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Genetic structure, demographic change and extinction dynamics in the collared lemming and woolly mammoth
Stockholm University, Faculty of Science, Department of Zoology.ORCID iD: 0000-0001-7382-7509
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In light of current climate change it is critical to understand how different species have been affected in the past by well-known climatic events. In this thesis, DNA was retrieved from ancient material to study the population dynamics of two cold-adapted taxa that capture the extremes of body size range in mammals: the collared lemming (Dicrostonyx sp.) and the woolly mammoth (Mammuthus primigenius). The aim was to reconstruct their histories to investigate possible associations between past population events and changes in climate. Mitochondrial DNA sequences from collared lemming fossil remains in western Europe suggested that the history of this small mammal was characterized by repeated population extinctions followed by recolonizations, and that these were related to millennial-scale climatic fluctuations. Further genetic sampling of more than 300 mitochondrial DNA sequences, covering a large part of the collared lemming’s historical distribution, showed that these population turnovers were not site-specific but widespread, occurring across Europe and western Russia. Extant populations were found to harbor only a small fraction of the historical genetic diversity demonstrating an extensive loss of genetic variation in this small mammal during the last 50,000 years. For the woolly mammoth, a comprehensive dataset of novel and publicly available mitochondrial DNA sequences was compiled, covering a broad geographical and temporal range. In addition, complete genome sequencing was performed on two mammoth specimens, the first representing one of the last surviving individuals from Wrangel Island and the second representing the ancestral Late Pleistocene Siberian population. Genome-wide as well as mitochondrial DNA data revealed that climatic changes have played a major role in shaping the demographic history of the woolly mammoth. For example, two severe population reductions were identified, with the first one encompassing the last warm interglacial period (~130,000 – 116,000 years ago) and the second coinciding with the end of the last Ice Age (~11,000 years ago). Moreover, climate-driven sea level changes appear to have had considerable impact by enabling increased gene flow across the Bering land bridge, as well as the isolation of mammoths on Wrangel Island. When comparing the two complete genomes, the one from Wrangel Island displayed 20% lower genome-wide diversity and a markedly higher fraction of runs of homozygosity. Consequently, loss of genetic variation and inbreeding may have contributed to the extinction of the woolly mammoth. Overall, the findings presented in this thesis illustrate the power of ancient DNA in providing unique insights into past evolutionary processes.

Place, publisher, year, edition, pages
Stockholm: Department of Zoology, Stockholm University , 2014. , 51 p.
National Category
Biological Sciences
Research subject
Systematic Zoology
Identifiers
URN: urn:nbn:se:su:diva-108951ISBN: 978-91-7649-044-0 (print)OAI: oai:DiVA.org:su-108951DiVA: diva2:761636
Public defence
2014-12-18, Nordenskiöldsalen, Geovetenskapens hus, Svante Arrhenius väg 12, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: Manuscript. 

Available from: 2014-11-26 Created: 2014-11-07 Last updated: 2014-12-17Bibliographically approved
List of papers
1. Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability
Open this publication in new window or tab >>Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability
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2012 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 50, 20532-20536 p.Article in journal (Refereed) Published
Abstract [en]

The Late Pleistocene global extinction of many terrestrial mammal species has been a subject of intensive scientific study for over a century, yet the relative contributions of environmental changes and the global expansion of humans remain unresolved. A defining component of these extinctions is a bias toward large species, with the majority of small-mammal taxa apparently surviving into the present. Here, we investigate the population-level history of a key tundra-specialist small mammal, the collared lemming (Dicrostonyx torquatus), to explore whether events during the Late Pleistocene had a discernible effect beyond the large mammal fauna. Using ancient DNA techniques to sample across three sites in North-West Europe, we observe a dramatic reduction in genetic diversity in this species over the last 50,000 y. We further identify a series of extinction-recolonization events, indicating a previously unrecognized instability in Late Pleistocene small-mammal populations, which we link with climatic fluctuations. Our results reveal climate-associated, repeated regional extinctions in a keystone prey species across the Late Pleistocene, a pattern likely to have had an impact on the wider steppe-tundra community, and one that is concordant with environmental change as a major force in structuring Late Pleistocene biodiversity.

Keyword
megafauna, palaeogenetics, palaeoclimate, modelling
National Category
Biological Sciences
Research subject
Systematic Zoology
Identifiers
urn:nbn:se:su:diva-87135 (URN)10.1073/pnas.1213322109 (DOI)000312605600081 ()
Note

AuthorCount:10;

Available from: 2013-01-29 Created: 2013-01-28 Last updated: 2017-12-06Bibliographically approved
2. Palaeogenetic analyses reveal wide-spread Pleistocene range fluctuations in the collared lemming
Open this publication in new window or tab >>Palaeogenetic analyses reveal wide-spread Pleistocene range fluctuations in the collared lemming
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(English)Manuscript (preprint) (Other academic)
National Category
Biological Sciences
Research subject
Systematic Zoology
Identifiers
urn:nbn:se:su:diva-108954 (URN)
Available from: 2014-11-07 Created: 2014-11-07 Last updated: 2014-11-08
3. Holarctic genetic structure and range dynamics in the woolly mammoth
Open this publication in new window or tab >>Holarctic genetic structure and range dynamics in the woolly mammoth
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2013 (English)In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 280, no 1770, 20131910- p.Article in journal (Refereed) Published
Abstract [en]

Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32-34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20-15 kyr BP, when a severe population size decline occurred.

Keyword
ancient DNA, Mammuthus primigenius, extinction, refugia, climate
National Category
Biological Sciences
Research subject
Systematic Zoology
Identifiers
urn:nbn:se:su:diva-101254 (URN)10.1098/rspb.2013.1910 (DOI)000330323300016 ()
Funder
Swedish Research Council
Note

AuthorCount:11;

Available from: 2014-03-03 Created: 2014-03-03 Last updated: 2017-12-05Bibliographically approved
4. Genome-wide signatures of demographic change and Holocene genetic decline in the extinct woolly mammoth
Open this publication in new window or tab >>Genome-wide signatures of demographic change and Holocene genetic decline in the extinct woolly mammoth
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(English)Manuscript (preprint) (Other academic)
National Category
Biological Sciences
Research subject
Systematic Zoology
Identifiers
urn:nbn:se:su:diva-108956 (URN)
Available from: 2014-11-07 Created: 2014-11-07 Last updated: 2014-11-08

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