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PubMed1995

Rapid multipoint linkage analysis of recessive traits in nuclear families, including homozygosity mapping.

Homozygosity mapping is a powerful strategy for mapping rare recessive traits in children of consanguineous marriages. Practical applications of this strategy are currently limited by the inability of conventional linkage analysis software to compute, in reasonable time, multipoint LOD scores for pedigrees with inbreeding loops. We have developed a new algorithm for rapid multipoint likelihood calculations in small pedigrees, including those with inbreeding loops. The running time of the algorithm grows, at most, linearly with the number of loci considered simultaneously. The running time is not sensitive to the presence of inbreeding loops, missing genotype information, and highly polymorphic loci. We have incorporated this algorithm into a software package, MAPMAKER/HOMOZ, that allows very rapid multipoint mapping of disease genes in nuclear families, including homozygosity mapping. Multipoint analysis with dozens of markers can be carried out in minutes on a personal workstation.

Algorithms↗
PubMed1995

[Population sturcture of the Gorno-Mariĭskiĭ region of the Mariĭ El Republic].

The genetic structure of the population of the Gorno-Mariiskii raion, Marii El Republic, was studied. The population consists of two major groups, highland Mari and Russians. The former constitute the majority of the rural population, and the latter, the majority of the urban one. A marked ethnicity-related marriage assortation was found. The value of random inbreeding was estimated using frequencies of surnames. It varied from 0.00015 to 0.00069 (the weighted average was 0.00026). The local inbreeding (a) for Gorno-Mariiskii raion estimated according to Malecot was 0.00029. The local inbreeding for marriages between Mari (0.0022) was five times higher than for marriages between Russians. The indices of endogamy were 0.84 in the rural population and 0.14 in the urban population. The matrix of genetic distances and its image in the form of genetic landscape suggest a regularly distorted isolation by distance and realized panmixia.

Consanguinity↗
PubMed1996

[A genetic and demographic study of Dagestan highland populations and migrants to the lowlands. The relationship between levels of consanguinity, homozygosity and physiologic sensitivity].

This is a continuation of a series of papers devoted to studying the genetic mechanisms of adaptation in migrants from isolated highland populations of Dagestan to new ecological conditions (lowlands). This paper describes the main results of studying the relationship between levels of inbreeding, homozygosity, and physiological sensitivity. Earlier, we found that decreased resistance to changing environmental factors in migrants to lowlands from the Dagestan highlands was connected with their high level of homozygosity. The data obtained allow us to assume that missing links in this chain of events include, in addition to parameters of inbreeding level, parameters of neurophysiological sensitivity, including absolute and differential sensitivity of various analyzers sensory systems, which are from 65 to 75% genetically determined. Migrants from highland auls (villages) to lowlands exhibited a decreased rate of sensomotor reactions in response to light and sound of various intensities, as well as decreased differential color sensitivity in the long-, medium-, and short-wave ranges of the spectrum, compared to highlanders. The results suggest the selective mortality of migrants from highlands to lowlands during adaptation to new conditions. Those migrants who dies were characterized by specific gene complexes that determined the characteristic features of expression of a number of interrelated polymorphic and quantitative traits. Thus, the high levels of homozygosity and inbreeding were accompanied by a greater neurophysiological sensitivity and lower indices of body weight and height.

Adaptation, Physiological↗
PubMed1996

Consanguinity and the sib-pair method: an approach using identity by descent between and within individuals.

To test for linkage between a trait and a marker, one can consider identical marker alleles in related individuals, for instance, sibs. For recessive diseases, it has been shown that some information may be gained from the identity by descent (IBD) of the two alleles of an affected inbred individual at the marker locus. The aim of this paper is to extend the sib-pair method of linkage analysis to the situation of sib pairs sampled from consanguineous populations. This extension takes maximum advantage of the information provided by both the IBD pattern between sibs and allelic identity within each sib of the pair. This is possible through the use of the condensed identity coefficients. Here, we propose a new test of linkage based on a chi2. We compare the performance of this test with that of the classical chi2 test based on the distribution of sib pairs sharing 0, 1, or 2 alleles IBD. For sib pairs from first-cousin matings, the proposed test can better detect the role of a disease-susceptibility (DS) locus. Its power is shown to be greater than that of the classical test, especially for models where the DS allele may be common and incompletely penetrant; that is to say for situations that may be encountered in multifactorial diseases. A study of the impact of inbreeding on the expected proportions of sib pairs sharing 0, 1, or 2 alleles IBD is also performed here. Ignoring inbreeding, when in fact inbreeding exists, increases the rate of type I errors in tests of linkage.

