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Once this was calculated for each of the 169 ancestral sequences, ancestral sequences were ordered by the number of covered (<5% divergence) extant sequences.
We then calculated the number of required RASs to achieve full coverage of extant sequences at divergence levels of 5, 10 and 15%; that is, when each extant sequence diverges by less than the chosen threshold from at least one ancestral sequence (Fig. 4).
Higher clades in subgenus Vitis diverged 16 – 5 Ma with overlapping confidence intervals, and ongoing divergence formed extant species at 12 – 1.3 Ma.
Point estimates for the basal divergence of extant cuckoos range from ∼47 to 79.5 Myr (Supplementary Table 10), a range that reflects the continuing debate over whether extant avian orders originated before or after the K T boundary 46,47.
In section Cochlopetalum, their common ancestor might lose either two telocentric chromosomes or a single metacentric chromosome before divergence of extant species (Cox et al. 1998).
The gene duplication leading to the closely related MPP paralogs occurred very early in eukaryote history, probably before the divergence of extant eukaryotes.
(II) 84.8 Ma MDD = 8.4) for the initial divergence of extant microhylid subfamilies (i.e., split of Phrynomerinae from other microhylids).
To estimate the age of the allodapine root node (earliest divergence among extant clades) we employed three calibration points.
Phylogenetic analyses indicate that the MHCIIa / MHCIIb duplication is more ancient than the divergence between extant metazoan lineages.
The accuracy of ancestral genome reconstruction also depends on the degree of divergence among extant taxa and taxon sampling.
We were interested in applying the genome-wide analysis of rare genomic changes associated with conserved amino acids (RGC_CAs) [ 36] to date the divergence of extant eukaryotes.
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