Excess of genomic defects in a woolly mammoth on Wrangel island
Rebekah L. Rogers , Montgomery Slatkin
Published: March 2, 2017 http://dx.doi.org/10.1371/journal.pgen.1006601
Source/Fonte: Flying Puff
Abstract
Woolly mammoths (Mammuthus primigenius) populated Siberia, Beringia, and North America during the Pleistocene and early Holocene. Recent breakthroughs in ancient DNA sequencing have allowed for complete genome sequencing for two specimens of woolly mammoths (Palkopoulou et al. 2015). One mammoth specimen is from a mainland population 45,000 years ago when mammoths were plentiful. The second, a 4300 yr old specimen, is derived from an isolated population on Wrangel island where mammoths subsisted with small effective population size more than 43-fold lower than previous populations. These extreme differences in effective population size offer a rare opportunity to test nearly neutral models of genome architecture evolution within a single species. Using these previously published mammoth sequences, we identify deletions, retrogenes, and non-functionalizing point mutations. In the Wrangel island mammoth, we identify a greater number of deletions, a larger proportion of deletions affecting gene sequences, a greater number of candidate retrogenes, and an increased number of premature stop codons. This accumulation of detrimental mutations is consistent with genomic meltdown in response to low effective population sizes in the dwindling mammoth population on Wrangel island. In addition, we observe high rates of loss of olfactory receptors and urinary proteins, either because these loci are non-essential or because they were favored by divergent selective pressures in island environments. Finally, at the locus of FOXQ1 we observe two independent loss-of-function mutations, which would confer a satin coat phenotype in this island woolly mammoth.
Author summary
We observe an excess of detrimental mutations, consistent with genomic meltdown in woolly mammoths on Wrangel Island just prior to extinction. We observe an excess of deletions, an increase in the proportion of deletions affecting gene sequences, and an excess of premature stop codons in response to evolution under low effective population sizes. Large numbers of olfactory receptors appear to have loss of function mutations in the island mammoth. These results offer genetic support within a single species for nearly-neutral theories of genome evolution. We also observe two independent loss of function mutations at the FOXQ1 locus, likely conferring a satin coat in this unusual woolly mammoth.
Citation: Rogers RL, Slatkin M (2017) Excess of genomic defects in a woolly mammoth on Wrangel island. PLoS Genet 13(3): e1006601. doi:10.1371/journal.pgen.1006601
Editor: Gregory S. Barsh, Stanford University School of Medicine, UNITED STATES
Received: July 20, 2016; Accepted: January 24, 2017; Published: March 2, 2017
Copyright: © 2017 Rogers, Slatkin. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: Previously published data for two woolly mammoths are available at http://www.ebi.ac.uk/ena, under accessions ERR852028 (Oimyakon) and ERR855944 (Wrangel Island). Previously published data for mammoths M4 and M25 are available at https://www.ncbi.nlm.nih.gov/sra accessions SRX1015606 and SRX1015608 (Maya/Uno); SRX1015711, SRX1015712, SRX1015714, SRX1015715, SRX1015717, SRX1015679, SRX1015671, SRX1015640, SRX1015634, and SRX1015625 (M4); SRX1015733, SRX1015732, SRX1015729, SRX1015727, and SRX1015726 (M25). VCF files are available at
Funding: RLR and MS are funded by grant R01-GM40282 from the National Institutes of Health to MS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
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