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Actually, in the lack of solid information on speciation time, we tested if dnuc is proportional to dmt.
If we take T1 as the known speciation time, corresponding to the time that each 3'LTR and 5'LTR take to coalesce into their common ancestors, and T2 as the unknown speciation time, for two species A and B we have that Integration time = Distance(5'LTR−3'LTR)/(rate5'+rate3').
These methods treat each ERV locus as having a distinct evolutionary rate for each LTR, and make use of consensual speciation time intervals between primates to calibrate the relaxed molecular clocks.
This suggests that Nei et al.'s conclusion about speciation time may not be so unrealistic.
The speciation time of Chinese hares was estimated at 3.116 MYA (± 0.731 MYA, Additional file 3).
Despite this proximity of sequence, neighborhood evidence shows that they evolved separately, at least since the speciation time of KLLA.
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Assuming known speciation times, we can estimate ERV integration times by using LTR sequence divergence and both 3' LTR and 5' LTR rates (figure 1).
The coincidence of speciation times across different families implied that environmental changes around that time may have played an essential role in the evolutionary processes of gibbons and other mammals [34], [35], [36].
Applying the values for the estimated genetic distances (D) and known speciation times (T) in the formula D = T*2k, where k is the substitution rate, a rate of substitutions per site per year can be inferred.
These speciation times were consistent with the fossil records.
Ancestral population sizes and speciation times were previously estimated with BPP.
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