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Only effective migration rate estimates with confidence intervals completely above 0.1 are considered significant.
Figures 3c-f, 4c-d indicate that increasing the number of sampled individuals reduces more drastically the variance of the migration rate estimates than does the number of loci analyzed.
When the method reveals nonzero migration rate estimates, the posterior distribution of the mean time of migration events was estimated for trees sampled from the Markov chain that had at least one migration event (given by the IM program) following Won and Hey [3].
Results from coalescent-based migration analyses are shown in Table 3. Effective migration rate estimates generally had very large confidence intervals, with lower ends of those intervals often far below 0.1, suggesting that a high degree of subdivision among these particular regions cannot be rejected.
The significance of migration rate estimates was measured by log-likelihood ratio tests (LLR) [ 73].
Historical migration rate estimates, M, ranged from 4.8 to 36.4 (see Fig. 6 and Additional file 2).
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Specifically, we converted their migration rate estimate of 0.0004 migrations per gene copy per generation (recalculated assuming a generation time of 20 years based on Hey [16]) to our units of migrations per mutation per generation (m) by dividing the former by the geometric mean of the mutation rates for the nine loci in this dataset (9.32×10−5 mutations per locus per generation ).
b Time of population splitting parameter c Migration rate estimate (m1 – from L. intermedia to L. whitmani; m2 – from L. whitmani to L. intermedia).
The conversion of the migration rate estimate to population migration rate per generation (m1 and m2) is not accurate when the population size is based on a single locus.
Peak posterior distribution of migration rate estimated asymmetrical gene flow between WA and SH, where migration to SH was significant (HiPt: 44.98, 95 % HPD: 0.0 2822) and migration to WA was negligible (HiPt: 0.3907, 95 % HPD: 0.0 2.030).
The migration rate estimate with the highest smoothed value of likelihood is m1 = 0.095 (average of 3 independent runs) and the 95% confidence intervals exclude the value zero for gene flow (Table 3).
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