Our data mining and filtering process retrieved 73 putative nuclear single-copy genes which are potentially useful for resolving phylogenetic relationships at a range of divergence depths within Cornales.
Prada, C. & Hellberg, M. E. Long prereproductive selection and divergence by depth in a Caribbean candelabrum coral.
Ingram [ 10] showed evidence that rockfish speciation is associated with the divergence of habitat depth and depth-related morphology, which supports that this group of fishes are undergoing ecological speciation along an environmental gradient.
In this study, we demonstrate that the previously described genetic partitioning of S. hystrix across depth-related habitats (rather than geographic locations) reflects a process of adaptive divergence along a depth gradient [ 27].
When we fix the proboscis length of pollinators (proboscis length is assigned to individuals at random, independently of the proboscis length of their parents, using the same probability distribution at each generation), there is absolutely no divergence in the depth of corolla tubes following 10000 generations (Fig. 4A).
This study confirms that the observed habitat partitioning of S. hystrix (and associated Symbiodinium) is reflective of adaptive divergence along a depth gradient.
GC content, read length and damage all had significant impacts on the proportion of read pools able to be mapped back to their reference at both levels of divergence, while coverage depth was not significantly correlated for either low or high divergence read pool mapping (Table 1).
In our comparative study within Ensatina, while we find a good qualitative agreement between mitochondrial and nuclear markers (i.e. major mtDNA lineages encompass distinct nDNA genetic clusters), we also find a quantitative disagreement in the depth of genetic divergence across pairs of populations.
Increasing the number of "pollen parcels" from two to ten, while keeping all other parameter values fixed, interferes with the divergence of corolla depths between the two plant species.
Particularly, given the strongly localised dispersal of S. hystrix [ 26], the selection-driven partitioning of ecotypes across habitats would result in assortative mating (i.e., mating with neighbours), which may drive and/or strengthen the genetic divergence of the depth-associated populations.
