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Nuclear copies of mitochondrial genes: another problem for ancient DNA
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
2010 (English)In: Genetica, ISSN 0016-6707, E-ISSN 1573-6857, Vol. 138, no 9-10, 979-984 p.Article in journal (Refereed) Published
Abstract [en]

The application of ancient DNA techniques is subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characterization of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplification of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occurred. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were utilized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another complication for ancient DNA studies, but it also suggests that more extensive inclusion of nuclear markers in ancient DNA studies should be feasible.

Place, publisher, year, edition, pages
2010. Vol. 138, no 9-10, 979-984 p.
Keyword [en]
Numt, aDNA, Sundasciurus, Mitochondria, Universal primers
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-134537DOI: 10.1007/s10709-010-9481-9ISI: 000282432000007OAI: oai:DiVA.org:uu-134537DiVA: diva2:373131
Available from: 2010-11-30 Created: 2010-11-29 Last updated: 2017-12-12Bibliographically approved
In thesis
1. Patterns and Processes of Evolution in Sundaland
Open this publication in new window or tab >>Patterns and Processes of Evolution in Sundaland
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Biodiversity in the tropics is disproportionately high compared to other habitats, and also under disproportionate threat from human impact. It is necessary to understand how this diversity evolved and how it is partitioned across space in order to preserve it. In this thesis I construct phylogenies of tropical forest dependent vertebrates from Southeast Asia and the islands of the Sunda shelf, a region referred to as Sundaland. I focus on the tree squirrels (genus Sundasciurus) and Asian barbets (Aves: Family Megalaimidae), two taxa with similar ecological characteristics. I use these phylogenies to test hypotheses that have been put forward to explain high levels of tropical diversity including the Pleistocene pump and museum hypotheses. I also use phylogenies to elucidate phylogeographic patterns within the region. I find no evidence for an increase in speciation in the Pleistocene, but I do find within species structure that dates to this period. Common phylogeographic patterns were identified between many forest dependent vertebrates that suggest that populations on the island of Sumatra are generally more closely related to Malay Peninsula populations than to populations on Borneo.

From a methodological viewpoint we propose careful usage of universal primers in ancient DNA studies because of our finding of increased risk of amplifying pseudogenes of the mtDNA.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2011. 27 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 835
National Category
Biological Sciences Biological Systematics Genetics
Research subject
Biology with specialization in Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-152213 (URN)978-91-554-8094-3 (ISBN)
Public defence
2011-06-09, Lindahlsalen, Norbyvägen 14, Uppsala, 13:00 (English)
Opponent
Supervisors
Available from: 2011-05-18 Created: 2011-04-27 Last updated: 2011-07-01Bibliographically approved

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