DOI: 10.5061/dryad.7c2n8
title: Data from: Landscape effects on gene flow for a climate-sensitive montane species, the American pika

description: Climate change is arguably the greatest challenge to conservation of our
 time. Most vulnerability assessments rely on past and current species
 distributions to predict future persistence but ignore species'
 abilities to disperse through landscapes, which may be particularly
 important in fragmented habitats and crucial for long-term persistence in
 changing environments. Landscape genetic approaches explore the
 interactions between landscape features and gene flow and can clarify how
 organisms move among suitable habitats, but have suffered from
 methodological uncertainties. We used a landscape genetic approach to
 determine how landscape and climate-related features influence gene flow
 for American pikas (Ochotona princeps) in Crater Lake National Park. Pikas
 are heat intolerant and restricted to cool microclimates; thus, range
 contractions have been predicted as climate changes. We evaluated the
 correlation between landscape variables and genetic distance using partial
 Mantel tests in a causal modelling framework, and used spatially explicit
 simulations to evaluate methods of model optimization including a novel
 approach based on relative support and reciprocal causal modelling. We
 found that gene flow was primarily restricted by topographic relief, water
 and west-facing aspects, suggesting that physical restrictions related to
 small body size and mode of locomotion, as well as exposure to relatively
 high temperatures, limit pika dispersal in this alpine habitat. Our model
 optimization successfully identified landscape features influencing
 resistance in the simulated data for this landscape, but underestimated
 the magnitude of resistance. This is the first landscape genetic study to
 address the fundamental question of what limits dispersal and gene flow in
 the American pika.
description: Castillo et al. CDPOP
 input filesThis Excel workbook
 contains all the necessary input files to re-run the simulations in
 CDPOP_v1.2.11. Note, each tab must be saved as a separate .csv in order
 for the program to run.Castillo_et_al_CDPOP_files.xlsxCastillo et al. Simulated genetic distance matricesGenetic distance (principle components analysis) matrices for the simulated genotypes from CDPOP. Each tab represents a different generation (grid#) and MC replicate (mcrun#). Only those individuals included in the analyses are included in the matrix.Castillo_et_al_GD_matrices.xlsxCastillo et al. Genetic distance matrix for empirical dataGenetic distance (principal components analysis) matrix for empirical data. Row/column names correspond to sample ID and are the same for the XY Coordinates file.Castillo_et_at_GD_matrix_real.csvCastillo et al. Pika LocalitiesXY coordinates for sampling localities. Data are in UTM zone 10, NAD83.Castillo_et_al_Pika_Localities.csvCastillo et al. GIS dataIncludes raster dataset for elevation, water, and land cover, as well as descriptions of original data sources and modifications to data.Castillo_et_al_GIS_data.7zCastillo et al. Pika Genotype FileRaw genotypes for pika fecal samples in Genepop format.Castillo_et_al_Genotypes_GenepopFile