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PubMed2002

Within-breed heterozygosity of canine single nucleotide polymorphisms identified by across-breed comparison.

Identification of single nucleotide polymorphisms (SNPs) by DNA sequence comparison across breeds is a strategy for developing genetic markers that are useful for many breeds. However, the heterozygosity of SNPs identified in this way might be severely reduced within breeds by inbreeding or genetic drift in the small effective population size of a breed (population subdivision). The effect of inbreeding and population subdivision on heterozygosity of SNPs in dog breeds has never been investigated in a systematic way. We determined the genotypes of dogs from three divergent breeds for SNPs in four canine genes (ACTC, LMNA, SCGB, and TYMS) identified by across-breed DNA sequence comparison, and compared the genotype frequencies to those expected under Hardy-Weinberg equilibrium (HWE). Although population subdivision significantly skewed allele frequencies across breeds for two of the SNPs, the deviations of observed heterozygosities compared with those expected within breeds were minimal. These results indicate that across-breed DNA sequence comparison is a reasonable strategy for identifying SNPs that are useful within many canine breeds.

Animals↗
PubMed2002

Population structure of an endangered species living in contrasted habitats: Parnassia palustris (Saxifragaceae).

In endangered species, it is critical to analyse the level at which populations interact (i.e. dispersal) as well as the levels of inbreeding and local adaptation to set up conservation policies. These parameters were investigated in the endangered species Parnassia palustris living in contrasted habitats. We analysed population structure in 14 populations of northern France for isozymes, cpDNA markers and phenotypic traits related to fitness. Within population genetic diversity and inbreeding coefficients were not correlated to population size. Populations seem not to have undergone severe recent bottleneck. Conversely to pollen migration, seed migration seems limited at a regional scale, which could prevent colonization of new sites even if suitable habitats appear. Finally, the habitat type affects neither within-population genetic diversity nor genetic and phenotypic differentiation among populations. Thus, even if unnoticed local adaptation to habitats exists, it does not influence gene flow between populations.

DNA, Chloroplast↗
PubMed2003

Subdivision and haplotype structure in natural populations of Arabidopsis lyrata.

High levels of inbreeding are expected to cause a strong reduction in levels of genetic variability, effective recombination rates and in adaptation compared with related outcrossing populations. We examined patterns of DNA polymorphism at five nuclear loci and one chloroplast locus within and between four populations of the outcrossing plant Arabidopsis lyrata, a close relative of the highly self-fertilizing model species A. thaliana. The observed patterns are compared with species-wide polymorphism at orthologous loci, as well as within- and between-population patterns at other studied loci in A. thaliana. In addition to evidence for much higher average within-population diversity, species-wide levels of silent polymorphism are generally higher in A. lyrata than in A. thaliana, unlike the results from a previous study of the ADH locus. However, polymorphism is also low in the North American A. lyrata subspecies lyrata compared with the European subspecies petraea, suggesting either a population bottleneck in North American populations or recent admixture involving diverged European populations. Differentiation between the two subspecies is strong, although there are few fixed differences, suggesting that their isolation is recent. Estimates of intralocus recombination rates and analysis of haplotype structure in European A. lyrata populations indicate lower recombination than predicted based on the variability together with physical recombination rates estimated from A. thaliana. This may be due to strong population subdivision, or to recent departures from demographic equilibrium such as a bottleneck or population admixture. Alternatively, there may be consistently lower recombination rates in the outcrossing species. In contrast, estimates of recombination rates from species-wide samples of A. thaliana are close to the values expected assuming a high rate of self-fertilization. Complex population histories in both A. thaliana and A. lyrata complicate theoretical predictions and empirical tests of the effects of inbreeding on polymorphism and molecular evolution.

Arabidopsis↗
PubMed2003

Fine-scale genetic structure in a free-living ungulate population.

