Alexei’s research interests are centered around probabilistic models of molecular evolution and population genetics.
“Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins.” Systematic Biology 66 (1): 57–73.
Many of our divergence-time estimates for major clades coincide well with both the known fossil record and with previous estimates.
However, our estimates for the origin of crown-clade angiosperms, which center on the Late Triassic, are considerably older than the unequivocal fossil record of flowering plants or than the molecular dates presented in recent studies.
“Inferring Ancestral Recombination Graphs from Bacterial Genomic Data.” Genetics 205 (2): 857–70.
“The Space of Ultrametric Phylogenetic Trees.” Journal of Theoretical Biology 403 (August): 197–208.
We present Clocksta R, a method for selecting the number of relaxed clocks for multigene datasets.
2016 "Bayesian inference of ancestral recombination grpahs for bacterial populations" bio Rxiv Ogilvie, Huw A., Joseph Heled, Dong Xie, and Alexei J. However, most datasets exhibit significant levels of rate variation among lineages.This can be caused by differences in population size, mutation rate or the strength of natural selection. “Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods.” Systematic Biology 65 (3): 381–96. Vaughan, Alex Gavryushkin, Stephane Guindon, Denise Kühnert, Gabriel E.