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[Maximum entropy principle and population genetic equilibrium].

A general mathematic model of population genetic equilibrium was constructed based on the maximum entropy principle. We proved that the maximum entropy probability distribution was equivalent to the Hardy-Weinberg equilibrium law. A population reached genetic equilibrium when the genotype entropy of the population reached the maximal possible value. In information theory, the entropy or the information content is used to measure the uncertainty of a system. In population genetics, we can use entropy to measure the uncertainty of the genotype of a population. The agreement of the maximum entropy principle and the hardy-Weinberg equilibrium law indicated that random crossing is an irreversible process, which increases the genotype entropy of the population, while inbreeding and selection decrease the genotype entropy of the population. In animal or plant breeding, we often use selection and/or inbreeding to decrease the entropy of a population, and use intercrossing to increase the entropy of the population. In this point of view, breeding is actually regulating the entropy of population. By applying the basic principle of informatics in population genetics, we revealed the biological significance of the genotype entropy and demonstrated that we can work over population genetic problems with the principles and methods of informatics and cybernetics.

Animals↗

[Heterogeneity and several clinico-genetic correlations in epilepsy under inbred conditions].

The types of inheritance and clinico-genetical correlatins of epilepsy in 291 probands in conditions of inbreeding were studied. The data obtained confirmed the multifactorial (gene-polygene+medium) inheritance of epileptic and convulsive predispositions and contradicted the hypothesis of primarily recessive inheritance of epilepsy. Together with family forms of the disease, which were communicated mainly according to an uncertained and dominant type (rarely recessive type), there were existed forms of eipilepsy with incomplete genetical hereditary predisposition (which were observed in relatives of 2-3 generations only by epileptic features) and phenotypical forms concentrated in sporadic groups. There were found the dependences onthe rate of occurrence of secondary epilepsy (with or without epileptoidness), epileptoid psychopathy and children convulsions in relatives, on the type of inheritance, the age of manifestations, the form, polymorphism of the attacks, the severity of the developement of epilepsy, the expressiveness of epileptoidness in probands and high severity of the disease with distinct epileptoidness inbreeding families. The hereditary heterogeneity of epilepsy, associated, perhaps, with pleiotropy of epileptic (with or without epileptoidness) genes, was assumed. The found clinico-genetical correlaltions mightbe taken into account in medico-genetical prognosis of families burdened by epilspsy in analogous populational-demographic conditions.

Adolescent↗

[Causes of mental retardation in children of immigrant background. A registry study of the occurrence of consanguinity among parents of mentally retarded children at the Center for Handicapped, Glostrup hospital, county of Copenhagen].

INTRODUCTION: In the County of Copenhagen the treatment of mentally retarded (MR) children is centralised in the Center for Handicapped (CFH). The aim of this study was to elucidate whether the frequency of MR is higher in children from ethnic minorities than in the background population and whether an increase could be ascribed to inbreeding. MATERIAL AND METHODS: The medical records of children with a non-Danish family name and where both parents were from countries other than Denmark were studied. RESULTS: A significant increase in the frequency of MR were found in the children from ethnic minorities: 16.6% of the children seen at CFH had an ethnic background compared to 14% in the background population, making a surplus of 18.5% more than expected. When a family was inbred other family members had Mr in 43.0%, whereas more family members with MR were found in only 14.2% of the families with no inbreeding. In the consanguineous families we found possible aetiological diagnoses in 21.5% of the children compared to 49% in the non-consanguineous families. In the entire group of children from ethnic minorities, we found Down's syndrome in 3.2% compared to 10.7% in Danish children with MR. DISCUSSION: There is a surplus of MR in children from ethnic minorities in the County of Copenhagen. The causes are not known, nor are aetiological factors for MR for a great part of the children. Consanguinity is likely to be a risk factor for MR, especially if it is already present in the family. This conforms with previously published data from other countries.

Adolescent↗

[Genetic analysis of markers of the performance test for herding dogs. 1. Performance traits].

