieties that perform well with honey bees as their primary pollinator. Further research is necessary to determine how the pollination deficit of blueberry varieties can be decreased as well as how to increase the effectiveness of honey bee pollination.
... Three profiles were measured for each sponge at every time point and each profile location was chosen randomly on each sponge. At every time point, statistical differences in dissolved oxygen concentration through the sponge tissue depth between treatments were determined by constructing repeated-measures linear mixed effect models where oxygen concentration was the response variable and depth and treatment were the explanatory variables (Pinheiro et al., 2021). ...
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Holobionts formed by a host organism and associated symbionts are key biological units in marine ecosystems where they are responsible for fundamental ecosystem services. Therefore, understanding anthropogenic impacts on holobionts is essential. Sponges (Phylum Porifera) are ideal holobiont models. They host a complex microbial community and provide ecosystem services including nutrient cycling. At bathyal depths, sponges can accumulate forming dense sponge ground habitats supporting biodiverse associated communities. However, the impacts of spilled oil and dispersants on sponge grounds cannot be understood without considering exposures mediated through sponge filtration of marine snow particles. To examine this, we exposed the model sponge Halichondria panicea to oil, dispersant and “marine oil snow” contaminated seawater and elucidate the complex molecular response of the holobiont through metatranscriptomics. While the host response included detoxification and immune response pathways, the bacterial symbiotic response differed and was at least partially the result of a change in the host environment rather than a direct response to hydrocarbon exposure. As the sponge host reduced its pumping activity and internal tissue oxygen levels declined, the symbionts changed their metabolism from aerobic to anaerobic pathways possibly via quorum sensing. Furthermore, we found evidence of hydrocarbon degradation by sponge symbionts, but sponge mortality (even when exposed to low concentrations of hydrocarbons) implied this may not provide the holobiont with sufficient resilience against contaminants. Given the continued proposed expansion of hydrocarbon production into deep continental shelf and slope settings where sponge grounds form significant habitats it is important that dispersant use is minimised and that environmental impact assessments carefully consider the vulnerability of sponge holobionts.
... The resulting data were log 10 transformed to satisfy the assumptions of normality and homoscedasticity. Independent mixed linear models were calculated for each behavior using the nlme package (Pinheiro and Bates 2022). For the time spent in self-grooming, allogrooming, fecal fluid grooming, and fungus grooming, the fixed factors were: (i) treatment (spraying with water or infection with M. anisopliae spores), (ii) time (baseline period, the first and second hours after the application of the challenge), and (iii) the interaction between time and treatment. ...
... Team, 2017) using the package 'nlme' (Pinheiro, Bates, DebRoy, & Sarkar, 2018). Linear regression identified possible predictors of outcome within each treatment. ...
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Background Cognitive therapy for social anxiety disorder (CT-SAD) is recommended by NICE (2013) as a first-line intervention. Take up in routine services is limited by the need for up to 14 ninety-min face-to-face sessions, some of which are out of the office. An internet-based version of the treatment (iCT-SAD) with remote therapist support may achieve similar outcomes with less therapist time. Methods 102 patients with social anxiety disorder were randomised to iCT-SAD, CT-SAD, or waitlist (WAIT) control, each for 14 weeks. WAIT patients were randomised to the treatments after wait. Assessments were at pre-treatment/wait, midtreatment/wait, posttreatment/wait, and follow-ups 3 & 12 months after treatment. The pre-registered (ISRCTN 95 458 747) primary outcome was the social anxiety disorder composite, which combines 6 independent assessor and patient self-report scales of social anxiety. Secondary outcomes included disability, general anxiety, depression and a behaviour test. Results CT-SAD and iCT-SAD were both superior to WAIT on all measures. iCT-SAD did not differ from CT-SAD on the primary outcome at post-treatment or follow-up. Total therapist time in iCT-SAD was 6.45 h. CT-SAD required 15.8 h for the same reduction in social anxiety. Mediation analysis indicated that change in process variables specified in cognitive models accounted for 60% of the improvements associated with either treatment. Unlike the primary outcome, there was a significant but small difference in favour of CT-SAD on the behaviour test. Conclusions When compared to conventional face-to-face therapy, iCT-SAD can more than double the amount of symptom change associated with each therapist hour.
... We next analyzed the magnitude of the absolute effects. To allow for the correlation of errors (four channels for each read) and unequal variances, we fitted a linear model to the absolute Cohen's d data by maximizing the restricted log-likelihood using generalized least squares (GLS) with the R package "nlme" (Pinheiro et al., 2019). A type-II analysis-of-variance table was calculated for the model using the Anova function of the R package "car" (Fox and Weisberg, 2019). ...
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A plethora of adaptive responses to predation has been described in microscopic aquatic producers. Although the energetic costs of these responses are expected, with their consequences going far beyond an individual, their underlying molecular and metabolic mechanisms are not fully known. One, so far hardly considered, is if and how the photosynthetic efficiency of phytoplankton might change in response to the predation cues. Our main aim was to identify such responses in phytoplankton and to detect if they are taxon-specific. We exposed seven algae and seven cyanobacteria species to the chemical cues of an efficient consumer, Daphnia magna, which was fed either a green alga, Acutodesmus obliquus, or a cyanobacterium, Synechococcus elongatus (kairomone and alarm cues), or was not fed (kairomone alone). In most algal and cyanobacterial species studied, the quantum yield of photosystem II increased in response to predator fed cyanobacterium, whereas in most of these species the yield did not change in response to predator fed alga. Also, cyanobacteria tended not to respond to a non-feeding predator. The modal qualitative responses of the electron transport rate were similar to those of the quantum yield. To our best knowledge, the results presented here are the broadest scan of photosystem II responses in the predation context so far.
... Note that digit sensitivity effects in these analyses would be reflected in negative t values, due the polarity of the N1 and testing for stronger (i.e., more negative) amplitudes for digits minus the control stimuli (letters or false fonts). The LMM was implemented with the function lme of the R package "Nlme" (Pinheiro et al., 2019). In our models, outliers were excluded if the normalized residuals exceeded the ±3 threshold, which resulted in exclusion of 7 data points (1% of the data) in the main model. ...
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Number processing abilities are important for academic and personal development. The course of initial specialization of ventral occipito-temporal cortex (vOTC) sensitivity to visual number processing is crucial for the acquisition of numeric and arithmetic skills. We examined the visual N1, the electrophysiological correlate of vOTC activation across five time points in kindergarten (T1, mean age 6.60 years), middle and end of first grade (T2, 7.38 years; T3, 7.68 years), second grade (T4, 8.28 years), and fifth grade (T5, 11.40 years). A combination of cross-sectional and longitudinal EEG data of a total of 62 children (35 female) at varying familial risk for dyslexia were available to form groups of 23, 22, 27, 27, and 42 participants for each of the five time points. The children performed a target detection task which included visual presentation of single digits (DIG), false fonts (FF), and letters (LET) to derive measures for coarse (DIG vs. FF) and fine (DIG vs. LET) digit sensitive processing across development. The N1 amplitude analyses indicated coarse and fine sensitivity characterized by a stronger N1 to digits than false fonts across all five time points, and stronger N1 to digits than letters at all but the second (T2) time point. In addition, lower arithmetic skills were associated with stronger coarse N1 digit sensitivity over the left hemisphere in second grade (T4), possibly reflecting allocation of more attentional resources or stronger reliance on the verbal system in children with poorer arithmetic skills. To summarize, our results show persistent visual N1 sensitivity to digits that is already present early on in pre-school and remains stable until fifth grade. This pattern of digit sensitivity development clearly differs from the relatively sharp rise and fall of the visual N1 sensitivity to words or letters between kindergarten and middle of elementary school and suggests unique developmental trajectories for visual processing of written characters that are relevant to numeracy and literacy.
... We used generalised linear mixed models to evaluate relationships between invertebrate community metrics and environmental and climate variables. All models were ran using the lme() function in the nlme package in R (Pinheiro et al., 2018). Invertebrate community metrics (i.e., abundance, richness, diversity, functional richness, Rao's Q, NMDS axis 1 score, NMDS axis 2 score) were modelled separately as independent response variables. ...
