A parameter to quantify the degree of genetic mixing among individuals in hybrid populations

Abstract

Hybridization between genetically distinct taxa is a complex evolutionary process. One challenge to studying hybrid populations is quantifying the degree to which non-native genes have become evenly mixed among individuals in the population. In this paper, we present a variance-based parameter, m d , that measures the degree to which non-native genes are evenly distributed among individuals in a population. The parameter has a minimum value of 0 for populations in which individuals from multiple taxa are present but have not interbred, and a maximum value of 1 for populations in which all individuals have the same amount of non-native ancestry. A recurrence equation showed that relatively few generations of random mating are required for m d to approach 1 (indicating a well-mixed population), and that m d is independent of initial amounts of non-native ancestry. The parameter is mathematically equivalent to F ST and we show how existing formulae for F ST can be used to estimate m d when diagnostic loci are available. Computer simulations showed this estimator to have very little bias for realistic amounts of data.

Patterns of hybridization among cutthroat trout and rainbow trout in northern Rocky Mountain streams

“…Yet we found, as have many others, that parental fish were common and allele distributions often nonrandom in hybrid zones, and consequently that hybrid swarms were rare. One could regard this as a semantic argument (e.g., Kalinowski and Powell 2015) that rests on the definition of a hybrid swarm, for example, the mere presence of hybridized individuals beyond the first generation (Rhymer and Simberloff 1996) or the more restrictive conditions that we and others (Allendorf et al. 2013) have adopted.…”

“…Yet we found, as have many others, that parental fish were common and allele distributions often nonrandom in hybrid zones, and consequently that hybrid swarms were rare. One could regard this as a semantic argument (e.g., Kalinowski and Powell 2015) that rests on the definition of a hybrid swarm, for example, the mere presence of hybridized individuals beyond the first generation (Rhymer and Simberloff 1996) or the more restrictive conditions that we and others (Allendorf et al 2013) have adopted. Regardless, the presumption that hybrid swarms will inevitably form following nonnative species introductions continues to influence the conservation of cutthroat trout (Allendorf et al 2005;Campton and Kaeding 2005;Shepard et al 2005) and of many other species (Blum et al 2010;Bean et al 2013;Hasselman et al 2014).…”

“…In those populations with both sufficient admixture (≥5%) and sample sizes (≥10) to provide meaningful tests of random mating, none of the sites lacking Yellowstone cutthroat trout alleles had allele distributions consistent with random mating and, at many of these sites, parental rainbow trout and westslope cutthroat trout were sympatric. Given the extended stocking histories associated with many of these sites, it is unlikely that these patterns represent transient phenomena; allele distributions consistent with binomial expectations can emerge in as little as five generations of random mating (Kalinowski and Powell 2015). It is also not the case that, due to processes such as within‐stream movement, drawn samples would never resemble swarms: Sites with significant numbers of alleles diagnostic for Yellowstone cutthroat trout produced samples consistent with random mating and lacking parental types.…”

Isolation, Migration, and Local Recruitment Drive Persistence of Cutthroat Trout in Tributaries near American Falls Reservoir

“…Evidence for the persistence of Yellowstone Cutthroat Trout Gunnell et al 2008;Kovach et al 2011) and Cutthroat Trout (McKelvey et al, in press) in sites threatened by Rainbow Trout and hybrid invasion is growing. Kalinowski and Powell (2015) used computer simulations to show that the complete loss of native genotypes is expected after only five generations of random mating between taxa. Further, a recent rangewide examination of Westslope Cutthroat Trout presented empirical evidence showing that apparently nonadmixed Cutthroat Trout persist in many populations facing hybrid invasions.…”

Analytical and Decision Support Tools for Genomics-Assisted Breeding

“…In this context, STRUCTURE [52] is the most extensively used software to detect population genetic structure. STRUCTURE generates clusters based on both transient Hardy-Weinberg disequilibrium and LD caused by admixture between populations [53,54]. EIGENSOFT is another widely used statistical package for the detection and correction of population stratification in GWAS using principal component analysis [55].…”