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Genomic analysis of the process leading up to the extinction of the woolly mammoth
Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History.ORCID iD: 0000-0001-9350-1987
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Species worldwide are subject to contractions in both abundance and geographical range, and their persistence in a changing environment may thus depend on the ability to survive in small and fragmented populations. Despite the urgent need to understand how extinction works, our knowledge of pre-extinction genetic processes is limited because techniques allowing population and conservation genomics to be studied in wild threatened populations have become available only recently. In this thesis, I used the last surviving population of the woolly mammoth (Mammuthus primigenius) as a model for studying pre-extinction population dynamics. I used ancient DNA as a tool to study microevolutionary processes in real time, analysing genetic changes in response to environmental shifts at the end of the last Ice Age and exploring impacts of genetic drift and inbreeding as woolly mammoths became isolated on Wrangel Island and survived for 6000 years at small population size. Using mitochondrial genomes, I found evidence of a founder effect that decreased the maternal diversity to a single lineage at the time when mammoths became trapped on Wrangel Island (~10,500 years ago). Moreover, a two- to three-fold higher mitochondrial mutation rate in Holocene and a fixed, potentially detrimental mutation in the ATP6 gene encoding for one of the key enzymes of the oxidative phosphorylation pathway, is consistent with the hypothesis that selection is less effective in removing deleterious mutations in small populations. A loss of diversity was also observed in an immunity gene that belongs to the major histocompatibility complex (MHC), even though the MHC is considered to be under balancing selection. Low-coverage genomic data was analysed in order to estimate endogenous DNA content and molecular sex of the mammoth samples. The observation of a male bias (69%) in the sex ratio led to the conclusion that male mammoths were more likely to die in a way that ensured good preservation. Another potential way of getting information about life history strategies of extinct species, which was explored here, is by measuring testosterone levels in mammoth hair shafts in connection with molecular sex inference. Finally, given that previous estimates have suggested a very small Holocene effective population size on Wrangel Island and thus that the population may have been too small to avoid genome erosion, four mammoths were sequenced to a high coverage in order to look for genomic consequences of small population size. When compared to mammoths from the Pleistocene mainland population, Wrangel Island mammoths had lower levels of genome-wide diversity and had a higher proportion of their genomes allocated in runs of homozygosity, which are large fragments completely depleted of diversity. Importantly, genome erosion appears to have accelerated in the last ten generations before the extinction, resulting in the last known woolly mammoth having almost 40% of its genome without any genetic diversity. Overall, these results highlight how genetic drift and inbreeding triggered genomic deterioration in the last surviving woolly mammoth population. Although Wrangel Island was a refugium, where mammoths survived for thousands of years after the last Ice Age, and the causal factors of the final extinction are not yet clear, isolation and small population size without any possibility of new gene flow may have contributed to reduced fitness, and thus to extinction. 

Place, publisher, year, edition, pages
Stockholm: Department of Zoology, Stockholm University , 2018.
Keyword [en]
woolly mammoth, Mammuthus primigenius, extinction, Wrangel Island, ancient DNA, palaeogenetics, population genetics, genomics, genomic erosion, genetic drift, inbreeding, population size
National Category
Evolutionary Biology
Research subject
Systematic Zoology
Identifiers
URN: urn:nbn:se:su:diva-149655ISBN: 978-91-7797-089-7 (print)ISBN: 978-91-7797-090-3 (electronic)OAI: oai:DiVA.org:su-149655DiVA, id: diva2:1164731
Public defence
2018-02-13, Vivi Täckholmssalen, NPQ-huset, Svante Arrhenius väg 20, 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 4: Manuscript. Paper 5: Manuscript.

Available from: 2018-01-19 Created: 2017-12-11 Last updated: 2018-01-11Bibliographically approved
List of papers
1. Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size
Open this publication in new window or tab >>Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size
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2017 (English)In: Evolution Letters, ISSN 2056-3744, Vol. 1, no 6, p. 292-303Article in journal, Letter (Refereed) Published
Abstract [en]

The onset of the Holocene was associated with a global temperature increase, which led to a rise in sea levels and isolation of the last surviving population of woolly mammoths on Wrangel Island. Understanding what happened with the population's genetic diversity at the time of the isolation and during the ensuing 6000 years can help clarify the effects of bottlenecks and subsequent limited population sizes in species approaching extinction. Previous genetic studies have highlighted questions about how the Holocene Wrangel population was established and how the isolation event affected genetic diversity. Here, we generated high-quality mitogenomes from 21 radiocarbon-dated woolly mammoths to compare the ancestral large and genetically diverse Late Pleistocene Siberian population and the small Holocene Wrangel population. Our results indicate that mitogenome diversity was reduced to one single haplotype at the time of the isolation, and thus that the Holocene Wrangel Island population was established by a single maternal lineage. Moreover, we show that the ensuing small effective population size coincided with fixation of a nonsynonymous mutation, and a comparative analysis of mutation rates suggests that the evolutionary rate was accelerated in the Holocene population. These results suggest that isolation on Wrangel Island led to an increase in the frequency of deleterious genetic variation, and thus are consistent with the hypothesis that strong genetic drift in small populations leads to purifying selection being less effective in removing deleterious mutations.

