A. Justin Nowakowski

Estimation of Larval Stream Salamander Densities in Three Proximate Streams in the Georgia Piedmont

Abstract Despite decades of research, there is still little known about the natural abundances and ecological importance of stream salamander larvae in eastern North America. Widely used methods for sampling larvae and estimating population densities can be significantly biased, which may have implications for monitoring efforts and studies addressing the effects of salamanders on stream processes such as nutrient dynamics. We compared the efficacy of two methods of capture, passive leaf litter trapping and dip netting, and performed mark–recapture (M-R) on larvae occurring in three adjacent streams. There was a significant size bias associated with at least one of our capture methods. Leaf litter traps captured a higher proportion of larger individuals (>15 mm SVL), whereas dip netting yielded a greater proportion of the smaller size class (≤15 mm). Density estimates were 1–2 orders of magnitude greater than estimates provided by other studies; however, count indices were comparable to those previously reported. Density estimates from M-R ranged from 23–169 salamander larvae per m2, which was remarkably consistent with estimates of 75–137 larvae per m2 from a contemporaneous study using nearly identical methodology in Appalachian streams in North Carolina. The coefficient of variation for mean density estimates generated from M-R was greater than that detected with count data, indicating that the use of replicated counts without adjustment for detection may be less effective for measuring spatial and temporal variation in larval stream salamander numbers.

Mechanistic insights into landscape genetic structure of two tropical amphibians using field‐derived resistance surfaces

Conversion of forests to agriculture often fragments distributions of forest species and can disrupt gene flow. We examined effects of prevalent land uses on genetic connectivity of two amphibian species in northeastern Costa Rica. We incorporated data from field surveys and experiments to develop resistance surfaces that represent local mechanisms hypothesized to modify dispersal success of amphibians, such as habitat‐specific predation and desiccation risk. Because time lags can exist between forest conversion and genetic responses, we evaluated landscape effects using land‐cover data from different time periods. Populations of both species were structured at similar spatial scales but exhibited differing responses to landscape features. Litter frog population differentiation was significantly related to landscape resistances estimated from abundance and experiment data. Model support was highest for experiment‐derived surfaces that represented responses to microclimate variation. Litter frog genetic variation was best explained by contemporary landscape configuration, indicating rapid population response to land‐use change. Poison frog genetic structure was strongly associated with geographic isolation, which explained up to 45% of genetic variation, and long‐standing barriers, such as rivers and mountains. However, there was also partial support for abundance‐ and microclimate response‐derived resistances. Differences in species responses to landscape features may be explained by overriding effects of population size on patterns of differentiation for poison frogs, but not litter frogs. In addition, pastures are likely semi‐permeable to poison frog gene flow because the species is known to use pastures when remnant vegetation is present, but litter frogs do not. Ongoing reforestation efforts will probably increase connectivity in the region by increasing tree cover and reducing area of pastures.

Tropical amphibians in shifting thermal landscapes under land-use and climate change

Land-cover and climate change are both expected to alter species distributions and contribute to future biodiversity loss. However, the combined effects of land-cover and climate change on assemblages, especially at the landscape scale, remain understudied. Lowland tropical amphibians may be particularly susceptible to changes in land cover and climate warming because many species have narrow thermal safety margins resulting from air and body temperatures that are close to their critical thermal maxima (CTmax ). We examined how changing thermal landscapes may alter the area of thermally suitable habitat (TSH) for tropical amphibians. We measured microclimates in 6 land-cover types and CTmax of 16 frog species in lowland northeastern Costa Rica. We used a biophysical model to estimate core body temperatures of frogs exposed to habitat-specific microclimates while accounting for evaporative cooling and behavior. Thermally suitable habitat area was estimated as the portion of the landscape where species CTmax exceeded their habitat-specific maximum body temperatures. We projected changes in TSH area 80 years into the future as a function of land-cover change only, climate change only, and combinations of land-cover and climate-change scenarios representing low and moderate rates of change. Projected decreases in TSH area ranged from 16% under low emissions and reduced forest loss to 30% under moderate emissions and business-as-usual land-cover change. Under a moderate emissions scenario (A1B), climate change alone contributed to 1.7- to 4.5-fold greater losses in TSH area than land-cover change only, suggesting that future decreases in TSH from climate change may outpace structural habitat loss. Forest-restricted species had lower mean CTmax than species that occurred in altered habitats, indicating that thermal tolerances will likely shape assemblages in changing thermal landscapes. In the face of ongoing land-cover and climate change, it will be critical to consider changing thermal landscapes in strategies to conserve ectotherm species.

