Data from: Testing models of refugial isolation, colonization and population connectivity in two species of montane salamanders

Rovito SM, Schoville SD

Date Published: May 19, 2017

DOI: http://dx.doi.org/10.5061/dryad.c197n

 

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Title Genepop file for northern lineage of Hydromantes
Downloaded 8 times
Description 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.
Download Hydro_genotypes_GENEPOP_HbHpN.txt (10.84 Kb)
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Title Genepop file for southern lineage of Hydromantes
Downloaded 6 times
Description 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.
Download Hydro_genotypes_GENEPOP_HpSOV.txt (9.773 Kb)
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Title Northern lineage Hydromantes STRUCTURE file
Downloaded 4 times
Description 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.
Download Hydro_msats_Structure_HpNHb.txt (11.94 Kb)
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Title Structure file for southern lineage of Hydromantes
Downloaded 2 times
Description 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.
Download Hydro_msats_Structure_HpSOV.txt (11.28 Kb)
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Title MSVAR input files
Downloaded 6 times
Description 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.
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Title ABC Model 1 input files
Downloaded 4 times
Description 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.
Download ABCrun_Model1.zip (2.332 Mb)
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Title ABC model 2 input files
Downloaded 2 times
Description 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.
Download ABCrun_Model2.zip (4.037 Mb)
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Title ABC Model 3 input files
Downloaded 2 times
Description 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.
Download ABCrun_Model3.zip (4.037 Mb)
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Title ABC model 4 input files
Downloaded 2 times
Description 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.
Download ABCrun_Model4.zip (4.037 Mb)
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Title ABC Model 5 input files
Downloaded 2 times
Description 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.
Download ABCrun_Model5.zip (4.037 Mb)
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Title ABC Model 1 with population size change
Downloaded 2 times
Description 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.
Download ABCrun_Model1wpopchange.zip (24.23 Mb)
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When using this data, please cite the original publication:

Rovito SM, Schoville SD (2017) Testing models of refugial isolation, colonization and population connectivity in two species of montane salamanders. Heredity, online in advance of print. http://dx.doi.org/10.1038/hdy.2017.31

Additionally, please cite the Dryad data package:

Rovito SM, Schoville SD (2017) Data from: Testing models of refugial isolation, colonization and population connectivity in two species of montane salamanders. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.c197n
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