Often phylogenetic studies recover basal divergences and exclusive groupings of lamprey sequences with long branches.
Our phylogenetic analyses revealed some topological differences between the phylogenies of the bacteria and their vectors, which led us to marginally reject a model of exclusive bacteria-vector co-divergence.
Our analyses also revealed that, although there is clearly congruence between the bacteria and vector/host trees, a model of exclusive bacteria-vector co-divergence can be rejected, albeit marginally.
These data support the idea that the paddlefish duplication is exclusive, and occurred after their divergence from sturgeon.
Several non-mutually exclusive processes can facilitate phenotypic divergence of castes, including caste-specific gene expression, alternative splicing, methylation and gene duplication.
Such a divergence is not exclusive to the ethylene receptors; the phytochromes of higher plants also originated from an ancestral His kinase but have now diverged so substantially that they completely lack His kinase activity (reviewed in Rockwell et al. 2006).
A second, non-mutually exclusive explanation for the evolutionary divergence in the requirement for Cdo/Ihog proteins is that, even though all family members bind Hh ligands and promote pathway activity, Cdo and Boc might function somewhat differently than Ihog and Boi.
My major comment concerning data analysis is towards the exclusive use of D. miranda for calculating divergence levels in Figure 1.
Differential introgression of loci across the genome between species due to hybridization is possible and common; gene flow and species divergence are not always mutually exclusive trajectories [ 89, 90, 94].
Moreover, we find consistent patterns of genomic divergence across sampling sites and mutually exclusive clustering of M and S populations using genetic distances based on all 400,000 SNPs, implying that M and S are evolving collectively across the study area.
