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- den Tex, Robert-Jan, et al.
(författare)
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Nuclear copies of mitochondrial genes : another problem for ancient DNA
- 2010
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Ingår i: Genetica. - : Springer Science and Business Media LLC. - 0016-6707 .- 1573-6857. ; 138:9-10, s. 979-984
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 3. |
- den Tex, Robert-Jan, et al.
(författare)
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Speciation dynamics in the SE Asian tropics : Putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus
- 2010
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 55:2, s. 711-720
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Tidskriftsartikel (refereegranskat)abstract
- Tropical rainforests are well known for their extraordinarily high levels of biodiversity. The origin of this species richness is still debated. For instance, the museum hypothesis states that over evolutionary time more and more species will accumulate with relatively few extinctions. In contrast, the Pleistocene diversification model argues that during the last 2 million years, climatic factors (glaciations) caused environmental changes that drove isolation and vicariant speciation events. In this study, we construct a molecular phylogeny of the Sundaland (Malay Peninsula, Sumata, Borneo, Palawan) and Greater Mindanao (Mindanao, Samar, Leyte) tree squirrels (genus Sundasciurus). Our results show that most speciation events in this forest dependent taxon occurred before the Pleistocene and that even the timing of intra-specific splits among populations from different landmasses are relatively old. Additionally, we found unexpectedly high divergence within and between highland populations of S. tenuis on Sumatra and the Malay Peninsula, highlighting the importance of Pliocene events in both speciation and within species divergences in this region. (C) 2010 Elsevier Inc. All rights reserved.
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| 4. |
- Leonard, Jennifer A., et al.
(författare)
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Phylogeography of vertebrates on the Sunda Shelf : a multi-species comparison
- 2015
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 42:5, s. 871-879
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Tidskriftsartikel (refereegranskat)abstract
- Aim Pleistocene environmental fluctuations had well-characterized impacts on the patterns of within-species divergences and diversity in temperate habitats. Here we examine the impact the Pleistocene had on widely distributed forest vertebrates in a tropical system where the distribution of the habitat was affected by those fluctuations. LocationSundaland, tropical Southeast Asia. Methods We conducted a comparative phylogeographical analysis of 28 non-migratory, forest-dependent vertebrates, for which we constructed rooted, intraspecifc phylogenies based on mitochondrial DNA sequences of individuals from at least the three major landmasses in the area (Borneo, Sumatra and the Malay Peninsula) and compared them to hypothetical phylogenies based on independent geological data and climate models regarding connections and relationships between the major landmasses of Sundaland. Java was included where possible. We dated the phylogenies to determine whether patterns of differentiation were concordant across species. Results In most species, populations on the Malay Peninsula and Sumatra were most closely related, and sister to those from Borneo. The dates of these divergences, however, varied extensively between species. Borneo harbours multiple deeply divergent lineages of many species compared to the diversity within those species. Javan populations of several birds were most divergent relative to those from the rest of the Sunda Shelf. Main conclusions These results suggest a dynamic history, including recurrent population extinctions and replacements and a strong priority effect for local populations. The close relationship between populations in Sumatra and the Malay Peninsula supports the existence of forest on the exposed shelf during the Pleistocene at many different times, and suggests that proximity was more important than the presence of palaeorivers for dispersal of forest taxa between landmasses.
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