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Allman, Elizabeth S.; Long, Colby; Rhodes, John A.

Species tree inference from genomic sequences using the log-det distance. (English) Zbl 1415.92127

SIAM J. Appl. Algebra Geom. 3, No. 1, 107-127 (2019).
Summary: 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.

Cited in 5 Documents

MSC:

92D15 Problems related to evolution
92D20 Protein sequences, DNA sequences
62P10 Applications of statistics to biology and medical sciences; meta analysis

Keywords:

distance-based methods; multispecies coalescent; mixture models; general time-reversible model; quadratic forms

Software:

MrBayes; ASTRAL-II; SVDquartets; ASTRID; STEM-hy
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Full Text: DOI arXiv

References:

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