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PubMed1991

Coevolution of self-fertilization and inbreeding depression. I. Mutation-selection balance at one and two loci.

Simple theories for the evolution of breeding systems suggest that the fate of an allele that modifies the rate of self-fertilization hinges only on the degree to which selfing reduces opportunities for outcrossing ("pollen discounting") and the extent of inbreeding depression. These theories predict that outcrossing evolves whenever deleterious mutations have a more severe effect in combination than expected from their individual effects. We study the evolutionary dynamics of a modifier of the rate of self-fertilization in populations subject to complete pollen discounting and recurrent mutations which impair viability at a single locus in diploids and at two loci in haploids. Our analysis indicates that genetic associations arising immediately upon the introduction of a rare modifier allele generate substantial quantitative and qualitative departures from expectation. Higher rates of segregation under selfing in our one-locus diploid model generate positive associations between enhancers of selfing and wild-type viability alleles, which in turn favor the evolution of selfing under a wider range of conditions than expected. Greater opportunities for recombination under outcrossing in our two-locus haploid model generate positive associations between enhancers of outcrossing and wild-type viability alleles. These associations favor the evolution of outcrossing under a wider range of conditions, and introduce the possibility of stable mixed mating systems involving both selfing and outcrossing. Our explicit analysis of genetic associations between loci affecting viability and the rate of self-fertilization indicates that modifiers that enhance the production of offspring with very high (and very low) viability by promoting segregation or recombination develop positive associations with high viability. This advantage of producing extremes can compensate for an initial disadvantage in offspring number.

Alleles↗
PubMed1991

Coevolution of self-fertilization and inbreeding depression. III. Homozygous lethal mutations at multiple loci.

We study the evolution of the rate of self-fertilization in response to deleterious mutations at multiple loci. Although partial selfing induces associations among loci even in the absence of linkage, associations among mutations at different loci are of a smaller order of magnitude than the mutation rate. Genotypes that carry homozygous lethal mutations in heterozygous form at i loci occur in frequencies of the order (Ti) mu i, in which T denotes the number of viability loci and mu the mutation rate. While associations between mutations at different loci remain small even under inbreeding, each viability locus develops an association with the modifier of the rate of self-fertilization that substantially affects the evolution of the breeding system. Positive associations between enhancers of selfing and haplotypes carrying multiple wild-type alleles and positive associations in heterozygosity between the modifier locus and the viability loci promote evolutionary increases in the rate of self-fertilization.

Biometry↗
PubMed2006

Evolution: inbreeding, multiple mating and embryonic aid.

Females frequently mate with more than one male, but it is rarely clear why. In species where related individuals frequently meet, multiple mating may allow females to avoid fertilising their eggs with sperm from a close relative. A new study suggests that promiscuous females do indeed suffer lower costs of inbreeding, but that this is because of interactions between embryos.

Animals↗
PubMed2004

Inbreeding coefficients for stochastically varying small population sizes-bias of calculation based on effective numbers.

The commonly used procedure to calculate inbreeding coefficients by effective population numbers (Ne) by the harmonic mean of generation-by-generation population sizes involves a computational bias. If the individual population sizes are considered as realizations of a binomially distributed random variable with sample size N and probability p, this bias can be investigated for the two cases p = constant and p = variable (Markov chain). The bias is of practical relevance only for small probabilities p, short period of initial successive generations, and small population sizes. The largest values for this computational bias are in the range of 0.05-0.06. It is concluded that for most practical purposes the approximate procedure is appropriate.

Animals↗
PubMed2004

The study of new SLA classical molecules in inbreeding Chinese Wuzhishan pig.

