Journal article
Linking branch lengths across sets of loci provides the highest statistical support for phylogenetic inference
DA Duchêne, KJ Tong, CSP Foster, S Duchêne, R Lanfear, SYW Ho
Molecular Biology and Evolution | OXFORD UNIV PRESS | Published : 2020
Abstract
Evolution leaves heterogeneous patterns of nucleotide variation across the genome, with different loci subject to varying degrees of mutation, selection, and drift. In phylogenetics, the potential impacts of partitioning sequence data for the assignment of substitution models are well appreciated. In contrast, the treatment of branch lengths has received far less attention. In this study, we examined the effects of linking and unlinking branch-length parameters across loci or subsets of loci. By analyzing a range of empirical data sets, we find consistent support for a model in which branch lengths are proportionate between subsets of loci: gene trees share the same pattern of branch lengths..
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Awarded by Australian Research Council
Funding Acknowledgements
This work was supported by funding from the Australian Research Council to D.A.D. (grant DE190100544), S.D. (grant DE190100805), and S.Y.W.H. (grant DP160104173). S.D. was also supported by a McKenzie Fellowship from the University of Melbourne. The authors acknowledge the Sydney Informatics Hub and the University of Sydney's high-performance computing cluster Artemis for providing the high-performance computing resources that have contributed to the research results reported in this paper. The authors thank Tal Pupko, two anonymous reviewers, and the editor for constructive comments on previous versions of the manuscript.