Effects of coancestry on accuracy of individual assignments to population of origin: examples using Great Lakes lake trout (Salvelinus namaycush)

Methods for assigning individuals to population of origin are widely used in ecological genetics, resources management, and forensics. Characteristics of genetic data obtained from putative source populations that enhance accuracy of assignment are well established. How non-independence within and among unknown individuals to be classified [i.e., gene correlations within individual (inbreeding) and gene correlations among individuals within group (coancestry)] affect assignment accuracy is poorly understood. We used empirical data for six microsatellite loci and offspring from full-sib crosses of hatchery strains of lake trout (Salvelinus namaycush; Salmonidae) representing known levels of coancestry (mean θ = 0.006 and 0.06) within families to investigate how gene correlations can affect assignment. Additional simulations were conducted to further investigating the influence of allelic diversity (2, 6 or 10 alleles per locus) and inbreeding (F = 0.00, 0.05, and 0.15) on assignment accuracy for cases of low and high inter-population variance in allele frequency (mean F _st = 0.01 and 0.1, respectively). Inbreeding had no effect on accuracy of assignments. In contrast, variance in assignment accuracy across replicated simulations, and for each empirical case study increased with increasing coancestry, reflecting non-independence of probabilities of correct assignment among members of kin groups. Empirical estimates of assignment error rates should be interpreted with caution if appreciable levels of coancestry are suspected. Additional emphasis should be placed on sampling designs (spatially and temporally) that define or minimize the potential for sampling related individuals.     

因子与巢式交配设计群体近交率的比较研究

探讨了因子和巢式交配设计群体近交率的形成机理,结果表明,这两种交配设计群体结构本身并不导致基近交率累积的差异。在育种选择情况下因子交配设计比巢式设计群体的近交率上升慢,而在完全随机留种和限制随机种情形这两种酱地群体近交率的影响没有差异,但在交配设计情况下,限制随机留种比完全随机留有有交地控制群体近交率的提高。这一结果显示,在动物的家畜遗传留种比完全随机留各 效地控制群体近交率的提高。这一结果显示,     

Family level inbreeding depression and the evolution of plant mating systems

Variation in the magnitude of inbreeding depression (ID) among families may have important consequences for mating system evolution. Experimental studies have shown that such variation is a common feature of natural plant populations. Unfortunately, the genetic and evolutionary significance of family level estimates remains obscure. Almost any kind of genetic variation will generate differences in ID among families, and as a consequence, a non-zero variance in family level ID is not sufficient to distinguish genetic architectures with wholly different implications for mating system evolution. Quantitative genetic methods provide a means to extract more information from ID experiments. Estimates of quantitative genetic variance components directly inform questions about the genetic basis of ID and should ultimately allow tests of alternative theories of mating system evolution.     

Sustainable long-term conservation of rare cattle breeds using rotational AI sires

The development of inbreeding in rotation breeding schemes, sequentially using artificial insemination (AI) sires over generations, was investigated for a full AI scheme. Asymptotic prediction formulae of inbreeding coefficients were established when the first rotation list of AI sires (possibly related) was in use. Simulated annealing provided the optimal rotation order of sires within this list, when the sires were related. These methods were also used for subsequent rotation lists, needed by the exhaustion of semen stores for the first bulls. Simulation was carried out starting with groups of independent sires, with different sizes. To generate a yearly inbreeding rate substantially lower than 0.05% (considered to be within reach by conventional conservation schemes using frequent replacements), the results obtained showed that the number of sires should be at least 10–15 and that the same sires should be used during at least 50 years. The ultimate objective was to examine the relevance of implementing rotation in breeding schemes on the actual rare French cattle breeds under conservation. The best candidate for such a test was the Villard-de-Lans breed (27 bulls and 73 000 doses for only 340 females) and it turned out to be the best performer with an inbreeding coefficient of only 7.4% after 500 years and five different sire lists. Due to the strong requirements on semen stores and on the stability of population size, actual implementation of this kind of conservation scheme was recommended only in special (''niche'') cattle populations.     

Inbreeding under a cyclical mating system

Summary General recursion formulae for the coefficient of inbreeding under a cyclical mating system were derived in which one male and one female are selected from each of the n families per generation (population size N = 2 n). Each male is given the family number of his sire in each generation, while his mate comes from another family, varying systematically in different generations. Males of the r-th family in generations 1, 2, 3,..., t = n–1 within each cycle mate with females from families r+1, r+2, r+3,..., r+t to produce generations 2, 3, 4,..., t+1=1, respectively. The change in heterozygosity shows a cyclical pattern of rises and falls, repeating in cycles of n–1 generations. The rate of inbreeding oscillates between <-3% to >6% in different generations within each cycle, irrespective of the population size. The average rate of inbreeding per generation is approximately 1/[4 N-(Log₂N+1)], which is the rate for the maximum avoidance of inbreeding. The average inbreeding effective population size is approximately 2 N–2.     