Keyword
Mammuthus primigenius, mitochondrial genomes, woolly mammoth, Wrangel Island
National Category
Evolutionary Biology
Research subject
Systematic Zoology
Identifiers
urn:nbn:se:su:diva-149647 (URN)10.1002/evl3.33 (DOI)
Available from: 2017-12-07 Created: 2017-12-07 Last updated: 2017-12-21Bibliographically approved
2. Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth
Open this publication in new window or tab >>Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth
2016 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 25274Article in journal (Refereed) Published
Abstract [en]

According to the nearly-neutral theory of evolution, the relative strengths of selection and drift shift in favour of drift at small population sizes. Numerous studies have analysed the effect of bottlenecks and small population sizes on genetic diversity in the MHC, which plays a central role in pathogen recognition and immune defense and is thus considered a model example for the study of adaptive evolution. However, to understand changes in genetic diversity at loci under selection, it is necessary to compare the genetic diversity of a population before and after the bottleneck. In this study, we analyse three fragments of the MHC DQA gene in woolly mammoth samples radiocarbon dated to before and after a well-documented bottleneck that took place about ten thousand years ago. Our results indicate a decrease in observed heterozygosity and number of alleles, suggesting that genetic drift had an impact on the variation on MHC. Based on coalescent simulations, we found no evidence of balancing selection maintaining MHC diversity during the Holocene. However, strong trans-species polymorphism among mammoths and elephants points to historical effects of balancing selection on the woolly mammoth lineage.

Keyword
Genetic variation, Molecular ecology, Molecular evolution, Palaeoecology
National Category
Biological Sciences
Research subject
Systematic Zoology
Identifiers
urn:nbn:se:su:diva-131207 (URN)10.1038/srep25274 (DOI)000375428500001 ()27143688 (PubMedID)
Available from: 2016-06-17 Created: 2016-06-14 Last updated: 2017-12-21Bibliographically approved
3. Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth
Open this publication in new window or tab >>Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth
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2017 (English)In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 27, no 22, p. 3505-3510.e3Article in journal (Refereed) Published
Abstract [en]

While present-day taxa are valuable proxies for understanding the biology of extinct species, it is also crucial to examine physical remains in order to obtain a more comprehensive view of their behavior, social structure, and life histories [1, 2]. For example, information on demographic parameters such as age distribution and sex ratios in fossil assemblages can be used to accurately infer socioecological patterns (e.g., [3]). Here we use genomic data to determine the sex of 98 woolly mammoth (Mammuthus primigenius) specimens in order to infer social and behavioral patterns in the last 60,000 years of the species' existence. We report a significant excess of males among the identified samples (69% versus 31%; p < 0.0002). We argue that this male bias among mammoth remains is best explained by males more often being caught in natural traps that favor preservation. Wehypothesize that this is a consequence of social structure in proboscideans, which is characterized by matriarchal hierarchy and sex segregation. Without the experience associated with living in a matriarchal family group, or a bachelor group with an experienced bull, young or solitary males may have been more prone to die in natural traps where good preservation is more likely.

Keyword
Mammuthus primigenius, sex ratio, sex bias, behaviour, ancient DNA, paleogenetics, mortality
National Category
Evolutionary Biology
Research subject
Systematic Zoology
Identifiers
urn:nbn:se:su:diva-149646 (URN)10.1016/j.cub.2017.09.064 (DOI)000415815800028 ()29103934 (PubMedID)
Available from: 2017-12-07 Created: 2017-12-07 Last updated: 2017-12-21Bibliographically approved
4. Testosterone in ancient hair from an extinct species
Open this publication in new window or tab >>Testosterone in ancient hair from an extinct species
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(English)Manuscript (preprint) (Other academic)
Keyword
endogenous steroids, hair-testing, woolly mammoth
National Category
Evolutionary Biology
Research subject
Systematic Zoology
Identifiers
urn:nbn:se:su:diva-149653 (URN)
Available from: 2017-12-07 Created: 2017-12-07 Last updated: 2017-12-21Bibliographically approved
5. Pre-extinction population dynamics and genome erosion in the woolly mammoth
Open this publication in new window or tab >>Pre-extinction population dynamics and genome erosion in the woolly mammoth
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(English)Manuscript (preprint) (Other academic)
Keyword
woolly mammoth, Mammuthus primigenius, Wrangel Island, complete genomes, genetic diversity
National Category
Evolutionary Biology
Research subject
Systematic Zoology
Identifiers
urn:nbn:se:su:diva-149654 (URN)
Available from: 2017-12-07 Created: 2017-12-07 Last updated: 2017-12-21Bibliographically approved

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