Palaeogenomic reconstruction of woolly mammoth evolutionary history and extinction dynamics
Biodiversity is declining globally. Yet, the biological and genetic processes associated with these declines on a longer timescale are still poorly understood. Ancient DNA is a powerful tool to study evolution in real-time. Despite advances in the field, there is further need for refinement of labor...
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Stockholms universitet, Zoologiska institutionen
2023
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ftstockholmuniv:oai:DiVA.org:su-214156 2023-05-15T17:58:16+02:00 Palaeogenomic reconstruction of woolly mammoth evolutionary history and extinction dynamics Dehasque, Marianne 2023 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-214156 eng eng Stockholms universitet, Zoologiska institutionen Stockholm : Department of Zoology, Stockholm University orcid:0000-0002-4640-8306 http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-214156 urn:isbn:978-91-8014-176-5 urn:isbn:978-91-8014-177-2 info:eu-repo/semantics/openAccess woolly mammoth Mammuthus primigenius extinction Wrangel Island ancient DNA palaeogenomics radiocarbon dating structural variants genome erosion population structure Biological Sciences Biologiska vetenskaper Doctoral thesis, comprehensive summary info:eu-repo/semantics/doctoralThesis text 2023 ftstockholmuniv 2023-02-23T21:44:27Z Biodiversity is declining globally. Yet, the biological and genetic processes associated with these declines on a longer timescale are still poorly understood. Ancient DNA is a powerful tool to study evolution in real-time. Despite advances in the field, there is further need for refinement of laboratory and computational techniques. In this thesis, I used mitochondrial and nuclear genomes, as well as radiocarbon data, to study the evolutionary history and extinction dynamics of the woolly mammoth (Mammuthus primigenius). In Chapter I, I developed and optimized a silica column-based extraction protocol for ancient DNA. Based on systematic tests, I advise against routine use of pretreatment methods, like bleach wash and/or predigestion, for well-preserved permafrost samples. Furthermore, I suggest that USER enzyme, which removes uracil from damaged DNA molecules, is effective at half the concentration compared to an established control protocol. Finally, I did not find a significant difference between different silica columns for the clean-up steps, or concentrator columns with different DNA retention sizes. In Chapter II, I used five high coverage Siberian mammoth genomes to develop a method based on differences in read depth to identify indels, insertions and deletions, in the mammoth genome. The results show that indels are enriched in intergenic regions, suggesting strong selection against structural variants affecting gene function. Nevertheless, 87 genes were identified that were severely affected. These genes are related to various functions like body-fat distribution, fur growth and hair shape, body temperature, and body size, and most likely represent important adaptations to the cold steppe-tundra. In Chapter III, I studied the population and extinction dynamics of the woolly mammoths in Siberia by combining Bayesian age models from radiocarbon data with inferences from complete mitogenomes. The results show that the woolly mammoth’s extinction was a complex process with consecutive extirpations, but ... Doctoral or Postdoctoral Thesis permafrost Tundra Wrangel Island Siberia Stockholm University: Publications (DiVA) Wrangel Island ENVELOPE(-179.385,-179.385,71.244,71.244) |
institution |
Open Polar |
collection |
Stockholm University: Publications (DiVA) |
op_collection_id |
ftstockholmuniv |
language |
English |
topic |
woolly mammoth Mammuthus primigenius extinction Wrangel Island ancient DNA palaeogenomics radiocarbon dating structural variants genome erosion population structure Biological Sciences Biologiska vetenskaper |
spellingShingle |
woolly mammoth Mammuthus primigenius extinction Wrangel Island ancient DNA palaeogenomics radiocarbon dating structural variants genome erosion population structure Biological Sciences Biologiska vetenskaper Dehasque, Marianne Palaeogenomic reconstruction of woolly mammoth evolutionary history and extinction dynamics |
topic_facet |
woolly mammoth Mammuthus primigenius extinction Wrangel Island ancient DNA palaeogenomics radiocarbon dating structural variants genome erosion population structure Biological Sciences Biologiska vetenskaper |
description |
Biodiversity is declining globally. Yet, the biological and genetic processes associated with these declines on a longer timescale are still poorly understood. Ancient DNA is a powerful tool to study evolution in real-time. Despite advances in the field, there is further need for refinement of laboratory and computational techniques. In this thesis, I used mitochondrial and nuclear genomes, as well as radiocarbon data, to study the evolutionary history and extinction dynamics of the woolly mammoth (Mammuthus primigenius). In Chapter I, I developed and optimized a silica column-based extraction protocol for ancient DNA. Based on systematic tests, I advise against routine use of pretreatment methods, like bleach wash and/or predigestion, for well-preserved permafrost samples. Furthermore, I suggest that USER enzyme, which removes uracil from damaged DNA molecules, is effective at half the concentration compared to an established control protocol. Finally, I did not find a significant difference between different silica columns for the clean-up steps, or concentrator columns with different DNA retention sizes. In Chapter II, I used five high coverage Siberian mammoth genomes to develop a method based on differences in read depth to identify indels, insertions and deletions, in the mammoth genome. The results show that indels are enriched in intergenic regions, suggesting strong selection against structural variants affecting gene function. Nevertheless, 87 genes were identified that were severely affected. These genes are related to various functions like body-fat distribution, fur growth and hair shape, body temperature, and body size, and most likely represent important adaptations to the cold steppe-tundra. In Chapter III, I studied the population and extinction dynamics of the woolly mammoths in Siberia by combining Bayesian age models from radiocarbon data with inferences from complete mitogenomes. The results show that the woolly mammoth’s extinction was a complex process with consecutive extirpations, but ... |
format |
Doctoral or Postdoctoral Thesis |
author |
Dehasque, Marianne |
author_facet |
Dehasque, Marianne |
author_sort |
Dehasque, Marianne |
title |
Palaeogenomic reconstruction of woolly mammoth evolutionary history and extinction dynamics |
title_short |
Palaeogenomic reconstruction of woolly mammoth evolutionary history and extinction dynamics |
title_full |
Palaeogenomic reconstruction of woolly mammoth evolutionary history and extinction dynamics |
title_fullStr |
Palaeogenomic reconstruction of woolly mammoth evolutionary history and extinction dynamics |
title_full_unstemmed |
Palaeogenomic reconstruction of woolly mammoth evolutionary history and extinction dynamics |
title_sort |
palaeogenomic reconstruction of woolly mammoth evolutionary history and extinction dynamics |
publisher |
Stockholms universitet, Zoologiska institutionen |
publishDate |
2023 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-214156 |
long_lat |
ENVELOPE(-179.385,-179.385,71.244,71.244) |
geographic |
Wrangel Island |
geographic_facet |
Wrangel Island |
genre |
permafrost Tundra Wrangel Island Siberia |
genre_facet |
permafrost Tundra Wrangel Island Siberia |
op_relation |
orcid:0000-0002-4640-8306 http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-214156 urn:isbn:978-91-8014-176-5 urn:isbn:978-91-8014-177-2 |
op_rights |
info:eu-repo/semantics/openAccess |
_version_ |
1766166837539635200 |