First, the average amount of nucleotide variation in the exons exceeds that in the non-coding regions, based on the proportions of variable sites as well as the mean numbers of different nucleotides per site.
However, this assumption can be overly restrictive as proportions of variable sites may vary in different lineages [ 22, 54].
Multiple alignments with outgroups were conducted for each Y chromosomal amplicon and the proportions of variable sites varied among amplicons (11.33%-21.65%; Table 3).
Although it is possible to model changes in proportions of variable sites using branch length mixtures, these can be complex under some scenarios and thus problematic to identify (Matsen and Steel 2007; Gruenheit et al. 2008; Lartillot et al. 2009).
This is because different proportions of variable sites are generated using pre-defined partitions, where each partition is simulated on a tree with different branch lengths (zero branch lengths are used for invariable sites).
The H data set contains genes involved in translation including the rpo genes, which previously have been shown to exhibit nonconservative substitutions, indels, and increased proportions of variable sites in green algae (Lockhart et al. 2006).
