PMC

Divergence Distance Estimation. Divergences estimated from tool alignments are overestimated at short divergence distances and underestimated at large divergence distances while divergences estimated from true simulated alignments are accurate to large divergence distances. A: Mean divergence distance estimated from simulated alignments and tool alignments for four species trees was measured as a function of total true divergence distance. B: Mean divergence estimation error (Estimate – True/True) for four species trees was measured as a function of total true divergence distance. C: Divergence estimation error from tool alignments is not correlated with alignment error. Mean divergence estimation error for four species trees was measured as a function of mean alignment error. D: Divergence estimation error varies across branches in a tree and is best for leaf-to-leaf alignments and worst for node-to-node alignments. Mean divergence estimation error along branches of equal true divergence from two, three and four species Mlagan alignments was measured as a function of true divergence distance.

(A) Neutral human-chimp divergence is negatively correlated with functional content. (B) Neutral human-orang divergence is negatively correlated with functional content. (C) Neutral human-chimp divergence is positively correlated with human recombination rate. (D) Neutral human-orang divergence is positively correlated with human recombination rate. Each point represents the mean divergence and functional content (A and B) or recombination rate (C and D) in 1% of the 100kb windows binned by functional content or recombination rate. Red lines indicate the loess curves fit to divergence and functional content (A and B) and divergence and recombination rate (C and D). The high variance of divergence at regions of low recombination rate is expected since the variance of divergence is inversely proportional to the recombination rate. Note that the last bin containing less than 1% of the windows was omitted from the plot. While the graph presents binned data, the correlations reported in the text are from the unbinned data.

For binning purposes, thresholds of divergence are set at a phenotypic score of 7 and at 5% genetic divergence. These thresholds partition the results into 4 bins: A) Populations diverging across both genetic and phenotypic thresholds, B) high phenotypic divergence with lower genetic divergence, C) high genetic divergence with lower phenotypic divergence, and D) populations whose divergences did not surpass thresholds. Comparisons are labeled and the labels correspond to case numbers in .

(A) Human-primate divergence versus functional content. (B) Human-primate divergence versus human recombination rate. (C) Human-rodent divergence versus functional content. (D) Human-rodent divergence versus McVicker’s B-values.