Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks.
OBJECTIVE
There is extensive variation in substitution rates among metazoan mitochondrial genomes, including differences among lineages and among sites. Differences in substitution rates among lineages are routinely taken into account in molecular phylogenetic and dating analyses. However, this is rarely the case for differences in the lineage-specific patterns of rate variation among sites.


METHODS
We analysed an alignment of 32 cetacean mitogenomes using a partitioned relaxed-clock approach, in which a separate relaxed-clock model was applied to each of the three codon positions of the protein-coding genes.


RESULTS
By comparing Bayes factors, we found overwhelming support for this model compared with a strict-clock model and less-complex models comprising fewer relaxed clocks. Our analyses reveal the presence of substantial rate heterogeneity among cetacean lineages, and that these patterns of variation differ between codon positions. However, we find no evidence of mitochondrial rate autocorrelation throughout the cetacean phylogeny.


CONCLUSIONS
Our study confirms the feasibility of applying a partitioned relaxed-clock model to mitogenomic data, and suggests that molecular phylogenetic and dating analyses may be improved by the application of these models.
Ho
Simon Y W
SY
Research School of Biology, Centre for Macroevolution and Macroecology, Australian National University, Canberra, ACT, 0200, Australia. simon.ho@sydney.edu.au
Lanfear
Robert
R
D000818:Animals; D001499:Bayes Theorem; D002591:Cetacea / Q000235:genetics*; D003062:Codon; D004272:DNA, Mitochondrial / Q000235:genetics*; D016678:Genome
D003062:Codon; D004272:DNA, Mitochondrial