The fine-scale genetic structure of wild animal populations has rarely been analysed, yet is potentially important as a confounding factor in quantitative genetic and allelic association studies, as well as having implications for population dynamics, inbreeding and kin selection. In this study, we examined the extent to which the three spatial subunits, or hefts, of the Village Bay population of Soay sheep (Ovis aries) on St Kilda, Scotland, are genetically structured using data from 20 microsatellite and protein loci. Allele frequencies differed significantly among three hefts in all the study years we considered (1987-2000 inclusive). Small but significantly positive F(ST) and negative F(IS) values were observed in most years, indicating that the hefts are genetically differentiated, and that within each heft there is more observed heterozygosity than would be expected if each were an isolated breeding population. Males showed less fidelity to their natal heft, and as a consequence higher levels of relatedness within hefts were observed among females than among males. There was a significant negative relationship between geographical proximity and relatedness in pairwise comparisons involving females, and on average pairs of females located within 50 m of each other were related at the equivalent level of second cousins. Structure is therefore largely driven by incomplete postnatal dispersal by females. Mating appears to be random with respect to the spatial-genetic substructure of the hefts, and therefore genetic structure does not contribute to the overall rate of inbreeding in the population. However, genetic substructure can lead to allelic associations and generate environmental effects within lineages that have the potential to confound heritability analyses and allelic association studies.

Adenosine Deaminase↗
PubMed2004

Population genetic structure of the sugar beet cyst nematode Heterodera schachtii: a gonochoristic and amphimictic species with highly inbred but weakly differentiated populations.

The sugar beet cyst nematode Heterodera schachtii is a soil-dwelling phytoparasitic nematode that feeds on beet roots. It is an important pest in most sugar beet growing areas, and better knowledge of its genetic variability is an important step to preserve the durability of resistant sugar beet varieties. The population genetic structure of this species in northern France was studied using five microsatellite markers. A hierarchical sampling design was used to investigate spatial structuring at the scale of the region, the field and the plant. Multilocus genotypes were obtained for single individual second-stage larvae, using only one individual per cyst in order to avoid the analysis of closely allied individuals (larvae from the same cyst share at least the same mother). A consistent trend of heterozygote deficit at all loci was observed at all spatial scales. Heterozygote deficit at the level of individual plants argues against its generation through a Wahlund effect. Inbreeding could be due to very limited active dispersal of larvae in the soil, favouring mating between siblings, such as larvae emerging from the same cyst. Such behaviour could have important consequences for the evolution of virulence in increasing the production of homozygous virulent individuals. Moreover, an analysis of molecular variance (amova) reveals that only 1.6% of the genetic variability is observed among regions, 3.7% among fields of the same region and 94.6% within fields. The very low level of genetic differentiation among fields is also indicated by low values of FST (</= 0.105) even for fields 150 km apart. We suggest that long-distance gene flows occur due to passive transport of cysts by human activities, water or wind. As such mechanisms of gene flow would involve cysts and not larvae, the strong signals of inbreeding observed at the local scale should not be disrupted. To our knowledge, this study constitutes the first investigation of the genetic structure of a phytoparasitic nematode based on neutral codominant genetic markers scored in single individuals.

Analysis of Variance↗
PubMed2005

"Clonal" population structure of the malaria agent Plasmodium falciparum in high-infection regions.

The population genetic structure of Plasmodium falciparum, the agent of malignant malaria, has been shown to be predominantly "clonal" (i.e., highly inbred) in regions of low infectivity; in high-infectivity regions, it is often thought to be panmictic, or nearly so, although there is little supporting evidence for this. The matter can be settled by investigating the parasite's genetic makeup in the midgut oocysts of the mosquito vector, where the products of meiosis can directly be observed. The developmental stages of P. falciparum are haploid, except in the oocysts of infected mosquito vectors, where two gametes fuse, diploidy occurs, and meiosis ensues. We have investigated genetic polymorphisms at seven microsatellite loci located on five chromosomes by assaying 613 oocysts in 145 mosquitoes sampled from 11 localities of Kenya, where malignant malaria is perennial and intense. There is considerable allelic variation, 16.3 +/- 2.1 alleles per locus, and considerable inbreeding, approximately 50% on the average. The inbreeding is caused by selfing (approximately 25%) and nonrandom genotype distribution of oocysts among mosquito guts (35%). The observed frequency of heterozygotes is 0.43 +/- 0.03; the expected frequency, assuming random mating, is 0.80 +/- 0.05. Linkage disequilibrium is statistically significant for all 21 pairwise comparisons between loci, even though 19 comparisons are between loci in different chromosomes, which is consistent with strong deviation from panmixia and the consequent reproduction of genomes as clones, without recombination between gene loci. This is of considerable evolutionary significance and of epidemiological consequence, concerning the spread of multilocus drug and vaccine resistance.