Article
Climate change is expected to alter rainfall and temperature regimes across the world. The hydrology and riparian zone vegetation of lotic ecosystems are tightly linked to rainfall and a mechanistic understanding of the effects of rainfall on lotic ecosystems is needed to forecast the ecological impacts of climate change. However, it is difficult to isolate rainfall effects from other environmental variables that covary across climates. To address this, we leveraged a unique steep rainfall gradient with few covarying changes in elevation, temperature, and geology to evaluate the effects of rainfall on stream invertebrate communities. We surveyed nine streams in the Texas Gulf Coast Prairie distributed along a 550–1,350 mm/year rainfall gradient. Four sites were classified as drier semi‐arid streams (<750 mm annual rainfall) and five sites were classified as wetter sub‐humid streams (>750 mm annual rainfall). A suite of characteristics including benthic invertebrate community metrics, flow conditions, and water quality variables were assessed monthly for 14 months at each site to relate precipitation regime to stream structure and function. Precipitation regime was observed to be a master explanatory variable. As annual rainfall increased, the flow environment became more stable within seasons and predictable across seasons, influencing spatial structure and temporal variability of invertebrate community composition. Wetter streams were dominated by slower growing taxa without adaptions for desiccation resistance and strong dispersal. Wetter sites displayed seasonal variation in community composition and species richness, whereas temporal variation in communities in drier streams was controlled by stochastic variation in flow conditions. These observations show that differences in local annual rainfall correlated with major changes to community structure and functional composition. We hypothesise that this association is related to the connection of rainfall to hydrological stability, particularly the frequency of low flow disturbances, and the subsequent effects on riparian vegetation and temporally available niches to stream invertebrates. Our work adds to evidence that alterations in precipitation patterns associated with climate change have sweeping impacts on lotic fauna.
... Statistically significant differences between group means for species and sites were initially determined by one-way ANOVA. We then evaluated the relationship between isotopic composition, and local precipitation and elevation, using a mixedeffect modeling approach on annual measurements in C. fissilis, and on 10-year bulk measurements for C. fissilis and C. odorata with nlme 3.1-148 (Pinheiro et al. 2020) and MuMIn 1.43.17 (Bunn et al. 2021) R packages. ...
Article
With increasing concerns about sustainable exploitation of tropical timber, there is a need for developing independent tools to check their origin. We evaluated the potential of tree-ring stable isotopes for identifying four Cedrela species (C. balansae, C. fissilis, C. odorata, and C. saltensis) and for identifying geographic origin of C. fissilis and C. odorata, two of the most intensively exploited species. We studied differences in 13C and 18O of wood among 11 forest sites (163 trees). We quantified isotope composition of 10-year bulk samples, and for a subset we also evaluated isotopic annual fluctuations for the last 10 years. Although annual isotopic variability was not correlated to precipitation or elevation, we found a significant relationship between the 10-year bulk stable-isotope composition and average precipitation and elevation. However these relationships were not consistent across all sites. We also explored isotopic site and species differentiation using Kernel Discriminant Analyses. Site discrimination was low: 30% accuracy for C. odorata, and 40% for C. fissilis sites. However, species discrimination was 57.5% for C. odorata and 95.3% for C. fissilis. These results suggest that although 13C and 18O isotopic analyses hold potential to verify species identification, discrimination of geographical origin within a country may still be challenging.
... Analyses were performed using generalized least squares (GLS) and phylogenetic generalized least squares (PGLS), recording the 95% confidence interval for parameter estimates, using the R packages "caper" (Orme et al., 2013) and "nlme" (Pinheiro et al., 2016). In all PGLS models, phylogenetic signal, lambda (λ) was estimated by maximum likelihood. ...
Article
Muroid rodents mostly have a complex stomach: one part is lined with a cornified (non‐glandular) epithelium, referred to as a 'forestomach,' whereas the rest is lined with glandular epithelium. Numerous functions for the forestomach have been proposed. We collated a catalog of anatomical depictions of the stomach of 174 muroid species from which the respective non‐glandular and glandular areas could be digitally measured, yielding a 'stomach ratio' (non‐glandular:glandular area) as a scale‐independent variable. Stomach ratios ranged from 0.13 to 20.15, and the coefficient of intraspecific variation if more than one picture was available for a species averaged at 29.7% (± 21.5). We tested relationships of the ratio with body mass and various anatomical and ecological variables, including diet. There was a consistent phylogenetic signal, suggesting that closely related species share a similar anatomy. Apart from classifying stomachs into hemiglandular and discoglandular, no anatomical or ecological measure showed a consistent relationship to the stomach ratio. In particular, irrespective of statistical method or the source of dietary information, dietary proxies did not significantly correlate with the stomach ratio, except for a trend towards significance for invertivory (insectivory). Yet, even this relationship was not convincing: whereas highly insectivorous species had high but no low stomach ratios, herbivorous species had both low and high stomach ratios. Thus, the statistical effect is not due to a systematic increase in the relative forestomach size with invertivory. The most plausible hypotheses so far associate the muroid forestomach and its microbiome with a generic protective role against microbial or fungal toxins and diseases, without evident correlates of a peculiar need for this function under specific ecological conditions. Yet, this function remains to be confirmed. While providing a catalog of published depictions and hypotheses, this study highlights that the function of the muroid rodent forestomach remains enigmatic to date. This article is protected by copyright. All rights reserved.
... (RStudio Team, 2018) using R version 3.5.1 (R Core Team, 2018). Most sediment and plant characteristics (%C, C/N, porewater NH 4 + , chl-a, above-and belowground biomass), microbial HC degrader relative abundances (Alteromonadales, Chromatiales, Desulfobacterales, Methylococcales, Rhizobiales, Rhodobacterales, Thiotrichales, total abundance), and N cycling rates (denitrification, DNRA, and percent denitrification) were analyzed using a one-way analysis of variance (ANOVA) with site as the factor on a linear mixed effects model (nlme package; Pinheiro et al., 2018) in which month of sampling was used as the random variable. All data were tested visually for normality of residuals using a quantile-quantile plot. ...
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Coastal marshes provide valuable ecosystem services including the removal of excess nitrogen (N) prior to reaching coastal waters. Crude oil contamination can disrupt N cycling processes, and while the impacts of crude oil on marsh structure and function are well studied, less is known about the effects of different oil components. The objective of this study was to determine how water accommodated fraction (WAF) of oil impacts marsh sediment N cycling capacity from three marshes with differing characteristics. One site was previously oiled following the Deepwater Horizon (DWH) oil spill while the other two sites had no known history of oil spills. We measured 16S rRNA gene composition from sediments collected from each marsh then conducted a laboratory incubation experiment on sediments treated with different concentrations (0%, 25%, 100%) of WAF. The DWH impacted site had a lower number of observed microbial taxa and lower Chao1 diversity, but a higher relative abundance of putative hydrocarbon degraders compared to the other sites. While there was no treatment effect of WAF on sediment denitrification, denitrification potential rates were 2.4 × higher in the DWH impacted sediment compared to the other sites. There were no differences in dissimilatory nitrate reduction to ammonium (DNRA) potential rates across sites, but 100% WAF treatments increased rates nearly twofold at one of the unoiled sites. These results suggest oil contamination alters the microbial community structure and impacts N cycling processes in salt marsh sediments.
... Female latencies to call and call rates in response to different males within a specific call type were compared using the lme function ('nlme' package, Pinheiro et al., 2004) to fit linear mixedeffect models with 'signaller class' as fixed factor and 'group' as random factor. Post hoc pairwise comparisons between different male categories (own, neighbour, unknown) were conducted by calculating estimated marginal means using the function emmeans ('emmeans' package, Lenth, 2022) including adjusted P values for multiple testing that were calculated with the Tukey method. ...