UNLABELLED: The pig may be used as an alternative organ donor source in the future. The Wuzhishan miniature pig (WZSP) is a Chinese inbred mini pig with the highest inbreeding coefficient and has been used in many biologic experiments. We studied the classical MHC molecules of WZSP to confirm its pure gene background and to provide information for xenotransplantation. METHODS: The classical class I (P1 and P14) and class II (DQA, DQB, DRA, and DRB) molecules were studied using RT-PCR. The products were cloned into a pGEM-T vector, respectively, sequenced and compared with related data for homology analysis. RESULTS: WZSP is highly homologous (>90%) with NIH miniature swine for class I and class II molecules amino acids in alpha-3 domain responsible for the binding of human T-cell CD8 were largely conserved; only two critical residues were altered. The critical residues of class I molecules recognized by human natural killer (NK) cells were completely different from humans. Furthermore, new class II molecules were homologous (>70%) with the Chinese south population in amino acids. The amino acids for binding to human CD4 were identical in DRB and showed only two differences in DRA. CONCLUSIONS: WZSP bears new alleles in porcine MHC-relevant loci. We might alter residues of class I molecules to avoid killing by human NK cells. The striking similarities of DRB would make WZSP less likely in compatible in xeno-rejection. We can also alter the two residues of the DRA sequence to make WZSP a better model for xenotransplant research in China.

Animals↗
PubMed1998

On the theory of partially inbreeding finite populations. V. The effective size of a partially selfing age-structured population.

Consider a large population, with the same age distribution at times 0, 1, 2, ..., in which there is reproduction by selfing with probability beta and by random mating with probability 1-beta. An individual between i and i + 1 units of age at time t is said to be in age group i at that time. Let L be the mean, among copies of an allele A in genotypes of offspring in age group 0, of ages of parents when the inbreeding coefficient has attained an equilibrium value. Then if there is no selection and allele A is originally present in one heterozygote, the probability that it is ultimately fixed is 1/(2N0L), where N0 is the number of individuals in age group 0 at any time. The effective population size can then be derived. It turns out to be the same as for a population with discrete generations having the same mean and variance of the number of successful gametes produced during a lifetime and the same number of individuals entering the population per generation.

Age Distribution↗
PubMed2002

Place and matching-to-place spatial learning affected by rat inbreeding (Dark-Agouti, Fischer 344) and albinism (Wistar, Sprague-Dawley) but not domestication (wild rat vs. Long-Evans, Fischer-Norway).

Domestication has been shown to produce a shift in both morphological and behavioral characteristics of animals. While changes in body weight, brain size, reproductive rates, and temperament are well documented, the effects of domestication on learning and memory are not as clearly understood. This issue is of particular importance to the use of rodent models in learning and memory where the domestication of Rattus norvegicus for research has resulted in the availability of numerous strains. To investigate cognitive effects resulting frm domestication, we examined the spatial performance of a number of rat strains: wild, Long-Evans, Fischer-Norway, Dark-Agouti, Wistar, Fischer 344, Sprague-Dawley. The wild rats served as a baseline for comparing inbred and outbred domestic strains and pigmented and albino domestic strains. Place (a measure of nonspatial and procedural learning), matching-to-place (spatial working memory), and probe (retention) performance were measured in the Morris swimming pool task. The task is an ideal means for comparing different rat strains because place learning has not been selected for in the domestication of Rattus norvegicus and because the task is ethologically relevant. The results indicated that wild rats and Long-Evans rats did not differ on any measure, with Fischer-Norway rats being only slightly inferior. Larger impairments were found in Wistar > Fischer 344 > Dark-Agouti > Sprague-Dawley strains. Impairments were more obvious on place acquisition but also occurred in matching-to-place performance. Platform crosses, but not quadrant preference was found to be correlated with place learning. In general, although nonspatial and spatial deficits were associated with both inbreeding and albinism, impaired spatial performance is not a necessary result of domestication.

Animals↗
PubMed1991

Inbreeding coefficients and coalescence times.

This paper describes the relationship between probabilities of identity by descent and the distribution of coalescence times. By using the relationship between coalescence times and identity probabilities, it is possible to extend existing results for inbreeding coefficients in regular systems of mating to find the distribution of coalescence times and the mean coalescence times. It is also possible to express Sewall Wright's FST as the ratio of average coalescence times of different pairs of genes. That simplifies the analysis of models of subdivided populations because the average coalescence time can be found by computing separately the time it takes for two genes to enter a single subpopulation and time it takes for two genes in the same subpopulation to coalesce. The first time depends only on the migration matrix and the second time depends only on the total number of individuals in the population. This approach is used to find FST in the finite island model and in one- and two-dimensional stepping-stone models. It is also used to find the rate of approach of FST to its equilibrium value. These results are discussed in terms of different measures of genetic distance. It is proposed that, for the purposes of describing the amount of gene flow among local populations, the effective migration rate between pairs of local populations, M, which is the migration rate that would be estimated for those two populations if they were actually in an island model, provides a simple and useful measure of genetic similarity that can be defined for either allozyme or DNA sequence data.

