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Because the divergence between human and chimpanzee is >0.5 (at synonymous sites and D-loop), simple models will underestimate evolutionary distances (Nei and Kumar 2000).
On the other hand, the low number of nucleotidic differences found between Platyrrhine species, because the divergence between many taxa was probably short, often limits the resolution of molecular studies.
In general, the FOU error of the Taxy method cannot be used for quantification of phylogenetic novelty because the divergence between the observed profile and the mixture model is forced to be minimized by the approximation method.
Of course, one must be careful when interpreting this result, because the divergence between genes does not necessarily reflect the same phylogenetic divergence between organisms that carry those genes.
Because the divergence between the two macaques is very recent (much later than the divergence between humans and chimpanzees), we must consider the segregation of polymorphisms in the common ancestral population to estimate the correct species divergence time [ 11, 12].
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Because of the divergence between ta-TRIM sequences in different taeniid species, the manually identified ta-TRIM sequences from each species were used for new BLASTN searches.
Because of the divergence between the SS and NSS protocols, we used real-time PCR as a reference to examine which protocol is less biased in determining expression profiles of the overlapped transcripts.
Because of the divergence between Y. pestis and Y. pseudotuberculosis, a number of gene sequences displayed high rates of missing bases and we removed genes where 20 or more modern Y. pestis samples had >10% missingness.
This exchange occurred after the divergence between Bp and Bm because all the Bp strains carried this cluster on chromosome I and all Bm stains on chromosome II.
The sushi-ichi-related retrotranposon that gave rise to the SIRH family was probably active around the time of the divergence between marsupials and eutherians, because PEG10/SIRH1 is conserved between the eutherians and marsupials, while SIRH3 11 seems to be eutherian-specific and SIRH12 evolved from a marsupial-specific retrotransposition event.
Because both major clades had already appeared by 65 mya, the divergence between the clades must have happened even earlier.
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