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Vocal recognition in social contexts is phylogenetically widespread and can be explained by kin and mate recognition or group coordination. It remains unclear why some species evolved alarm calls that also provide cues to signaller identity as the function of these calls is thought to predominantly serve predation avoidance. One hypothesis is that individually distinct alarms facilitate the detection of unreliable callers, which is in line with the idea of reputation-based mate choice. However, it remains unknown whether receivers use provided cues to identify the signaller and, if yes, how vocal signaller recognition impacts on their own behaviour during predation events. In many nonhuman primates, males provide risky antipredator services to the rest of the group while uttering conspicuous alarm calls. In putty-nosed monkeys, some male alarm types have been shown to be individually distinct and females have been shown to vocally recruit males for predation defence. Whether females are sensitive to the identity of the male supporting them in predation defence is unknown. We tested 16 groups of putty-nosed monkeys in the Nouabalé Ndoki National Park (Republic of Congo) with different alarm types from different males. Specifically, we broadcast pyow, hack and kek calls from the group's own male, a neighbouring male and an unknown male, respectively, to each group. Female receivers were sensitive to signaller identity and consistently varied their own antipredator behaviour between different males for two call types but not for eagle-related hacks. We explored different possible explanations for male recognition based on risky male antipredator services and conclude that our results are strongly in line with the reputation-based mate choice hypothesis.
... The effect of coral species on microbial alpha diversity (Shannon index, using the diversity() function in "vegan" R package [69]) was tested using the Kruskal-Wallis rank-sum test on raw counts following rarefaction. To account for variance due to coral species while testing other factors, a nested ANOVA approach was employed by fitting mixed models using the lme() function in the "nlme" R package [70]. Model terms were fit by maximizing the restricted log-likelihood (i.e., REML method). ...
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Background The importance of symbiosis has long been recognized on coral reefs, where the photosynthetic dinoflagellates of corals (Symbiodiniaceae) are the primary symbiont. Numerous studies have now shown that a diverse assemblage of prokaryotes also make-up part of the microbiome of corals. A subset of these prokaryotes is capable of fixing nitrogen, known as diazotrophs, and is also present in the microbiome of scleractinian corals where they have been shown to supplement the holobiont nitrogen budget. Here, an analysis of the microbiomes of 16 coral species collected from Australia, Curaçao, and Hawai’i using three different marker genes (16S rRNA, nifH, and ITS2) is presented. These data were used to examine the effects of biogeography, coral traits, and ecological life history characteristics on the composition and diversity of the microbiome in corals and their diazotrophic communities. Results The prokaryotic microbiome community composition (i.e., beta diversity) based on the 16S rRNA gene varied between sites and ecological life history characteristics, but coral morphology was the most significant factor affecting the microbiome of the corals studied. For 15 of the corals studied, only two species Pocillopora acuta and Seriotopora hystrix, both brooders, showed a weak relationship between the 16S rRNA gene community structure and the diazotrophic members of the microbiome using the nifH marker gene, suggesting that many corals support a microbiome with diazotrophic capabilities. The order Rhizobiales, a taxon that contains primarily diazotrophs, are common members of the coral microbiome and were eight times greater in relative abundances in Hawai’i compared to corals from either Curacao or Australia. However, for the diazotrophic component of the coral microbiome, only host species significantly influenced the composition and diversity of the community. Conclusions The roles and interactions between members of the coral holobiont are still not well understood, especially critical functions provided by the coral microbiome (e.g., nitrogen fixation), and the variation of these functions across species. The findings presented here show the significant effect of morphology, a coral “super trait,” on the overall community structure of the microbiome in corals and that there is a strong association of the diazotrophic community within the microbiome of corals. However, the underlying coral traits linking the effects of host species on diazotrophic communities remain unknown. 2iUFYDy-sBVn2WqgoVCqfbVideo Abstract
... When a variable from one category was selected, other variables from the same category were systematically avoided to prevent correlated variables being present in the same model (except topographical factors). The function "nlme" from the R package "nlme" (Pinheiro et al. (2021)) was used to run these models. Evaluation of the models was done by comparing graphical predictions made by different models and their ecological significance, and by comparing the observed vs. predicted values, along with the Akaike Information Criteria ...
Thesis
Global environmental changes are affecting tree population demography with potentially significant impacts on forest biodiversity and wood industry. Forest regeneration processes include seed production, growth and survival of saplings to the recruitment sizes at which trees are considered in forest inventories. Changes in regeneration dynamics directly affect forest composition and structure and can jeopardize the sustainability of forest management. This is especially the case in mountain forests where environmental gradients are strong and where forests are often uneven-aged, i.e. combining trees of all ages in a single stand. Regeneration processes are difficult to monitor. Large data sets often give only fixed pictures of sapling densities with little information on demographic processes. In this thesis, we quantified the effects of different biotic and abiotic factors on regeneration dynamics of Picea abies (spruce), Abies alba (fir) and Fagus sylvatica (beech) in the French Alps and Jura mountains. We also predicted changes in tree recruitment fluxes in these forests, for potential climate change situations. We recorded sapling height increment and density of spruce, fir and beech in 152 plots across the French Alps and Jura mountains. We then analysed how biotic and abiotic factors known to affect regeneration, namely altitude, slope, aspect, light availability, soil characteristics, ungulate browsing, temperature, precipitation and evapotranspiration, affected sapling density and growth using non-linear mixed models. We showed that temperature has a positive non-linear effect on sapling height growth and water resource availability has a positive effect on sapling density. Terminal shoot browsing, which prevents sapling height growth, is especially frequent on fir. In a second analysis, we built a more comprehensive model of regeneration dynamics, representing explicitly the process of new seedling production, sapling growth, browsing and survival, and finally their recruitment into adult trees. We predicted parameters for these processes in combination, using Approximate Bayesian Computation (ABC), based on the field data collected earlier. The results imply that more frequent and intense heat and drought events could negatively influence sapling growth and survival of the three species, with probable reduction of forest renewal fluxes. An increase of ungulate populations leading to increased browsing could be especially detrimental to fir and possibly also to beech saplings. We also predicted the potential tree recruitment fluxes for different IPCC climate projection scenarios for the year 2100, and showed that a reduction in tree recruitments is highly likely. This study shows that the ABC method can be efficiently used to estimate regeneration dynamic processes, based on sapling density, height increment and browsing data. It highlights the vulnerability of future forest regeneration to water availability and ungulate presence, urging researchers and forest managers alike to anticipate future potential important changes in mountain forest dynamics.
... The heart rate performance curve was generated by fitting data using the general additive mixed model (GAMM) with the R packages MGCV version 1.8 (Wood, 2004) and NLME version 3.1 (Pinheiro, 2011 ...
Article
Species range shift is one of the most significant consequences of climate change in the Anthropocene. A comprehensive study, including demographic, physiological, and genetic factors linked to poleward range expansion, is crucial for understanding how the expanding population occupies the new habitat. In the present study, we investigated the demographic, physiological, and genetic features of the intertidal gastropod Nerita yoldii, which has extended its northern limit by ~200 km over the former biogeographic break of the Yangtze River Estuary during recent decades. The neutral SNPs data showed that the new marginal populations formed a distinct cluster established by a few founders. Demographic modelling analysis revealed that the new marginal populations experienced a strong genetic bottleneck followed by recent demographic expansion. Successful expansion that overcame the founder effect might be attributed to its high capacity of rapid population growth and multiple introductions. According to the non‐neutral SNPs under diversifying selection, there were high levels of heterozygosity in the new marginal populations, which might be beneficial for adapting to the novel thermal conditions. The common garden experiment showed that the new marginal populations have evolved divergent transcriptomic and physiological responses to heat stress, allowing them to occupy and survive in the novel environment. Lower transcriptional plasticity was observed in the new marginal populations. These results suggest a new biogeographic pattern of N. yoldii has formed with the occurrence of demographic, physiologic, and genetic changes, and emphasize the roles of adaptation of marginal populations during range expansion.
... We therefore had to exclude air temperature as an explanatory variable in all models. In all further analysis, linear mixed effect models (LMEs, function lme in nlme package) (Pinheiro et al. 2013) were used to predict bark intake, expressed as the daily average in gram per week. Enclosure was used as random factor. ...
