| 1. |
- Anderung, Cecilia, 1972-
(författare)
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Genetic Analyses of Bovid Remains and the Origin of Early European Cattle
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The aurochs Bos primigenius, extinct since 1627, was the wild progenitor of cattle. It is believed that all European cattle originate from one domestication event in the Near East 10 000 years ago. However, it is evident from the archaeological record that the aurochs survived into historic time and spent many years existing alongside domestic cattle. Thus, a question posed is whether aurochsen were locally domesticated or incorporated into early domestic cattle stock.In this thesis, genetic techniques are applied to ancient and modern DNA from bovids in order to study questions relating to the origin of early European cattle. DNA from ancient specimens is fragmented and in greatly reduced quantity. Therefore mitochondrial DNA, present in many copies in the living cell, has long been dominating the ancient DNA research field. Analyses of ancient DNA presented in this work are based on both mitochondrial DNA and nuclear DNA, through the study of Single Nuclear Polymorohism (SNPs). A method for typing ancient SNPs was developed and applied to ancient cattle bones.Mitochondrial DNA of cattle is structured into five geographically distributed lineages, the dominant lineage in Europe is also found in the Near East where additional lineages are found. This pattern has been attributed to the proposed domestication event in the Near East from where cattle carrying the single lineage were brought to Europe. However, the results presented here show that cattle domestication was more complicated than previously suggested. SNP data from extant cattle and bones from cattle and aurochs point towards a hybridisation event. European cattle appear indeed to have been domesticated in the Near East and brought in to the European continent from there. However, once in Europe, hybridisation with local aurochsen took place. It appears therefore that today’s cattle descend both from both Anatolian and European aurochsen.
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| 2. |
- Axelsson, Erik, et al.
(författare)
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The effect of ancient DNA damage on inferences of demographic histories.
- 2008
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 25:10, s. 2181-7
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Tidskriftsartikel (refereegranskat)abstract
- The field of ancient DNA (aDNA) is casting new light on many evolutionary questions. However, problems associated with the postmortem instability of DNA may complicate the interpretation of aDNA data. For example, in population genetic studies, the inclusion of damaged DNA may inflate estimates of diversity. In this paper, we examine the effect of DNA damage on population genetic estimates of ancestral population size. We simulate data using standard coalescent simulations that include postmortem damage and show that estimates of effective population sizes are inflated around, or right after, the sampling time of the ancestral DNA sequences. This bias leads to estimates of increasing, and then decreasing, population sizes, as observed in several recently published studies. We reanalyze a recently published data set of DNA sequences from the Bison (Bison bison/Bison priscus) and show that the signal for a change in effective population size in this data set vanishes once the effects of putative damage are removed. Our results suggest that population genetic analyses of aDNA sequences, which do not accurately account for damage, should be interpreted with great caution.
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| 3. |
- Gilbert, M. Thomas P., et al.
(författare)
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Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes
- 2008
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 105:24, s. 8327-8332
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Tidskriftsartikel (refereegranskat)abstract
- We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, approximate to 1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the C-14 ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.
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| 4. |
- Gilbert, M. Thomas P., et al.
(författare)
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Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland
- 2008
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 320:5884, s. 1787-1789
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Tidskriftsartikel (refereegranskat)abstract
- The Paleo- Eskimo Saqqaq and Independence I cultures, documented from archaeological remains in Northern Canada and Greenland, represent the earliest human expansion into the New World's northern extremes. However, their origin and genetic relationship to later cultures are unknown. We sequenced a mitochondrial genome from a Paleo- Eskimo human by using 3400- to 4500- year- old frozen hair excavated from an early Greenlandic Saqqaq settlement. The sample is distinct from modern Native Americans and Neo- Eskimos, falling within haplogroup D2a1, a group previously observed among modern Aleuts and Siberian Sireniki Yuit. This result suggests that the earliest migrants into the New World's northern extremes derived from populations in the Bering Sea area and were not directly related to Native Americans or the later Neo- Eskimos that replaced them.
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| 5. |
- Gilbert, M. Thomas P., et al.
