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When comparing the two groups, no statistically significant differences were found (p > 0.05) for any of the parameters, and the mandibular divergence parameter was found to be of borderline significance.
The marginal posterior probability distribution of the divergence parameter, t, revealed a sharp peak at 0.477 (Figure 7), which converted into a divergence time of 0.758 MYA with the 90% HPD interval ranged from 0.599 to 0.953 MYA (Table 4).
In the divergence parameter estimation the three independent runs consistently showed a sharp peak in each dataset, however, the marginal posterior probability distribution of the parameter did not drop to zero when sufficiently high values were reached.
For each of the three genome sequences we defined a confounding divergence parameter (CDP) as the amount of divergence between paralogous sequences that would mirror average allelic divergence within the organism.
The DR ¯ scheme is defined by setting the UV divergence parameter Δ = 0. We however work with Δ ≠ 0 and take for the coupling CTs only the parts ∝ Δ.
Although this timing perfectly matches the respective point estimate drawn from cpDNA alone [ 15], single-locus cpDNA analysis suffered from a lack of convergence of the lineage divergence parameter (t), a problem that has been overcome with the present multi-locus approach (Additional file 9: Figure S2).
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The MLEs of the divergence parameters were ca. 25,000 years ago 900% HPD 9074 3,131,867 years ago) for A. linearis and A. apiculata and ca. 9000 years ago 900% HPD 1815 3,624,008 years ago) for A. oblonga and A. macroclinidioides.
To evaluate all possible scenarios of divergence, which differ in the number of unique divergence parameters and therefore divergence complexity, we used model-based inference and model-based selection to calculate evidence ratios and rank all possible models [ 90- 92].
Oaks et al. [ 7] discuss how placing a uniform prior over the number of divergence parameters (denoted | τ | here, and as Ψ in [ 4]) imposes an "U-shaped" prior over divergence models (t; see Figure five(B) of [ 7]).
As a further test of the utility at the phylogeographic scale, we used the anchor hybrid enriched loci to infer lineage divergence parameters using coalescent models of isolation with migration.
Further, given their high level of conservation, purifying selection could result in strongly biased estimates of population diversity, and thus of phylogenetic estimates via species trees or divergence parameters [ 18, 19].
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