From a theoretical point of view, two main factors may bias our intraspecific assessment of COI divergence: disequilibrium in the representation of some taxa or incorrect taxonomic classification (i.e., cryptic (morphological indistinguishable, but genetically distinct), or non-monophyletic species).
We performed a global assessment of the divergence distributions, phylogenies, and consensus sequences of CR1 repeats in the chicken genome.
Likewise, the assessment of population divergence will be complicated since the sample size (sequencing coverage) available for allele frequency estimation varies among loci.
Hence, our data do not allow an accurate assessment of the divergence time between red and arctic foxes - the focus of this paper is on much more recent phylogeographic events within red foxes.
Furthermore, we made a detailed quantitative assessment of TCS divergence regarding the HisKA site (see Supplementary material, Figure S2) and performed various analyses about the different context in which TCS domains can occur.
Therefore, this analysis provides a large-scale and unbiased assessment of genome divergences and regional variations of substitution rates among cattle, dog and human.
This analysis provides a large-scale and unbiased assessment of genomic divergences and regional variation of substitution rates among cattle, dog and human.
The results presented here were concordant with this result, but also provided an assessment of patterns of divergence among geographic transects.
The common-garden study design employed in this study allows for assessment of parallelism in divergence for pairs of demes belonging to the same temperature regime.
These observations led them to propose that the MMR system is involved in the assessment of the degree of divergence when heteroduplex DNA is formed.
