Habitat availability and gene flow influence diverging local population trajectories under scenarios of climate change: a place-based approach

Ecological niche theory holds that species distributions are shaped by a large and complex suite of interacting factors. Species distribution models (SDMs) are increasingly used to describe species’ niches and predict the effects of future environmental change, including climate change. Currently, SDMs often fail to capture the complexity of species’ niches, resulting in predictions that are generally limited to climate-occupancy interactions. Here, we explore the potential impact of climate change on the American pika using a replicated place-based approach that incorporates climate, gene flow, habitat configuration, and microhabitat complexity into SDMs. Using contemporary presence–absence data from occupancy surveys, genetic data to infer connectivity between habitat patches, and 21 environmental niche variables, we built separate SDMs for pika populations inhabiting eight US National Park Service units representing the habitat and climatic breadth of the species across the western United States. We then predicted occurrence probability under current (1981–2010) and three future time periods (out to 2100). Occurrence probabilities and the relative importance of predictor variables varied widely among study areas, revealing important local-scale differences in the realized niche of the American pika. This variation resulted in diverse and – in some cases – highly divergent future potential occupancy patterns for pikas, ranging from complete extirpation in some study areas to stable occupancy patterns in others. Habitat composition and connectivity, which are rarely incorporated in SDM projections, were influential in predicting pika occupancy in all study areas and frequently outranked climate variables. Our findings illustrate the importance of a place-based approach to species distribution modeling that includes fine-scale factors when assessing current and future climate impacts on species’ distributions, especially when predictions are intended to manage and conserve species of concern within individual protected areas.Keywords: genetic neighborhood, species distribution modeling, functional connectivity, Random Forest, realized niche, American pika, Ochotona princeps, National Park

The idiosyncrasies of place: geographic variation in the climate–distribution relationships of the American pika

Although climate acts as a fundamental constraint on the distribution of organisms, understanding how this relationship between climate and distribution varies over a species’ range is critical for addressing the potential impacts of accelerated climate change on biodiversity. Bioclimatic niche models provide compelling evidence that many species will experience range shifts under scenarios of global change, yet these broad, macroecological perspectives lack specificity at local scales, where unique combinations of environment, biota, and history conspire against generalizations. We explored how these idiosyncrasies of place affect the climate–distribution relationship of the American pika (Ochotona princeps) by replicating intensive field surveys across bioclimatic gradients in eight U.S. national parks. At macroecological scales, the importance of climate as a constraint on pika distribution appears unequivocal; forecasts suggest that the species’ range will contract sharply in coming decades. However, the species persists outside of its modeled bioclimatic envelope in many locations, fueling uncertainty and debate over its conservation status. Using a Bayesian hierarchical approach, we modeled variation in local patterns of pika distribution along topographic position, vegetation cover, elevation, temperature, and precipitation gradients in each park landscape. We also accounted for annual turnover in site occupancy probabilities. Topographic position and vegetation cover influenced occurrence in all parks. After accounting for these factors, pika occurrence varied widely among parks along bioclimatic gradients. Precipitation by itself was not a particularly influential predictor. However, measures of heat stress appeared most influential in the driest parks, suggesting an interaction between the strength of climate effects and the position of parks along precipitation gradients. The combination of high elevation, cold temperatures, and high precipitation lowered occurrence probabilities in some parks, suggesting an upper elevational limit for pikas in some environments. Our results demonstrate that the idiosyncrasies of place influence both the nature and strength of the climate–distribution relationship for the American pika. Finegrained, but geographically extensive, studies replicated across multiple landscapes offer insights important to assessing the impacts of climate change that otherwise may be masked at macroecological scales. The hierarchical approach to modeling provides a coherent conceptual and technical framework for gaining these insights.Keywords: Conservation, Climate change, American pika, Bayesian hierarchical model, Occupancy, Sign surveys, Presence–absence, Turnover, Place-based contingencies, Ochotona princeps, National park

Supplement 1. OpenBUGS code for hierarchical multi-park distribution models.

<h2>File List</h2><div> <a href="OpenBUGScode.txt">OpenBUGScode.txt</a> (MD5: )</div><h2>Description</h2><div> <p>OpenBUGScode.txt – provides OpenBUGS model code for three Bayesian hierarchical site-occupancy models used to evaluate geographic variation in the climate-distribution relationships of the American pika across eight U.S. National Park study areas. Code can be copied from this file and pasted directly into OpenBUGS or into text editors for use with other software such as R.</p> </div

Appendix B. Exploratory plots showing the relationship between site occurrence probabilities and site distances to nearest roads for each park unit.

Exploratory plots showing the relationship between site occurrence probabilities and site distances to nearest roads for each park unit

Appendix A. Maps of the park potential pika habitat and sampling frame with survey locations and results, and summary of occupancy survey results by park.

Maps of the park potential pika habitat and sampling frame with survey locations and results, and summary of occupancy survey results by park

SchwalmHabitatAvailabilityGeneAppendixS1FiguresS1-S6.pdf

Ecological niche theory holds that species distributions are shaped by a large and complex suite of interacting factors. Species distribution models (SDMs) are increasingly used to describe species’ niches and predict the effects of future environmental change, including climate change. Currently, SDMs often fail to capture the complexity of species’ niches, resulting in predictions that are generally limited to climate-occupancy interactions. Here, we explore the potential impact of climate change on the American pika using a replicated place-based approach that incorporates climate, gene flow, habitat configuration, and microhabitat complexity into SDMs. Using contemporary presence–absence data from occupancy surveys, genetic data to infer connectivity between habitat patches, and 21 environmental niche variables, we built separate SDMs for pika populations inhabiting eight US National Park Service units representing the habitat and climatic breadth of the species across the western United States. We then predicted occurrence probability under current (1981–2010) and three future time periods (out to 2100). Occurrence probabilities and the relative importance of predictor variables varied widely among study areas, revealing important local-scale differences in the realized niche of the American pika. This variation resulted in diverse and – in some cases – highly divergent future potential occupancy patterns for pikas, ranging from complete extirpation in some study areas to stable occupancy patterns in others. Habitat composition and connectivity, which are rarely incorporated in SDM projections, were influential in predicting pika occupancy in all study areas and frequently outranked climate variables. Our findings illustrate the importance of a place-based approach to species distribution modeling that includes fine-scale factors when assessing current and future climate impacts on species’ distributions, especially when predictions are intended to manage and conserve species of concern within individual protected areas.Keywords: Random Forest, functional connectivity, species distribution modeling, genetic neighborhood, American pika, National Parks, Ochotona princeps, realized nicheKeywords: Random Forest, functional connectivity, species distribution modeling, genetic neighborhood, American pika, National Parks, Ochotona princeps, realized nich

Genetic Distance Matrices

One .csv file per study site including the genetic distances among individual pika samples. Genetic distances were calculated from individual genotypes as a principal conponents distance calculated using the ecodist package in R

Pika Genetic Sample Localities

One .csv file including the xy coordinates (UTM, NAD83) for each pika genetic sample used in analyses. Data was collected in the field on handheld GPS units