Computational Phylogenetics Group

New paper by Silvestro et al on “Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors” in Syst Biol.

Abstract: New World Monkeys (NWM) (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Herein, we integrate paleontological and molecular evidence to assess the evolutionary dynamics of extinct and extant platyrrhines. We develop novel analytical frameworks to infer the evolution of body mass, changes in latitudinal ranges through time, and species diversification rates using a phylogenetic tree of living and fossil taxa. Our results show that platyrrhines originated 5–10 million years earlier than previously assumed, dating back to the Middle Eocene. The estimated ancestral platyrrhine was small—weighing 0.4 kg—and matched the size of their presumed African ancestors. As the three platyrrhine families diverged, we recover a rapid change in body mass range. During the Miocene Climatic Optimum, fossil diversity peaked and platyrrhines reached their widest latitudinal range, expanding as far South as Patagonia, favored by warm and humid climate and the lower elevation of the Andes. Finally, global cooling and aridification after the middle Miocene triggered a geographic contraction of NWM and increased their extinction rates. These results unveil the full evolutionary trajectory of an iconic and ecologically important radiation of monkeys and showcase the necessity of integrating fossil and molecular data for reliably estimating evolutionary rates and trends.

New paper by Ren et al on “Species divergence and maintenance of species cohesion of three closely related Primula species in the Qinghai–Tibet Plateau” published in J Biogeo.

Abstract: Aim: Understanding the relative roles of geography and ecology in driving speciation, population divergence and maintenance of species cohesion is of great interest to molecular ecology. Closely related species that are parapatrically distributed in mountainous areas provide an ideal model to evaluate these key issues, especially when genomic data are analyzed within a spatially and ecologically explicit context. Here, we used three closely related species of Primula that occur in the Himalayas, the Hengduan Mountains and north-east Qinghai–Tibet Plateau (QTP) to examine spatial and ecological effects on interspecific divergence and maintenance of species cohesion. Location: Himalayas, the Hengduan Mountains and north-east QTP. Methods: We used genomic data for 770 samples of the three species using double?digest restriction site?associated DNA (ddRAD) sequencing and combined approximate Bayesian computation (ABC) modeling, generalized linear mixed modeling (GLMM) and niche?based species distribution modeling (SDM). Results: The three species are clearly delimited by the RADseq data. Further ABC modeling indicates that Primula tibetica diverged first followed by a later divergence between Primula nutans and Primula fasciculata. The time frames of the divergences among the three species coincide with the uplifts of the Hengduan Mountains and the northern QTP during the late Miocene and Pliocene followed by a long period of founder events. SDMs indicate that the three species might have survived in different refugia during glaciations and came into secondary contact during the postglacial expansions but with no significant introgression. Finally, GLMM suggests that both the geographical and ecological factors play roles in population differentiation in P. fasciculata and P. tibetica, while for P. nutans, geography is the major driver of genomic variation. The different roles played by geographical and ecological factors in the three species may have affected the maintenance of species cohesion. Main conclusion: Our results provide insights of unprecedented details into the start and maintenance of interspecific divergence in the context of changing environments in mountains. Our findings highlight the significance of combining population genomics with environmental data when evaluating the effects of geography and ecology on interspecific divergence and maintenance of closely related species.

New paper by Rolland et al on the link between micro- and macro-evolution in clownfishes accepted in Proc R Soc B.

Abstract: The difference between rapid morphological evolutionary changes observed in populations and the long periods of stasis detected in the fossil record has raised a decades-long debate about the exact role played by intraspecific mechanisms at the interspecific level. Although they represent different scales of the same evolutionary process, micro- and macroevolution are rarely studied together and few empirical studies have compared the rates of evolution and the selective pressures between both scales. Here, we analyze morphological, genetic and ecological traits in clownfishes at different evolutionary scales and demonstrate that the tempo of molecular and morphological evolution at the species level can be, to some extent, predicted from parameters estimated below the species level, such as the effective population size or the rate of molecular evolution within population. We also show that similar codons in the gene of the rhodopsin RH1, a light-sensitive receptor protein, are under positive selection at the intra and interspecific scales, suggesting that similar selective pressures are acting at both levels.