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Any impact of the last Glacial Maximum (21,000 years ago; [16]) would be apparent in genetic homogeneity over large areas (reflecting recent recolonisation) and/or the elimination of the genetic signatures of more ancient divergence events (because of extirpation of populations over wide areas).
The decrease in collinearity between classes reflects the more ancient divergence of the two classes.
Phylogenetic evidence suggests a much more ancient divergence of Peromyscus from laboratory mice (Mus) and rats (Rattus) than that separating latter two.
Thus, one may select genes that will perform best for the epoch of interest, whether for recent divergence times or for more ancient divergence times.
For example, under the IM model, the median Akaike weight reached 1.0 (100% support for the true model) at a sample size of n = 3 per population for models with more ancient divergence.
While the approach was sensitive enough for moderate divergence, it has been pointed out conserved gene order may be too strict for more ancient divergence [ 3], as inversion is another dominant force for the degeneration of CHSs.
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We therefore asked whether the TREx metric might be applied to more ancient divergences.
This evidence indicates that Tolypocladium peptaibiotic genes are not highly similar but are the products of more ancient divergences.
The slowly evolving proteins may reflect more ancient divergences, but the exclusion of fast-evolving proteins decreases the number of analysed amino-acid positions by a factor of two and the issue of dataset size is critical in plastid multi-gene phylogenetic studies [ 34].
For the divergence time τS, we used a log-uniform prior, thus assigning substantial probability to recent post-glaciation divergence while still allowing for more ancient divergent times.
Although in trees of life obtained from rRNAs or concatenated proteins and rooted between Bacteria and Archaea-Eukaryota Aquificales are found very close to the root of Bacteria, the divergence between Aquifex and Sulfurihydrogenibium should not be more ancient than the divergence of epsilon-Proteobacteria from other Proteobacteria.
Related(20)
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