Although individual species show clear codon preferences, it has been recognized for more than 20 years that individual mammalian genes can have codon contents that diverge substantially from the average [11].
We used a significance threshold alpha value of 0.05 adjusted for the number of windows examined by Bonferroni correction to identify individual windows that diverged substantially from expectation.
But when heterogeneity was larger (τ=2.5 in scenarios B, D and E) then this method produced point estimates of the pooled log IRR that diverge substantially from their true values.
The draft plan suggested that hatchery fish that had "diverged substantially from the evolutionary lineage" of their wild counterparts would not be considered part of the population being considered for protection.
However, surprisingly, none of the D. pulex GNBP homologues are members, indicating that it is missing from the draft assembly, that it has been lost, or that it diverged substantially since the separation of these species.
Because eight of these ten tRNA introns lie at the same site within the anticodon loop, it is possible that they arose through proliferation of a founding intron in the Chlorokybus lineage (perhaps the trnG ucc) intron that is also found in Chaetosphaeridium mtDNA) and that they diverged substantially in sequence following their insertion in different tRNA genes.
The pairwise distance data (Fig. 6B) reveal that the OFC mutations are localized to regions of the protein that have diverged substantially between MSX1 and MSX2.
In addition, Stevison and Noor examined Drosophila species that have diverged substantially from D. melanogaster.
For the majority of these diversifications, it is clear from which LECA Rab they descended; however, we found a number of lineage-specific Rab types that have diverged substantially from their ancestors, making them difficult to place with one of the LECA Rabs.
In addition, the significance of a BLAST search depends on the length of the query sequence; therefore, short sequences are rarely matched to known genes [ 15], or these sequences may represent rapidly evolving parts of genes that have diverged substantially from their homologs [ 16].
