In general, sex-linked genes are expected to contribute progressively more to heritable differences between taxa as time passes because initial selection on standing genetic variation favours divergence on autosomes [26], whereas divergence due to new mutations will be biased towards sex chromosomes [4], [7], and this divergence accumulates over time.
This will determine the timescales over which the models can reliably detect random variation in divergence times and avoid spurious inference of clustered divergence models.
The overall differentiation between these sympatric divergent haplotypes involves two likely sources of variation: (i) divergence which already existed within the common ancestral populations; (ii) divergent haplotypes originating from previously isolated lineages [ 19].
The modifications also improve the method's power to detect random variation in divergence times, reducing the tendency to estimate clustered divergences.
If two, recently diverged clades are now genetically isolated but share retained ancestral variation, their divergence and genetic isolation follow a continuum and no single percentage is going to work in all cases.
Of eight taxa examined through phylogeographic analyses, five species showed acute genetic variation and divergence in mitochondrial sequences.
Median joining haplotype networks constructed for both captive and free-ranging white-tailed deer revealed extensive mitochondrial haplotype variation and divergence (Figure 2).
Although the degrees of intraspecific variation and divergence between closely related species have been investigated by some authors (e.g. 7.93% between and 0.43% within bird species for COI [33]; 5.7% between and 1.5% within Stenella species for cyt b [22]), these are generally poorly studied.
DNA variation and divergence at sequenced loci for the laboratory strains.
MEGA 2.0 [ 53] was used to determine nucleotide variation and divergence values.