Animals↗
PubMed1999

Genetic study of embryonic mortality in White Leghorn lines selected for egg production traits.

The present study compares embryonic mortality between lines selected for different production traits, assesses the effects of inbreeding of the hen and embryo on embryonic mortality, and estimates genetic parameters of embryonic mortality. The experiment covered 10 generations of selection for increased egg number (EN), egg weight (EW), egg mass (EM) and a control line (C). The data included age at 1st egg, egg number and egg weight. Percent fertile eggs (PF), percent hatched of fertile eggs (PHF) and percent dead chick at hatch (PDH) were also recorded for the selected parents. PDH was higher in the selected lines than in the control line. Among the selected lines, the EW line had the highest embryonic mortality. Inbreeding of the hen and embryo had no significant effect on PDH in any of the lines. Estimates of heritability for PDH were 0.10+/-0.05, 0.02+/-0.02, 0.03+/-0.02 and 0.02+/-0.02 for lines EN, EW, EM and C, respectively. There was a positive genetic correlation between egg weight and PDH in line EW indicating that selection for increased egg weight was associated with high embryonic mortality. A negative genetic correlation between PDH and reproductive traits in line EN was observed, which is favourable.

Animals↗
PubMed2001

Population parameters to compare dog breeds: differences between five Dutch purebred populations.

Differences in five purebred dog populations born in 1994 in the Netherlands were evaluated using different parameters. Numerically, the Golden Retriever was the largest breed (840 litters of 234 sires) and the Kooiker Dog (101 litters of 41 sires) the smallest. The litter per sire ratio was largest in the Bernese Mountain Dog (4.59) and lowest in the Kooiker Dog (2.46). The mean relatedness and the actual mean level of inbreeding in the studied generations were 0.102 and 0.056 respectively for the Bernese Mountain Dog, 0.041 and 0.046 for the Bouvier des Flandres, 0.087 and 0.061 for the Boxer, 0.020 and 0.018 for the Golden Retriever, and 0.146 and 0.070 for the Kooiker Dog. Quantification and visualization of population parameters for purebred dogs will facilitate the comparison of breeds and the comparison of breeds in different periods or countries. It appears unlikely that the increase in inbreeding is a major determinant of the possible increase in the frequency of genetic diseases.

Animals↗
PubMedDate not supplied

Elements of the surname structure of Austria.

The isonymy structure of Austria was studied using the surname distributions in 1081002 private telephone users selected from about 4000000 registered in a 1996 commercial CD-ROM, which contains all Austrian users. The sample was distributed in 120 towns representing an approximately uniform distribution over the country. The number of different surnames found in the whole analysis was 140766. Lasker's distance, the negative value of the logarithm of isonymy between localities, was found to be linearly and significantly correlated with the log of geographic distance, with r = 0.565 +/- 0.011. A dendrogram was built with the matrix of isonymy distance, using the Unweighted Pair-Group Method using Arithmetic averages, UPGMA. It separates the Austrian towns in five main clusters, one along the central portion of the country, another one which occupies the northern region of central Austria; then comes a third cluster at the north-eastern part, a fourth cluster in the western region, and finally a small cluster towards the border with Slovenia. Within each, small subclusters with specific geographic distributions could be delimited. The main clusters correspond fairly well to the classic regions of Austria. The results were compared with those obtained in similar analyses of Switzerland, Germany, Italy and Venezuela. From the present analysis, isolation by distance emerges clearly, and it is stronger than in Germany but smaller than that observed in Italy, Switzerland and Venezuela. The random component of inbreeding estimated from isonymy, at the level of resolution used here, indicates that the inbreeding level in Austria is rather uniform.

Austria↗
PubMedDate not supplied

Mating patterns of the Abbad tribe in Jordan.

The mating patterns of the Abbad tribe in Jordan are examined based on empirical data obtained from four male samples representing the different levels of the Abbad's substructure as well as on nonempirical information and pedigrees collected during field work. From the total matings in each sample, at least one-third were first-cousin marriages, and some 90 per cent were marriages within the Abbad. The estimated inbreeding coefficient (mean F = 0.018) was relatively high. Relatedness, geographic locality, maternal links, and the type of economy are suggested as the factors which influenced the mating behavior of the Abbad. The study also indicates the vital role of matings in the formation and make-up of the tribe. The Abbad tribe could be described as an endogamic population consisting of more or less inbreeding subunits.