Article
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The distribution and population density of red deer (Cervus elaphus) are increasing in several regions of Europe. The deer may cause severe damage in commercial forestry and agriculture. Bark stripping is the main problem in forests, especially on Norway spruce (Picea abies), and is thought to mostly occur during winter when other forage is scarce. It has been suggested that an imbalance in the nutrient intake, and especially a diet including high amounts of easily-digestible macronutrients, such as agricultural crops, can lead to an increased urge to consume bark. Feeding on brassicas, for example rapeseed (Brassica napus) might have this effect. The aim with this study was to investigate the relationship between intake of rapeseed and bark stripping on Norway spruce by red deer during early spring. We did this by a controlled feeding experiment with four groups of captive red deer in southern Sweden. All groups were given spruce logs every week, while only two groups had access to freshly harvested rapeseed plants. In addition, influence of air temperature and forage nutritional composition was taken into account. Our results show that red deer bark stripping can be considerable not only during winter but also during spring green-up. We found no significant influence of rapeseed on bark stripping performed by the deer. However, at a threshold temperature, deer suddenly started to ingest large amounts of bark biomass, coinciding with a significant change in the bark’s concentration of starch. We suggest that the lack of effect of rapeseed feeding can partly be explained by overshadowing effects caused by such seasonal changes of bark characteristics, and partly by the fact that the rapeseed plants in our study contained lower than expected concentrations of easily-digestible macronutrients (apart from protein). We conclude that the risk of damage on spruce can be especially high during certain periods, something that is important to consider when mitigating bark stripping. However, several interactive effects are involved and must be considered in order to more efficiently mitigate damage.
... All data were checked for normality, using the Shapiro-Wilk's test (p > 0.05), and for extreme outliers. To assess the effects of different predictors on speed performance response, several linear mixed models (LMMs) were conducted with distinct combinations of the predictors, using the lme function from the nlme R package (Pinheiro et al., 2020). The LMMs were performed considering the following predictors: POP, BT, adult sex (females vs. males; SEX), and juvenile age (15-and 30-day-old; AGE), and their interactions, with SVL and weight (W) as covariates. ...
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Locomotion performance in reptiles is deeply associated with habitat use, escape from predators, prey capture and territory defence. As ectotherms, this trait in lizards is extremely sensitive to body temperature. However, most studies rarely look at locomotion patterns in an ontogenic perspective. The Moorish gecko, Tarentola mauritanica, was used to investigate the possible effects of distinct body temperatures on the locomotor performance within juveniles and adults. Not surprisingly, adult individuals significantly outperform the juveniles in speed at every body temperature. Moreover, except in the 30-day old juveniles, there is a general trend for an increase of speed with body temperature. The comparison of these speed values with the ones obtained for diurnal lizard species, corroborates the premise that because nocturnal species are subject to low thermal heterogeneity, little selection for behavioural thermoregulation, but strong selection for high performance at relatively cool temperatures are expected. Furthermore, the higher locomotor performance in adults at 29 ºC, roughly coincides with previously obtained preferred body temperatures. However, further studies need to be conducted to build the full performance curve, and to validate the existence of coadaption between behavioural thermoregulation and thermal sensitivity of physiological performance. Finally, this study has found that adult males run significantly faster than females at the highest body temperatures, highlighting the importance in understanding sex differences, and its potential to drive sex-specific behaviours, ecology and ultimately fitness.
... We carried out all the analyses in R software 4.0.5 (R Core Team, 2021), and used the packages FactoMineR v1.41 (Lê et al., 2008), vegan v2.5-7 (Oksanen et al., 2007), MuMIn v1.43.17 (Barto n, 2022), car v3.0-11 (Fox et al., 2012), and nlme v3.1-152 (Pinheiro et al., 2007) to run these analyses. ...
Article
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In addition to landscape changes, urbanization also brings about changes in environmental factors that can affect wildlife. Despite the common referral in the published literature to multiple environmental factors such as light and noise pollution, there is a gap in knowledge about their combined impact. We developed a multidimensional environmental framework to assess the effect of urbanization and multiple environmental factors (light, noise, and temperature) on life-history traits and breeding success of Barn Swallows (Hirundo rustica) across rural to urban gradients in four locations spanning over 2500 km from North to South China. Over a single breeding season, we measured these environmental factors nearby nests and quantified landscape urbanization over a 1 km2 radius. We then analysed the relationships between these multiple environmental factors through a principal component analysis and conducted spatially explicit linear-mixed effects models to assess their effect on life-history traits and breeding success. We were particularly interested in understanding whether and how Barn Swallows were able to adapt to such environmental conditions associated with urbanization. The results show that there is significant variation in the exposure to environmental conditions experienced by Barn Swallows breeding across urbanization gradients in China. These changes and their effects are complex due to the behavioural responses ameliorating potential negative effects by selecting nesting sites that minimize exposure to environmental factors. However, significant relationships between landscape urbanization, exposure to environmental factors, and life-history traits such as laying date and clutch size were pervasive. Still, the impact on breeding success was, at least in our sample, negligible, suggesting that Barn Swallows are extremely adaptable to a wide range of environmental features.
... Second, we estimated the extent to which purported state-level emotion regulatory behaviors at epoch t-1, including attempt-to-escape, support-seeking, distraction, and focus-on-restraint, predicted changes in the level of anger expression at epoch t after controlling for anger expression at epoch t-1, mean levels of emotion regulatory behaviors, and time interval, using 1-epoch lagged multilevel models (Snijders & Bosker, 2011). The model was estimated using Linear and Nonlinear Mixed Effects Models package (NLME) in R (Pinheiro et al., 2013). The equations for this step are presented in Supplemental Appendix S2. ...
Article
The present study is focused on anger expression and regulation within the National Institute of Mental Health (NIMH) Research Domain Criteria (RDoC) construct of Frustrative Nonreward. Although previous studies have examined associations between child anger regulation and expression, these studies do not directly address the dynamic processes involved in Frustrative Nonreward using microlongitudinal methods. The current study used data from 561 adopted children, their adoptive parents, and birth parents and aimed to address gaps in the literature by examining: (a) temporal associations between anger expression during a frustrating situation, and behaviors thought to regulate emotions (e.g., attempt-to-escape, support-seeking, distraction, and focus-on-restraint) on a microlongitudinal scale during an arm restraint task assessed at 27 months; (b) birth parent externalizing problems and overreactive parenting by adoptive parents as predictors of child anger expression and moderators of the moment-to-moment associations estimated in Step 1; and (c) longitudinal associations (linear vs. quadratic) between anger expressions and externalizing behaviors at 4.5 years. Findings indicated that children's attempt-to-escape and support-seeking predicted an increase in anger expression in the following 3-s interval, whereas distraction and focus-on-restraint were not associated with changes in anger expression. Furthermore, we found that birth parents' externalizing problems were significantly associated with child anger expression, suggesting heritable influences. Anger expression showed a U-shaped longitudinal association with paternal report of externalizing behaviors at 4.5 years. Taken together, the findings emphasize the significance of integrating microlongitudinal analysis approaches into the RDoC framework, helping to advance our understanding of dynamic processes underlying reactions to Frustrative Nonreward. (PsycInfo Database Record (c) 2022 APA, all rights reserved).
... La significancia estadística de cada grupo de variables es calculada para cada tratamiento utilizando el test de permutación de Monte Carlo (499 permutaciones). Las variables de suelo, riqueza de hongos y abundancia de hongos se comparan para los distintos tratamientos utilizando modelos lineales de efectos mixtos (LME por sus siglas en inglés, p ≤ 0,05), desarrollados por medio del paquete Nlme (PINHEIRO et al., 2016), donde el sitio fue definido como aleatorio y los tratamientos de prevención de incendios forestales como factor. Se utiliza también el test de Tukey HSD cuando es necesario. ...
Conference Paper
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Los ecosistemas mediterráneos de matorrales pirófitos sin gestión son un combustible forestal con alto riesgo de incendios forestales. Los tratamientos de prevención se presentan como una herramienta eficaz para revertir esta situación. En este contexto, los hongos pueden jugar un papel importante desde los puntos de vista económico y ecológico. Para investigar los efectos a largo plazo de tratamientos de prevención de incendios forestales sobre las comunidades de hongos, hemos analizado dichas comunidades 9 años después de la aplicación de quemas prescritas y desbroces, realizados sobre matorrales dominados por Halimium lasianthum. Nuestros resultados indican que los tratamientos de prevención de incendios forestales no han tenido un efecto negativo sobre la abundancia o riqueza de hongos ectomicorrícicos, aunque hemos encontrado una menor riqueza general en los tratamientos de quema. Nuestro trabajo ha permitido detectar la presencia de Boletus edulis, especie que no ha sido afectada por los tratamientos realizados. Estos resultados apuntan a que las prácticas de gestión forestal relacionadas con la prevención de incendios forestales son compatibles con la conservación de las comunidades de hongos del suelo, algunos de ellos de alto potencial económico.
