Evidence for Positive Selection at the Pantophysin (Pan I) Locus in Walleye Pollock, Theragra chalcogramma
Nucleotide polymorphism at the pantophysin ( Pan I) locus in walleye pollock, Theragra chalcogramma , was examined using DNA sequence data. Two distinct allelic lineages were detected in pollock resulting from three amino acid replacement mutations in the first intravesicular domain of the protein....
Published in: | Molecular Biology and Evolution |
---|---|
Main Authors: | , |
Format: | Text |
Language: | English |
Published: |
Oxford University Press
2004
|
Subjects: | |
Online Access: | http://mbe.oxfordjournals.org/cgi/content/short/msh141v1 https://doi.org/10.1093/molbev/msh141 |
id |
fthighwire:oai:open-archive.highwire.org:molbiolevol:msh141v1 |
---|---|
record_format |
openpolar |
spelling |
fthighwire:oai:open-archive.highwire.org:molbiolevol:msh141v1 2023-05-15T15:27:22+02:00 Evidence for Positive Selection at the Pantophysin (Pan I) Locus in Walleye Pollock, Theragra chalcogramma Canino, M. F. Bentzen, P. 2004-04-14 12:53:01.0 text/html http://mbe.oxfordjournals.org/cgi/content/short/msh141v1 https://doi.org/10.1093/molbev/msh141 en eng Oxford University Press http://mbe.oxfordjournals.org/cgi/content/short/msh141v1 http://dx.doi.org/10.1093/molbev/msh141 Copyright (C) 2004, Society for Molecular Biology and Evolution Original Articles TEXT 2004 fthighwire https://doi.org/10.1093/molbev/msh141 2013-05-27T15:52:47Z Nucleotide polymorphism at the pantophysin ( Pan I) locus in walleye pollock, Theragra chalcogramma , was examined using DNA sequence data. Two distinct allelic lineages were detected in pollock resulting from three amino acid replacement mutations in the first intravesicular domain of the protein. The common Pan I allelic group, comprising 94% of the samples, was less polymorphic (π = 0.005) than the uncommon group (π = 0.008) and nucleotide diversity in both was higher than for two allelic lineages in the related Atlantic cod, Gadus morhua . Phylogenetic analyses of Pan I sequences from these two species did not clearly resolve orthology among allelic groups, in part due to recombination that has occurred between the two pollock lineages. Conventional tests of neutrality comparing polymorphisms within and between homologous regions of the Pan I locus in walleye pollock and Atlantic cod did not detect the effects of selection. This result is likely attributed to low levels of synonymous divergence among allelic lineages and a lack of mutation-drift equilibrium inferred from nucleotide mismatch frequency distributions. However, the ratio of nonsynonymous to synonymous substitutions per site (d N /d S ) exceeded unity in two intravesicular domains of the protein and the influence of positive selection at multiple codon sites was strongly inferred through the use of maximum likelihood analyses. In addition, the frequency spectrum of linked neutral variation showed indirect effects of adaptive hitchhiking in pollock due to a selective sweep of the common allelic lineage. Recombination between the two allelic classes may have prevented complete loss of the older, more polymorphic lineage. The results suggest that recurrent sweeps driven by positive selection is the principle mode of evolution at the Pan I locus in gadid fishes. Text atlantic cod Gadus morhua Theragra chalcogramma HighWire Press (Stanford University) Molecular Biology and Evolution 21 7 1391 1400 |
institution |
Open Polar |
collection |
HighWire Press (Stanford University) |
op_collection_id |
fthighwire |
language |
English |
topic |
Original Articles |
spellingShingle |
Original Articles Canino, M. F. Bentzen, P. Evidence for Positive Selection at the Pantophysin (Pan I) Locus in Walleye Pollock, Theragra chalcogramma |
topic_facet |
Original Articles |
description |
Nucleotide polymorphism at the pantophysin ( Pan I) locus in walleye pollock, Theragra chalcogramma , was examined using DNA sequence data. Two distinct allelic lineages were detected in pollock resulting from three amino acid replacement mutations in the first intravesicular domain of the protein. The common Pan I allelic group, comprising 94% of the samples, was less polymorphic (π = 0.005) than the uncommon group (π = 0.008) and nucleotide diversity in both was higher than for two allelic lineages in the related Atlantic cod, Gadus morhua . Phylogenetic analyses of Pan I sequences from these two species did not clearly resolve orthology among allelic groups, in part due to recombination that has occurred between the two pollock lineages. Conventional tests of neutrality comparing polymorphisms within and between homologous regions of the Pan I locus in walleye pollock and Atlantic cod did not detect the effects of selection. This result is likely attributed to low levels of synonymous divergence among allelic lineages and a lack of mutation-drift equilibrium inferred from nucleotide mismatch frequency distributions. However, the ratio of nonsynonymous to synonymous substitutions per site (d N /d S ) exceeded unity in two intravesicular domains of the protein and the influence of positive selection at multiple codon sites was strongly inferred through the use of maximum likelihood analyses. In addition, the frequency spectrum of linked neutral variation showed indirect effects of adaptive hitchhiking in pollock due to a selective sweep of the common allelic lineage. Recombination between the two allelic classes may have prevented complete loss of the older, more polymorphic lineage. The results suggest that recurrent sweeps driven by positive selection is the principle mode of evolution at the Pan I locus in gadid fishes. |
format |
Text |
author |
Canino, M. F. Bentzen, P. |
author_facet |
Canino, M. F. Bentzen, P. |
author_sort |
Canino, M. F. |
title |
Evidence for Positive Selection at the Pantophysin (Pan I) Locus in Walleye Pollock, Theragra chalcogramma |
title_short |
Evidence for Positive Selection at the Pantophysin (Pan I) Locus in Walleye Pollock, Theragra chalcogramma |
title_full |
Evidence for Positive Selection at the Pantophysin (Pan I) Locus in Walleye Pollock, Theragra chalcogramma |
title_fullStr |
Evidence for Positive Selection at the Pantophysin (Pan I) Locus in Walleye Pollock, Theragra chalcogramma |
title_full_unstemmed |
Evidence for Positive Selection at the Pantophysin (Pan I) Locus in Walleye Pollock, Theragra chalcogramma |
title_sort |
evidence for positive selection at the pantophysin (pan i) locus in walleye pollock, theragra chalcogramma |
publisher |
Oxford University Press |
publishDate |
2004 |
url |
http://mbe.oxfordjournals.org/cgi/content/short/msh141v1 https://doi.org/10.1093/molbev/msh141 |
genre |
atlantic cod Gadus morhua Theragra chalcogramma |
genre_facet |
atlantic cod Gadus morhua Theragra chalcogramma |
op_relation |
http://mbe.oxfordjournals.org/cgi/content/short/msh141v1 http://dx.doi.org/10.1093/molbev/msh141 |
op_rights |
Copyright (C) 2004, Society for Molecular Biology and Evolution |
op_doi |
https://doi.org/10.1093/molbev/msh141 |
container_title |
Molecular Biology and Evolution |
container_volume |
21 |
container_issue |
7 |
container_start_page |
1391 |
op_container_end_page |
1400 |
_version_ |
1766357806206681088 |