Adult↗
PubMed2003

Delayed selfing as an optimal mating strategy in preferentially outcrossing species: theoretical analysis of the optimal age at first reproduction in relation to mate availability.

The evolution of mating systems and that of life history have usually been modeled separately. However, they may be to some extent coupled in natural situations because they rely on the same phenotypic traits. Here, we focus on one of these traits, the age at first reproduction, in a species able to self- and cross-fertilize. When inbreeding depression is strong, self-fertile species preferentially cross-fertilize. However, outcrossing is not always possible when the availability of sexual partners is limited. The optimal reproductive strategy in this case would be to wait for a sexual partner for a certain period of time (the waiting time) and then switch to selfing if no mates have been encountered (reproductive assurance strategy). We predict the evolution of an optimal waiting time depending on the efficiency of resource reallocation to late fecundity, on the inbreeding depression, and on the instantaneous probability of encountering a partner versus dying. As a consequence of reduced mate availability, intermediate selfing rates can be generated in preferentially outcrossing populations, but they are lowered by the existence of a waiting time. Our model may thus explain low selfing rates observed in natural populations of many self-fertile, preferentially outcrossing plants or animal species.

Age Factors↗
PubMed2026

Genotypic and phenotypic consequences of domestication in dogs.

Runs of homozygosity (ROH) are genomic regions that arise when identical haplotypes are inherited from a shared ancestor. In this study, we explored ROH across 556 whole-genome sequences from domesticated and non-domesticated dogs. Then, we leveraged ROH from 466 breed dogs, representing 13 breed groups and 13 phenotypic traits, to investigate associations between genetic diversity and non-disease phenotypes. We identified significant associations between the ROH-based inbreeding coefficient (FROH) and multiple phenotypes. These include three quantitative traits (height, weight, lifespan) and ten morphological and coat-related traits. After correcting for population structure, we identified more than 45 genes associated with quantitative traits that exceeded suggestive or genome-wide significance (GWS) thresholds. We also observed distinct patterns of inbreeding across dog populations, including elevated levels of long ROH in modern breed dogs relative to more ancient breeds, consistent with intensive breeding practices during Victorian-era breed formation. Together, our results demonstrate how domestication, demographic bottlenecks, and selective breeding have shaped patterns of homozygosity and contributed to the genetic architecture of complex traits in dogs, highlighting an important role for non-additive genetic variation and polygenicity.

Animals↗
PubMed1991

FST in a hierarchical island model.

It is shown that in a hierarchical island model, in which demes within a neighborhood exchange migrants at a much higher rate than do demes in different neighborhoods, hierarchical F statistics introduced by S. Wright can indicate the extent of gene flow within and between neighborhoods. At equilibrium, the within-neighborhood inbreeding coefficient, FSN, is approximately 1/(1 + 4Nm1) where N is the deme size and m1 is the migration rate among demes in the same neighborhood. The between-neighborhood inbreeding coefficient, FNT, is approximately 1/(1 + 4Ndm2) where d is the number of demes in a neighborhood and m2 is the migration rate among demes in different neighborhoods.

Animals↗
PubMed1992

Effective size of nonrandom mating populations.

Nonrandom mating whereby parents are related is expected to cause a reduction in effective population size because their gene frequencies are correlated and this will increase the genetic drift. The published equation for the variance effective size, Ne, which includes the possibility of nonrandom mating, does not take into account such a correlation, however. Further, previous equations to predict effective sizes in populations with partial sib mating are shown to be different, but also incorrect. In this paper, a corrected form of these equations is derived and checked by stochastic simulation. For the case of stable census number, N, and equal progeny distributions for each sex, the equation is [formula: see text], where Sk2 is the variance of family size and alpha is the departure from Hardy-Weinberg proportions. For a Poisson distribution of family size (Sk2 = 2), it reduces to Ne = N/(1 + alpha), as when inbreeding is due to selfing. When nonrandom mating occurs because there is a specified system of partial inbreeding every generation, alpha can be substituted by Wright's FIS statistic, to give the effective size as a function of the proportion of inbred mates.

