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It thus appeared that the inconsistent root height (red/arctic fox divergence time) only slightly impacted our time estimates for phylogeographic events within red foxes, which is likely in part due to our additional use of interior tip calibrations based on ancient DNA sequences from known-age fossil remains.
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After 1000 random permutations, the clade and nested clade distances (D c and D n ), the interior-tip distances (I-T c and I-T n ) were calculated.
Clade distances (Dc) and nested clade distances (Dn) were measured and interior and tip clade differences estimated.
Contrasts of interior versus tip clades within a nested clade strongly indicate contrasts of older versus younger clades.
ASUMZ, Arkansas State University Museum of Zoology; bp, basepairs; cox1, cytochrome oxidase 1; Dc, clade distance; Dn, nested clade distance; I-T, interior to tip; JFBM, John Ford Bell Museum; MVZ, Museum of Vertebrate Zoology NCAA, nested clade analysis; PF, past fragmentation; RE, range expansion; RGF, restricted gene flow.
When non-random associations of haplotypes with geography were detected, the geographic distribution of ancestral versus derived haplotypes (interior and tip haplotypes, respectively) was further explored to identify possible refugial areas and the directionality of previously detected demographic and spatial expansions.
GeoDis version 2.0 [ 89] was used to calculate (1) the clade distance Dc, which measures the average distance of haplotypes in a nested group from its geographical center, (2) the nested clade distance Dn, which measures how far a haplotype group is from the geographic center of other groups with which it is nested, and 3) the average Dc and Dn separating interior and tip groupings of haplotypes.
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