... Los datos han sido transformados cuando fue necesario para cumplir los criterios de normalidad y homocedasticidad. La riqueza de hongos a nivel de filo y grupos funcionales, la 5/14 abundancia de hongos comestibles, y las diferencias en las variables del suelo en los distintos tratamientos fueron estudiadas utilizando un modelo lineal mixto (LME, p ≤ 0,05), desarrollado mediante el paquete Nlme (PINHEIRO et al., 2016) de R (R CORE TEAM, 2019). El test de Tukey se utilizó para confirmar las diferencias significativas (p ≤ 0,05) entre tratamientos cuando fue necesario, empleando para ello el mismo software. ...
Conference Paper
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En un contexto de cambio climático, los incendios forestales suponen una grave amenaza para los ecosistemas arbolados de todo el mundo, modificando sus dinámicas naturales. Los ecosistemas mediterráneos están comúnmente afectados por incendios forestales, y las quemas prescritas se presentan en ellos como una herramienta eficaz para reducir su riesgo de ocurrencia y severidad. Aunque los efectos de la quema prescrita son un tema de estudio recurrente, la estación en la que deben aplicarse es un campo menos explorado. En este estudio se analiza el efecto de las quemas prescritas en dos estaciones diferentes (primavera y otoño) sobre las comunidades de hongos asociadas con bosques naturales de Pinus nigra. Cuatro años después del tratamiento, los resultados no muestran diferencias en la riqueza total y composición de las comunidades de hongos entre las dos estaciones de aplicación. No obstante, se perciben distintas tendencias poblacionales asociadas al comportamiento de filos y grupos funcionales. Además, se ha detectado la presencia de hongos comestibles, los cuales no se han visto afectados por los tratamientos de quema prescrita. Nuestros resultados sugieren que la aplicación de quemas prescritas en primavera y otoño son compatibles con la conservación de las comunidades de hongos del suelo.
... We examined two game outcomes measured at the individual participant level: (1) decisions to provide wildlife habitat and (2) decisions to scare lions. We modelled these outcomes as the number of scare or habitat provisioning decisions using linear mixed-effects (LME) models in the nlme package (Pinheiro et al., 2021). Both outcomes were measured as counts and were, therefore, log transformed to normalise the data. ...
Article
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Reconciling conflicts between wildlife conservation and other human activities is a pervasive, multifaceted issue. Large carnivores, such as the African lion Panthera leo are often the focus of such conflicts as they have significant ecological and cultural value but impose severe social and financial costs on the communities that live alongside them. To effectively manage human–lion conflict, it is vital to understand stakeholder decision‐making and preferences regarding mitigation techniques and coexistence strategies. We used a novel experimental game framed around lions and livestock protection, played across eight villages in Tanzania, to examine stakeholder behaviour in response to three incentive structures: support for non‐lethal scaring, and individual‐ and community‐level subsidies for provision of wildlife habitat. We found that non‐lethal deterrent methods were the preferred mitigation strategy and that individual subsidies most increased the provision of wildlife habitat. Subsidies that were conditional on other community members' decisions were less effective at increasing habitat choices. Player characteristics and attitudes appeared to have little influence on game behaviour. However, there was some evidence that gender, wealth, perceptions of respect, and the behaviour of other players affected decision‐making. Achieving success in managing conservation conflicts requires genuine stakeholder participation leading to mutually beneficial results. Our findings suggest that, while incentive‐based instruments can promote pro‐conservation behaviour, these may be more effective when targeted at individuals rather than groups. We demonstrate how experimental games offer a practical and engaging approach that can be used to explore preferences and encourage discussion of conflict management. Read the free Plain Language Summary for this article on the Journal blog. Read the free Plain Language Summary for this article on the Journal blog.
... Linear models were first inspected for assumption violations using the hist and plot function in base R coupled with the ncvTest function (Breusch-Pagan test for heteroscedasticity) in the "car" package (Fox & Weisberg, 2019). Mixed-effects models were implemented using "nlme" package (Pinheiro et al., 2020) and graphs were built using "ggplot2" (Wickham, 2016). Cohen's F effect sizes were calculated using WebPower (Zhang & Yuan, 2018) and confidence intervals, marginal and conditional R 2 , intraclass correlation coefficients (ICC), and other summary statistics were generated using the "sjPlot" package (Lüdecke, 2021). ...
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Long‐distance insect migration is poorly understood despite its tremendous ecological and economic importance. As a group, Nearctic hover flies (Diptera: Syrphidae: Syrphinae), which are crucial pollinators as adults and biological control agents as larvae, are almost entirely unrecognized as migratory despite examples of highly migratory behavior among several Palearctic species. Here, we examined evidence and mechanisms of migration for four hover fly species (Allograpta obliqua, Eupeodes americanus, Syrphus rectus, and Syrphus ribesii) common throughout eastern North America using stable hydrogen isotope (δ2H) measurements of chitinous tissue, morphological assessments, abundance estimations, and cold‐tolerance assays. Although further studies are needed, nonlocal isotopic values obtained from hover fly specimens collected in central Illinois support the existence of long‐distance fall migratory behavior in Eu. americanus, and to a lesser extent S. ribesii and S. rectus. Elevated abundance of Eu. americanus during the expected autumn migratory period further supports the existence of such behavior. Moreover, high phenotypic plasticity of morphology associated with dispersal coupled with significant differences between local and nonlocal specimens suggest that Eu. americanus exhibits a unique suite of morphological traits that decrease costs associated with long‐distance flight. Finally, compared with the ostensibly nonmigratory A. obliqua, Eu. americanus was less cold tolerant, a factor that may be associated with migratory behavior. Collectively, our findings imply that fall migration occurs in Nearctic hover flies, but we consider the methodological limitations of our study in addition to potential ecological and economic consequences of these novel findings.
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Research on several social fishes has revealed that shoals constituted by familiar individuals behave remarkably differently compared to shoals formed by unfamiliar individuals. However, whether these behavioural changes may arise also in shoals composed by a mixture of familiar and unfamiliar individuals, a situation that may commonly occur in nature, is not clear. Here, we observed the behaviour of Mediterranean killifish ( Aphanius fasciatus ) shoals that were composed by both familiar and unfamiliar individuals (i.e. individuals were familiar to each other in pairs) and compared it with shoals entirely made by either unfamiliar or familiar individuals. Shoals formed by familiar individuals took longer to emerge from a refuge and swam more cohesively compared to shoals formed by unfamiliar fish. Shoals formed by a mixture of familiar and unfamiliar individuals behaved as shoals formed by unfamiliar individuals. Moreover, mixed shoals did not segregate in pairs according to their familiarity. This study suggests that mixed shoals do not show the behavioural effects of familiarity. Significance statement Laboratory studies have compared the behaviour of shoals formed by familiar fish versus shoals formed by unfamiliar fish, finding notable advantages in the former ones, such as improved antipredator and foraging behaviour. However, comparing these two opposite shoal types may not provide information on the natural situation, because in nature, shoals often change composition. We investigated how shoals formed by a mixture of familiar and unfamiliar fish behaved. We analysed shoals’ preference for open environment versus covers and shoals’ swimming cohesion. Results showed that shoals formed by both familiar and unfamiliar individuals mostly behave like shoals entirely formed by unfamiliar individuals. This suggests that the advantages of social groups formed by familiar fish might be hardly seen in nature for species in which shoal composition changes frequently.
Article
Purpose Fatigue is frequently experienced during treatment for cancer and persists for months to years after treatment completion in a subset of patients. The underlying mechanisms remain poorly understood. We postulated that reduced cellular energy metabolism may underlie fatigue in cancer patients and survivors and tested this hypothesis in a sample of patients newly diagnosed with early-stage breast cancer (n=49) followed for approximately 1 year from before the start of neoadjuvant chemotherapy (NACT) till after treatment completion. Methods Patient-reported fatigue was assessed with the Checklist Individual Strength, and blood samples were obtained before, during, and shortly after NACT. A final assessment was completed after surgery and radiation therapy, 4-6 months after NACT. At each study time point, mitochondrial oxygen consumption and glycolytic activity were measured in peripheral blood mononuclear cells (PBMC). Associations of these measures of PBMC energy metabolism with fatigue were assessed in multilevel models. Results Before NACT, higher mitochondrial oxygen consumption and glycolytic activity were associated with higher fatigue, whereas after completion of all primary treatment, these assessments were associated with lower fatigue. Conclusion These findings suggest that lower cellular energy metabolism after treatment may be a novel target for interventions aimed at preventing or reducing persistent fatigue. Earlier studies investigated the use of supplements for maintaining mitochondrial health during treatment, with mixed results; when proven to be safe, such interventions may be more effective after treatment and in individuals with reduced mitochondrial oxygen consumption rates.
