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On the basis of the 21,419 cotton orthologous gene sets for G. raimondii, G. arboreum, and the two subgenomes each of G. hirsutum and G. barbadense, the synonymous divergence levels (Ks) for all four cotton species were calculated.
High divergence levels between the two copies of each trn might indicate duplication events followed by random loss and mutations in the anticodon.
Here, we show that sequence motifs, polymorphism levels, and divergence levels around a gene can be used to predict commonly imbalanced genes in a human data set.
High divergence levels could be detected among these homologous miRNA genes (Figure 3 and Figure 4).
Low divergence levels were observed (0.065%) also between Pachygrapsus maurus and P. marmoratus.
The consistence of divergence levels between the chromosomal and plasmid sequences strongly suggests the vertical inheritance nature of the plasmids.
This corresponds to the optimal divergence levels and so insures good accuracy of Bayesian prediction results reported here.
Pairwise molecular divergence levels among basins were converted to dates using Weir and Schluter's [47] estimate of 2.1% per Mya, averaged from 36 independent passeriform calibrations.
A second challenge for PHYLORPH was to provide phylogenetic markers (candidate SCPCH) able to resolve phylogenetic relationships at low divergence levels.
These datasets were manually curated to retain only sequences that corresponded to the divergence levels considered in the four experimental validations (i.e. E. alphitoides/E. quercicola in different populations in France, H. albidus/H.
Branch lengths were chosen to give a symmetric (unrooted) tree with silent divergence levels between maximum likelihood [63] and Nei-Gojobori (NG) [64] estimates (see Figure 2 legend for details).
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