Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data.
Understanding when species diverged aids in identifying the drivers of speciation, but the end of gene flow between populations can be difficult to ascertain from genetic data. We explore the use of pairwise sequential Markovian coalescent (PSMC) modelling to infer the timing of divergence between species and populations. PSMC plots generated using artificial hybrid genomes show rapid increases in effective population size at the time when the two parent lineages diverge, and this approach has been used previously to infer divergence between human lineages. We show that, even without high coverage or phased input data, PSMC can detect the end of significant gene flow between populations by comparing the PSMC output from artificial hybrids to the output of simulations with known demographic histories. We then apply PSMC to detect divergence times among lineages within two real datasets: great apes and bears within the genus Ursus Our results confirm most previously proposed divergence times for these lineages, and suggest that gene flow between recently diverged lineages may have been common among bears and great apes, including up to one million years of continued gene flow between chimpanzees and bonobos after the formation of the Congo River.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95060, USA.
James A
0000-0002-7145-0215
JA
Cahill
Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95060, USA.
André E R
0000-0002-7768-2199
AE
Soares
Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95060, USA.
Richard E
RE
Green
Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95060, USA bashapir@ucsc.edu.
Beth
0000-0002-2733-7776
B
Shapiro
D000818:Animals; D019143:Evolution, Molecular; D051456:Gene Flow; D049810:Genetic Speciation; D016678:Genome; D015186:Hominidae / Q000235:genetics*; D006801:Humans; D008390:Markov Chains; D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D001503:Ursidae / Q000235:genetics*
PSMC; bears; great apes; species divergence