Detection of mitochondrial insertions in the nucleus (NuMts) of Pleistocene and modern muskoxen

Kolokotronis, Sergios‐Orestis; MacPhee, R. D. E.; Greenwood, Alex D.

doi:10.1186/1471-2148-7-67

Cited by 20 publications

(17 citation statements)

References 40 publications

(45 reference statements)

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“…The absence of any clearly identifiable alternative sequence among these clones, coupled with the absence of any mismatch when the heavily overlapping primers in our amplification strategies were used, suggests that nuclear-encoded copies of mitochondrial sequences were not recovered, although they have been obtained from ancient and modern musk ox (54). Sequences were found to be totally consistent between fragments generated by different primer pairs and replicable between amplifications when the same primer pairs were used.…”

Section: Methodsmentioning

confidence: 74%

Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox ( Ovibos moschatus ) population dynamics

Campos

Willerslev

Sher

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

205

159

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The causes of the late Pleistocene megafaunal extinctions are poorly understood. Different lines of evidence point to climate change, the arrival of humans, or a combination of these events as the trigger. Although many species went extinct, others, such as caribou and bison, survived to the present. The musk ox has an intermediate story: relatively abundant during the Pleistocene, it is now restricted to Greenland and the Arctic Archipelago. In this study, we use ancient DNA sequences, temporally unbiased summary statistics, and Bayesian analytical techniques to infer musk ox population dynamics throughout the late Pleistocene and Holocene. Our results reveal that musk ox genetic diversity was much higher during the Pleistocene than at present, and has undergone several expansions and contractions over the past 60,000 years. Northeast Siberia was of key importance, as it was the geographic origin of all samples studied and held a large diverse population until local extinction at ≈45,000 radiocarbon years before present ( 14 C YBP). Subsequently, musk ox genetic diversity reincreased at ca. 30,000 14 C YBP, recontracted at ca. 18,000 14 C YBP, and finally recovered in the middle Holocene. The arrival of humans into relevant areas of the musk ox range did not affect their mitochondrial diversity, and both musk ox and humans expanded into Greenland concomitantly. Thus, their population dynamics are better explained by a nonanthropogenic cause (for example, environmental change), a hypothesis supported by historic observations on the sensitivity of the species to both climatic warming and fluctuations.

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Section: Methodsmentioning

confidence: 74%

Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox ( Ovibos moschatus ) population dynamics

Campos

Willerslev

Sher

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

205

159

View full text Add to dashboard Cite

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“…The amplification of numts has been problematic in analyses of closely related bovid species (e.g. Ovibos moschatus; Kolokotronis et al, 2007). Tests of our mitochondrial control region primers on a modern goat extract yielded sequences that were nearly identical (>99% identity) to a few of the artefact sequences.…”

Section: Origin Of the Artefact Sequencesmentioning

confidence: 96%

A flock of sheep, goats and cattle: ancient DNA analysis reveals complexities of historical parchment manufacture

Campana

Bower

Bailey

et al. 2010

Journal of Archaeological Science

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“…This problem appears not to be limited to historic specimens. Numts have also been inadvertently amplified in much older Pleistocene material (Orlando et al 2003;Kolokotronis et al 2007). …”

Section: Discussionmentioning

confidence: 99%

Nuclear copies of mitochondrial genes: another problem for ancient DNA

et al. 2010

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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.R.-J. den Tex · J. A. Leonard (&)

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Detection of mitochondrial insertions in the nucleus (NuMts) of Pleistocene and modern muskoxen

Cited by 20 publications

References 40 publications

Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox ( Ovibos moschatus ) population dynamics

Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox ( Ovibos moschatus ) population dynamics

A flock of sheep, goats and cattle: ancient DNA analysis reveals complexities of historical parchment manufacture

Nuclear copies of mitochondrial genes: another problem for ancient DNA

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