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Since population recombination rates are dependent on the effective population size (ρ = 4Ner), estimates of the population recombination rate in each population were normalized by θ = 4Neµ, a scaled population mutation rate obtained from the same individuals and populations, where µ is the genome-wide average microsatellite mutation rate per locus and per generation [13].
In addition, these values encompass the Ne estimate based on BSP [ 116] by our inference of the mutation rate obtained from BEAST across all four clades.
An additional calibration scenario employed a fixed mutation rate obtained from human Y chromosomes: 0.76 × 10−/site/year (Fu et al. 2014).
The BSPs computed for the U6 and U5 haplogroups (based on the mutation rate obtained with the internal calibration) display quite interesting patterns.
Branch lengths were saved and a mutation rate obtained by dividing the distance from the most recent common ancestor (mrca) of Trichosanthes to the present (0.01416) by 65 my, based on the oldest seeds assigned to this genus [ 43].
Excluding the polymorphic 9 pb deletion, typical of haplogroup B; Data from Santos et al. [37] The mutation rate obtained for the coding region of mtDNA considering only germinal mutations was 0.2334 mutations/site/Myr, the highest value reported so far, and much higher than those obtained by phylogenetic methods (Table 3).
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Results shown in figure 3 indicate that the mutation rates obtained in vitro and in vivo are very similar (95% confidence interval).
Mean mutation rates obtained with the five demographic models under the relaxed molecular clock ranged from 1.39 to 4.89×10−4 substitutions/site/year.
Single colony PCR analysis of expansions were done as previously described and rates were corrected by multiplying the percent bona fide expansions by the apparent mutation rates obtained by fluctuation analysis [68].
Table 2 gives estimates of the 13 Y-STR mutation rates obtained using MAL1 and MAL8.
The mutation rates obtained for individual microsatellite markers provide guidelines for divergence time estimates that can be applied in P. pacificus next-generation sequencing approaches of wild isolates.
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