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.
Genepop file for northern lineage of Hydromantes
Genotypes 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.txt
Genepop file for southern lineage of Hydromantes
Genotypes 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.txt
Northern lineage Hydromantes STRUCTURE file
STRUCTURE 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.txt
Structure file for southern lineage of Hydromantes
STRUCTURE 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.txt
MSVAR input files
Input 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.zip
ABC Model 1 input files
Input 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.zip
ABC model 2 input files
Input 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.zip
ABC Model 3 input files
Input 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.zip
ABC model 4 input files
Input 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.zip
ABC Model 5 input files
Input 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.zip
ABC Model 1 with population size change
Input 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