Quantifying inbreeding in natural populations of hermaphroditic organisms

Abstract

We review molecular methods for estimating selfing rates and inbreeding in populations. Two main approaches are available: the population structure approach (PSA) and progeny-array approach (PAA). The PSA approach relies on single-generation samples and produces estimates that integrate the inbreeding history over several generations, but is based on strong assumptions (for example, inbreeding equilibrium). The PSA has classically relied on single-locus inbreeding coefficients averaged over loci. Unfortunately PSA estimates are very sensitive to technical problems such as the occurrence of null alleles at one or more of the loci. Consequently inbreeding might be substantially overestimated, especially in outbred populations. However, the robustness of the PSA has recently been greatly improved by the development of multilocus methods free of such bias. The PAA, on the other hand, is based on the comparison between offspring and mother genotypes. As a consequence, PAA estimates do not reflect long-term inbreeding history but only recent mating events of the maternal individuals studied ('here and now' selfing). In addition to selfing rates, the PAA allows estimating other mating system parameters, including biparental inbreeding and the correlation of selfing among sibs. Although PAA estimates could also be biased by technical problems, incompatibilities between the mother's genotype and her offspring allow the identification and correction of such bias. For all methods, we provide guidelines on the required number of loci and sample sizes. We conclude that the PSA and PAA are equally robust, provided multilocus information is used. Although experimental constraints may make the PAA more demanding, especially in animals, the two methods provide complementary information, and can fruitfully be conducted together.

A Bayesian method for the joint estimation of outcrossing rate and inbreeding depression

“…However, the platform may also prove useful if small families are an inherent feature of a species. Animal mating system studies commonly use single-generation approaches to estimate t and F because progeny arrays of sufficient size are rarely obtainable (Jarne and David, 2008). In this case, sampling of more families with fewer offspring per family is a natural experimental design and BORICE may here allow improved estimation.…”

“…ID is estimated from the magnitude of the change in F from zygote to adult with the zygote F inferred from the outcrossing rate. In plants, t and F are typically estimated from progeny arrays (Jarne and David, 2008). Seed families are collected from natural populations, grown in a greenhouse, and individuals from each seed family are genotyped at variable marker loci.…”

“…One benefit of using experimental crosses over field-based methods is that population substructure (for example, biparental inbreeding or the Wahlund effect) may be less of a concern (Jarne and David, 2008). Experimental crosses are also often less expensive and avoid the technical problems associated with marker selection and genotyping.…”

Mixed Mating in Homostylous Species: Genetic and Experimental Evidence from an Alpine Plant with Variable Herkogamy,Primula halleri

“…The outcrossing rate of each population was estimated using a progeny array approach (see Ritland and Jain 1981;Shaw et al 1981; reviewed by Jarne and David 2008; sample sizes per population in table A2; tables A1, A2 available online). To establish whether each population has a mixed mating system (question i), we estimated multilocus outcrossing rates (t m ), average single-locus outcrossing rates (t s ), and the level of biparental inbreeding (t m 2 t s ).…”

Reconstruction of pedigrees in clonal plant populations

“…It has been used mainly to find correlations between phenotypes and reproductive success, or to estimate pollen-mediated gene flow (Smouse and Meagher, 1994;Burczyk et al, 1996;Smouse et al, 1999;Meagher et al, 2003;Wright and Meagher, 2004). To a lesser extent, parentage inference and related methods are used to estimate recent rates of self-fertilization (selfing) in a population (Ritland and Jain, 1981;David et al, 2007;Wilson and Dawson, 2007;Jarne and David, 2008).…”