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Patterns and Processes of Evolution in Sundaland
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
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: urn:nbn:se:uu:diva-152213ISBN: 978-91-554-8094-3OAI: oai:DiVA.org:uu-152213DiVA: diva2:413274
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
List of papers
1. Biogeography of the Sunda Shelf: a multi species comparison
Open this publication in new window or tab >>Biogeography of the Sunda Shelf: a multi species comparison
Show others...
(English)Manuscript (preprint) (Other academic)
Identifiers
urn:nbn:se:uu:diva-152227 (URN)
Available from: 2011-04-27 Created: 2011-04-27 Last updated: 2011-07-01
2. Speciation and extinction in the tropics: insights from Asian barbets
Open this publication in new window or tab >>Speciation and extinction in the tropics: insights from Asian barbets
(English)Manuscript (preprint) (Other academic)
Identifiers
urn:nbn:se:uu:diva-152223 (URN)
Available from: 2011-04-27 Created: 2011-04-27 Last updated: 2011-07-01
3. Speciation dynamics in the SE Asian tropics: Putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus
Open this publication in new window or tab >>Speciation dynamics in the SE Asian tropics: Putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus
2010 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 55, no 2, 711-720 p.Article in journal (Refereed) Published
Abstract [en]

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.

Keyword
Cytochrome b, Fib6, c-myc, FTH, POR, GBG, HMG1, Sunda shelf, Pleistocene species pump, Molecular dating, RY coding
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-136338 (URN)10.1016/j.ympev.2009.12.023 (DOI)000276875300031 ()
Available from: 2010-12-13 Created: 2010-12-11 Last updated: 2011-07-01Bibliographically approved
4. Red and yellow: the phylogeography of the coppersmith barbet (Aves: Megalaima haemacephala)
Open this publication in new window or tab >>Red and yellow: the phylogeography of the coppersmith barbet (Aves: Megalaima haemacephala)
(English)Manuscript (preprint) (Other academic)
Identifiers
urn:nbn:se:uu:diva-152224 (URN)
Available from: 2011-04-27 Created: 2011-04-27 Last updated: 2011-07-01
5. Nuclear copies of mitochondrial genes: another problem for ancient DNA
Open this publication in new window or tab >>Nuclear copies of mitochondrial genes: another problem for ancient DNA
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.

Keyword
Numt, aDNA, Sundasciurus, Mitochondria, Universal primers
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-134537 (URN)10.1007/s10709-010-9481-9 (DOI)000282432000007 ()
Available from: 2010-11-30 Created: 2010-11-29 Last updated: 2011-07-01Bibliographically approved

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