Recent perspectives focus on the two-way interplay between vegetation and hillslope geomorphology, where establishing cause-and-effect linkages is made difficult by confounding factors (spatial temporal scale, location, convergence, divergence, nonlinearity, thresholds, feedbacks).
I propose a new method for inferring the location of divergence points in phylogenies.
The location of divergence between VSGs is consistent with selection for strain-specific VSG repertoires, possibly to allow superinfection of an animal by a second strain.
The fifth column shows the average location of divergence times when they are represented as a fraction between 0 and 1, 1 being the weak end and 0 the strong end.
The location of divergence between VSG homologues was not random but was more prevalent in positions consistent with selection for the production of antigenically novel VSGs and thus strain-specific VSG repertoires.
In some locations the divergence from the long-term average has been an eye-watering 20C.
The wheat - barley synteny at the RAR1 locus together with the observation that the B. distachyon RAR1 copy is located on chromosome 3 (BrAdditional.1; Additional file 1: Table S1), which is syntenic with rice chromosome 2, suggests that the RAR1 locus change in chromosomes location occurred after divergence between B. distachyon and wheat, but before the wheat barley divergence.
The precise location of the divergence point along the branch is poorly estimated, but the selected branch is highly supported.
As humans and rodents shared a more recent common ancestor than either humans and dogs, or humans and chickens, it thus appears likely that one or more PRAME genes were translocated into this genomic location after the divergence with the Laurasiatherian lineage containing extant carnivores (approximately 95 MYA), but before the rodent-primate split (approximately 85 MYA) [ 26].
Our finding that 37% of maize genes supported by full-length cDNA are not retained at a syntenic position in other grass species, and almost 50% of cDNA supported genes apparently inserted into their present locations prior to divergence of the BEP clade, represented by both rice and brachypodium, is in agreement with previous studies.
