Branch models were used to test for significant differences in dN/dS between the bottlenose dolphin and the cow (divergence c. 50 my), between the elephant and the hyrax (divergence c. 80 mya), and between humans and the bushbaby (chosen to provide a similar branch length, divergence c. 80 mya).
Once the two pollinator species differ in tongue length, divergence in corolla-tube depth between the two plant species ensues.
The AlexSys (Aniba et al., 2010) strategy is built on this approach and combines features measured on the unaligned sequences (length, divergence, etc).
The exon-increase model involves more in the variation of existed exons/introns, e.g., their length, divergence and GC content, but less in their gain and loss.
However, it should be noted that the power of LRT is affected by sequence length, divergence and number of species [ 28] and may lead to a lower power in our case.
In ants telomere length divergence between sexes seems to start earlier and the difference in lifespan and telomere length between males and females is more pronounced than in mammals.
However, in contrast to mammals, where these patterns are established in the course of extra-uterine life (Okuda et al., 2002; Cherif et al., 2003), telomere length divergence appears to already have taken place during early larval development in ants.
As a first surprise, ITS2 proved to be well alignable across the entire order due to its high structural conservation and low sequence length divergence, and thus allowed reconstructions of the phylogenetic branching pattern even above the level of the sampled families.
Given that most of the variation in the molecular mass of SvsII is presumably produced through insertions and deletions, this was so far the only evidence suggesting that indels may explain adaptive length divergence in reproductive proteins under scenarios of sperm competition.
In addition to codon frequencies, we also have to fix or choose ranges of other parameters for the simulation, including sequence length, divergence time (t), two ratios of transitional rate between purines (κR) and between pyrimidines (κY) to transversional rate, and selective pressure ω.