Invasion of sibmating genes in diploid and haplodiploid populations

Summary Existing genetic models of the evolution of sibmating behaviour in diploids incorporate inbreeding depression in terms of reduced fecundity of consanguineous mating pairs rather than reduced survival or fecundity of the progeny of such matings. Here we derive a model to correct this deficiency and extend the model to haplodiploids where differential effects of inbreeding in males and females is a crucial consideration. Our analyses indicate that sibmating can readily evolve in both diploids and haplodiploids in which male mating costs and inbreeding depression are reasonably low, provided there is some mechanism to permit sibmating such as siblings being reared in nests or other forms of aggregation. Our analyses also indicate that once sibmating invades, it typically will go to fixation, although sib-/randommating polymorphisms can persist in both diploids and haplodiploids if male mating costs are close to zero and inbreeding depression reduces survival by around one-third. The conditions favouring sibmating are slightly more restrictive in haplodiploids than in diploids. In light of this we may ask why we see intense sibmating in many haplodiploids such as parasitic wasps, fig wasps, ants, bark beetles and mites, and only rarely in diploid animals. The common factor could be certain kinds of aggregation behaviour that are a prerequisite for sibmating in the absence of kin recognition. Another possibility is that inbreeding depression is likely to be more severe in diploids than in haplodiploids because deleterious recessives are purged from haplodiploid populations when expressed by haploid males. Thus, lower levels of inbreeding depression might be one important reason why sibmating appears to arise more frequently in haplodiploids than diploids. Phylogenetic analysis of groups, such as bark beetles and mites, exhibiting both diploid and haplodiploid populations may be useful in elucidating the relative importance of gregarious behaviour and haplodiploidy in facilitating sibmating systems.     

When does female multiple mating evolve to adjust inbreeding? Effects of inbreeding depression,direct costs,mating constraints,and polyandry as a threshold trait

Polyandry is often hypothesized to evolve to allow females to adjust the degree to which they inbreed. Multiple factors might affect such evolution, including inbreeding depression, direct costs, constraints on male availability, and the nature of polyandry as a threshold trait. Complex models are required to evaluate when evolution of polyandry to adjust inbreeding is predicted to arise. We used a genetically explicit individual‐based model to track the joint evolution of inbreeding strategy and polyandry defined as a polygenic threshold trait. Evolution of polyandry to avoid inbreeding only occurred given strong inbreeding depression, low direct costs, and severe restrictions on initial versus additional male availability. Evolution of polyandry to prefer inbreeding only occurred given zero inbreeding depression and direct costs, and given similarly severe restrictions on male availability. However, due to its threshold nature, phenotypic polyandry was frequently expressed even when strongly selected against and hence maladaptive. Further, the degree to which females adjusted inbreeding through polyandry was typically very small, and often reflected constraints on male availability rather than adaptive reproductive strategy. Evolution of polyandry solely to adjust inbreeding might consequently be highly restricted in nature, and such evolution cannot necessarily be directly inferred from observed magnitudes of inbreeding adjustment.     

Genetic structure and reproductive strategy of the ant Cardiocondyla elegans: strictly monogynous nests invaded by unrelated sexuals

Cardiocondyla elegans is a Mediterranean ant that nests on river banks. It rears only wingless (ergatoid) males that live peacefully in the same nest as opposed to other species of the same genus, which have both peaceful, winged and mutually aggressive 'ergatoid' males. Using microsatellite analysis, we investigated the genetic structure of 21 colonies from three different locations as well as the parentage of sexuals of two colonies of C. elegans. We show that C. elegans is strictly monogynous, and that its nests can contain foreign sexuals. The presence of alien sexuals inside ant nests is described for the first time and probably counteracts inbreeding resulting from matings between siblings. In the laboratory, aggression tests showed that workers only allow alien males to enter their nests, while all winged female sexuals attempting to enter were attacked. Nevertheless, the presence of alien female sexuals in nests in the field seems to result from active carrying behaviour by workers during the reproductive period.     

Sex‐specific effects of inbreeding in wild‐caught Drosophila melanogaster under benign and stressful conditions

In animal populations, sib mating is often the primary source of inbreeding depression (ID). We used recently wild‐caught Drosophila melanogaster to test whether such ID is amplified by environmental stress and, in males, by sexual selection. We also investigated whether increased ID because of stress (increased larval competition) persisted beyond the stressed stage and whether the effects of stress and sexual selection interacted. Sib mating resulted in substantial cumulative fitness losses (egg to adult reproduction) of 50% (benign) and 73% (stressed). Stress increased ID during the larval period (23% vs. 63%), but not during post‐stress reproductive stages (36% vs. 31%), indicating larval stress may have purged some adult genetic load (although ID was uncorrelated across stages). Sexual selection exacerbated inbreeding depression, with inbred male offspring suffering a higher reproductive cost than females, independent of stress (57% vs. 14% benign, 49% vs. 11% stress).