Grouping substitution types into different relaxed molecular clocks.
Different types of nucleotide substitutions experience different patterns of rate change over time. We propose clustering context-dependent (or context-independent) nucleotide substitution types according to how their rates change and then using the grouping for divergence time estimation. With our models, relative rates among types that are in the same group are fixed, whereas absolute rates of the types within a group change over time according to a shared relaxed molecular clock. We illustrate our procedure by analysing a 0.15 Mb intergenic region to infer divergence times relating eight primates. The different groupings of substitution types that we explore have little effect on the posterior means of divergence times, but the widths of the credibility intervals decrease as the number of groups increases.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA hlee12@ncsu.edu.
Hui-Jie
HJ
Lee
Laboratory of Biometrics and Bioinformatics, University of Tokyo, Tokyo, Japan.
Hirohisa
H
Kishino
Department of Biology, Institute of Biochemistry, and School of Mathematics and Statistics, Carleton University, Ottawa, Ontario, Canada.
Nicolas
N
Rodrigue
Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA.
Jeffrey L
0000-0003-3779-5743
JL
Thorne
D000818:Animals; D021901:DNA, Intergenic / Q000235:genetics*; D019143:Evolution, Molecular; D008957:Models, Genetic; D010802:Phylogeny; D011323:Primates / Q000235:genetics*; D013995:Time
D021901:DNA, Intergenic
CpG transition rate; context-dependent substitution; divergence time estimation; relaxed molecular clock