DOI: 10.5061/dryad.c197n
title: Data from: Testing models of refugial isolation, colonization and population connectivity in two species of montane salamanders

description: Pleistocene glaciations have profoundly affected patterns of genetic
 diversity within many species. Temperate alpine organisms likely
 experienced dramatic range shifts, given that much of their habitat was
 glaciated during this time. While the effects of glaciations are
 relatively well understood, the spatial locations of refugia and processes
 that gave rise to current patterns of diversity are less well known. We
 use a microsatellite data set to test hypotheses of population
 connectivity and refugial isolation in the web-toed salamanders
 (Hydromantes) of the Sierra Nevada. We reject models of refugia with
 subsequent expansion into either the high southern Sierra or low-elevation
 Owens Valley, in favor of a simple isolation model with no migration
 between current populations. We find no evidence of migration at even
 moderate spatial scales using a variety of analyses in the southern
 Sierra, and limited migration in the northern Sierra. These results
 suggest that divergence in isolation following fragmentation is the
 dominant process structuring genetic variation in these salamander
 species. In the context of anthropogenic climate change and habitat
 degradation, these results imply that salamanders and other low-vagility
 alpine organisms are at risk of decline as they are unlikely to migrate
 across large distances.
description: Genepop file for
 northern lineage of HydromantesGenotypes for 10
 microsatellite loci for 136 individuals of Hydromantes platycephalus and
 H. brunus from 12 localities in northern Sierra Nevada, California in
 Genepop format. This file was generated using the program GeneMapper,
 which was also used to call genotypes. The program Genepop V4 was used to
 calculate Fst between populations as well as genetic diversity statistics
 for each population.Hydro_genotypes_GENEPOP_HbHpN.txtGenepop file for southern lineage of HydromantesGenotypes for 10 microsatellite loci for 122 individuals from 9 localities of Hydromantes platycephalus from the southern Sierra Nevada, California in Genepop format. This file was generated using the program GeneMapper, which was also used to call genotypes. The program Genepop V4 was used to calculate Fst between populations as well as genetic diversity statistics for each population.Hydro_genotypes_GENEPOP_HpSOV.txtNorthern lineage Hydromantes STRUCTURE fileSTRUCTURE input file for genotypes of 10 microsatellite loci for 136 individuals of Hydromantes from 12 localities in the northern Sierra Nevada, California, USA. This file was generated using the Genepop file of genotypes (Hydro_genotypes_GENEPOP_HbHpN.txt) in the program STRUCTURE, which was also used to analyze the data at K values of 2, 3, and 6 in order to determine the level of population structure. Data were summarized in CLUMPP and visualized using DISTRUCT.Hydro_msats_Structure_HpNHb.txtStructure file for southern lineage of HydromantesSTRUCTURE input file for genotypes of 10 microsatellite loci for 122 individuals of Hydromantes from 9 localities in the northern Sierra Nevada, California, USA. This file was generated using the Genepop file of genotypes (Hydro_genotypes_GENEPOP_HbHpN.txt) in the program STRUCTURE, which was also used to analyze the data at K values of 6 in order to determine the level of population structure. Data were summarized in CLUMPP and visualized using DISTRUCT.Hydro_msats_Structure_HpSOV.txtMSVAR input filesInput files for MSVAR analyses of bottlenecks for populations of Hydromantes platycephalus from the southern Sierra Nevada. The files were generated manually and analyzed using the program MSVAR to detect past demographic bottlenecks for each population. The results were summarized and visualized using the R script provided.MSVAR.zipABC Model 1 input filesInput files for isolation with no migration model for ABC analysis. These files were generated using ABCToolkit or manually. The files 'arl_run.txt' and 'arl_run.ars' were used to calculated summary statistics in Arlequin. The file 'hydromantesSTR.obs' contains summary statistics for observed data. The file 'hydromantesSTR.par' contains parameters for the coalescence simulation program simcoal. 'hydromantes.input' is the input file for the program ABCSampler. 'ssDefs.txt' contains information on which summary statistics were calculated. The script 'Process_ABC_commands.R' was used to compare models and determine the posterior probability of each.ABCrun_Model1.zipABC model 2 input filesInput files for ABC analysis of Owens Valley refuge model. These files were generated using ABCToolkit or manually. The files 'arl_run.txt' and 'arl_run.ars' were used to calculated summary statistics in Arlequin. The file 'hydromantesSTR.obs' contains summary statistics for observed data. The file 'hydromantesSTR.par' contains parameters for the coalescence simulation program simcoal. 'ssDefs.txt' contains information on which summary statistics were calculated. 'hydromantes.input' is the input file for the program ABCSampler. The script 'Process_ABC_commands.R' was used to compare models and determine the posterior probability of each.ABCrun_Model2.zipABC Model 3 input filesInput files for ABC analysis of High Sierra refuge model. These files were generated using ABCToolkit or manually. The files 'arl_run.txt' and 'arl_run.ars' were used to calculated summary statistics in Arlequin. The file 'hydromantesSTR.obs' contains summary statistics for observed data. The file 'hydromantesSTR.par' contains parameters for the coalescence simulation program simcoal. 'hydromantes.input' is the input file for the program ABCSampler. 'ssDefs.txt' contains information on which summary statistics were calculated. The script 'Process_ABC_commands.R' was used to compare models and determine the posterior probability of each.ABCrun_Model3.zipABC model 4 input filesInput files for ABC analysis of model with persistence in both Owens Valley and High Sierra Nevada with migration between geographic neighbors. These files were generated using ABCToolkit or manually. The files 'arl_run.txt' and 'arl_run.ars' were used to calculated summary statistics in Arlequin. The file 'hydromantesSTR.obs' contains summary statistics for observed data. The file 'hydromantesSTR.par' contains parameters for the coalescence simulation program simcoal. 'hydromantes.input' is the input file for the program ABCSampler. 'ssDefs.txt' contains information on which summary statistics were calculated. The script 'Process_ABC_commands.R' was used to compare models and determine the posterior probability of each.ABCrun_Model4.zipABC Model 5 input filesInput files for ABC analysis with alternative divergence history of populations. These files were generated using ABCToolkit or manually. The files 'arl_run.txt' and 'arl_run.ars' were used to calculated summary statistics in Arlequin. The file 'hydromantesSTR.obs' contains summary statistics for observed data. The file 'hydromantesSTR.par' contains parameters for the coalescence simulation program simcoal. 'hydromantes.input' is the input file for the program ABCSampler. 'ssDefs.txt' contains information on which summary statistics were calculated. The script 'Process_ABC_commands.R' was used to compare models and determine the posterior probability of each.ABCrun_Model5.zipABC Model 1 with population size changeInput files for ABC analysis of isolation with no migration model including population size changes. Subfolders correspond for to the model with a bottleneck in the population included in the folder name. These files were generated using ABCToolkit or manually. The files 'arl_run.txt' and 'arl_run.ars' were used to calculated summary statistics in Arlequin. The file 'hydromantesSTR.obs' contains summary statistics for observed data. The file 'hydromantesSTR.par' contains parameters for the coalescence simulation program simcoal. 'hydromantes.input' is the input file for the program ABCSampler. 'ssDefs.txt' contains information on which summary statistics were calculated. The script 'Process_ABC_commands.R' was used to compare models and determine the posterior probability of each.ABCrun_Model1wpopchange.zip