Detecting non-random mating or selection in natural populations using
multi-locus gene families
Abstract
New sequencing technologies have opened the door to many new research
opportunities, but these advances in data collection are not always
compatible with some important methods for data analysis. Fis has been a
staple calculation in the field of population genetics. Fis can be used
to measure either a departure from random mating, or measure underlying
selective pressures for or against heterozygote genotypes. However, when
using Next Generation Sequencing (NGS) technology on multi-locus gene
families it is often impossible to discern which allelic variants are
present at each locus. Some important multi-locus gene families are: the
major histocompatibility complex (MHC) in animals; homeobox genes in
fungi; or the self-incompatibility genes in plants. This in turn makes
it impossible to calculate either locus-specific expected
heterozygosity, or observed heterozygosity, both of which are required
to calculate Fis. Without the ability to calculate Fis from NGS of
multi-locus gene families, we need a new multi-locus measure that will
allow us to detect the underlining mating, and selective patterns
present in such multi-locus genes. This paper provides such a novel
multi-locus measure, called 1His. We demonstrate the accuracy of the
1His equation using simulated data, and two datasets taken from natural
populations of dolphins and penguins. The introduction of this new
measure is particularly important because of the great interest in
mating patterns and selection of multi-locus gene families, such as MHC.