(författare)
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Whole-genome shotgun sequencing of mitochondria from ancient hair shafts
- 2007
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 317:5846, s. 1927-1930
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Tidskriftsartikel (refereegranskat)abstract
- Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.
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| 6. |
- Johnson, Sarah Stewart, et al.
(författare)
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Ancient bacteria show evidence of DNA repair
- 2007
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 104:36, s. 14401-14405
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Tidskriftsartikel (refereegranskat)abstract
- Recent claims of cultivable ancient bacteria within sealed environments highlight our limited understanding of the mechanisms behind long-term cell survival. It remains unclear how dormancy, a favored explanation for extended cellular persistence, can cope with spontaneous genomic decay over geological timescales. There has been no direct evidence in ancient microbes for the most likely mechanism, active DNA repair, or for the metabolic activity necessary to sustain it. In this paper, we couple PCR and enzymatic treatment of DNA with direct respiration measurements to investigate long-term survival of bacteria sealed in frozen conditions for up to one million years. Our results show evidence of bacterial survival in samples up to half a million years in age, making this the oldest independently authenticated DNA to date obtained from viable cells. Additionally, we find strong evidence that this long-term survival is closely tied to cellular metabolic activity and DNA repair that over time proves to be superior to dormancy as a mechanism in sustaining bacteria viability.
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| 7. |
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| 8. |
- Malmström, Helena, et al.
(författare)
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Ancient DNA Reveals Lack of Continuitybetween Neolithic Hunter-Gatherersand Contemporary Scandinavians
- 2009
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Ingår i: Current Biology. - : Elsevier. - 0960-9822 .- 1879-0445. ; 19:20, s. 1758-1762
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Tidskriftsartikel (refereegranskat)abstract
- The driving force behind the transition from a foraging to a farming lifestyle in prehistoric Europe (Neolithization) has been debated for more than a century [1–3]. Of particular interest is whether population replacement or cultural exchange was responsible [3–5]. Scandinavia holds a unique place in this debate, for it maintained one of the last major hunter-gatherer complexes in Neolithic Europe, the Pitted Ware culture [6]. Intriguingly, these late hunter-gatherers existed in parallel to early farmers for more than a millennium before they vanished some 4,000 years ago [7, 8]. The prolonged coexistence of the two cultures in Scandinavia has been cited as an argument against population replacement between the Mesolithic and the present [7, 8]. Through analysis of DNA extracted from ancient Scandinavian human remains, we show that people of the Pitted Ware culture were not the direct ancestors of modern Scandinavians (including the Saami people of northern Scandinavia) but are more closely related to contemporary populations of the eastern Baltic region. Our findings support hypotheses arising from archaeological analyses that propose a Neolithic or post-Neolithic population replacement in Scandinavia [7]. Furthermore, our data are consistent with the view that the eastern Baltic represents a genetic refugia for some of the European hunter-gatherer populations.
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| 9. |
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| 10. |
- Malmström, Helena, et al.
(författare)
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Barking up the wrong tree : Modern northern European dogs fail to explain their origin
- 2008
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Background: Geographic distribution of the genetic diversity in domestic animals, particularly mitochondrial DNA, has often been used to infer centers of domestication. The underlying presumption is that phylogeographic patterns among domesticates were established during, or shortly after the domestication. Human activities are assumed not to have altered the haplogroup frequencies to any great extent. We studied this hypothesis by analyzing 24 mtDNA sequences in ancient Scandinavian dogs. Breeds originating in northern Europe are characterized by having a high frequency of mtDNA sequences belonging to a haplogroup rare in other populations (HgD). This has been suggested to indicate a possible origin of the haplogroup (perhaps even a separate domestication) in central or northern Europe. Results: The sequences observed in the ancient samples do not include the haplogroup indicative for northern European breeds (HgD). Instead, several of them correspond to haplogroups that are uncommon in the region today and that are supposed to have Asian origin. Conclusion: We find no evidence for local domestication. We conclude that interpretation of the processes responsible for current domestic haplogroup frequencies should be carried out with caution if based only on contemporary data. They do not only tell their own story, but also that of humans.
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