Article
A more efficient use of limited canopy space and, thus, a higher canopy space occupation (CSO) in forests can result in an increased absorption of photosynthetically active radiation, which in turn can promote productivity. Although there is some evidence for a positive relationship between tree diversity (TD) and CSO, the generality of this hypothesis is still under debate. Here, we propose a conceptual framework that accounts for both the spatial complexity of canopy space and size-dependent interspecific tree interactions and tested it using mobile laser scanning data across larger spatial scales. We assessed the CSO at high resolution with two diversity indices, tree species richness (TSR) and the effective number of species (ENS) along a TSR gradient ranging from monocultures to 8-species mixtures in a mature and structurally complex mixed-species temperate forest. We found that the direction and strength of the TD-CSO relationship largely depended on the way how canopy space is defined and which tree size classes are considered to calculate TSR. Using an broad deliniation of canopy space no significant relationship between TD and CSO was evident. In contrast, when considering only the upper canopy space, a significant effect of TSR on CSO emerged. Importantly, the direction of this relationship was critically dependent on the tree size threshold underlying the TSR determination. For all trees with a diameter at breast height > 7 cm, we observed a significant negative relationship, while the opposite was the case when considering only large-sized trees. Our novel conceptual framework demonstrates that accurate estimation of canopy space complexity and tree size dependence is key to better understanding the processes underlying CSO. However, further information on diversity-canopy space occupation relationships from studies in different forests and forest types is needed.
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Species of the genus Trichoderma sp. are used to control leaf-cutting ants. However, knowledge about the collective immune responses of ants against this antagonist is scarce. Therefore, this study assessed the frequency of hygienic behaviors deployed by medium workers of Atta cephalotes. For this purpose, suspensions of Trichoderma sp. spores were sprayed on sub-colonies composed of workers and a portion of the mutualist. As a control, the sub-colonies were sprayed with water. Independent of whether the workers were treated with spores of Trichoderma sp. or water, they increased the frequency of self-grooming while reducing the frequency of fungus grooming. These findings suggest that medium workers prioritize the removal of contaminants from their bodies over the interaction with the mutualist, possibly to avoid further contamination in the garden. In the field, this strategy may minimize the possibility that foraging ants exposed to contaminants from the exterior can transfer potentially hazardous materials to the nest where they can reach the garden, risking the colony’s productivity.
Article
Bacille Calmette-Guerin (BCG) is a potential tool in the control of Mycobacterium bovis in European badgers (Meles meles). A five year Test and Vaccinate or Remove (TVR) research intervention project commenced in 2014 using two BCG strains (BCG Copenhagen 1331 (Years 1–3/ BadgerBCG) and BCG Sofia SL2222 (Years 4–5). Badgers were recaptured around 9 weeks after the Year 5 vaccination and then again a year later. The Dual-Path Platform (DPP) Vet TB assay was used to detect serological evidence of M. bovis infection. Of the 48 badgers, 47 had increased Line 1 readings (MPB83 antigen) between the Year 5 vaccination and subsequent recapture. The number of BCG Sofia vaccinations influenced whether a badger tested positive to the recapture DPP VetTB assay Line 1 (p < 0.001) while the number of BadgerBCG vaccinations did not significantly affect recapture Line 1 results (p = 0.59). Line 1 relative light units (RLU) were more pronounced in tests run with sera than whole blood. The results from an in_house MPB83 ELISA results indicated that the WB DPP VetTB assay may not detect lower MPB83 IgG levels as well as the serum DPP VetTB assay. Changes in interferon gamma assay (IFN-γ) results were seen in 2019 with significantly increased CFP-10 and PPDB readings. Unlike BadgerBCG, BCG Sofia induces an immune response to MPB83 (the immune dominant antigen in M. bovis badger infection) that then affects the use of immunodiagnostic tests. The use of the DPP VetTB assay in recaptured BCG Sofia vaccinated badgers within the same trapping season is precluded and caution should be used in badgers vaccinated with BCG Sofia in previous years. The results suggest that the DPP VetTB assay can be used with confidence in badgers vaccinated with BadgerBCG as a single or repeated doses.
Article
Mangroves are coastal wetland ecosystems of tropical and subtropical regions. Water and substrate salinities are important drivers of their development and trajectories. Therefore, understanding how main mangrove species respond to salinity gradient when transplanted in natural environment is essential for their restoration. This study assessed the survival, growth, and productivity of Rhizophora racemosa seedlings in response to gradient of salinity. Seedlings were grown in nursery under low (3–5 psu) and medium (15–17 psu) water salinities for thirty days and transplanted to three mangrove sites with various salinities (4.6, 11.41, and 18.27 psu). Seedling survival and growth were monitored monthly for 6 months. At the end of month 6, total biomass was harvested and partitioned among plant parts. Results showed that growth, survival, and productivity of R. racemosa were mainly influenced not by the salinity under which the seedlings were raised in nursery but rather by site. Survival was higher (88.33%) at the site with the highest salinity. Total plant biomass was similar across sites, but root biomass and root weight ratio were higher on sites with higher salinity. Biomass was disproportionately higher in stems (45–54%) than in roots (28–37%), and leaves (15–18%). We suggest that restoration is done in appropriate period, ideally one month before the start of rainy season. This will not only allow seedlings to well establish their rooting system before rains start but also favour seedling growth, because of substrate salinity dilution by fresh water from rains and flows from uplands.
Article
Species in the mammalian order Carnivora have extremely diverse diets. The association between diet and craniodental morphology in carnivorans has been the subject of a number of studies. The distance from the jaw joint to the tooth positions may contribute to the ability to acquire and process food because it corresponds to the outlever arm when the jaw functions as a lever to generate a bite force. A shorter outlever arm relative to the inlever arm of the masticatory muscle generates a higher bite force. This study measured the distances from the jaw joint to different points of the teeth as the outlever lengths in the crania of terrestrial Carnivora species to show that outlever lengths corrected for phylogeny and a measure of the inlever length differ according to dietary habits among carnivorans. The distance from the jaw joint to the last molar was shortest in folivores, followed by aquatic prey specialists, suggesting that consumption of tough plant materials and, to some extent, aquatic prey with hard exoskeletons has favoured the evolution of a shorter outlever to allow stronger bites with enlarged molars. In contrast, among Canidae species, a shorter outlever to canines was associated with feeding on large prey, but this association was not found across carnivorans, suggesting that the correlated evolution of a shorter outlever at the canines and specialization for feeding on large prey depends on foraging and hunting behaviours. Combined, these findings provide some evidence that distances from the jaw joint to different points of the teeth are adapted to different feeding ecologies in carnivorans. In craniodental morphology, the distance from the jaw joint to the teeth corresponds to the outlever arm when the jaw functions as a lever to generate a bite force, with a shorter outlever converting more muscle force into bite force. We performed phylogenetic comparative analyses to show that the outlever lengths at different points of the teeth in the cranium differ according to dietary habits in the mammalian order Carnivora. This study provides evidence for adaptations of the distance from the jaw joint to the teeth to different feeding ecologies in Carnivora.
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Flowers produce local humidity that is often greater than that of the surrounding environment, and studies have shown that insect pollinators may be able to use this humidity difference to locate and identify suitable flowers. However, environmental humidity is highly heterogeneous, and is likely to affect the detectability of floral humidity, potentially constraining the contexts in which it can be used as a salient communication pathway between plants and their pollinators. In this study, we use differential conditioning techniques on bumblebees Bombus terrestris audax (Harris) to explore the detectability of an elevated floral humidity signal when presented against different levels of environmental noise. Artificial flowers were constructed that could be either dry or humid, and individual bumblebees were presented with consistent rewards in either the humid or dry flowers presented in an environment with four levels of constant humidity, ranging from low (~20% RH) to highly saturated (~95% RH). Ability to learn was dependent upon both the rewarding flower type and the environment: the bumblebees were able to learn rewarding dry flowers in all environments, but their ability to learn humid rewarding flowers was dependent on the environmental humidity, and they were unable to learn humid rewarding flowers when the environment was highly saturated. This suggests that floral humidity might be masked from bumblebees in humid environments, suggesting that it may be a more useful signal to insect pollinators in arid environments.
