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The first method uses the molecular clock.
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We could also use the molecular clock to estimate the time of divergence of H. naledi to the other hominins.
The advantage of using the molecular clock to determine speciation rates is that it works well for all species, whether common or rare.
The main reason is that geneticists use the molecular clock theory to infer the time to the most recent common ancestor (TMRCA) of each set of haplotypes clustered together (i.e., each haplogroup) in the molecular phylogenies obtained for uniparentally inherited mtDNA and Y chromosome genetic markers.
In addition, we used the molecular clock to calculate the mean age of multiple tip haplotypes, which form star-like phylogenies in the tree.
Age estimates were calculated using the molecular clock rate for E. coli as an approximation (3.4×10−9 synonymous mutations/generation) and assuming 300 generations per year, as per the method employed for age estimates in Yersinia pestis [42].
Divergence time from a common ancestor was estimated by using the molecular clock calculator.
The age of the proposed transfer was estimated using the molecular clock equation (t = Ks/2r).
These tests are fully equipped to decipher interspecific rate changes using the molecular clock as a null hypothesis.
To reinforce the HT hypothesis, the divergence times of both retroelements were calculated using the molecular clock (see Material and Methods).
Maximum likelihood (ML) tree of AGOs showing the approximate relative time of divergence of all the nodes using the molecular clock test on 'plant AGO dataset II'.
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