The objective of the present study was to analyse data based on records of sheep dog trials in order to evaluate the importance of genetic and environmental sources of variation and to draw conclusions for breeding purposes. The data analysed consisted of 2745 test results recorded at 48 sheep dog trials carried out in Germany from 1994 to 1998, on which a total of 337 sheep dogs had attended. Tested dogs descended from 147 sires and 201 dams, with a mean inbreeding coefficient of about 2.8%. Variance components of working traits were estimated applying Restricted Maximum Likelihood methods. Additive genetic effects, permanent environmental effects of the animal and the effect of the handler were treated as random factors using multivariate linear models. Additionally, the model included the fixed effects of the age of the dogs at the sheep dog trial, sex, the level of difficulty of the exercises as well as the event itself, the starting number of the dog, the number of the dogs' tests at the particular event and the number of dogs presented on sheep dog trials by their handlers. The inbreeding coefficient was regarded as a linear covariate. Sex of the dog and starting number did not explain a significant proportion of variance for traits analysed, whereas the event of the sheep dog trial and the starting class usually were of significant importance. The analyses were performed using all sheep dog trial classes and for each of the three classes separately. Repeatabilities of herding traits within the same event of sheep dog trial estimated from animal effect mostly varied within a range from w = 0.1 to w = 0.5 whereas repeatabilities estimated over all events of sheep dog trials mostly gave estimates from w = 0.1 to w = 0.3. The estimated heritabilities for the herding performance traits ranged from h2 < or = 0.001 to h2 = 0.13 with standard errors in the range between 0.001 and 0.08. The selection possibilities appear to be rather limited given the heritability estimates and the low number of progeny of parents.

Animal Husbandry↗

How high should paternity index be for reliable identification of war victims by DNA typing?

AIM: To analyze statistically and logically the significance of genetic matches between skeletal remains and relatives of missing persons in the process of identification of war victims by DNA typing. METHODS: DNA was isolated from bone and blood samples and short tandem repeat (STR) loci were typed by using AmpFLSTR Profiler, Profiler Plus, and Identifiler kits. Novel mini-haplotype analysis that compares matches in all three-locus combinations of alleles was developed and used in the analysis of inbreeding in the group of 295 unrelated individuals. RESULTS: While comparing 98 skeletal remains exhumed in the process of identification of war victims in Croatia with over 3,000 genotypes of relatives of missing persons, we revealed 20 cases of 14-locus matches and 4 cases of 15-locus matches between unrelated people. We hypothesized that this unexpectedly high number of false matches might be a consequence of local inbreeding and supported this hypothesis with very low correlation between the probability of a genotype and the number of matching genotypes in the database (R(2) = 0.36). Further support for the hypothesis was obtained by the analysis of mini-haplotypes, which revealed up to 90% overrepresentation of some mini-haplotypes. CONCLUSIONS: STR DNA typing is the "golden standard" of human identification, but evidential value of a genetic match can be easily misinterpreted. Therefore, careful use of statistical methods is essential for the proper evaluation of laboratory results. Whenever possible, multiple relatives should be analyzed and other evidence based on the information about time, place, and other conditions of disappearance, as well as anthropological and other "classical" forensic data should always be put together and compared before any final decision about the identity is made.

Consanguinity↗

[Integrated population genetic and medical genetic study of two raions of the Tver oblast].

An integrated medical genetic an population genetic study has been performed in two raions (administrative districts) of the Tver oblast (region) of Russia: the Udomlya raion located in the zone affected by the Kalininskaya Nuclear Power Plant and the Ostashkov raion, which served as a control district. No significant differences has been found with respect to the genetic parameters studied. The values of these parameters in the populations of the town of Udomlya, the town of Ostashkov, the Udomlya raion, and the Ostashkov raion, respectively, are the following: random inbreeding, 0.00006, 0.00011, 0.000167, and 0.000366; endogamy index, 0.05, 0.43, 0.30, and 0.42; local inbreeding, 0.0003, 0.00045, 0.0009, and 0.0011; the degree of isolation by distance, 0.0003, 0.00045, 0.0009, and 0.0005; sigma, 2098, 1338, 1473, and 1189; the load of autosomal dominant (AD) diseases, 0.71, 0.92, 0.92, and 1.37; the load of autosomal recessive (AR) diseases, 0.68, 0.69, 0.67, and 0.82; and the load of X-linked diseases, 0.18, 0.64, 0.83, and 0.27.

Consanguinity↗

[Genetic demographic description of the Ust-Aldan rural population of Sakha Republic (Yakutia): migrations and marriage structure].

