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Table 2 shows two alternatives based on divergence time estimates.
The earliest estimated dates of formation of the allopolyploids, based on divergence time analyses, were within the last 6 Ma.
Within Oryza, two early rapid diversification events were hypothesized based on divergence time estimates [ 13], involving two and three extant lineages, respectively.
Based on divergence time estimates from Pochon et al. [ 18], these divergences equate to an overall substitution rate of ~3.1-3.4×10-9 per site per year From the 2418 pairwise analyses, dN/dS could not be estimated in three instances because dS=0 (dN was also 0 in two cases).
These dates are somewhat older than those found by Sessa et al. [ 16] based on divergence time analysis using a plastid dataset, which indicated that D. carthusiana and D. cristata descended from a Eurasian species (the "D. semicristata" lineage) that had diverged from its closest relative ca. 10 Ma, with the polyploids having formed subsequent to that.
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Through these observations, we estimate that the duplication that generated DPY19L2 arose between 173 (Marsupilia) and 360 (Lissamphibia) MYA (based on divergence times in [ 32]).
Some phylogeographic evidence supports the latter scenario based on divergence times among three clades that date to the early to mid Pleistocene [ 55].
Branch lengths of angiosperms were assigned based on divergence times estimated by Wikström et al. (2001) using the bladj algorithm in PYLOCOM 4.2 (Webb et al. 2008).
These two lineages ('coastal' and 'interior') are thought to have diverged from each other anywhere from 1 to 4 million years ago (Ma) based on divergence times calibrated with a fossil and estimated molecular substitution rates [ 24].
Other time points are based on the divergence time estimated using the nuclear data from human populations (Green et al. 2006; Gutenkunst et al. 2009) and from human/Neanderthal (Green et al. 2006) comparisons, respectively.
The divergence of the mimetic from non-mimetic lineage in model R1 was based on the divergence time estimate of Mullen et al. [ 16].
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