dXYi

dXYi is a locus-specific measure used in population genetics to quantify genetic divergence between two populations at a given genomic locus i. It represents the per-locus component of the broader statistic dXY, which denotes the average number of nucleotide differences per site between sequences sampled from populations X and Y. By focusing on locus i, dXYi provides higher-resolution insight into regional differentiation across the genome, beyond a genome-wide average.

Computation of dXYi can be performed directly from sequence data by calculating the mean pairwise differences between sequences from the two populations at locus i, normalized by the locus length. When only allele frequency data are available, dXYi can be approximated using p_i and q_i, the allele frequencies in populations X and Y at locus i, with a form such as dXYi ≈ p_i(1 − q_i) + (1 − p_i)q_i. These locus-specific estimates can be averaged across loci to obtain genome-wide dXY or scanned to identify regions with unusually high or low divergence.

Applications of dXYi include identifying genomic regions where gene flow is restricted or where local adaptation may have occurred, as well as detecting regions of potential introgression or conserved function. It complements relative measures like FST by providing an absolute measure of divergence, which can be informative for understanding the scale of differentiation.

Limitations and caveats include sensitivity to sample size, missing data, and recombination within loci. Demographic history, selection, and ascertainment bias can influence interpretation, so comparisons should account for sampling schemes and data quality.

See also: dXY, FST, nucleotide diversity, population genomics, introgression.