During the first iteration of the agglomerative process, clades are reduced to a single taxon, so that for any of the O(n) pairs of such trivial connected component C A and C B, the values N mft +(C A, C B ) and N mft −(C A, C B ) correspond to the creation of new triplets AB|X, where A and B are fixed taxa and where X can take n − 2 label values.
Assessing the topological performance for the lineage model presents a significant challenge due to two related issues: that the number of taxa is not fixed and that the taxa themselves are not uniquely identifiable.
Accordingly, the ancestor of Trachypithecus, Semnopithecus and T. [ pileatus] carried multiple DNA lineages with one lineage being randomly fixed in two taxa, but not in the third.
In small hybridizing populations, mtDNA might sometimes get fixed into foreign taxa via drift or founder effects, even with little or no gene flow at nuclear loci [ 31].
Additional analyses (not shown) that included incomplete taxa (formalin-fixed human case samples) did not alter tree topology but decreased nonparametric bootstrap proportions for nodes, including formalin-fixed taxa.
However, high-order (partial) correlation has the advantage over pairwise correlation, because it measures the conditional dependency between two taxa given the effect of other taxa being removed or fixed, and reflects direct correlation between taxa and excludes the between-taxon dependency due to other taxa.
Because ESPs have been discovered only recently [66], [67], it is not yet known whether any of them show fixed differences between rodent taxa.
The physically unlinked centromeric regions on all three chromosomes of these closely related taxa contain fixed nucleotide differences which have been found in nearly complete linkage disequilibrium in geographic areas of no or low M-S hybridization.
Values of median relative error and median relative HPD range are plotted against the number of loci, where the number of taxa is fixed to 15.
Specific classes of these conserved elements seem to have been generated before the divergence of taxa and fixed during the process of evolution.
As the modes of action of the genes involved in domestication and the metabolic pathways leading to particular phenotypes become better understood, it should be possible to determine whether similar phenotypes have similar underlying genetic controls, or whether human selection in genetically related but independently domesticated taxa has fixed different mutants with similar phenotypic effects.
