Motivating our study was the hypothesis that the genes important for interaction with the host, e.g., those encoding the T3SS and in particular the effector proteins, which are translocated across the eukaryotic cell membrane and into the host cell cytoplasm [7], might be driving divergence, similar to the genes determining beak morphology in Darwin's finches.
Niche modeling suggests that the absence of each lineage in the distribution gap correlates with ecological variables and therefore suggests that not only do the two lineages inhabit different habitats but there might be ecological divergence between the lineages.
We then analyzed the motifs contained in the cIRK1 5'-flanking region, based on the presumption that there might be significant divergence between chicken and mammal IRK1/Kir2.1 promoter regions that could account for their different gene expression patterns.
One possible explanation for this stark difference in evolutionary conservation might be the early divergence of T. brucei from other eukaryotes.
The differences might be attributable to divergence in the levels of these cell cycle regulators in different cell lines.
One explanation why molecular data do not support a monophyly of H. pelagica (Table 3) might be a deep divergence followed by a rapid radiation.
This suggests that homologous recombination might be reducing the divergence of repC, potentially also explaining the low CAI values for this gene (homologous recombination would be erasing any improvement in the CAI values).
Concordantly, antennae of both male and female E. dilemma are more sensitive to HNDB than those of E. viridissima suggesting that behavioral differences might be based on divergence in the antennal periphery ([ 27]; T. Eltz, unpublished).
Finally more intensive population sampling in the southern genetic clusters could reveal ecological differences between them and help to discover local adaptations that might be involved in divergence between lineages.
We measured several population genetic parameters that can help to distinguish between the various forces, including demographic and selective pressures, that might be influencing genetic divergence in this species complex.