Chromosome Mapping↗
PubMed1977

[Method of computer processing of genealogic material].

The essential moments of the computer algorithms - a construction of pedigree patterns and determination of inbreeding coefficients - are described. The main attention is given to the field material prossesing for the computer system. The common program is composed to three subprograms: pedigree construction, F estimation and evaluation of information quantity concerning the ancestors. The principal algorithms of the pedigree subprogram is based on computations of a parents computer adress from the proband's code. Such a run is repeated from generation to generation, until the information of ancestors comees to zero. Common ancestors for Wright's inbreeding estimation have been found by sorting out and comparison of husband's and wife's ancestors. The inbreeding coefficient has been formed as the kinship coefficient of parents.

Computers↗
PubMed1997

[Consanguinity among Arabs in Israel].

In a previous nationwide study, we examined the rate of consanguineous matings in the Israeli Arab community. The average inbreeding coefficient was 0.0192, much higher than that reported for the general population of Israel, 0.0038 in 1956-7. The inbreeding coefficients of 69 Arab villages, towns and cities (excluding the Bedouin in the South) were determined. Knowledge of the inbreeding coefficients of the various local populations is of value for geneticists, pediatricians and gynecologists and for planning suitable health programs.

Arabs↗
PubMed1998

The significance of relatedness and gene flow on population genetic structure in the®subsocial spider Eresus cinnaberinus (Araneae: Eresidae)

Interdemic selection, inbreeding and highly structured populations have been invoked to explain the evolution of cooperative social behaviour in the otherwise solitary and cannibalistic spiders. The family Eresidae consists of species ranging from solitary and intermediate subsocial to species exhibiting fully cooperative social behaviour. In this study we, in a hierarchical analysis, investigated relatedness of putative family clusters, inbreeding and population genetic structure of the subsocial spider Eresus cinnaberinus. Five hierarchical levels of investigation ranging from large scale genetic structure (distances of 250 and 50 km level 1 and 2) over microgeographic structure (20 km2 and 4 km2, level 3 and 4) to a single hill transect of 200 m (level 5) were performed. The purpose of level 5 was two-fold: (1) to investigate the relatedness of putative family groups, and (2) to evaluate the influence of both family living and sampling design on higher level estimates. Relatedness estimates of putative family groups showed an average relatedness of R=0.26. There was no indication of inbreeding. In contrast to social spiders, genetic variation was abundant, Heapproximately0.10. The population genetic structure was intermediate between social and asocial spiders. Genetic variance increased continually across hierarchical levels. Family structured neighbourhoods biased differentiation estimates among level 5 samples (FST=0.04) and level 3 and 4 samples (0.07 0, was caused by disjunct sampling from separate neighbourhoods. Larger scale samples were highly differentiated 0.12<FST<0.26, depending on level and sampling design. Due to a distance effect family living did not influence estimates of the higher level 1. Although the dispersing sex among social spiders and the subsocial E. cinnebarinus differ, females versus males, female behaviour of both sociality classes lead to high genetic variance.Copyright 1998 The Linnean Society of London

Journal Article↗
PubMed1998

Effect of reference database on frequency estimates of polymerase chain reaction (PCR)-based DNA profiles.

