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We also use some historical evidence to calibrate differentiation speed and give estimates of time since separation for the different cases studied.
The mountain-forming events in New Guinea correspond with our molecular clock estimates of time since divergence, Fst estimates, and phylogenetic structure (geologic dates in Table 1, molecular estimates in Table 4).
Estimates of time since expansion in mutational units are calculated from the mismatch distribution with their 95% confidence intervals.
Median synonymous substitution levels were converted into estimates of time since divergence using an estimate of 6.1 × 10-9 substitutions per synonymous site per year [ 35].
These results suggest that measures of average sequence divergence observed in CanSINE lineages, calibrated by the feliform phylogeny, are estimates of time since periods of active proliferation.
Although estimates of time since divergence increased with the taxonomic separation of taxa, the relationship was noisy and non-linear (see Additional file 4: Figure S3).
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The individual estimates of time-since-infection for each serum sample in the cross-sectional surveys were converted to an estimate of the annual infection incidence ("sero-incidence") in the sampled population; point estimates and 95% credible intervals are reported.
Estimate of time since expansion is most recent in M. rutilus at 4.31 Ka (95% CI range 2.12 6.74 KaKa).
Applying the equation τ = 2 μt where μ is the mutation rate and t is time in generations [ 66], allows an estimate of time since expansion.
Consequently, we calculated a microsatellite-based estimate of time since divergence of F. radicans and F. vesiculosus using a coalescent approach.
These differing estimates are no doubt affected by the inflated estimate of time since expansion due to the lack of a value for μ expressed in generations rather than years (see Methods).
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