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All the MTC strains were VNTR typed using the loci ETR A-E (see Additional file 1) [ 14].
Akey et al. (2002) [ 10] suggested using the loci in the tails of the empirical distribution as candidate targets of selection.
Strains of the same species (including the type strain) share more than 60% mutual AFLP band pattern similarity and more than 95% similarity in MLSA (using the loci rpoA, recA, pyrH, ftsZ, topA, mreB gyrB and gapA).
The extensive sampling also provides a genus-wide context in which to evaluate the amounts and patterns of divergence among putative species that can be detected using the loci we sampled.
Genomic changes such as inversion and translocation events among the three A genome pairs, Aj-An, Aj-Ar, and Ar-An, were identified by comparative genetic mapping using the loci with known sequence information in the linkage groups of the A genome of the SY-PM population and their corresponding alignment matches in the Ar and An genomes.
Similar(53)
The value of IA is known to increase with the number of loci tested; therefore, multilocus linkage disequilibrium was also measured using the locus number independent measure rD, [61].
FSTs were calculated using the locus by locus AMOVA function in Arlequin v. 3.5.
We see the strongest enrichment signal by using the locus definition closest to the known locations of the HM.
We estimated genetic differentiation using the Locus Specific Branch Length (LSBL), as described in Shriver et al., 2004 [ 36].
When using more than one gene, the maximum-likelihood number of partners for each female is estimated using the locus showing the highest degree of putative partners.
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