Migrations, dynamics of the gametic structure of rural populations, and marriage structure with respect to birthplaces and inbreeding estimated from isonymy have been studied in the Ust-Aldan ulus (administrative district) of Sakha Republic (Yakutia). The villages studied (Byadi, Dyupsya, and Cheriktey) are characterized by intense migration; however, the migration radius is small (most migrations occur within the district). The rural populations studied differ in the intensities and directions of gamete flows and their dynamics. There is no substantial gamete flow into the Ust-Aldan population from outside Sakha Republic. About 50% of marriages contracted in this population are homolocal (between residents of the same district); the endogamy is low (15%). In most cases of heterolocal marriages (contracted between residents of different districts), one of the spouses is a local resident. The inbreeding estimated from isonymy is FTT = 0.002930 in Yakuts; it is mainly accounted for by the nonrandom component (FIS = 0.002232 and FST = 0.000700).

Consanguinity↗

[Genetic diversity and differentiation of Gmelin larch Larix gmelinii populations from Evenkia (Central Siberia)].

Within- and among-population diversity of Gmelin larch Larix gmelinii (Rupr.) Rupr. from Evenkia was inferred from data on 17 genes determining allozyme diversity of ten enzymes. More than 50% of the genes proved to be polymorphic. On average, each tree was heterozygous at 9.2% genes. Heterozygosity expected from the Hardy-Weinberg proportions was higher, 12.5%. A deficit of heterozygous genotypes was observed in all populations under study and attributed to inbreeding. With Wright's F statistics, average individual inbreeding was estimated at 26.6% relative to the population (F(IS)) and at 27.8% relative to the species (F(IT)). The greatest deficit of heterozygosity was observed for the youngest population. Within-population variation accounted for more than 98% of the total variation, while the contribution of among-population variation was 1.66%. Genetic distance between populations varied from 0.0025 to 0.0042, averaging 0.0035.

Enzymes↗

A PCR multiplex and database for forensic DNA identification of dogs.

Animal-derived trace evidence is a common finding at crime scenes and may provide an important link between victim(s) and suspect(s). A database of 558 dogs of pure and mixed breeds is described and analyzed with two PCR multiplexes of 17 microsatellites. Summary statistics (number of alleles, expected and observed heterozygosity and power of exclusion) are compared between breeds. Marked population substructure in dog breeds indicates significant inbreeding, and the use of a conservative theta value is recommended in likelihood calculations for determining the significance of a DNA match. Evidence is presented that the informativeness of the canine microsatellites, despite inbreeding, is comparable to the human CODIS loci. Two cases utilizing canine DNA typing, State of Washington v. Kenneth Leuluaialii and George Tuilefano and Crown v. Daniel McGowan, illustrate the potential of canine microsatellite markers for forensic investigations.

Animals↗

Analysis of marital structure in Massachusetts using repeating pairs of surnames.

Analysis of surnames from marriages is now a well-established method in the study of marital and genetic structure. Traditional methods of partitioning inbreeding into random and nonrandom components rely on the total number of isonymous marriages. Because this number is often low, standard errors of inbreeding estimates tend to be high. Lasker and Kaplan (1985) devised a method that circumvents this problem by focusing on the total number of repeating pairs (RP) of surnames among marriages. The observed value of RP can be compared with the value expected at random (RPr) to assess patterns of subdivision within a population. The RP method is applied here to data from 3431 marriages that took place from 1800 to 1849 in 4 Massachusetts towns. The level of excess RP [(RP-RPr)/RPr] is positively associated with population size and exogamy rate. These results indicate a tendency for greater relative subdivision in larger, more exogamous populations. One possible reason for increased subdivision is preferential marriage by social class, although adequate data are not available for a test of this hypothesis.

Consanguinity↗

[Genetic analysis of the outcome of behavioural tests in puppies of the Hovawart breed].

The objective of the present study was to evaluate the importance of genetic and environmental sources of variation for results of puppy behavioural tests in the Hovawart dog. For these analyses test results of 5,608 puppies born in 1995 to 2000 have been used. Variance component estimation was performed for the traits contact, optical and acoustical influences, hunting affinity, appearance and temperament using multivariate linear animal models and Restricted Maximum Likelihood (REML). The models included test-year-season, sex, litter size, region of kennel, inbreeding coefficient of the animal and the test inspector as fixed effects. Additive genetic effects of the animal, permanent environmental effect of the litter and the effect of the kennel were considered as random factors. An extended model included the additive genetic maternal effect. The region of the kennel was significant for all traits and the most important factor among the fixed effects. The sex of the puppy was significant for the temperament. Test-year-season was significant for hunting affinity, whereas the test inspector was significant for optical and acoustical influences. The effects litter size and inbreeding coefficient of the animal did not influence any of the traits significantly. The estimated heritabilities for the traits of puppy behaviour tests ranged from h2 = 0.02 to h2 = 0.13 with standard errors of up to 0.03. Common environment of the puppies significantly influenced all behaviour tests and the estimates were between c2 = 0.13 and 0.22. The maternal heritabilities amounted up to h2 = 0.04. The additive genetic correlations between the traits were always highly positive (r(g) = 0.6 bis 1).

