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Even when the topology is estimated correctly, divergence dates are likely to be affected by error in rate estimation, particularly if only a few calibration points are used.
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Therefore this estimate more correctly represents the divergence time of Lepidosauromorpha rather than Squamata.
Using artificial varieties simulated with known parameters, we showed that our method was able to correctly estimate the divergence time.
Re-evaluation of the C′ and D′ sequences confirmed that, while the original consensus sequence was correctly identified, significant divergence is tolerated in this motif.
Out of a total of 887 pairs containing an inconsistent coalescence event occurring after the pair divergence, JML correctly detected 95 and falsely detected 48.
However, on the basis of the results of a simulation study, the estimated substitution rates should still be reliable indicators of the average rate of evolution and can be used to infer the divergence times correctly also in this case (10).
The ability of AT- and TC-specific probes to correctly predict the expression divergence from the mid-parent value was verified experimentally by hybridizing Affymetrix microarray chips with the 1 1 mix of AT and TC RNA samples and fitting the model assuming the 1 1 ratio of AT and TC expression in the mix.
Results solely for best-fit linear models are shown except for "%indels called correctly" at low and high divergence and "% SNPs called correctly" at low divergence.
It is important in this type of analysis to count the numbers of synonymous and nonsynonymous sites correctly and consistently across the divergence and polymorphism data.
The models used in the analyses might fail to capture the actual patterns of rate variation and correctly estimate branch lengths and divergence times.
Accordingly, a high percentage of correctly assigned individuals may indicate strong genetic divergence among populations and, conversely, low assignment success may indicate weak divergence [ 45].
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