Animals↗
PubMed2002

Polyandrous females avoid costs of inbreeding.

Why do females typically mate with more than one male? Female mating patterns have broad implications for sexual selection, speciation and conflicts of interest between the sexes, and yet they are poorly understood. Matings inevitably have costs, and for females, the benefits of taking more than one mate are rarely obvious. One possible explanation is that females gain benefits because they can avoid using sperm from genetically incompatible males, or invest less in the offspring of such males. It has been shown that mating with more than one male can increase offspring viability, but we present the first clear demonstration that this occurs because females with several mates avoid the negative effects of genetic incompatibility. We show that in crickets, the eggs of females that mate only with siblings have decreased hatching success. However, if females mate with both a sibling and a non-sibling they avoid altogether the low egg viability associated with sibling matings. If similar effects occur in other species, inbreeding avoidance may be important in understanding the prevalence of multiple mating.

Animals↗
PubMed2002

The cost of inbreeding in Arabidopsis.

Population geneticists have long sought to estimate the distribution of selection intensities among genes of diverse function across the genome. Only recently have DNA sequencing and analytical techniques converged to make this possible. Important advances have come from comparing genetic variation within species (polymorphism) with fixed differences between species (divergence). These approaches have been used to examine individual genes for evidence of selection. Here we use the fact that the time since species divergence allows combination of data across genes. In a comparison of amino-acid replacements among species of the mustard weed Arabidopsis with those among species of the fruitfly Drosophila, we find evidence for predominantly beneficial gene substitutions in Drosophila but predominantly detrimental substitutions in Arabidopsis. We attribute this difference to the Arabidopsis mating system of partial self-fertilization, which corroborates a prediction of population genetics theory that species with a high frequency of inbreeding are less efficient in eliminating deleterious mutations owing to their reduced effective population size.

Amino Acid Substitution↗
PubMed2025

Quantifying genetic and genotypic gain gaps in Eucalyptus: the hidden cost of ignoring inbreeding and dominance.

Understanding the mating system of Eucalyptus species is necessary to accurately estimate genetic parameters and improve breeding programs. Eucalyptus species often exhibit mixed mating systems, leading to complex relationships among progenies. Traditional tree breeding programs that assume a half-sibling relationship for open-pollinated (OP) trials may overestimate genetic gains by neglecting the effects of inbreeding and dominance. This study focuses on Eucalyptus pellita, a species with a mixed mating system, to quantify the impact of selfing and dominance on breeding strategies. We simulated OP trial growth data for 100 randomly selected families in a randomized complete block design, using published estimated parameters for diameter at breast height (DBH). Our analysis indicated that marker-based models, particularly those incorporating dominance effects, provide more accurate genetic parameter estimates and larger predicted genetic gains than pedigree-based models. These results reveal pronounced genetic and genotypic gain gaps when traditional models are employed, underscoring the imperative for integrating dominance-informed genomic selection strategies. Thus, our study provides essential guidance for optimizing breeding programs to sustainably enhance productivity and genetic quality in Eucalyptus plantations.

Eucalyptus↗
PubMed2004

Population genetic structure of and inbreeding in an insular cattle breed, the Jersey, and its implications for genetic resource management.