A variety of general, regional, ancestral and ethnic databases is available for the polymerase chain reaction (PCR)-based loci LDLR, GYPA, HBGG, D7S8, Gc, DQA1, and D1S80. Generally, we observed greater differences in frequency estimations of DNA profiles between racial groups than between ethnic or geographic subgroups. Analysis revealed few forensically significant differences within ethnic subgroups, particularly within general United States groups, and multi-locus frequency estimates typically differ by less than a factor of ten. Using a database different from the one to which a target profile belongs tends to overestimate rarity. Implementation of the general correction of homozygote frequencies for a population substructure, advised by the 1996 National Research Council report, The Evaluation of Forensic DNA Evidence, has a minimal effect on profile frequencies. Even when it is known that both the suspect and all possible perpetrators must belong to the same isolated population, the special correction for inbreeding, which was proposed by the 1996 National Research Council report for this special case, has a relatively modest effect, typically a factor of two or less for 1% inbreeding. The effect becomes more substantial (exceeding a factor of ten) for inbreeding of 3% or more in multi-locus profiles rarer than about one in a million.

Alleles↗
PubMed1998

[Distribution of family names in rural populations of Kursk region].

The coefficient of inbreeding and its components were calculated for populations of rural districts of Kursk oblast with the use of the isonymic method. The following values were obtained: F(it) = 0.000567, Fst = 0.000650, and Fis = 0.000083. The Fst value agreed with the value of Malecot's local inbreeding coefficient (0.000201). In the districts where the proportions of families with frequent family names (FFNs; a frequency of 0.001 and more) were 50% and over, these family names were sufficient to adequately describe the population structure. The migration index and the index of family-name diversity were calculated. Significant correlations were revealed between Fst, the migration index, the index of family-name diversity, Malecot's local inbreeding, the mean square distance between birthplaces of spouses, the effective migration pressure, and the coefficient of linear systematic pressure.

Biomarkers↗
PubMed2026

REVIEW: CAUSES AND CONSEQUENCES OF DOING IT WITH ONESELF-SYNTHESIS AND META-ANALYSIS OF NEODERMATAN HERMAPHRODITIC MATING SYSTEMS.

Hermaphroditic mating systems profoundly influence evolution, yet in parasitic flatworms (Neodermata) they remain strikingly understudied. For decades, sweeping claims have oscillated between pervasive selfing and near-universal outcrossing, reflecting a lack of comprehensive synthesis. This review, the first in more than 40 yr, integrates nearly a century of research, from early observational studies to modern genetic analyses, to reveal a far more nuanced picture. Our meta-analysis of population-genetic data shows a sharp departure from the bimodal selfing patterns typical of plants and other hermaphroditic animals: neodermatan parasites are strongly skewed toward outcrossing. We link variation in mating systems to parasite demography and life-history traits, especially in species exhibiting mixed mating or elevated selfing. Current evidence suggests outcrossing is common, but taxonomic and life-history gaps preclude definitive conclusions. Beyond patterns and causes, we explore evolutionary consequences ranging from fitness costs such as inbreeding depression to trait evolution, including delayed selfing, sex allocation, and complex life cycles. Evidence for inbreeding depression is mixed and limited, yet emerging approaches using selfing-rate comparisons offer promising avenues for future research. Notably, demographic constraints, such as infection intensity and life-cycle architecture, often explain mixed mating without invoking selection, challenging classical models. Similarly limited in number, studies on sex allocation indicate that hermaphroditic mating systems can shape reproductive investment, with patterns consistent with local sperm competition in some taxa. By consolidating historical observations with modern genetic insights, this review provides the most comprehensive synthesis of hermaphroditic mating systems in the Neodermata to date. We highlight critical gaps in taxonomic coverage and experimental data and point to future opportunities for integrating genomic approaches with ecological and demographic frameworks. Such integration will be essential to illuminate how mating systems shape parasite evolution and to resolve long-standing questions about the persistence of mixed mating despite theoretical expectations.

Animals↗
PubMed1997

Determinants of female dispersal in Thomas langurs.