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This study aimed to quantify the mobilization of body energy of alpine goats slaughtered at fixed time intervals from parturition to 56 days of lactation. Fifty-one multiparous Alpine dairy goats were used to determine the body composition of the animals. Three goats were slaughtered to estimate the initial body composition of the animals that remained in the experiment. Forty-eight goats were assigned to a completely randomized design, and the treatments were the eight subsequent weeks of lactation (7th, …, 56th days). Six goats were slaughtered per week. We used linear and non-linear models to analyze the variables with and without repeated measures. The animals' dry matter intake reached the maximum of 1.5±0.21 kg/day at 40±3 days of lactation. The milk yield reached the maximum of 2.52±0.32 kg/day at 28 ± 9 days of lactation. The rate of secretion of the milk components such as fat, protein, lactose, and energy reached maximum values of 141.0±17.5, 102.2±16.1, 100.5±24 g/day, and 9.44±1.01 MJ/day at 7±2, 2±5, 18±12, and 7±2 days of lactation, respectively. Empty body mass, non-carcass components, carcass, and omental and visceral fat reduced with the advance of the lactation weeks. In conclusion, dairy goats in early lactation mobilize not only energy reserves from omental and visceral fats but also from the carcass and non-carcass components, ash, and water. The body energy of alpine goats is mobilized with higher intensity in the first eight weeks of lactation due to the more significant mobilization of omental and visceral fats (average of 130 g/day) in the empty body weight. Body energy decreased linearly, and the total amount of energy mobilized during the first eight weeks of lactation was considerable: 352MJ, with an average of 6.24 MJ/day.
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This chapter is aimed to overview the joint modeling through the harmonization of longitudinal data and time-to-event data with a Bayesian approach. We considered a randomized clinical trial in which both longitudinal data and survival data were collected to compare the efficacy and the safety of two antiretroviral drugs in treating patients who had failed or were intolerant of zidovudine (AZT) therapy. Using these data, we demonstrated the advantages of the Bayesian joint modeling over the classical approach of separately analyzing these types of data with Cox proportional hazard model and longitudinal linear mixed-effects model. We found that the Bayesian joint modeling can better address information loss on outcome-dependent missingness, which can preserve information from both longitudinal data and time-to-event data. The Bayesian joint modeling can produce unbiased estimates and retain higher statistical power for public health data analysis.
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Mountain lakes experience interannual variability in spring snowpack and ice cover that can lead to differences in physical, chemical, and biological properties in the succeeding summer. Lake studies that capture extreme years of snow and ice would be useful to understand and anticipate effects of climate change, but such data are rare for remote mountain lakes. Monitoring of lakes in Olympic, North Cascades, and Mount Rainier National Parks from 2007 to 2018 allowed us to examine limnological differences along interannual and elevation‐driven climate gradients that included unusually high (2011–2012) and 100‐yr record low (2015) snowpack years. Years with lower spring snowpack had earlier ice‐out. Across lakes, our analysis suggested an average of 0.075°C lake warming per day of lost ice duration (0.525°C per week), giving rise to other ecosystem changes linked to temperature such as lower dissolved oxygen, higher total dissolved N, higher chlorophyll, and higher abundance of cladoceran zooplankton. Conversely, in years with higher snowpack and a shorter ice‐free season, lakes were colder and clearer (1 m deeper Secchi depth for every 1 m May snow water equivalent), with more dilute ions as well as lower algal biomass and zooplankton abundance. These results add to evidence that changes in snowpack or ice‐out dates alter mountain lake ecology through multiple processes associated with hydrology, terrestrial‐aquatic connection, water temperature, productivity, ion composition, and plankton communities.
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Body size and shape play fundamental roles in organismal function and it is expected that animals may possess body proportions that are well-suited to their ecological niche. Tetrapods exhibit a diverse array of body shapes, but to date this diversity in body proportions and its relationship to ecology have not been systematically quantified. Using whole-body skeletal models of 410 extinct and extant tetrapods, we show that allometric relationships vary across individual body segments thereby yielding changes in overall body shape as size increases. However, we also find statistical support for quadratic relationships indicative of differential scaling in small-medium versus large animals. Comparisons of locomotor and dietary groups highlight key differences in body proportions that may mechanistically underlie occupation of major ecological niches. Our results emphasise the pivotal role of body proportions in the broad-scale ecological diversity of tetrapods.
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For human-audible vocalizations (below 20 kHz) of rodents, subterranean lifestyle results in low-frequency calls coupled with low-frequency hearing. For ultrasonic vocalizations (above 20 kHz), the effect of subterranean lifestyle on the acoustics is unknown. This study fills this gap of knowledge, by comparing vocalizations of two closely related species, the surface-dwelling Brandt’s vole Lasiopodomys brandtii (17 pups, 19 adults) and the subterranean mandarin vole L. mandarinus (15 pups, 16 adults). As predicted, the audible calls (AUDs) were substantially higher-frequency in L. brandtii than in L. mandarinus, in either pups or adults. In contrast to AUDs, the ultrasonic calls (USVs) did not differ in frequency variables between species, in either pups or adults. Interspecies differences were found in duration: AUDs were shorter in adult L. brandtii than in adult L. mandarinus, USVs were longer in pup L. brandtii than in pup L. mandarinus, and the low-frequency USVs of adult L. brandtii were longer than low-frequency USVs of adult L. mandarinus. We advance a hypothesis that shift towards higher-frequency AUDs in L. brandtii compared to L. mandarinus was triggered by the evolutionary emergence of the high-frequency audible alarm call, which is only present in L. brandtii but absent in L. mandarinus. We discuss that USVs may be resistant to these selection pressures as close-distant social signals. Significance statement Relationship between ecological specialization, such as subterranean or surface-dwelling lifestyle, and the acoustic traits of communicative signals in rodents evoke interest for over than 30 years. So far, the relationship between vocalization and subterranean life (low-frequency calls and low-frequency hearing) was only reported for calls produced by rodents in human-audible range of frequencies. No data was available for ecological adaptations of ultrasonic calls; moreover, even the existence of ultrasonic calls in subterranean rodents was unknown to recent time. Comparative studies of closely related subterranean and surface-dwelling rodent species might highlight the evolution of acoustic traits related to these ecological specializations.
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Rationale Second-generation antipsychotic (SGA) medications can produce abnormal weight gain and metabolic dysfunction in children, but little is known about the post-treatment consequences of adolescent SGA exposure. Objectives The objective of this study was to determine the long-term, post-treatment effects of adolescent olanzapine exposure on weight and metabolic function and whether dietary fish oil (FO) modulated any observed effects of olanzapine. Methods Male and female mice were fed a high-fat, high-sugar (HF-HS) diet or an HF-HS diet supplemented with fish oil (HF-HS-FO) and were treated with olanzapine or vehicle for 29 days beginning on postnatal day 37. Results In male mice, adolescent olanzapine treatment suppressed weight gain during and after treatment and improved metabolic function in adulthood; dietary fish oil reduced weight gain, increased expression of fatty acid oxidation genes, and decreased expression of genes associated with fatty acid synthesis and inflammation. In contrast, few effects were observed in female mice. Conclusions The current results suggest that adolescent olanzapine exposure can produce long-term alterations in weight and metabolic function in male mice and that dietary fish oil can reduce adverse effects of lifelong consumption of an HF-HS diet. Because expected adverse effects of adolescent olanzapine treatment were not observed, the potential beneficial effects of dietary fish oil for SGA-induced weight gain and metabolic dysfunction could not be evaluated.
