These observations, along with the findings on large-scale genome reduction associated with gradual increase in genomic A+T-content and extensive chromosomal rearrangements between different strains, strongly suggest a stepwise diversification of Prochlorococcus strains, in course of their adaptive evolution.
Our analyses indicate that the ecotype-specific molecular signatures exhibited by P. marinus strains under study are not mere remnants of a continuous genetic drift, but a potential outcome of niche-oriented stepwise diversification of Prochlorococcus, orchestrated by an array of interplaying adaptive forces.
RAG1: recombination activating gene; FSGD: fish-specific whole-genome duplication event; MEDUSA: Modeling Evolutionary Diversification Using Stepwise AIC; Ma: million years ago; My: million years.
We used the R [ 70] module MEDUSA (modeling evolutionary diversification using stepwise AIC) [ 43] implemented in the GEIGER package [ 42] to estimate changes in the diversification rate based on the consensus chronogram attained from the BEAST [ 41] analysis.
One such model (Enquist et al. 2011) explains characteristic patterns of technological change, such as diversification and stepwise modification, in terms of dependencies between technologies, and therefore without assuming any specific learning mechanisms.
MEDUSA (Modeling Evolutionary Diversification Using Stepwise AIC), a recently developed comparative method that integrates taxonomic and phylogenetic information, allows exceptionally radiating clades to be identified on an incompletely sampled phylogeny [ 36, 37].
This involves the stepwise acquisition of cell diversification programs in both cell types, each of which leads to the generation of distinct subtypes, the subsequent matching of each motor pool with its cognate target muscle through topographical arrangement of their axonal projections, and finally a process that allows numerical matching of MN pool size to the size of the target muscle [ 1, 2].
MEDUSA detects, using a stepwise AIC approach, significant shifts of diversification rates across a given phylogeny by evaluating the fit of different pairwise birth-death models.
We also sought shifts in diversification rates using a stepwise birth-death model fitting approach based on the AIC implemented as MEDUSA in the R package GEIGER [ 65, 66].
It is thought that this habitat diversification occurred in a stepwise manner, where the ancestors of the group occupied solid wet substrate, followed by the invasion of the shore water intersection, and finally there was the diversification into the open-water habitats.
MEDUSA utilized a stepwise AIC approach to adding clade-wise diversification models Yule or birth-death to a tree until the decrease in AIC failed to exceed a set threshold, which was dependent on tree size.
