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DnaSP version 4 [58] was used to calculate Tajima's D [59], the pairwise nucleotide diversities as well as the gene wise population recombination [60] and mutation rates, respectively, and to detect genetic differentiation of subpopulations by calculating Ks* and Z* [61] as well as Snn [62] statistics with 1000 replicates to assess statistical significance in the permutation test.
Allele frequencies, a pair wise population matrix of Nei's genetic distance were computed by GENEALEX[ 32].
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The FST values for all pair-wise population comparisons are shown in Table 4.
Inter- and intra- population genetic differences were quantified by the inflation factor lambda (ranging from 1.00 to 4.21), fixation index (Fst) (ranging from 0.000 to 0.023), and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons.
Pair-wise population FST and FST corrected for null alleles.
District-wise population for 2008 was obtained from the Population Projections of India [ 10].
This procedure assumes that the pair-wise population comparisons are statistically independent, which is questionable, since each population is involved in several different comparisons.
Pair-wise population comparisons of neutral genetic variation (FST-values between populations) ranged from 0.0057 to 0.52 when P. g. weigandi was included and between 0.0057 and 0.36 within P. g. gaigeae only (Table 1).
Pair-wise population differentiation (FST) and summary statistics (heterozygosity, number of alleles per locus) were calculated using GENEPOP v4.2 [ 85, 86] and the Excel Microsatellite Toolkit v3.1.1 [ 87], respectively.
In addition, cox1 pair-wise population F ST values were generally high (F ST = 0.5-0.99) and highly significant, with the exception of between neighbouring populations (viz., 19 vs. 10-15, 24 vs. 28).
Implementation of the pair-wise population differentiation test in the software GENEPOP 4.07 [ 20] showed that all breed pairs were significantly differentiated, including the six breed pairs that included the four Lacaune subpopulations.
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