Divergent bit scores were re-evaluated by comparing them to other fungal vs. animal/plant scores to exclude divergences only proper to the two fungi initially considered.
Moreover, demographic inference based on genetic data supplements morphological records in the quest towards understanding the natural history of organisms on deeper time scales [eg. [ 6] and can aid in discriminating between different scenarios of population differentiation and speciation, for instance, between speciation models including or excluding post-divergence gene-flow [ 7, 8].
When SNPs that are observed in human populations were excluded, the divergence was significantly reduced (ranging from 0.002 to 0.022 and averaging 0.0112), especially within the region that showed high nucleotide diversity in humans (Fig. 2D).
The outlier Pinus uncinata sample (UN2), defined based on PCoA analysis, was excluded from divergence estimates in UPGMA and the species genetic differentiation analysis.
The distribution of the mass probability of the divergence time posterior density suggests that the Quechua and the Shimaa populations diverged recently: If the point estimate appears implausible, the upper limit of the 90% density interval excludes a divergence older than 5300 years ago.
Given such a history we should expect a level of sequence divergence of 1.3 1.6% [ 23]; in fact between these repeats we observe 1.1% sequence divergence (excluding indels).
However, in this note we show that for the case of cubic symmetry this form of the Green's function contains strong divergences, excluding possibilities of direct application of well-known numerical schemes.
In marine plants (excluding phytoplankton), adaptive phenotypic divergence at the population level was mainly studied with respect to temperature regimes (Table 2), either in common garden or in reciprocal transplant designs.
Interestingly, variations in these three properties were interrelated in that divergence in one excludes the need for divergence in the other two but they are not directly predictive of each other.
Divergence could be estimated for 489 proviral LTRrs, 239 solo-LTRs, and 10 unclassified LTRrs (Dataset S1); the remaining 307 copies were excluded from the divergence analysis due to ambiguous alignments.
