Data from: Population genomic analysis of Brook Trout Salvelinus fontinalis in Pennsylvania’s Appalachian region ...
Informed conservation of stream fishes requires detailed understanding of the effects of both natural processes and anthropogenic activities on genetic diversity. Brook Trout Salvelinus fontinalis, a salmonid native to eastern North America, typically resides in cold, high-quality stream ecosystems....
| Main Authors: | , , , , |
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| Format: | Dataset |
| Language: | English |
| Published: |
Dryad
2018
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| Subjects: | |
| Online Access: | https://dx.doi.org/10.5061/dryad.vk405 https://datadryad.org/stash/dataset/doi:10.5061/dryad.vk405 |
| Summary: | Informed conservation of stream fishes requires detailed understanding of the effects of both natural processes and anthropogenic activities on genetic diversity. Brook Trout Salvelinus fontinalis, a salmonid native to eastern North America, typically resides in cold, high-quality stream ecosystems. The species has not only faced historical anthropogenic pressures, but also confronts current and future pressures. In a genetic analysis we used a reduced representation sequencing method (ddRADseq) to characterize 63 individuals from 23 streams where Brook Trout are native in the Appalachian region of Pennsylvania. A total of 2,590 loci passed filtering criteria, and 53% displayed significant association with a major stream drainage basin (Susquehanna or Allegheny; mean FST = 0.085). Mapping of the sequencing reads to the Atlantic Salmon Salmo salar genome revealed no clustering of high interdrainage FST values to specific genome regions. Evidence for genetic heterogeneity within each drainage basin was also ... : Stacks and Genepop filesStacks v 1.36 catalog files and alleles.tsv, matches.tsv, snps.tsv, and tags.tsv files for each individual mapped to Atlantic salmon reference genome. Also included are sumstats.tsv file "batch_1.sumstats.tsv" for individuals grouped into either Susquehanna or Allegheny river basins, and the final filtered GENEPOP file, "batch_1_genepop_HWE001_poolBias.txt" used for analysis after filtering for Hardy Weinberg deviations and for loci that were associated with library pool.Sfontinalis.tar.gzSupplementFile2R script "tryRollWindows.R" – for performing genome-anchored smoothed FST and diversity significance analysis. Also included is the data file "Fig3_data_forMark.csv" referenced in the script. ... |
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