We also did a locus-by-locus analysis of molecular variance (AMOVA) with fields grouped into townships to hierarchically partition genetic variance into regions, fields and individuals.
Neutrality was tested through FST comparisons: FST values[ 17] were calculated for all loci by a locus-by-locus analysis of molecular variance (AMOVA) using ARLEQUIN.
We used a locus-by-locus analysis of molecular variance, using 20,000 simulations, which was performed by Arlequin using its default values (constant model; Excoffier et al. 2005).
The degree of genetic divergence between the two species, F ST, was assessed by a locus-by-locus analysis of molecular variance (AMOVA) in Arlequin version 3.5.1.2 (Excoffier et al. 2005).
A locus-by-locus analysis of deviations from Hardy-Weinberg equilibrium frequencies indicated that one marker (Ren181K04) showed a heterozygote deficiency for all breeds and groups of poodles, suggesting presence of null alleles, genotyping errors or tight physical linkage to a selected trait.
Although the results from our locus-by-locus analysis showed some evidence of altered methylation with arsenic exposure, these results did not withstand multiple comparison corrections.
We performed quantitative trait locus analysis of Klrd1 expression by using BXD lines with different generation times and found that the expression difference in Klrd1 in the later BXD set is driven by a strong cis-acting expression quantitative trait locus.
In a locus-by-locus analysis, the markers with the highest frequencies of null alleles were SPS115 (9.7 %) and INRA063 (6.6 %) (see Additional file 2: Table S2).
The asymptotic connection between the standard log-likelihood ratio statistic and the χ metrics used for multi-locus analysis of LD by Hill (1975) and more recently by Zhao et al. (2005) is given, for example, in Agresti (2002).
To ascertain the proportions of genetic variance due to differences within and between populations, genetic variance was hierarchically apportioned according to geographic criteria through the locus by locus AMOVA (analysis of molecular variance) [51], using the Arlequin 3.01 software [43].
