Er is nauwelijks een ander deel van onze aarde aan te wijzen, waar de dierenwereld zulk een verscheidenheid vertoont, als in den Indo-Australischen archipel. Dr. L.F. de Beaufort, Zoögeographie van den Indischen Archipel (1926) Writing a book is an adventure. To begin with, it is a toy and an amusement; then it becomes a mistress, and then it becomes a master, and then a tyrant. The last phase is that just as you are about to be reconciled to your servitude you kill the monster, and fling him out to the public. Sir Winston Churchill Voor K., J. & F. Cover design by Kathelijne Balfoort Kathelijne Balfoort List of papers This thesis is based on the following papers, referred to by their roman nu- merals. I. Den Tex, R.-J., Roberts, M., Maldonado, J.E., Munoz-Fuentes, V., Thorington, R. and Leonard, J.A. 2011. Biogeography of the Sunda shelf: a multi species comparison. Manuscript II. Den Tex, R.-J., and Leonard, J.A. 2011. Speciation and extinction in the Tropics: insights from Asian barbets. Manuscript. III. Den Tex, R.-J., Thorington, R., Maldonado, J.E., and Leonard, J.A. 2010a. Speciation dynamics in the SE Asian tropics: putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus. Molecular Phylogenetics and Evolution 55: 711-720. IV. Den Tex, R.-J., and Leonard, J.A. 2011. Red and yellow: the phy- logeography of the coppersnith barbet (Aves: Megalaima hae- macephala). Manuscript. V. Den Tex, R.-J., Maldonado, J.E., Thorington, R., and Leonard, J.A. 2010b. Nuclear copies of mitochondrial genes: another problem for ancient DNA. Genetica 138: 979-984. Papers number III ( Elsevier) and V ( Springer) are reproduced with permission from the publishers. This thesis, or the reproduction in it of any of its manuscripts presented, is not intended for permanent scientific record in the meaning of the Interna- tional Code of Zoological Nomenclature. Thus, any nomenclatural changes proposed here are not valid nomenclatural acts (ICZN, Fourth Edition, Chap- ter 3, Articles 8.2 and 8.3). Contents Introduction ..................................................................................................... 9 Tropical biodiversity .................................................................................. 9 Origin of tropical biodiversity .................................................................. 10 Biogeography ........................................................................................... 10 Sundaland ................................................................................................. 12 Samples and the importance of natural history museums ........................ 13 Ancient DNA and historic DNA .............................................................. 13 Main study organisms .............................................................................. 14 Tree squirrels of the genus Sundasciurus ............................................ 14 The Asian barbets (Aves: Megalaimidae) ........................................... 15 Research goals .............................................................................................. 17 Specific aims ............................................................................................ 17 Summaries of papers ..................................................................................... 18 Paper I: Biogeography of the Sunda shelf: a multi species comparison. 18 Paper II: Speciation and extinction in the Tropics: insights from Asian barbets. ..................................................................................................... 18 Paper III: Speciation dynamics in the SE Asian tropics: putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus. ............................................................................ 19 Paper IV: Red and yellow: the phylogeography of the coppersnith barbet (Aves: Megalaima haemacephala). ......................................................... 20 Paper V: Nuclear copies of mitochondrial genes: another problem for ancient DNA. ............................................................................................ 21 Conclusions and prospects ............................................................................ 22 Svensk sammanfattning ................................................................................ 24 Nederlandse samenvatting ............................................................................ 27 Acknowledgements ....................................................................................... 30 References ..................................................................................................... 32 Abbreviations aDNA Ancient DNA bp Base pair(s) DNA Deoxy-ribo-nucleic acid LTT plot Lineage through time plot ML Maximum likelihood MP Maximum parsimony mtDNA Mitochondrial DNA MY Million years MYA Million years ago NUMT Nuclear insert of mtDNA origin PCR Polymerase chain reaction SE Asia Southeast Asia Introduction Tropical biodiversity The bewildering array of different life forms, called biodiversity, is not equally distributed over the earth’s surface. Areas of high species richness and high levels of species endemism, that is species that are occurring only in a particular area, are especially found around the earth’s equator (Myers et al. 2000). These areas have a tropical climate and are mainly located in South America, Africa and SE Asia each with particular properties that have shaped the patterns of their own unique biodiversity. The tropical region of SE Asia is fundamentally different from the other two regions. Scattered over thousands of islands, both large and small with different grades of isolation to each other and the mainland of SE Asia to- gether with its very dynamic geological history, makes this region especially atractive for biogeographers to study the processes that have shaped the pat- terns of biodiversity in this region (Heaney 1986; Gorog et al. 2004). Due to the rapid economical development of this region, large parts of tropi- cal forest habitat, mainly lowland tropical rain forests, are under the serious danger of destruction (Sodhi et al. 2004). These lowland rainforests are the most biodiverse (Lambert and Collar 2002). Threads to these forests are mainly transformation into palm oil plantations and direct logging but also forest fires related to drought years can destroy huge areas of this vegetation (Curran et al. 2004). The importance of tropical rainforests for human soci- ety as a rich source of all kinds of products and from an aesthetic point can- not be overemphasized (Woodruff 2010). Therefore it is important that we should manage these rich sources in such a way that our use of forest prod- ucts will be sustainable and therefore also available to future generations. With the current rate of human induced transformations and population growth, SE Asia is one of the most threatened and vulnerable regions of the tropics (Sodhi et al. 2004; Woodruff 2010). The need for conservation is urgent but to make decisions about where and what to conserve basic and more fundamental knowledge about its biodiversity is necessary (Whittaker et al. 2005). It is in this light that I present my thesis. 9 Origin of tropical biodiversity One of the clearest patterns of earth’s biodiversity is that tropical regions house many more different life forms than temperate regions, the so-called latitudinal gradient (Mittelbach et al. 2007). The huge abundance of biodi- versity in the tropics as compared to higher latitudes demands explanation and several hypotheses have been put forward (Mittelbach et al. 2007). The species present in any place is a result of local speciation and extinction dy- namics, and immigration of species from other places (Heaney 2000; Wiens and Donoghue 2004). The two main hypotheses that have been suggested to explain the high density of species in the tropics are the Pleistocene pump hypothesis and the museum hypothesis. One explains the higher diversity through higher speciation, and the other through lower extinction. The Pleistocene pump hypothesis postulates that much of the diversity present in the tropics today arose in the Pleistocene, as widespread popula- tions were broken into smaller, isolated populations as the climate fluctu- ated. Some of the populations then diverged in isolation, and when the forest was reconnected they increased their distributions and became sympatric with their sister species, and this happened repeatedly. This hypothesis pre- dicts that many of the species in the tropics have a Pleistocene origin. The Museum hypothesis on the other hand postulates that gradual species built-up through time is responsible for the high levels of biodiversity. Tropical regions are seen as benign environments where extinction rates are low. Biogeography Biogeography is the study concerned with explaining the observed patterns in distribution of species both in a spatial (geographic) and temporal (his- tory) framework (Whittaker et al. 2005). A phylogenetic approach, by which one tries to reconstruct the evolutionary relationships among species or populations, is imperative for biogeographical studies. Only then, it can teach us to understand about the relative importance of speciation, extinction and dispersal as main drivers that yielded today’s biogeographical patterns. Scale, both spatial and temporal, is important too in biogeographical studies. On a small scale the ecophysiology