Besides, a fragment of the cpr gene, a locus involved in metabolic insecticide resistance and odorant clearance in insects, was used to analyze the divergence between An. cruzii populations from south and southeast Brazil (Florianópolis SC, Cananéia and Juquitiba SP, Itatiaia RJ, Santa Teresa ES).
We did not intensively analyze the divergence between humans and cynomolgus monkeys, because a study on rhesus genome has investigated this thoroughly [ 5]; it also identified and discussed positively selected genes or extensively duplicated genomic regions during the evolution of Catarrhine primates.
We analyzed the divergence time between the two lineages with a coalescent-based approach using the program MDIV [ 59].
In this study, we analyzed the divergence of transcriptome sequence between the two aphid species, and similar genes/pathways were identified to be involved in the divergence of two aphid species through both comparative transcriptomic analysis and Ka/Ks analysis.
We analyzed the profile divergence between partly assembled data and simulated short read data for a human gut sample (Kurokawa et al., 2007) where we compared Taxy with WebCARMA (Gerlach et al., 2009) and the NBC web server tool (Rosen et al., 2011) on phylum level (see Supplementary Material).
The results were used to analyze the functional divergence between each pair of clades and to infer the functional variation of amino acid sites among the distinct OR subfamilies using the method of Gu [ 29].
For dating the insertion events of the autonomous and nonautonomous Fatima elements, we analyzed the nucleotide divergence rate between two LTRs in the case when both LTRs were present in the elements' structure.
In order to obtain meaningful estimates of dN and dS on the scale of individual genes by cross-species comparison, the divergence between the analyzed species should not be too low.
The reason is as follows: initially we intended to analyze the sequence divergence patterns between the orthologous coding regions of human, chimpanzee, and rhesus monkey.
We also analyzed the relationship between various characteristics of postzygotic reproductive isolation and genetic divergence.