Breeding↗
PubMed2001

High genetic load in the Pacific oyster Crassostrea gigas.

The causes of inbreeding depression and the converse phenomenon of heterosis or hybrid vigor remain poorly understood despite their scientific and agricultural importance. In bivalve molluscs, related phenomena, marker-associated heterosis and distortion of marker segregation ratios, have been widely reported over the past 25 years. A large load of deleterious recessive mutations could explain both phenomena, according to the dominance hypothesis of heterosis. Using inbred lines derived from a natural population of Pacific oysters and classical crossbreeding experiments, we compare the segregation ratios of microsatellite DNA markers at 6 hr and 2-3 months postfertilization in F(2) or F(3) hybrid families. We find evidence for strong and widespread selection against identical-by-descent marker homozygotes. The marker segregation data, when fit to models of selection against linked deleterious recessive mutations and extrapolated to the whole genome, suggest that the wild founders of inbred lines carried a minimum of 8-14 highly deleterious recessive mutations. This evidence for a high genetic load strongly supports the dominance theory of heterosis and inbreeding depression and establishes the oyster as an animal model for understanding the genetic and physiological causes of these economically important phenomena.

Alleles↗
PubMed2003

On the determination of recombination rates in intermated recombinant inbred populations.

The recurrent intermating of F(2) individuals for some number of generations followed by several generations of inbreeding produces an intermated recombinant inbred (IRI) population. Such populations are currently being developed in the plant-breeding community because linkage associations present in an F(2) population are broken down and a population of fixed inbred lines is also created. The increased levels of recombination enable higher-resolution mapping in IRI populations relative to F(2) populations. Herein we derive relationships, under several limiting assumptions, for determining the expected recombination fraction in IRI populations from the crossover rate per meiosis. These relationships are applicable to situations where the inbreeding component of IRI population development is by either self-fertilization or full-sib mating. Additionally, we show that the derived equations can be solved for the crossover rate per meiosis if the recombination fraction is known for the IRI population. Thus, the observed recombination fraction in any IRI population can be expressed on an F(2) basis. The implications of this work on the expansion of genetic maps in IRI populations and limits for detecting linkage between markers are also considered.

Chromosome Mapping↗
PubMed1972

Origin of reproductive isolation in the absence of apparent genic differentiation in a geographic isolate of Drosophila pseudoobscura.

F(1) males obtained from the cross of D. pseudoobscura females from Bogotá (Colombia) x males of this species from mainland, i.e. populations from various locations in the United States and from Guatemala, are sterile. This sterility is due to genes located on the X chromosome and the autosomes; the Y chromosome is not involved. The percentage of sterile males in backcrosses can be explained by assuming an interaction between two loci on the Bogotá X chromosome and probably two loci, one each on two of the mainland autosomes. The role of founder events, inbreeding and geographic isolation in the development of reproductive isolation and the magnitude of gene differences responsible for the origin of reproductive isolation is discussed. It is concluded that founder events, inbreeding and geographic isolation play a major role in the development of reproductive isolation and that major adaptive incorporation of new alleles at a large number of structural loci is not necessary for the origin of reproductive isolation.

Animals↗
PubMed1974

An experimental comparison of individual, family and combination selection.

Two selection experiments comparing the relative efficiencies of individual, family, and combination selection were conducted. The expected results for larval weight of Tribolium (h(2) = 0.20) and for pupal weight (h(2) = 0.40) were that combination selection would be a more efficient method than family selection, and that family selection would exceed individual selection. In experiment I, individual selection produced more response (P < 0.05) than did combination or family, which was not in agreement with expectation. There was confounding of inbreeding levels and random drift due to differential effective population sizes in the lines selected by different methods. Experiment II consisted of ten single-generation selection tests. An advantage of this approach is that it eleminates the inherent problems of differential inbreeding levels and differential rates of genetic drift due to unequal population sizes among the methods of selection. There were no statistically significant differences in efficiency among the three methods of selection for both traits. This was contrary to theoretical expectations but does suggest that with traits of 20% h(2) or higher, and where feasible, one may be justified in basing selection decisions on the phenotype of the individual only. Other advantages of single generation testing are that it allows more precise testing of selection theory and unbiased standard errors for estimates of realized heritability.

Animals↗