november, 2019

12nov1:00 pm2:00 pmPhylogenetic incongruences - opportunities to improve the reconstruction of a dated tree of lifeDR Dominik Schrempf


Event Details


The increasing amount of sequence data that has recently become available has not brought relief to many questions in evolutionary biology but instead has highlighted the complex and ambivalent histories of genes. It is long known that gene trees are not species trees, but the effect of processes such as Incomplete Lineage Sorting (ILS), gene Duplication and Loss (DL) and Horizontal Gene Transfer (HGT) on phylogenetic inference has been underestimated.We focus our attention on these processes causing incongruence. After all,the strength of ILS is proportional to the population size; the timing of DL can provide information about the evolution of gene functions or pathways; and HGT only occurs between co-existing species and, hence, gives indication about the order of speciation events and the position of the root.We plan to perform joint inference in the presence of ILS, DL and HGT using a hierarchical model. On the top level, species form and decay according to a linear birth and death process. The resulting species tree which includes extinct species acts as a constraint for genes that develop in populations, are duplicated,lost or transferred. For this combined model, we aim to derive the likelihood of specific parameters given data and, consequently, develop an MCMC sampler to perform Bayesian parameter inference.We hope that modeling incongruences helps resolve, e.g., the timing of microbial evolution and its relationship to Earth history, where dating methods are limited by the paucity of fossils; or the position of eukaryotes among archaea.

If you like to meet with Dominik please contact Carolin Kosiol.



(Tuesday) 1:00 pm - 2:00 pm


Dyer's Brae Seminar Room

Dyers Brae, School of Biology, University of St Andrews, St Andrews, Greenside Place, Fife, KY16 9TH, UK


Carolin Kosiol, Niki Khan, Miguel Barbosa, Nick Jones