title: Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays.
abstract: Estimates of the timing of divergence are central to testing the underlying causes of speciation. Relaxed molecular clocks and fossil calibration have improved these estimates; however, these advances are implemented in the context of gene trees, which can overestimate divergence times. Here we couple recent innovations for dating speciation events with the analytical power of species trees, where multilocus data are considered in a coalescent context. Divergence times are estimated in the bird genus Aphelocoma to test whether speciation in these jays coincided with mountain uplift or glacial cycles. Gene trees and species trees show general agreement that diversification began in the Miocene amid mountain uplift. However, dates from the multilocus species tree are more recent, occurring predominately in the Pleistocene, consistent with theory that divergence times can be significantly overestimated with gene-tree based approaches that do not correct for genetic divergence that predates speciation. In addition to coalescent stochasticity, Haldane's rule could account for some differences in timing estimates between mitochondrial DNA and nuclear genes. By incorporating a fossil calibration applied to the species tree, in addition to the process of gene lineage coalescence, the present approach provides a more biologically realistic framework for dating speciation events, and hence for testing the links between diversification and specific biogeographic and geologic events.
authors.affiliation: Museum of Zoology, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA. jmccormack@lsu.edu
authors.forename: John E
authors.initials: JE
authors.lastname: McCormack
authors.forename: Joseph
authors.initials: J
authors.lastname: Heled
authors.forename: Kathleen S
authors.initials: KS
authors.lastname: Delaney
authors.forename: A Townsend
authors.initials: AT
authors.lastname: Peterson
authors.forename: L Lacey
authors.initials: LL
authors.lastname: Knowles
mesh_terms: D000818:Animals; D005075:Biological Evolution; D002467:Cell Nucleus / Q000235:genetics; D002489:Central America; D004272:DNA, Mitochondrial / Q000235:genetics; D005580:Fossils; D051456:Gene Flow; D049810:Genetic Speciation; D014644:Genetic Variation; D055593:Geological Phenomena; D008800:Mexico; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D020308:Songbirds / Q000145:classification / Q000235:genetics*; D014481:United States
chemical_list: D004272:DNA, Mitochondrial