The importance of defining focal assemblages when evaluating amphibian and reptile responses to land use

Habitat loss and degradation are primary threats to amphibians and reptiles, but the relative effects of common land uses on assemblages and the mechanisms that underlie faunal responses are poorly studied. We reviewed the effects of four prevalent types of habitat alteration (urbanization, agriculture, livestock grazing, and silviculture) on amphibian and reptile species richness and abundance by summarizing reported responses in the literature and by estimating effect sizes across studies for species richness in each land-use type. We then used a multinomial model to classify species as natural habitat specialists, generalists, and disturbed habitat specialists and examined variation in effect sizes for each land-use type according to habitat specialization categories. There were mixed conclusions from individual studies, some reporting negative, neutral, or positive effects of land use on species richness and total abundance. A large proportion of studies reported species-specific effects of individual species abundance. However, in our analysis of effect sizes, we found a general trend of negative effects of land use on species richness. We also demonstrate that habitat associations of common species and species turnover can explain variation in the effect of land use on herpetofauna. Our review highlights the pervasive negative effects of common land uses on amphibians and reptiles, the importance of identifying groups vulnerable to land-use change (e.g., forest-associated species) in conservation studies, and the potential influence of disturbance-associated species on whole assemblage analyses.

Evaluating connectivity for tropical amphibians using empirically derived resistance surfaces.

Agricultural expansion continues to drive forest loss in species-rich tropical systems and often disrupts movement and distributions of organisms. The ability of species to occupy and move through altered habitats likely depends on the level of contrast between natural forest and surrounding land uses. Connectivity models, such as circuit theory models, are widely used in conservation biology, and their primary input consists of resistance surfaces representing movement costs associated with landscape features. Cost values are most frequently determined by expert opinion, which may not capture relevant levels of contrast among features. We developed resistance surfaces using experiments that represent different local mechanisms hypothesized to affect connectivity for two Neotropical amphibian species. Response ratios were calculated to translate experimental results to cost values used in connectivity modeling. We used relative abundance data in three land-cover types to generate resistance surfaces for evaluating independent support of models derived from experiments. Finally, we analyzed agreement among movement pathways predicted for each species and among three commonly used connectivity measures: Euclidean, least cost, and resistance distances. Experiments showed that extreme microclimates associated with altered habitats significantly increased desiccation and mortality risk for both species. Resistances estimated from microclimate experiments were concordant with those from survey data for both species. For one focal species, resistance estimates derived from predator encounter rates were also highly correlated with abundance-derived resistances. There was generally low agreement among the three alternative distance measures, which underscores the importance of choosing connectivity models that are most appropriate for the study objectives. Overall, similarity among linkages modeled for each species was high, but decreased with declining forest cover. Our results highlight the value of experiments for drawing inferences about processes in resistance modeling, as well as the need to consider model differences and species-specific responses when developing strategies to maintain connectivity.

Matrix type alters structure of aquatic vertebrate assemblages in cypress domes

Management of communities in fragmented systems requires application of models for predicting and understanding patterns of diversity at relevant scales. Metacommunity models may help explain patterns of beta-diversity, but more empirical investigations are needed to determine the generality of these models and the importance of matrix identity as a mediator of metacommunity processes. We studied patterns of beta diversity among cypress domes in a landscape composed of two different matrix types within Big Cypress National Preserve to determine whether community composition differed by matrix type and to evaluate predictions of metacommunity models. We sampled fully-aquatic vertebrates in 16 cypress domes. A causal modeling framework was used to assess the relative importance of space and environmental variables measured in the domes and in the nearby matrix in explaining variation in community similarities. Our results show that community composition was influenced by matrix type, which violates the common metacommunity assumption that matrix identity has negligible effect on patch patterns. We found different drivers of beta-diversity patterns between matrix types; similarities among dome communities within cypress-prairie matrix were influenced by local environmental conditions and matrix characteristics, while communities in pine-rockland domes were most influenced by conditions in the matrix. Our results have implications for use of metacommunity models in conservation planning and we suggest that future research should focus on the importance of matrix identity and complexity in mediating community patterns in patchy landscapes.

Phylogenetic homogenization of amphibian assemblages in human-altered habitats across the globe

Significance Widespread conversion of natural habitats to human land use creates evolutionarily novel environments and causes declines of native species. Stemming biodiversity loss requires an understanding of why some species persist while others decline in these novel habitats. We analyzed survey data of amphibian species from around the globe to determine whether closely related species respond similarly to habitat conversion. We find that species that persist in converted habitats tend to come from the same clades within the amphibian tree of life and that by favoring these widely distributed clades, habitat conversion leads to nonrandom extirpations and loss of evolutionary history. Our results show that the identity of winners and losers during the Anthropocene can be tightly linked to their evolutionary history. Habitat conversion is driving biodiversity loss and restructuring species assemblages across the globe. Responses to habitat conversion vary widely, however, and little is known about the degree to which shared evolutionary history underlies changes in species richness and composition. We analyzed data from 48 studies, comprising 438 species on five continents, to understand how taxonomic and phylogenetic diversity of amphibian assemblages shifts in response to habitat conversion. We found that evolutionary history explains the majority of variation in species’ responses to habitat conversion, with specific clades scattered across the amphibian tree of life being favored by human land uses. Habitat conversion led to an average loss of 139 million years of amphibian evolutionary history within assemblages, high species and lineage turnover at landscape scales, and phylogenetic homogenization at the global scale (despite minimal taxonomic homogenization). Lineage turnover across habitats was greatest in lowland tropical regions where large species pools and stable climates have perhaps given rise to many microclimatically specialized species. Together, our results indicate that strong phylogenetic clustering of species’ responses to habitat conversion mediates nonrandom structuring of local assemblages and loss of global phylogenetic diversity. In an age of rapid global change, identifying clades that are most sensitive to habitat conversion will help prioritize use of limited conservation resources.