The Jersey is a ubiquitous and successful breed of cattle that originates from the UK Channel Island of Jersey. While the breed has been exported extensively, no imports have taken place to the island since 1789, leading to a concern regarding possible losses of genetic diversity and increased inbreeding. We have conducted the first large-scale genetic analysis of the Jersey cattle using only samples from the island. A total of 223 cattle from all parishes except one were genotyped for 12 microsatellite loci. The average number of alleles per locus and expected heterozygosity were found to be comparatively high (n(A)=4, H(e)=0.64) with respect to that observed in a number of continental breeds. Only breeds that have been upgraded and are therefore the result of admixture are clearly more variable than the Jersey. We also found a significant but limited amount of genetic differentiation between parishes (F(st)=0.013), or even between farms (F(st)=0.035) despite an apparent lack of movement. This is confirmed by the application of two recent statistical methods. A Bayesian partition analysis shows that the most probable value of K, the number of possible hidden partitions, is 1 (P approximately 0.98). K=2 has a much lower probability (P approximately 0.02) while other values are essentially zero. Similarly, we were able to show that there was no support for departure from panmixia other than due to population structure, and thus that there is sufficient background gene flow across the island to overcome local drift. Overall, it appears that the current level of genetic diversity and its distribution within the island means it is unnecessary to import unrelated genetic material to the island for management purposes.

Alleles↗
PubMed2004

Intergenomic interactions affect female reproduction: evidence from introgression and inbreeding depression in a haplodiploid mite.

Nuclear and cytoplasmic genomes can coevolve antagonistically or harmoniously to affect fitness. One commonly used test for nuclear-cytoplasmic coadaptation relies on the breakup of coadapted gene complexes by introgression, potentially resulting in an increased frequency of nuclear alleles in deleterious interaction with an alien cytoplasm. We investigated the phenotypic effect of such genes on female reproduction in outbred and inbred introgressed lines of the haplodiploid mite Tetranychus urticae. Introgression changed female lifetime fecundity and increased male production, in ways suggesting a control of fecundity by nuclear genes. Conversely introgression reduced the fertilization rate, possibly due to sperm-egg incompatibility or maternal effects. The intensity of inbreeding depression expressed as a reduction in fecundity was more severe in introgressed females than in nonintrogressed ones, giving evidence for recessive interacting alleles contributing to residual nucleo-cytoplasmic incompatibility. Overall, our data suggest recessive negative interactions between nuclear and cytoplasmic genes. This study is the first report of a contribution of nuclear polymorphism within a population to deleterious interactions with an alien cytoplasmic genome.

Animals↗
PubMed2005

The relationship between flower size, inbreeding coefficient and inferred selfing rate in British Euphrasia species.

The genus Euphrasia in Britain comprises a taxonomically complex group of self-compatible, morphologically similar, hemi-parasitic, annual plant species of high conservation importance. The 19 diploid and tetraploid taxa currently recognised show striking variation in flower size. The objective of this paper is to determine whether a relationship exists between flower size and breeding system within Euphrasia. Following a survey of flower size variation among the 19 taxa, seven diploid populations, encompassing a broad range of flower sizes, were selected for detailed study. Four nuclear microsatellite loci were used to estimate the inbreeding coefficient Fis within each population. Fis values varied from to 0.17-0.77 and showed a significant, negative correlation with flower size. These results are best explained as the consequence of variation in selfing rate among the Euphrasia populations, with selfing rate increasing as flower size decreases. The potential factors influencing breeding system evolution in Euphrasia are discussed, together with the role of autogamy in generating taxonomic complexity and facilitating lineage differentiation within the genus.

Euphrasia↗
PubMed2004

Limited pollen dispersal and biparental inbreeding in Symphonia globulifera in French Guiana.

In this paper, we report a study of the mating system and gene flow of Symphonia globulifera, a hermaphroditic, mainly bird-pollinated tree species with a large geographic distribution in the tropical Americas and Africa. Using three microsatellites, we analysed 534 seeds of 28 open pollinated families and 164 adults at the experimental site 'Paracou' in French Guiana. We observed, compared to other tropical tree species, relatively high values for the effective number of alleles. Significant spatial genetic structure was detected, with trees at distances up to 150 m more genetically similar than expected at random. We estimated parameters of the mating system and gene flow by using the mixed mating model and the TwoGener approach. The estimated multilocus outcrossing rate, tm, was 0.920. A significant level of biparental inbreeding and a high proportion of full-sibs were estimated for the 28 seed arrays. We estimated mean pollen dispersal distances between 27 and 53 m according to the dispersal models used. Although the adult population density of S. globulifera in Paracou was relatively high, the joint estimation of pollen dispersal and density of reproductive trees gave effective density estimates of 1.6 and 1.3 trees/ha. The parameters of the mating system and gene flow are discussed in the context of spatial genetic and demographic structures, flowering phenology and pollinator composition and behaviour.