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Trichinellosis is a notifiable zoonotic disease caused by parasitic nematode larvae belonging to the genus Trichinella. Domestic pig and wild boar are important hosts within the natural cycle of T. spiralis, the last one being an animal whose populations have experienced an important growth. Therefore, this paper studies the prevalence of Trichinella infection in wild boar in Spain, as well as its relation with hunting and its impact on public health during the period 2006–2019. For this purpose, different sources of information were consulted and analyzed depending on the autonomous communities of Spain and years. During the fourteen years of study, the number of wild boars hunted and the number of cases of Trichinella infection in them increased (from 172 cases in 2006 to 421 in 2019), although prevalence values remained low as the number of animals analyzed also increased. On the other hand, trichinellosis in humans tended to decrease (from a peak of 107 cases in 2007 to 11 cases in 2019). Nevertheless, the numbers of both wild boars and humans infected with Trichinella in Spain are among the highest in Europe, and this emphasizes the importance of food safety, sanitary controls of game meat and citizen awareness campaigns, which prevent the spread of Trichinella through the human population.
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The Atlantic salmon (Salmo salar) aquaculture industry is growing, and with it, the need to source and optimise sustainable ingredients for aquafeeds. Black soldier fly (BSF) larvae (Hermetia illucens) have received increasing research attention since they are a good source of protein that can efficiently convert a wide range of low-value organic material into valuable resources. This study investigated the impact of three differently processed BSF meals, an untreated BSF diet (BSFC+), a dechitinated BSF diet (BSFC-) and a fermented BSF diet (BSFC+P+) at a 10% inclusion level replacing fish meal in a fish meal control (FM) and a marine and soy protein concentrate based control diet (SPC). Growth performance, gut microbiome and gut histology of salmon fry was assessed. The inclusion and processing methods of BSF showed no adverse impacts on either growth performance or gut histology. However, the gut microbiome of fish was significantly altered by both the protein source and the processing method of the BSF larvae. Fish fed BSFC+, had an increased diversity and evenness of the community compared with conventional protein sources alone, and compared with the other BSF processing methods. However, control diets had a greater presence of lactic acid bacteria and genera associated with faster growing hosts. Fish fed BSF had a high relative abundance of the genus, Exiguobacterium, a chitin-degrading bacterium and in BSFC+P+ fed fish this bacterium completely dominated the community, indicating the presence of dysbiosis. Future studies should determine, why Exiguobacterium has dominated the community for the BSFC+P+ diet, and if it provides a digestive function to the host and identify bacteria that are indicators of optimal host performance and resilience. The results confirmed that BSF is a promising fish meal replacement for salmon, and it demonstrated that BSFC+ has a potential prebiotic impact on the gut microbiome of Atlantic salmon.
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Species range sizes and realized niche breadths vary tremendously. Understanding the source of this variation has been a long‐term aim in evolutionary ecology and is a major tool in efforts to ameliorate the impacts of changing climates on species distributions. Species ranges that span a large climatic envelope can be achieved by a collection of specialized genotypes locally adapted to a small range of conditions, by genotypes with stable fitness across variable environments, or a combination of these factors. We asked whether fitness expressed along a key niche axis, water availability, could explain a species’ realized niche breadth‐‐its geographic range and climate breadth‐‐ in 11 species from a clade of jewelflowers whose range sizes vary by two orders of magnitude. Specifically, we explored whether the range size of a species was related to the ability of genotypes (maternal families) to maintain fitness across a range of experimental water availabilities based on 30‐year historical field precipitation regimes. We operationally characterized fitness homeostasis through the coefficient of variation (CV) in fitness of a genotype (family) across the experimental water gradient. We found that species with genotypes that had high fitness homeostasis ‐‐ low variation in fitness over our treatments ‐‐had larger climatic niche breadth and geographic range in their field distributions. The result was robust to alternate measures of fitness homeostasis. Our results show that the fitness homeostasis of genotypes can be a major factor contributing to niche breadth and range size in this clade. Fitness homeostasis can buffer species from loss of genetic diversity and under changing climates, provides time for adaptation to future conditions.
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Environmental stress is a major driver of ecological and evolutionary processes in nature. To cope with stress, organisms can adjust through phenotypic plasticity and/or adapt through genetic change. Here, we compared short-term behavioural (activity) and physiological (corticosterone levels, CORT) responses of Rana arvalis tadpoles from two divergent populations (acid origin, AOP, versus neutral origin, NOP) to acid and predator stress. Tadpoles were initially reared in benign conditions at pH 7 and then exposed to a combination of two pH (acid versus neutral) and two predator cue (predator cue versus no predator cue) treatments. We assessed behavioural activity within the first 15 min, and tissue CORT within 8 and 24 h of stress exposure. Both AOP and NOP tadpoles reduced their activity in acidic pH, but the response to the predator cue differed between the populations: AOP tadpoles increased whereas NOP tadpoles decreased their activity. The AOP and NOP tadpoles differed also in their CORT responses, with AOP being more responsive (CORT levels of NOP tadpoles did not differ statistically across treatments). After 8 h exposure, AOP tadpoles had elevated CORT levels in the acid-predator cue treatment and after 24 h exposure they had elevated CORT levels in all three stress treatments (relative to the benign neutral–no-cue treatment). These results suggest that adaptation to environmental acidification in R. arvalis is mediated, in part, via behavioural and hormonal plasticity.
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Many areas are experiencing increasing stream temperatures due to climate change, and some are experiencing reduced summer stream flows and water availability. Because dam building and pond formation by beaver can increase water storage, stream cooling, and riparian ecosystem resilience, beaver have been proposed as a potential climate adaption tool. Despite the large number of studies that have evaluated how beaver activity may affect hydrology and water temperature, few experimental studies have quantified these outcomes following beaver relocation. We evaluated changes in temperature and water storage following the relocation of 69 beaver into 13 headwater stream reaches of the Skykomish River watershed within the Snohomish River basin, Washington, USA. We evaluated how beaver dams affected surface and groundwater storage and stream temperature. Successful relocations created 243 m3 of surface water storage per 100 m of stream in the first year following relocation. Dams raised water table elevations by up to 0.33 m and stored approximately 2.4 times as much groundwater as surface water per relocation reach. Stream reaches downstream of dams exhibited an average decrease of 2.3°C during summer base‐flow conditions. We also assessed how dam age, condition, maintenance frequency, and pond morphology influenced stream temperature at naturally colonized wetland complexes. Our findings demonstrate that dam building can increase water storage and reduce stream temperatures in the first year following successful beaver relocation. Fluvial and floodplain morphology of candidate reaches for relocation is an important consideration because it determines the type and magnitude of response. Relocation to reaches with existing small, abandoned ponds may address thermal criteria by conversion from warming to cooling reaches, whereas relocation within large, abandoned complexes or vacant habitat may result in greater water storage. Although beaver relocation can be an effective climate adaptation strategy to retain more stable hydrologic regimes and water quality in our study area, there appear to be regionally specific environmental and geomorphic factors that influence how beaver affect water storage and temperature. More research is needed to investigate how and why these regional differences affect water storage and stream temperature response in beaver‐influenced systems.
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The increase in species diversity from temperate to tropical regions is one of the most widespread patterns in biogeography. As humans continue to drastically modify natural habitats, land‐use changes such as the development of cities could potentially alter typical latitudinal diversity gradients. Cities could depress or enhance biodiversity through filtering, localised extirpations, or increasing niche availability, respectively. To address these possibilities and the consequences for the latitudinal diversity gradient, we constructed a global dataset of urban species diversity (richness) and community composition across ~60° of absolute latitude and from 63 cities. We focused our study on ants, for which comparable urban and non‐urban diversity data are broadly available. We found that urbanisation significantly dampened the latitude‐diversity cline. The effects of urbanisation varied with latitude: at lower latitudes, cities were relatively species poor and harboured distinct ant communities relative to nearby non‐urban communities. In higher latitude cities, both species richness and community composition were more similar to the surrounding non‐urban ant communities. Our analyses suggest that the strongest impacts of urbanisation on ant diversity may be in the tropics, where biological diversity is already expected to experience the greatest risk of extinction in the face of climate change. We constructed a global dataset of urban ant species diversity (richness) and community composition. We found that urbanisation significantly dampened the latitude‐diversity cline, with varying impacts across latitude. Lower latitude cities were species poor with distinct ant communities relative to nearby non‐urban communities. Urban and non‐urban species richness and community composition were more similar at higher latitudes. The strongest impacts of urbanisation on ant diversity may be in the tropics, where biological diversity is expected to experience the greatest risk of extinction due to climate change.
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