Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

BMC Evolutionary Biology

Thomas J Near⁴  Matt Friedman³  Jeffrey P Townsend²  Alex Dornburg¹ 

[1] Department of Ecology and Evolutionary Biology, Yale University, New Haven 06520, Connecticut, USA;Program in Computational Biology and Bioinformatics, Yale University, New Haven 06510, Connecticut, USA;Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK;Yale Peabody Museum of Natural History, New Haven 06520, Connecticut, USA

关键词: Homoplasy;    Nucleotide Saturation;    Actinopterygii;    Molecular clock;   

Others  :  1118028
DOI  :  10.1186/s12862-014-0169-0

 received in 2014-04-03, accepted in 2014-07-21,  发布年份 2014

【 摘 要 】

Background

Discordance among individual molecular age estimates, or between molecular age estimates and the fossil record, is observed in many clades across the Tree of Life. This discordance is attributed to a variety of variables including calibration age uncertainty, calibration placement, nucleotide substitution rate heterogeneity, or the specified molecular clock model. However, the impact of changes in phylogenetic informativeness of individual genes over time on phylogenetic inferences is rarely analyzed. Using nuclear and mitochondrial sequence data for ray-finned fishes (Actinopterygii) as an example, we extend the utility of phylogenetic informativeness profiles to predict the time intervals when nucleotide substitution saturation results in discordance among molecular ages estimated.

Results

We demonstrate that even with identical calibration regimes and molecular clock methods, mitochondrial based molecular age estimates are systematically older than those estimated from nuclear sequences. This discordance is most severe for highly nested nodes corresponding to more recent (i.e., Jurassic-Recent) divergences. By removing data deemed saturated, we reconcile the competing age estimates and highlight that the older mtDNA based ages were driven by nucleotide saturation.

Conclusions

Homoplasious site patterns in a DNA sequence alignment can systematically bias molecular divergence time estimates. Our study demonstrates that PI profiles can provide a non-arbitrary criterion for data exclusion to mitigate the influence of homoplasy on time calibrated branch length estimates. Analyses of actinopterygian molecular clocks demonstrate that scrutiny of the time scale on which sequence data is informative is a fundamental, but generally overlooked, step in molecular divergence time estimation.

【 授权许可】

   
2014 Dornburg et al.; licensee BioMed Central Ltd.

【 图 表 】

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