Data from: Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata)
The importance of speciation-with-gene-flow scenarios is increasingly appreciated. However, the specific processes and the resulting genomic footprints of selection are subject to much discussion. We studied the genomics of speciation between the two panmictic, sympatrically spawning sister-species;...
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ftdryad:oai:v1.datadryad.org:10255/dryad.69479 2023-05-15T13:27:25+02:00 Data from: Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata) Jacobsen, Magnus W. Pujolar, Jose Martin Bernatchez, Louis Munch, Kasper Jian, Jianbo Niu, Yongchao Hansen, Michael M. Ringhals Lough Erne Valencia Riviere Blanche St. Jonhs River Mira River Holocene present-day 2014-08-27T16:11:48Z http://hdl.handle.net/10255/dryad.69479 https://doi.org/10.5061/dryad.f2313 unknown doi:10.5061/dryad.f2313/1 doi:10.5061/dryad.f2313/2 doi:10.1111/mec.12896 PMID:25155907 doi:10.5061/dryad.f2313 Jacobsen MW, Pujolar JM, Bernatchez L, Munch K, Jian J, Niu Y, Hansen MM (2014) Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata). Molecular Ecology 23(19): 4785-4798. http://hdl.handle.net/10255/dryad.69479 Fish Genomics/Proteomics SNP data Article 2014 ftdryad https://doi.org/10.5061/dryad.f2313 https://doi.org/10.5061/dryad.f2313/1 https://doi.org/10.5061/dryad.f2313/2 https://doi.org/10.1111/mec.12896 2020-01-01T15:11:06Z The importance of speciation-with-gene-flow scenarios is increasingly appreciated. However, the specific processes and the resulting genomic footprints of selection are subject to much discussion. We studied the genomics of speciation between the two panmictic, sympatrically spawning sister-species; European (Anguilla anguilla) and American eel (A. rostrata). Divergence is assumed to have initiated more than 3 million years ago, and although low gene flow still occurs strong postzygotic barriers are present. Restriction-site Associated DNA (RAD) sequencing identified 328,300 SNPs for subsequent analysis. However, despite the presence of 3,757 strongly differentiated SNPs (FST > 0.8), sliding window analyses of FST showed no larger genomic regions (i.e. hundreds of thousands to millions of bases) of elevated differentiation. Overall FST was 0.041 and linkage disequilibrium was virtually absent for SNPs separated by more than 1000 bp. We suggest this to reflect a case of genomic hitchhiking, where multiple regions are under directional selection between the species. However, low but biologically significant gene flow and high effective population sizes leading to very low genetic drift preclude accumulation of strong background differentiation. Genes containing candidate SNPs for positive selection showed significant enrichment for gene ontology (GO) terms relating to developmental processes and phosphorylation, which seems consistent with assumptions that differences in larval phase duration and migratory distances underlie speciation. Most SNPs under putative selection were found outside coding regions, lending support to emerging views that non-coding regions may be more functionally important than previously assumed. In total, the results demonstrate the necessity of interpreting genomic footprints of selection in the context of demographic parameters and life-history features of the studied species. Article in Journal/Newspaper Anguilla anguilla Dryad Digital Repository (Duke University) Blanche ENVELOPE(140.018,140.018,-66.663,-66.663) Mira ENVELOPE(10.500,10.500,-70.417,-70.417) |
institution |
Open Polar |
collection |
Dryad Digital Repository (Duke University) |
op_collection_id |
ftdryad |
language |
unknown |
topic |
Fish Genomics/Proteomics SNP data |
spellingShingle |
Fish Genomics/Proteomics SNP data Jacobsen, Magnus W. Pujolar, Jose Martin Bernatchez, Louis Munch, Kasper Jian, Jianbo Niu, Yongchao Hansen, Michael M. Data from: Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata) |
topic_facet |
Fish Genomics/Proteomics SNP data |
description |
The importance of speciation-with-gene-flow scenarios is increasingly appreciated. However, the specific processes and the resulting genomic footprints of selection are subject to much discussion. We studied the genomics of speciation between the two panmictic, sympatrically spawning sister-species; European (Anguilla anguilla) and American eel (A. rostrata). Divergence is assumed to have initiated more than 3 million years ago, and although low gene flow still occurs strong postzygotic barriers are present. Restriction-site Associated DNA (RAD) sequencing identified 328,300 SNPs for subsequent analysis. However, despite the presence of 3,757 strongly differentiated SNPs (FST > 0.8), sliding window analyses of FST showed no larger genomic regions (i.e. hundreds of thousands to millions of bases) of elevated differentiation. Overall FST was 0.041 and linkage disequilibrium was virtually absent for SNPs separated by more than 1000 bp. We suggest this to reflect a case of genomic hitchhiking, where multiple regions are under directional selection between the species. However, low but biologically significant gene flow and high effective population sizes leading to very low genetic drift preclude accumulation of strong background differentiation. Genes containing candidate SNPs for positive selection showed significant enrichment for gene ontology (GO) terms relating to developmental processes and phosphorylation, which seems consistent with assumptions that differences in larval phase duration and migratory distances underlie speciation. Most SNPs under putative selection were found outside coding regions, lending support to emerging views that non-coding regions may be more functionally important than previously assumed. In total, the results demonstrate the necessity of interpreting genomic footprints of selection in the context of demographic parameters and life-history features of the studied species. |
format |
Article in Journal/Newspaper |
author |
Jacobsen, Magnus W. Pujolar, Jose Martin Bernatchez, Louis Munch, Kasper Jian, Jianbo Niu, Yongchao Hansen, Michael M. |
author_facet |
Jacobsen, Magnus W. Pujolar, Jose Martin Bernatchez, Louis Munch, Kasper Jian, Jianbo Niu, Yongchao Hansen, Michael M. |
author_sort |
Jacobsen, Magnus W. |
title |
Data from: Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata) |
title_short |
Data from: Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata) |
title_full |
Data from: Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata) |
title_fullStr |
Data from: Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata) |
title_full_unstemmed |
Data from: Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata) |
title_sort |
data from: genomic footprints of speciation in atlantic eels (anguilla anguilla and a. rostrata) |
publishDate |
2014 |
url |
http://hdl.handle.net/10255/dryad.69479 https://doi.org/10.5061/dryad.f2313 |
op_coverage |
Ringhals Lough Erne Valencia Riviere Blanche St. Jonhs River Mira River Holocene present-day |
long_lat |
ENVELOPE(140.018,140.018,-66.663,-66.663) ENVELOPE(10.500,10.500,-70.417,-70.417) |
geographic |
Blanche Mira |
geographic_facet |
Blanche Mira |
genre |
Anguilla anguilla |
genre_facet |
Anguilla anguilla |
op_relation |
doi:10.5061/dryad.f2313/1 doi:10.5061/dryad.f2313/2 doi:10.1111/mec.12896 PMID:25155907 doi:10.5061/dryad.f2313 Jacobsen MW, Pujolar JM, Bernatchez L, Munch K, Jian J, Niu Y, Hansen MM (2014) Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata). Molecular Ecology 23(19): 4785-4798. http://hdl.handle.net/10255/dryad.69479 |
op_doi |
https://doi.org/10.5061/dryad.f2313 https://doi.org/10.5061/dryad.f2313/1 https://doi.org/10.5061/dryad.f2313/2 https://doi.org/10.1111/mec.12896 |
_version_ |
1766398255273345024 |