Excess of genomic defects in a woolly mammoth on Wrangel island.
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 spe...
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ftdoajarticles:oai:doaj.org/article:a363f6d3686a4a6fa36ec0cc0be6ac83 2023-05-15T18:44:23+02:00 Excess of genomic defects in a woolly mammoth on Wrangel island. Rebekah L Rogers Montgomery Slatkin 2017-03-01T00:00:00Z https://doi.org/10.1371/journal.pgen.1006601 https://doaj.org/article/a363f6d3686a4a6fa36ec0cc0be6ac83 EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC5333797?pdf=render https://doaj.org/toc/1553-7390 https://doaj.org/toc/1553-7404 1553-7390 1553-7404 doi:10.1371/journal.pgen.1006601 https://doaj.org/article/a363f6d3686a4a6fa36ec0cc0be6ac83 PLoS Genetics, Vol 13, Iss 3, p e1006601 (2017) Genetics QH426-470 article 2017 ftdoajarticles https://doi.org/10.1371/journal.pgen.1006601 2022-12-31T06:30:34Z 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. Article in Journal/Newspaper Wrangel Island Beringia Siberia Directory of Open Access Journals: DOAJ Articles Wrangel Island ENVELOPE(-179.385,-179.385,71.244,71.244) PLOS Genetics 13 3 e1006601 |
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Directory of Open Access Journals: DOAJ Articles |
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English |
topic |
Genetics QH426-470 |
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Genetics QH426-470 Rebekah L Rogers Montgomery Slatkin Excess of genomic defects in a woolly mammoth on Wrangel island. |
topic_facet |
Genetics QH426-470 |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Rebekah L Rogers Montgomery Slatkin |
author_facet |
Rebekah L Rogers Montgomery Slatkin |
author_sort |
Rebekah L Rogers |
title |
Excess of genomic defects in a woolly mammoth on Wrangel island. |
title_short |
Excess of genomic defects in a woolly mammoth on Wrangel island. |
title_full |
Excess of genomic defects in a woolly mammoth on Wrangel island. |
title_fullStr |
Excess of genomic defects in a woolly mammoth on Wrangel island. |
title_full_unstemmed |
Excess of genomic defects in a woolly mammoth on Wrangel island. |
title_sort |
excess of genomic defects in a woolly mammoth on wrangel island. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2017 |
url |
https://doi.org/10.1371/journal.pgen.1006601 https://doaj.org/article/a363f6d3686a4a6fa36ec0cc0be6ac83 |
long_lat |
ENVELOPE(-179.385,-179.385,71.244,71.244) |
geographic |
Wrangel Island |
geographic_facet |
Wrangel Island |
genre |
Wrangel Island Beringia Siberia |
genre_facet |
Wrangel Island Beringia Siberia |
op_source |
PLoS Genetics, Vol 13, Iss 3, p e1006601 (2017) |
op_relation |
http://europepmc.org/articles/PMC5333797?pdf=render https://doaj.org/toc/1553-7390 https://doaj.org/toc/1553-7404 1553-7390 1553-7404 doi:10.1371/journal.pgen.1006601 https://doaj.org/article/a363f6d3686a4a6fa36ec0cc0be6ac83 |
op_doi |
https://doi.org/10.1371/journal.pgen.1006601 |
container_title |
PLOS Genetics |
container_volume |
13 |
container_issue |
3 |
container_start_page |
e1006601 |
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