CALIBRATING DIVERGENCE TIMES ON SPECIES TREES VERSUS GENE TREES: IMPLICATIONS FOR SPECIATION HISTORY OF APHELOCOMA JAYS

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 coup...

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Bibliographic Details
Published in:Evolution 2011-01, Vol.65 (1), p.184-202
Main Authors: McCormack, John E., Heled, Joseph, Delaney, Kathleen S., Peterson, A. Townsend, Knowles, L. Lacey
Format: Article
Language:English
Subjects:
Animals
Aphelocoma
BEAST
Biogeography
Biological Evolution
Biological taxonomies
Birds
Calibration
Cell Nucleus - genetics
Central America
divergence times
Divergent evolution
DNA, Mitochondrial - genetics
Estimated taxes
fossil calibration
Fossils
Gene Flow
gene tree
Genes
Genetic Speciation
Genetic Variation
Geological Phenomena
glaciations
Mexico
Mitochondrial DNA
Molecules
mountain uplift
Phylogenetics
Phylogeny
Pleistocene
Sequence Alignment
Sequence Analysis, DNA
Songbirds - classification
Songbirds - genetics
Speciation
species tree
Stochastic models
Trees
United States
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Summary: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 Plesitocene, 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.
ISSN:0014-3820
1558-5646
DOI:10.1111/j.1558-5646.2010.01097.x