The first measure of the divergence of duplicated genes compares sets of their transcriptional regulators.
The first occurred in the common ancestor of the Asteraceae and the second after the divergence of the Mutisioideae from the other tribes, but before the birth of the Anthemideae tribe.
However, the consensus points to one duplication prior to the divergence of lamprey/hagfish and gnathostomes, and the second after the divergence of these lineages [ 32] (figure 4).
Second, at the divergence of the two cyclostome lineages, the hagfish and lampreys, these ancestral cyclostome Dlx genes were segregated into the two species lineages.
The first occurred ∼600 Mya before the existence of the common ancestor of the Vertebrata, and the second occurred after the divergence of the jawless vertebrates around 450 Mya, and the third one, the fish specific WGD, happened at ∼350 Mya but only in Actinopterygii [22], [23], [24].
Pairwise divergence between the Vei and Vtu genomes accounts for about one-third of the total divergence in each of the unrooted ortholog phylogenies with 1 and 0.1 expected synonymous and nonsynonymous substitution per site, respectively (mean d S ± standard deviation [SD] = 1.05 ± 0.33; mean d N ± SD = 0.1 ± 0.05; supplementary fig. S2 and table S6, Supplementary Material online).
This ancestral type-3 copper protein gene underwent two duplication events, the first prior to the divergence of the unikont eukaryotic lineages and the second before the diversification of animals.
The first occurred after the divergence of monotremes and placentals/marsupials, and the number of T2R genes increased almost five-fold in the mammalian lineages.
The H. sapiens CK1δ and CK1ϵ form the first branch after the divergence of S. cerevisiae, with a bootstrap confidence of 99%. A. thaliana contains many CK1 paralogs, of which CKL1-13 are the most conserved.
Among them, N. concolor branched off first, followed by the divergence of N. gabriellae and N. leucogenys/N.
In instances in which a divergence time was not available for two species we used the conservatively estimated date of first appearance as the divergence time taken from the Paleobiology Database (Alroy et al. 2008).
