Bias-corrected paralinear and LogDet distances and tests of molecular clocks and phylogenies under nonstationary nucleotide frequencies

Molecular Biology and Evolution
X Gu, W H Li

Abstract

The statistical properties of the paralinear and LogDet distances under nonstationary nucleotide frequencies were studied. First, we developed formulas for correcting the estimation biases of the paralinear and LogDet distances, i.e., the bias-corrected distance is estimated by dc = d - 2var(d), where d and var(d) are the estimated distance and sampling variance, respectively. The performances of these formulas and the formulas for sampling variances were examined by computer simulation. Second, we developed a method for estimating the variance-covariance matrix of paralinear distances, so that statistical tests of DNA phylogenies can be conducted in the nonstationary case. Third, a new LogDet-based method for testing the molecular clock hypothesis was developed under nonstationary nucleotide frequencies.

Citations

May 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·X Gu, W H Li
Nov 13, 2015·Systematic Biology·Jesús Fernández-Sánchez, Marta Casanellas
May 9, 2001·Molecular Phylogenetics and Evolution·G M Plunkett, P P Lowry
Dec 17, 2014·Systematic Biology·Benjamin D KaehlerGavin A Huttley
May 18, 1999·Theoretical Population Biology·E Baake, A von Haeseler
Sep 25, 2002·Molecular Biology and Evolution·Koichiro Tamura, Sudhir Kumar
Nov 9, 2000·Molecular Biology and Evolution·F Rodríguez-TrellesF J Ayala
Jul 9, 2004·Molecular Biology and Evolution·Tomoaki NishiyamaMitsuyasu Hasebe
Feb 25, 2003·Molecular Biology and Evolution·Naoko TakezakiJan Klein
Feb 13, 2021·NAR Genomics and Bioinformatics·Lars S JermiinBarbara R Holland

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