Journal
SIAM JOURNAL ON APPLIED ALGEBRA AND GEOMETRY
Volume 3, Issue 1, Pages 107-127Publisher
SIAM PUBLICATIONS
DOI: 10.1137/18M1194134
Keywords
distance-based methods; multispecies coalescent; mixture models; general time-reversible model; quadratic forms
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Funding
- National Institutes of Health under the Joint DMS/NIGMS Initiative to Support Research at the Interface of the Biological and Mathematical Sciences [R01 GM117590]
- Mathematical Biosciences Institute
- National Science Foundation [DMS-1440386]
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The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple nonmixture models of sequence evolution. Here we prove that the log-det distance, coupled with a distance-based tree construction method, also permits consistent inference of species trees under mixture models appropriate to aligned genomic-scale sequences data. Data may include sites from many genetic loci, which evolved on different gene trees due to incomplete lineage sorting on an ultrametric species tree, with different time-reversible substitution processes. The simplicity and speed of distance-based inference suggest log-det-based methods should serve as benchmarks for judging more elaborate and computationally intensive species trees inference methods.
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