Data from: Latitudinal divergence in a wide-spread amphibian: contrasting patterns of neutral and adaptive genomic variation ...
Stochastic effects from demographic processes and selection are expected to shape the distribution of genetic variation in spatially heterogeneous environments. As the amount of genetic variation is central for long-term persistence of populations, understanding how these processes affect variation...
| Main Authors: | , , , , , |
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| Format: | Dataset |
| Language: | English |
| Published: |
Dryad
2019
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| Subjects: | |
| Online Access: | https://dx.doi.org/10.5061/dryad.fk560dg https://datadryad.org/stash/dataset/doi:10.5061/dryad.fk560dg |
| Summary: | Stochastic effects from demographic processes and selection are expected to shape the distribution of genetic variation in spatially heterogeneous environments. As the amount of genetic variation is central for long-term persistence of populations, understanding how these processes affect variation over large-scale geographic gradients is pivotal. We investigated the distribution of neutral and putatively adaptive genetic variation, and reconstructed demographic history in the moor frog (Rana arvalis) using 136 individuals from 15 populations along a 1700 km latitudinal gradient from northern Germany to northern Sweden. Using ddRAD-seq we obtained 27590 SNPs, and identified differentiation outliers and SNPs associated with growing season length. Populations grouped into a southern and a northern cluster, representing two phylogeographical lineages from different post-glacial colonization routes. Hybrid index estimation and demographic model selection showed strong support for a southern and northern lineage ... : barcodelist_processradtagsList of barcodes and indices for process_radtagsprocess_arvalisScript used to run process_radtagsdenovo_arvalis_noreplicExample script from parameter optimization in the denovomap pipelinepopmap_arvalis_noreplicatesPopulation map used for STACKS and main analysespopmap_arvalis_noreplicatesregions_demographicPopulation map used to create vcf file to crease mSFS in easySFS.easySFS_projectionDown projection results from easySFSRUN_easySFSExample command to run easySFSarvalis_latitudinal_MSFSmultidimensional folded SFS created by easySFS and used for demographic analysis in fsc26denovo_arvalis_noreplicScript used to run fsc26fsc2_runall.shBoot_fsc26Script used to bootstrap 95% CI around parameter estimate for the best model identified in fsc26fsc2_runallScript to run all models in fsc26batch_1.summary.sumstatsStacks summary ouputbatch_1.sumstatsStacks summary outputbatch_1Final filtered vcf file used for the main analyses. ... |
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