Low Diversity in the Mitogenome of Sperm Whales Revealed by Next-Generation Sequencing
Large population sizes and global distributions generally associate with high mitochondrial DNA control region (CR) diversity. The sperm whale ( Physeter macrocephalus ) is an exception, showing low CR diversity relative to other cetaceans; however, diversity levels throughout the remainder of the s...
Published in: | Genome Biology and Evolution |
---|---|
Main Authors: | , , , , , , , |
Format: | Text |
Language: | English |
Published: |
Oxford University Press
2013
|
Subjects: | |
Online Access: | http://gbe.oxfordjournals.org/cgi/content/short/5/1/113 https://doi.org/10.1093/gbe/evs126 |
id |
fthighwire:oai:open-archive.highwire.org:gbe:5/1/113 |
---|---|
record_format |
openpolar |
spelling |
fthighwire:oai:open-archive.highwire.org:gbe:5/1/113 2023-05-15T17:59:26+02:00 Low Diversity in the Mitogenome of Sperm Whales Revealed by Next-Generation Sequencing Alexander, Alana Steel, Debbie Slikas, Beth Hoekzema, Kendra Carraher, Colm Parks, Matthew Cronn, Richard Baker, C. Scott 2013-01-21 00:08:01.0 text/html http://gbe.oxfordjournals.org/cgi/content/short/5/1/113 https://doi.org/10.1093/gbe/evs126 en eng Oxford University Press http://gbe.oxfordjournals.org/cgi/content/short/5/1/113 http://dx.doi.org/10.1093/gbe/evs126 Copyright (C) 2013, Society for Molecular Biology and Evolution Research Article TEXT 2013 fthighwire https://doi.org/10.1093/gbe/evs126 2013-05-27T13:03:06Z Large population sizes and global distributions generally associate with high mitochondrial DNA control region (CR) diversity. The sperm whale ( Physeter macrocephalus ) is an exception, showing low CR diversity relative to other cetaceans; however, diversity levels throughout the remainder of the sperm whale mitogenome are unknown. We sequenced 20 mitogenomes from 17 sperm whales representative of worldwide diversity using Next Generation Sequencing (NGS) technologies (Illumina GAIIx, Roche 454 GS Junior). Resequencing of three individuals with both NGS platforms and partial Sanger sequencing showed low discrepancy rates (454-Illumina: 0.0071%; Sanger-Illumina: 0.0034%; and Sanger-454: 0.0023%) confirming suitability of both NGS platforms for investigating low mitogenomic diversity. Using the 17 sperm whale mitogenomes in a phylogenetic reconstruction with 41 other species, including 11 new dolphin mitogenomes, we tested two hypotheses for the low CR diversity. First, the hypothesis that CR-specific constraints have reduced diversity solely in the CR was rejected as diversity was low throughout the mitogenome, not just in the CR (overall diversity π = 0.096%; protein-coding 3rd codon = 0.22%; CR = 0.35%), and CR phylogenetic signal was congruent with protein-coding regions. Second, the hypothesis that slow substitution rates reduced diversity throughout the sperm whale mitogenome was rejected as sperm whales had significantly higher rates of CR evolution and no evidence of slow coding region evolution relative to other cetaceans. The estimated time to most recent common ancestor for sperm whale mitogenomes was 72,800 to 137,400 years ago (95% highest probability density interval), consistent with previous hypotheses of a bottleneck or selective sweep as likely causes of low mitogenome diversity. Text Physeter macrocephalus Sperm whale HighWire Press (Stanford University) Genome Biology and Evolution 5 1 113 129 |
institution |
Open Polar |
collection |
HighWire Press (Stanford University) |
op_collection_id |
fthighwire |
language |
English |
topic |
Research Article |
spellingShingle |
Research Article Alexander, Alana Steel, Debbie Slikas, Beth Hoekzema, Kendra Carraher, Colm Parks, Matthew Cronn, Richard Baker, C. Scott Low Diversity in the Mitogenome of Sperm Whales Revealed by Next-Generation Sequencing |
topic_facet |
Research Article |
description |
Large population sizes and global distributions generally associate with high mitochondrial DNA control region (CR) diversity. The sperm whale ( Physeter macrocephalus ) is an exception, showing low CR diversity relative to other cetaceans; however, diversity levels throughout the remainder of the sperm whale mitogenome are unknown. We sequenced 20 mitogenomes from 17 sperm whales representative of worldwide diversity using Next Generation Sequencing (NGS) technologies (Illumina GAIIx, Roche 454 GS Junior). Resequencing of three individuals with both NGS platforms and partial Sanger sequencing showed low discrepancy rates (454-Illumina: 0.0071%; Sanger-Illumina: 0.0034%; and Sanger-454: 0.0023%) confirming suitability of both NGS platforms for investigating low mitogenomic diversity. Using the 17 sperm whale mitogenomes in a phylogenetic reconstruction with 41 other species, including 11 new dolphin mitogenomes, we tested two hypotheses for the low CR diversity. First, the hypothesis that CR-specific constraints have reduced diversity solely in the CR was rejected as diversity was low throughout the mitogenome, not just in the CR (overall diversity π = 0.096%; protein-coding 3rd codon = 0.22%; CR = 0.35%), and CR phylogenetic signal was congruent with protein-coding regions. Second, the hypothesis that slow substitution rates reduced diversity throughout the sperm whale mitogenome was rejected as sperm whales had significantly higher rates of CR evolution and no evidence of slow coding region evolution relative to other cetaceans. The estimated time to most recent common ancestor for sperm whale mitogenomes was 72,800 to 137,400 years ago (95% highest probability density interval), consistent with previous hypotheses of a bottleneck or selective sweep as likely causes of low mitogenome diversity. |
format |
Text |
author |
Alexander, Alana Steel, Debbie Slikas, Beth Hoekzema, Kendra Carraher, Colm Parks, Matthew Cronn, Richard Baker, C. Scott |
author_facet |
Alexander, Alana Steel, Debbie Slikas, Beth Hoekzema, Kendra Carraher, Colm Parks, Matthew Cronn, Richard Baker, C. Scott |
author_sort |
Alexander, Alana |
title |
Low Diversity in the Mitogenome of Sperm Whales Revealed by Next-Generation Sequencing |
title_short |
Low Diversity in the Mitogenome of Sperm Whales Revealed by Next-Generation Sequencing |
title_full |
Low Diversity in the Mitogenome of Sperm Whales Revealed by Next-Generation Sequencing |
title_fullStr |
Low Diversity in the Mitogenome of Sperm Whales Revealed by Next-Generation Sequencing |
title_full_unstemmed |
Low Diversity in the Mitogenome of Sperm Whales Revealed by Next-Generation Sequencing |
title_sort |
low diversity in the mitogenome of sperm whales revealed by next-generation sequencing |
publisher |
Oxford University Press |
publishDate |
2013 |
url |
http://gbe.oxfordjournals.org/cgi/content/short/5/1/113 https://doi.org/10.1093/gbe/evs126 |
genre |
Physeter macrocephalus Sperm whale |
genre_facet |
Physeter macrocephalus Sperm whale |
op_relation |
http://gbe.oxfordjournals.org/cgi/content/short/5/1/113 http://dx.doi.org/10.1093/gbe/evs126 |
op_rights |
Copyright (C) 2013, Society for Molecular Biology and Evolution |
op_doi |
https://doi.org/10.1093/gbe/evs126 |
container_title |
Genome Biology and Evolution |
container_volume |
5 |
container_issue |
1 |
container_start_page |
113 |
op_container_end_page |
129 |
_version_ |
1766168251696414720 |