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One such method introduced by Theil [1950. A rank-invariant method of linear and polynomial regression analysis. I, II, III. Proc. Ned. Akad. Wet. 53, 386 392, 521 525, 1397 1412] is based on pairwise estimates.
Nielsen et al. (2005) provided a list with the top 50 candidates showing the strongest evidence for positive selection based on pairwise estimates of ω with subsequent likelihood ratio tests.
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But MIL2 shows much stronger divergence than MIL3 based on pairwise ΦST estimates (Table 1) and AMOVA results.
For methylation tree construction, we first calculated the absolute methylation level in sliding windows of 50 kb with steps of 25 kb across the whole genome for the four samples, and then clustered the samples based on pairwise Spearman correlation coefficients estimated from the above whole genome sliding methylation level matrix.
Briefly, parsimonious scenarios are estimated based on pairwise comparisons of gene order between all available sequenced genomes (1378 comparisons in Genomicus v56.01).
The extent of LD and the average trend of LD decay rate in this association panel were estimated based on pairwise LD squared correlation coefficients (r) for all intrachromosomal SNP loci.
In a first step, estimates were only based on pairwise alignments between human and all other species (fig. 1 A and B ) instead of branch-specific estimates based on multiple alignments (fig. 1 C ).
Secondly, estimates of Fst based on pairwise genetic distances [80] were contrasted between neutral (non-coding or synonymous alleles) and functional alleles (i.e. alleles differing in putative ABS amino acid residues).
The reconstructed haplotypes were inserted into HAPLOVIEW v4.1 [ 19] to estimate LD statistics based on pairwise r and to construct the blocking pattern in the candidate regions of interest to enable selection signature analysis.
Estimates of genetic differentiation based on pairwise FST and Dest values were also obtained to further investigate the overall stability between sampling locations and temporal sampling periods.
This is mainly due to that 1) our estimates is not directly based on pairwise distances, but on a given tree with branch lengths; 2) we use different calibration point from those studies [ 31, 32].
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