Female dispersal occurs in a number of primate species. It may be related to: avoidance of inbreeding, reduction in food competition, reduction of predation risk, or avoidance of infanticide in combination with mate choice. Female dispersal was studied for a 5-year period in a wild population of Thomas langurs (Presbytis thomasi) that lived in one-male multi-female groups. Juvenile and adult individuals of both sexes were seen to disperse. Females appeared to transfer unhindered between groups, mostly from a larger group to a recently formed smaller one. They transferred without their infants and when not pregnant, and seemed to transfer preferentially during periods when extra-group males were harassing their group. During these inter-group encounters extra-group males seemed to try to commit infanticide. Thus, the timing of female transfer was probably closely linked to infanticide avoidance. Moreover, females seemed to transfer when the resident male of their group was no longer a good protector. The observations in the present study suggest that females transferred to reduce the risk of infanticide. Female dispersal may have another ultimate advantage as well, namely inbreeding avoidance. Due to the dispersal of both females and males the social organization of Thomas langurs was rather fluid. New groups were formed when females joined a male; male takeovers were not observed. Bisexual groups had only a limited life span, because all adult females of a bisexual group could emigrate. This pattern of unhindered female dispersal affects male reproductive strategies, and in particular it might lead to infanticidal behavior during inter-group encounters.

Animals↗
PubMed1978

Three mice, two blind.

In a closed colony of approximately one million mice which had been rigidly pedigreed (brother to sister) from a few original mice, three unusual mice have appeared. These three have obviously deviated from what would be expected according to the accepted laws of inbreeding geneity. Thus three unexpected incidences of increased variability have occurred three times in addition to the occasional appearance of new mutations (approximately one in 26,000 mice). The first mouse developed a sudden increase in susceptibility to spontaneous tumors of mammary origin. She became the mother of the well-known C family used extensively in cancer research. The second mouse clearly exhibited, among clear-cut altered biological characteristics, several somatic mutations, thus indicating an unstable genetic condition. The third mouse developed a highly significant capacity to regress and eliminate spontaneous tumor tissue. The conclusion is reached that unstable biological states arise occasionally during the process of inbreeding.

Animals↗
PubMed1997

The evolutionary dynamics of selfish replicators: a two-level selection model.

The aim of the present paper is to study the evolutionary dynamics of selfish replicators in a constant genetic background. Selfish replicators are viewed as alleles at a single locus, having a pleiotropic effect. Infinitely many alleles are possible; they act on individual fitness and have various levels of ability to distort segregation. This results in a two-level process of selection, including inter-individual selection (effect on individual fitness) and intra-individual selection (ability to distort segregation). The model takes other parameters into account, such as dominance, inbreeding and inbreeding depression. The system can have two different behaviours. (1) In some cases, evolutionary cycles are possible. The cycles correspond to an alternation of phases with predominant inter-individual selection, corresponding to major-effect mutations, and phases with predominant intra-individual selection, corresponding to small-effect mutations. (2) For other values of the parameters, a synthetic fitness can be defined: this absolute allelic fitness is estimated as a function of one's fitness due to both inter-individual and intra-individual selection. During the course of evolution, the synthetic fitness increases. The optimisation of a synthetic fitness is the most general process. The optimised value is essentially homologous to the value optimised for resource allocation to male and female function in hermaphrodites (female function being homologous to the effect on individual fitness, and male function being homologous to distortion ability). The relative importance of both behaviours is discussed. It is argued that repeated sequences causing some human degenerative hereditary diseases may follow a two-step evolutionary process: a progressive increase in number of sequences accompanied by a decrease of the individual fitness would be followed by massive elimination of such sequences. But in general the optimisation of the synthetic fitness seems to be more likely.

Animals↗
PubMed2000

Predicting response to selection on a quantitative trait: a comparison between models for mixed-mating populations.

Two different theoretical frameworks have been developed to predict response to selection in a mixed mating population (in which reproduction occurs by a mixture of outcrossing and self-fertilization). The genotypic covariance model (GCM) and the structured linear model (SLM) rely on the same assumptions regarding quantitative trait inheritance, but use different genetic summary statistics. Here, we demonstrate the algebraic relationships between the various genetic metrics used in each theory. This is accomplished by reformulating the GCM in terms of the Wright-Kempthorne equation. We use stochastic simulations to investigate the relative accuracy of each theory for a range of selfing rates. The SLM is generally more accurate than the GCM, the most pronounced differences emerging in simulations with inbreeding depression for fitness. In fact, with strong inbreeding depression and high selfing rates, evolution can occur opposite the direction predicted by the GCM. The simulations also indicate that direct application of random mating models to partially selfing populations can produce very inaccurate predictions if quantitative trait loci exhibit dominance.

