Inference of assortative mating and selection on heterozygotes from
multi-locus gene families.
Abstract
1. The fixation index, FIS has been a staple measure to detect selection
or departures from random mating in populations. However, current Next
Generation Sequencing (NGS) cannot easily estimate Fis, in multi-locus
gene families, which contain multiple loci having similar or identical
arrays of variant sequences of ≥1 kilobase, which differ at multiple
positions. In these families, high-quality short-read NGS data typically
identify variants, but not the genomic location, which is required to
calculate Fis (based on locus-specific observed and expected
heterozygosity). Thus, to assess assortative mating, or selection on
heterozygotes, from NGS of multi-locus gene families, we need a method
that does not require knowledge of which variants are allelic at which
locus in the genome. 2. We developed such a method. Like Fis, our novel
measure, 1His, is based on the principle that positive assortative
mating, or selection against heterozygotes, reduces within-individual
variability relative to the population. 3. We demonstrate high accuracy
of 1His on a wide-range of simulated scenarios, and two datasets from
natural populations of penguins and dolphins. 4. 1His is important
because multi-locus gene families are often involved in assortative
mating, or selection on heterozygotes. 1His is particularly useful for
multi-locus gene families such as toll-like receptors, the
major-histocompatibility-complex in animals, homeobox genes in fungi and
self-incompatibility genes in plants.