Abstract
BackgroundMany factors have been identified as correlates of the rate of molecular evolution, such as body size and generation length. Analysis of many molecular phylogenies has also revealed correlations between substitution rates and clade size, suggesting a link between rates of molecular evolution and the process of diversification. However, it is not known whether this relationship applies to all lineages and all sequences. Here, in order to investigate how widespread this phenomenon is, we investigate patterns of substitution in chloroplast genomes of the diverse angiosperm family Proteaceae. We used DNA sequences from six chloroplast genes (6278bp alignment with 62 taxa) to test for a correlation between diversification and the rate of substitutions.ResultsUsing phylogenetically-independent sister pairs, we show that species-rich lineages of Proteaceae tend to have significantly higher chloroplast substitution rates, for both synonymous and non-synonymous substitutions.ConclusionsWe show that the rate of molecular evolution in chloroplast genomes is correlated with net diversification rates in this large plant family. We discuss the possible causes of this relationship, including molecular evolution driving diversification, speciation increasing the rate of substitutions, or a third factor causing an indirect link between molecular and diversification rates. The link between the synonymous substitution rate and clade size is consistent with a role for the mutation rate of chloroplasts driving the speed of reproductive isolation. We find no significant differences in the ratio of non-synonymous to synonymous substitutions between lineages differing in net diversification rate, therefore we detect no signal of population size changes or alteration in selection pressures that might be causing this relationship.
Highlights
Many factors have been identified as correlates of the rate of molecular evolution, such as body size and generation length
Using a phylogenetic comparative analysis of sister pairs [34], we investigated the relationship between rates of molecular evolution and net diversification in chloroplast genes of the plant family Proteaceae
A model where every branch in the phylogeny had an independent rate of substitutions had a significantly higher likelihood than the constant rates model in all the rates estimations, and ω (P value < 0.01 for all tests; see Methods section), indicating that the rate of molecular evolution of the chloroplast genes analysed varies significantly between lineages of the family Proteaceae
Summary
Many factors have been identified as correlates of the rate of molecular evolution, such as body size and generation length. Analysis of many molecular phylogenies has revealed correlations between substitution rates and clade size, suggesting a link between rates of molecular evolution and the process of diversification. It is not known whether this relationship applies to all lineages and all sequences. One intriguing relationship that has been revealed through studies of branch lengths on molecular phylogenies is a link between the rate of molecular evolution and the net diversification rate. One study of a large number of phylogenies found a relationship between root-to -tip branch lengths and net diversification in around half of the phylogenies tested, but it is not clear whether this was due to low power or lack of a common trend [10].
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