Polymorphic microsatellite loci for a neotropical leaf-litter frog (Craugastor bransfordii) characterized through Illumina sequencing

There are relatively few molecular resources for amphibians in the tropics where widespread habitat loss, disease, and contamination threaten the world’s most diverse assemblages. We used Illumina sequencing to develop microsatellite primers for a dominant amphibian species in Costa Rica that has recently experienced population declines. We characterized 12 polymorphic loci and have provided sequences for over 200 additional primers. These novel molecular resources will be useful for future studies of population genetic structure and may help explain recent declines in one of many species that are decreasing in Central America.

Salinity tolerances and use of saline environments by freshwater turtles: implications of sea level rise: Freshwater turtles in saline environments

The projected rise in global mean sea levels places many freshwater turtle species at risk of saltwater intrusion into freshwater habitats. Freshwater turtles are disproportionately more threatened than other taxa; thus, understanding the role of salinity in determining their contemporary distribution and evolution should be a research priority. Freshwater turtles are a slowly evolving lineage; however, they can adapt physiologically or behaviourally to various levels of salinity and, therefore, temporarily occur in marine or brackish environments. Here, we provide the first comprehensive global review on freshwater turtle use and tolerance of brackish water ecosystems. We link together current knowledge of geographic occurrence, salinity tolerance, phylogenetic relationships, and physiological and behavioural mechanisms to generate a baseline understanding of the response of freshwater turtles to changing saline environments. We also review the potential origins of salinity tolerance in freshwater turtles. Finally, we integrate 2100 sea level rise (SLR) projections, species distribution maps, literature gathered on brackish water use, and a phylogeny to predict the exposure of freshwater turtles to projected SLR globally. From our synthesis of published literature and available data, we build a framework for spatial and phylogenetic conservation prioritization of coastal freshwater turtles. Based on our literature review, 70 species (∼30% of coastal freshwater turtle species) from 10 of the 11 freshwater turtle families have been reported in brackish water ecosystems. Most anecdotal records, observations, and descriptions do not imply long‐term salinity tolerance among freshwater turtles. Rather, experiments show that some species exhibit potential for adaptation and plasticity in physiological, behavioural, and life‐history traits that enable them to endure varying periods (e.g. days or months) and levels of saltwater exposure. Species that specialize on brackish water habitats are likely to be vulnerable to SLR because of their exclusive coastal distributions and adaptations to a narrow range of salinities. Most species, however, have not been documented in brackish water habitats but may also be highly vulnerable to projected SLR. Our analysis suggests that approximately 90% of coastal freshwater turtle species assessed in our study will be affected by a 1‐m increase in global mean SLR by 2100. Most at risk are freshwater turtles found in New Guinea, Southeast Asia, Australia, and North and South America that may lose more than 10% of their present geographic range. In addition, turtle species in the families Chelidae, Emydidae, and Trionychidae may experience the greatest exposure to projected SLR in their present geographic ranges. Better understanding of survival, growth, reproductive and population‐level responses to SLR will improve region‐specific population viability predictions of freshwater turtles that are increasingly exposed to SLR. Integrating phylogenetic, physiological, and spatial frameworks to assess the effects of projected SLR may improve identification of vulnerable species, guilds, and geographic regions in need of conservation prioritization. We conclude that the use of brackish and marine environments by freshwater turtles provides clues about the evolutionary processes that have prolonged their existence, shaped their unique coastal distributions, and may prove useful in predicting their response to a changing world.

Restored Wetlands Can Support Mammalian Assemblages Comparable to Those in Nonmitigated Reference Wetlands

Abstract Restoration of wetland ecosystems has typically focused on hydrology, soil, and vegetation; taking an, “If you build it, they will come” strategy for the recovery of wetland fauna. We tested this assumption by quantifying mammal richness and abundance in recently restored and nonmitigated reference wetland habitats to determine if mammalian community composition varies with wetland condition. Our study consisted of live trapping and infrared photography at three restored and three reference (“natural”) wetland sites in Northeastern Ohio. After 3000 potential trap nights and 120 potential camera nights, we documented the presence of nine species and nearly 300 unique individuals in reference and restored wetlands. We found no significant differences in mammalian richness, abundance, or species composition between reference and restored wetlands; however, mammal abundance in terms of individual captures was 62% higher in restored wetland patches (n  =  194) than in reference wetlands (n  =  104). Restored wetlands – if managed correctly – can harbor mammalian communities as rich as those found in nonmitigated wetland habitats. Our results support the “Field of Dreams” hypothesis which suggests, among other things, that if the necessary physical conditions are present then desired fauna will subsequently colonize the patch. For small to midsized mammals in our study area, this appears to be the case.