Speciation dynamics in the SE Asian tropics: Putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus

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 diver- sification model argues that during the last 2 million years, climatic factors (glaciations) caused environ- mental 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 Minda- nao (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 regionPeer reviewe

The phylogeography of red and yellow coppersmith barbets (Aves: Megalaima haemacephala)

Understanding the evolution of color in birds is important because it is used for both inter- and intra-specific communication and is often linked to other important traits including life history, behavior, immunology, and mate choice. The coppersmith barbet (Megalaima haemacephala) is widely distributed across southern Asia and many islands of the Sunda shelf and the Philippines. It occurs in two well-differentiated and completely allopatrically distributed color morphs, a red- and a yellow-headed form. We constructed a phylogeny of coppersmith barbets from both color morphs and from across their range using sequences from two mitochondrial and one nuclear loci. Strong geographical patterns were found, in which India and Sri Lanka, the Philippines and mainland tropical east Asia (TE Asia) and the islands on the Sunda shelf (Sundaland) each formed a divergent group. The red birds formed two clades within the diversity of yellow animals. Major clades were dated using a molecular clock calibrated on a larger phylogeny. The phylogeographic patterns suggest that the species likely originated in TE Asia/Sundaland and then colonized the Philippines from the south in the mid-Pleistocene, via a now extinct population on Borneo. More recently, coppersmith barbets colonized India and Sri Lanka, also from TE Asia/Sundaland. Coppersmith barbets were also likely distributed on the Malay Peninsula, but went extinct there too. The population that now inhabits this region derives from a natural recolonization of yellow morph birds about 80 years ago. The red morph evolved at least twice independently from the yellow morph in the late Pleistocene, suggesting that this change does not require very many mutational steps, and thus can arise relatively frequently, on an evolutionary timescale. This system may be ideal for further studies of the genetics of carotenoid coloration.Peer Reviewe

Patterns and Processes of Evolution in Sundaland

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

Evolution of acoustic and visual signals in Asian barbets

The study of animal communication systems is an important step towards gaining greater understanding of the processes influencing diversification because signals often play an important role in mate choice and can lead to reproductive isolation. Signal evolution can be influenced by a diversity of factors such as biophysical constraints on the emitter, the signalling environment, or selection to avoid heterospecific matings. Furthermore, because signals can be costly to produce, trade-offs may exist between different types of signals. Here, we apply phylogenetic comparative analyses to study the evolution of acoustic and visual signals in Asian barbets, a clade of non-Passerine, forest-dependent birds. Our results suggest that evolution of acoustic and visual signals in barbets is influenced by diverse factors, such as morphology and signalling environment, suggesting a potential effect of sensory drive. We found no trade-offs between visual and acoustic signals. Quite to the contrary, more colourful species sing significantly longer songs. Song characteristics presented distinct patterns of evolution. Song frequency diverged early on and the rate of evolution of this trait appears to be constrained by body size. On the other hand, characteristics associated with length of the song presented evidence for more recent divergence. Finally, our results indicate that there is a spatial component to the evolution of visual signals, and that visual signals are more divergent between closely related taxa than acoustic signals. Hence, visual signals in these species could play a role in speciation or reinforcement of reproductive isolation following secondary contacts. © 2013 European Society For Evolutionary Biology.Peer Reviewe

Nuclear copies of mitochondrial genes: another problem for ancient DNA

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. © 2010 Springer Science+Business Media B.V.Peer Reviewe

Société d'Histoire du Droit des Pays Flamands, Picards et Wallons. Journées d'histoire des institutions tenues a Bréda (21, 22 et 23 mai 1953)

Lepointe Gabriel, Houwens Post H., Janne d'Othée X., Schaap H.P., Warlomont René, Feenstra Robert, Spijkerboer G., Fockema Andreae S. J., Feuchère P., Den Tex Jan, Dereine Charles, Dieleman P. Société d'Histoire du Droit des Pays Flamands, Picards et Wallons. Journées d'histoire des institutions tenues a Bréda (21, 22 et 23 mai 1953) . In: Revue du Nord, tome 36, n°141, Janvier-mars 1954. pp. 69-82

Société d'Histoire du Droit des Pays Flamands, Picards et Wallons. Journées d'histoire des institutions tenues a Bréda (21, 22 et 23 mai 1953)

Lepointe Gabriel, Houwens Post H., Janne d'Othée X., Schaap H.P., Warlomont René, Feenstra Robert, Spijkerboer G., Fockema Andreae S. J., Feuchère P., Den Tex Jan, Dereine Charles, Dieleman P. Société d'Histoire du Droit des Pays Flamands, Picards et Wallons. Journées d'histoire des institutions tenues a Bréda (21, 22 et 23 mai 1953) . In: Revue du Nord, tome 36, n°141, Janvier-mars 1954. pp. 69-82

Neutral markers mirror small-scale quantitative genetic differentiation in an avian island population

We still know remarkably little about the extent to which neutral markers can provide a biologically relevant description of population structure. In the present study, we address this question, and quantify microsatellite differentiation among a small, structured island population of great tits (Parus major), and a large mainland population 150 km away. Although only a few kilometres apart, we found small but statistically significant levels of differentiation between the eastern and the western part of the island. On the other hand, there was no differentiation between the western part of the island and the mainland population, whereas the eastern part and the mainland did differ significantly. This initially counterintuitive result provides powerful support for the hypothesis that the large genetic difference in clutch size between both parts of the island found earlier is maintained by different levels of gene flow into both parts of the island, and illustrates the capacity of microsatellites to provide a meaningful description of population structure. Importantly, because the level of microsatellite differentiation is very low, we were unable to infer any population structure without grouping individuals a priori. Hence, these low levels of differentiation in neutral markers could easily remain undetected, or incorrectly be dismissed as biologically irrelevant. Thus, although microsatellites can provide a powerful tool to study genetic structure in wild populations, they should be used in conjunction with a range of other sources of information, rather than as a replacement