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Subgenotypes have been described within these HBV genotypes based on a divergence in the complete nucleotide sequence greater than 4% and less than 8% [4].
Finally, diversification within each of these intraspecific lineages occurred from the Upper Miocene in lineage VIII of B. duperreyi (based on a divergence rate of 1.3% Myr−1; 2.0 Myr 95% HPD: 1.0 2.1) to the Middle Pleistocene in lineage III of B. duperreyi (based on a divergence rate of 2.3% Myr−1; 0.2 Myr 95% HPD: 0.2 0.4; see Fig. 3 for more details about the dating results).
HBV as a highly variable virus is at least classified into eight genotypes based on a divergence in the entire nucleotide sequence greater than 8% [ 3- 21].
Based on a divergence analysis calibrated with hypotheses from previous studies and fossil data, it appears that microhylid genera inhabiting the New World originated during a period of gradual cooling from the late Oligocene to mid Miocene.
I first reduced the dimensionality of the 11 shape variables by calculating morphological divergence scores for each individual along the stream reservoir gradient based on a divergence vector (referred to as habitat divergence vector hereafter) as defined by Langerhans (2009).
Based on a divergence of East Asians from Africans of 55,000 years ago (Nei and Roychoudhury 1974 , 1993, and assuming that RST is proportional to time, we can estimate the evolutionary rate of Y-STR by using the Y-STR tree.
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The numerical procedure is based on a divergence-free finite element method and is applicable to multiply connected domains.
Therefore, the estimates of nonvertically acquired virulence genes based on a sequence divergence of 0.0021 should be considered conservative.
A total of 10 HBV genotypes (A J) have been identified based on a sequence divergence of >8% across the entire HBV genome and >4% in the preS/S region of the HBV genome.
A third rate was based on a known divergence time of approximately 16 years between the separation of Dehalococcoides ethenogenes strain 195 ("strain 195") [ 6] from its mother culture - the "TCE/MeOH" culture (Prof. S. Zinder, pers. comm).
Di Rienzi et al. (2013) concluded that the two groups are sister phyla rather than a single phylum based on a combined divergence slightly greater than a recommended threshold of 85%16SS rRNA gene sequence identity for distinguishing new phyla (Hugenholtz et al. 1998).
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Justyna Jupowicz-Kozak
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