Then, we analyzed the accumulation of different TEs based on divergence from the consensus sequence, which resembles the motifs of ancestral repeats, and found different patterns in the Chinese alligator, green anole lizard, chicken (Gallus gallus), and zebra finch (Taeniopygia guttata) (Supplementary information, Figure S3).
Based on divergence time estimates from Pochon et al. [ 18], these divergences equate to an overall substitution rate of ~3.1-3.4×10-9 per site per year From the 2418 pairwise analyses, dN/dS could not be estimated in three instances because dS=0 (dN was also 0 in two cases).
Based on divergence age estimates, gibbons separated from great apes and humans 16.26 million years ago (mya) (for 95% credibility intervals see Table 2).
The transformation presented in this paper is based on divergence theorem.
Table 2 shows two alternatives based on divergence time estimates.
Booth and Holland (2004) determined the relative evolutionary ages of the NANOG pseudogenes based on substitutional divergence from the NANOG parent gene and concluded that NANOGP8 is the most recent.
To test if proximity to genes affected piRNA coverage independent of RTE age, members of each RTE family were divided into three equally sized groups based on their divergence from their consensus sequence (called 'young'median'and and 'old' loci, respectively).
For brevity, we report the results of the pooled Ka and KS, which are based on the divergence data from the study of Bustamante et al. (2005), unless stated otherwise.
Sequential experimental design, based on the divergence criterion and tools from computational statistics such as the deviance information criterion estimated by a Markov Chain Monte Carlo technique, were used to discriminate among 12 possible kinetic models.
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.
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.
