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: | , , , , |
---|---|
Format: | Dataset |
Language: | unknown |
Published: |
Dryad
2018
|
Subjects: | |
Online Access: | https://doi.org/10.5061/dryad.vk405 |
id |
fttriple:oai:gotriple.eu:50|dedup_wf_001::43e9838a93889d3067ffe58d9cac6dd5 |
---|---|
record_format |
openpolar |
spelling |
fttriple:oai:gotriple.eu:50|dedup_wf_001::43e9838a93889d3067ffe58d9cac6dd5 2023-05-15T15:31:55+02:00 Data from: Population genomic analysis of Brook Trout Salvelinus fontinalis in Pennsylvania’s Appalachian region Buonaccorsi, Vince P. Malloy, Jacob Peterson, Mark Brubaker, Kristen Grant, Chris J. 2018-03-02 https://doi.org/10.5061/dryad.vk405 undefined unknown Dryad https://dx.doi.org/10.5061/dryad.vk405 http://dx.doi.org/10.5061/dryad.vk405 lic_creative-commons 10.5061/dryad.vk405 oai:easy.dans.knaw.nl:easy-dataset:101493 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:101493 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 Salvelinus fontinalis population genomics salmonid Pennsylvania USA Life sciences medicine and health care envir geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2018 fttriple https://doi.org/10.5061/dryad.vk405 2023-01-22T17:15:55Z 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 detected. Stepwise regression of observed heterozygosity against geographic and environmental features revealed that drainage basin and effective area of watersheds were significant predictors of observed heterozygosity of Brook Trout within streams. Natural features such as waterfalls and major drainage basin, as well as the effects of dams and acid-mine drainage have fragmented habitat and shaped genetic diversity within Brook Trout populations in the Appalachian region of Pennsylvania, overall indicating the vulnerability of this species to increased industrialization. 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 ... Dataset Atlantic salmon Salmo salar Unknown |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Salvelinus fontinalis population genomics salmonid Pennsylvania USA Life sciences medicine and health care envir geo |
spellingShingle |
Salvelinus fontinalis population genomics salmonid Pennsylvania USA Life sciences medicine and health care envir geo Buonaccorsi, Vince P. Malloy, Jacob Peterson, Mark Brubaker, Kristen Grant, Chris J. Data from: Population genomic analysis of Brook Trout Salvelinus fontinalis in Pennsylvania’s Appalachian region |
topic_facet |
Salvelinus fontinalis population genomics salmonid Pennsylvania USA Life sciences medicine and health care envir geo |
description |
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 detected. Stepwise regression of observed heterozygosity against geographic and environmental features revealed that drainage basin and effective area of watersheds were significant predictors of observed heterozygosity of Brook Trout within streams. Natural features such as waterfalls and major drainage basin, as well as the effects of dams and acid-mine drainage have fragmented habitat and shaped genetic diversity within Brook Trout populations in the Appalachian region of Pennsylvania, overall indicating the vulnerability of this species to increased industrialization. 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 ... |
format |
Dataset |
author |
Buonaccorsi, Vince P. Malloy, Jacob Peterson, Mark Brubaker, Kristen Grant, Chris J. |
author_facet |
Buonaccorsi, Vince P. Malloy, Jacob Peterson, Mark Brubaker, Kristen Grant, Chris J. |
author_sort |
Buonaccorsi, Vince P. |
title |
Data from: Population genomic analysis of Brook Trout Salvelinus fontinalis in Pennsylvania’s Appalachian region |
title_short |
Data from: Population genomic analysis of Brook Trout Salvelinus fontinalis in Pennsylvania’s Appalachian region |
title_full |
Data from: Population genomic analysis of Brook Trout Salvelinus fontinalis in Pennsylvania’s Appalachian region |
title_fullStr |
Data from: Population genomic analysis of Brook Trout Salvelinus fontinalis in Pennsylvania’s Appalachian region |
title_full_unstemmed |
Data from: Population genomic analysis of Brook Trout Salvelinus fontinalis in Pennsylvania’s Appalachian region |
title_sort |
data from: population genomic analysis of brook trout salvelinus fontinalis in pennsylvania’s appalachian region |
publisher |
Dryad |
publishDate |
2018 |
url |
https://doi.org/10.5061/dryad.vk405 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
10.5061/dryad.vk405 oai:easy.dans.knaw.nl:easy-dataset:101493 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:101493 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 |
op_relation |
https://dx.doi.org/10.5061/dryad.vk405 http://dx.doi.org/10.5061/dryad.vk405 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.vk405 |
_version_ |
1766362413645430784 |