Animals↗
PubMed2000

Epistasis and the conversion of non-additive to additive genetic variance at population bottlenecks.

The effect of population bottlenecks on the mean and the additive variance generated by two neutral independent epistatic loci has been studied theoretically. Six epistatic models, used in the analysis of binary disease traits, were considered. Ancestral values in an infinitely large panmictic population were compared with their expectations at equilibrium, after t consecutive bottlenecks of equal size N (derived values). An increase in the additive variance after bottlenecks (inversely related to N and t) will occur only if the frequencies of the negative allele at each locus are: (1) low, invariably associated to strong inbreeding depression; (2) high, always accompanied by an enhancement of the mean with inbreeding. The latter is an undesirable property, making the pertinent models unsuitable for the genetic analysis of disease. For the epistatic models considered, it is unlikely that the rate of evolution may be accelerated after population bottlenecks, in spite of occasional increments of the derived additive variance over its ancestral value.

Animals↗
PubMed1989

Blood biochemical polymorphisms as markers for genetic characteristics of wild Spanish and domestic rabbits.

Seventeen blood proteins were studied in a sample of 412 Spanish wild rabbits and in 598 domestic rabbits belonging to various breeds. The wild rabbit populations showed a high level of genetic polymorphism. Six loci were monomorphic, while the remaining ten loci were segregating for at least two alleles. Two of the loci that were polymorphic in the wild rabbits were monomorphic in the domestic ones. Wright's inbreeding coefficient in the total Spanish wild rabbit population was F = 5.66, indicating subdivision of the total population. Inbreeding coefficients, estimated by Kidd et al.'s method (Anim. Blood Grps, Biochem. Genet. 11: 21-38), differed significantly from zero, being 15.62%, in wild rabbits and 6-12% in domestic breeds, indicating consanguinity. Genetic distances between wild rabbit populations showed that factors other than geographic distance (e.g., bottlenecks, barriers such as rivers, mountains, etc.) may explain the result that a northern population forms a cluster with two central populations whereas the northeastern populations form a different cluster with another central population. Populations of the first cluster are more closely related to the captive populations than others. There are three population clusters of domestic rabbits, namely (1) New Zealand White and a hybrid combination; (2) Spanish Common, Butterfly, Burgundy, and Californian; and (3) Spanish Giant.

Animals↗
PubMed1988

The founder effect theory: quantitative variation and mdg-1 mobile element polymorphism in experimental populations of Drosophila melanogaster.

One of the main points of Mayr's 'founder's principle' is the role played by inbreeding in the first generations after the foundation of a population. To test this role, we studied 10 experimental populations of Drosophila melanogaster, each founded by one brother-sister pair; these sib pairs differed for their values of viability components of their F1 offsprings. The populations so formed were maintained en masse with non-overlapping generations. Under our uniform laboratory environmental conditions, the mean viability and within-family component of variance (measured on wing length) values of the first generations depended on the viability component values of the founders. After about twenty generations, all but one of these populations reached equilibrium values similar to those of the parental population. Moreover, the insertion patterns of the mdg-1 mobile element were analysed in the founded populations by in situ hybridization on polytene chromosomes. The patterns differed between the founded populations. More than forty generations were needed before movements of transposable elements reshaped the genome in a significant way. Although it is classically admitted that inbreeding resulting from founder event ultimately leads to extinction, our results show that once the first generations are over, the founded populations become firmly established and present the characteristics of the parental population.

Animals↗
PubMed1993

Half-sib mating structures.

All ways in which all matings in a population can be between half-sibs under a generalization of regular systems of inbreeding are characterized for both finite and infinite populations. A model of random half-sib mating is developed and analyzed, and the asymptotic configuration of populations subject to it is described. The classical model of half-sib mating which ensues from the standard definition of regular systems of inbreeding is only one of many ways a population can propagate by half-sib mating, and a wide range of genetic identity is possible dependent on which half-sib mating structure governs a population.

Animals↗