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Low Diversity in theMitogenome of Sperm Whales Revealed by Next-Generation Sequencing Public Deposited

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https://ir.library.oregonstate.edu/concern/articles/sx61dm694

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  • 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 pi]=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.
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  • Alexander, A., Steel, D., Slikas, B., Hoekzema, K., Carraher, C., Parks, M., & Cronn, R. ... (2013). Low Diversity in theMitogenome of Sperm Whales Revealed by Next-Generation Sequencing. Genome Biology and Evolution, 5(1), 113-129. doi:10.1093/gbe/evs126
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  • 5
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  • This work was supported by a Mamie Markham Award and a Lylian Brucefield Reynolds Award from the Hatfield Marine Science Center; and a 2008–2011 International Fulbright Science & Technology award to A.A; and co-funded by the ASSURE program of the Department of Defense in partnership with the National Science Foundation REU Site program to K.H and C.S.B. [grant number NSF OCE-1004947]. Publication of this paper was supported, in part, by the Thomas G. Scott Publication Fund.
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