French Guiana↗
PubMed2001

Distribution of individual inbreeding coefficients, relatedness and influence of stocking on native anadromous brown trout (Salmo trutta) population structure.

We examined polymorphism at seven microsatellite loci in 4023 brown trout (Salmo trutta) collected from 32 tributaries to the Limfjord, Denmark (approximately 200 km) and from two hatcheries used for stocking. Populations differ in their estimated sizes and stocking histories. Mean individual inbreeding coefficients do not differ among locations within rivers. Relatedness varies between sites within rivers indicating varied local dynamics at a very small geographical scale. Relatedness is sometimes lower than expected among an equal number of simulated individuals with randomized genotypes, suggesting structure within locations. Five per cent of the genetic variance is distributed among rivers (F(ST) = 0.049), but in the western, less heavily stocked, area of the Limfjord a higher proportion of the genetic variance is distributed among rivers than among locations within rivers. The reverse is true of the eastern, more heavily stocked, area of the Limfjord. Here, a higher proportion of the genetic variance is distributed among locations within rivers than among rivers. Assignment tests reveal that the majority of trout (mean 77% of all fish) are more probably of local origin than hatchery origin but this proportion varies regionally, with rivers in the western area of the Limfjord showing a relatively high (mean 88%) and those in the eastern area showing a relatively low (mean 72%) proportion of locally assigned trout. These results can be interpreted as reflecting stocking impact. Also, the proportion of locally assigned trout correlates with the populations' stocking histories, with rivers presently subjected to stocking (hatchery trout) showing low (mean approximately 0.73), and rivers where stocking was discontinued showing high (mean approximately 0.84) proportions of local fish, probably reflecting lower survival of hatchery than of wild trout. There is evidence for isolation by distance at a large geographical scale when individual river populations are pooled into nine geographical regions but not at a small geographical scale when populations are considered individually. We reject the null hypothesis that stocking has had no impact on population structure but the relatively high proportion of locally assigned trout in populations where stocking with domestic fish no longer takes place suggests limited long-term success of stocking.

Animals↗
PubMed1972

How genetic background masks single-gene heterosis in Drosophila (polymorphism-selection-isoenzymes-inbreeding-fly).

Conditional heterosis associated with two isoallelic forms of octanol dehydrogenase in Drosophila pseudoobscura has been detected in flies that have been (a) inbred for several generations to make the background genotype as homozygous as practicable, and (b) grown on a medium containing a small amount of octanol. The heterosis was first found in inbred males. The possibility that the effect in females was masked by X-linked polymorphic genes affecting the same fitness components as the locus for octanol dehydrogenase was shown to be correct when, on further inbreeding, heterosis was found in the females of one of the lines. The implications of this and other findings for the current understanding of the genetic structure of natural populations is discussed.

Alcohol Oxidoreductases↗
PubMed1990

DNA "fingerprinting" reveals high levels of inbreeding in colonies of the eusocial naked mole-rat.

Using the technique of DNA fingerprinting, we investigated the genetic structure within and among four wild-caught colonies (n = 50 individuals) of a eusocial mammal, the naked mole-rat (Heterocephalus glaber; Rodentia: Bathyergidae). We found that DNA fingerprints of colony-mates were strikingly similar and that between colonies they were much more alike than fingerprints of non-kin in other free-living vertebrates. Extreme genetic similarity within colonies is due to close genetic relationship (mean relatedness estimate +/- SE, r = 0.81 +/- 0.10), which apparently results from consanguineous mating. The inbreeding coefficient (F = 0.45 +/- 0.18) is the highest yet recorded among wild mammals. The genetic structure of naked mole-rat colonies lends support to kin selection and ecological constraints models for the evolution of cooperative breeding and eusociality.

Animals↗