Animals↗

Mating system and the evolution of quantitative traits: an experimental study of Mimulus guttatus.

The mating system of a population profoundly influences its evolution. Inbreeding alters the balance of evolutionary forces that determine the amount of genetic variation within a population. It redistributes that variation among individuals, altering heritabilities and genetic correlations. Inbreeding even changes the basic relationships between these genetic statistics and response to selection. If populations differing only in mating system are exposed to the same selection pressures, will they respond in qualitatively different ways? Here, we address this question by imposing selection on an index of two negatively correlated traits (flower size and development rate) within experimental populations that reproduce entirely by outcrossing, entirely by self-fertilizing, or by a mixture of outcrossing and selfing. Entirely selfing populations responded mainly by evolving larger flowers whereas outcrossing populations also evolved more rapid development. Divergence occurred despite an equivalent selection regime and no direct effect of mating system on fitness. The study provides an experimental demonstration of how the interaction of selection, genetic drift, and mating system can produce dramatic short-term changes in trait means, variances, and covariances.

Crosses, Genetic↗

Will population bottlenecks and multilocus epistasis increase additive genetic variance?

We apply new analytical methods to understand the consequences of population bottlenecks for expected additive genetic variance. We analyze essentially all models for multilocus epistasis that have been numerically simulated to demonstrate increased additive variance. We conclude that for biologically plausible models, large increases in expected additive variance--attributable to epistasis rather than dominance--are unlikely. Naciri-Graven and Goudet (2003) found that as the number of epistatically interacting loci increases, additive variance tends to be inflated more after a bottleneck. We argue that this result reflects biologically unrealistic aspects of their models. Specifically, as the number of loci increases, higher-order epistatic interactions become increasingly important in these models, with an increasing fraction of the genetic variance becoming nonadditive, contrary to empirical observations. As shown by Barton and Turelli (2004), without dominance, conversion of nonadditive to additive variance depends only on the variance components and not on the number of loci per se. Numerical results indicating that more inbreeding is needed to produce maximal release of additive variance with more loci follow directly from our analytical results, which show that high levels of inbreeding (F > 0.5) are needed for significant conversion of higher-order components. We discuss alternative approaches to modeling multilocus epistasis and understanding its consequences.

Biological Evolution↗

Genetic trend for milk yield in Guzerat herds participating in progeny testing and MOET nucleus schemes.

Genetic trends for 305-day milk yield (P305) in Brazilian Guzerat herds under selection were compared. Data from 4898 lactations of 3179 purebred and crossbred cows from various regions of Brazil were used. Milk yield was adjusted for mature age and the contemporary groups were defined as herd and calving year. Genetic parameters were estimated using the MTDFREML program. The model included the random effects of animals and permanent environment, and herd-calving year, calving season and genetic composition as fixed effects. Genetic trends were estimated by linear regression of weighted average estimated breeding values as a function of calving year. The average P305 was 2065 +/- 922 kg and the heritability was 0.23 +/- 0.03. The annual genetic trend in estimated breeding values of cows for P305 was 7.09 +/- 0.71 kg between 1987 and 2004, and 6.47 +/- 2.35 kg between 1997 and 2004. For cows born and raised in the multiple ovulation and embryo transfer (MOET) nucleus, this trend was 36.46 +/- 24.54 kg/year between 1997 and 2004, 183.14 +/- 47.94 kg/year between 1997 and 2000, and 9.13 +/- 19.19 kg/year between 2001 and 2004. An average inbreeding coefficient of 0.04 was found for inbred MOET cows in 2004. Increasing the size of the family and introducing new progenies changed reliabilities and predicted transmitting ability estimates of MOET sires. In conclusion, there was a positive genetic trend for milk yield in the MOET nucleus at low inbreeding coefficients due to the increased accuracy and estimated genetic merit, but no changes in the average milk yield were observed.

Animals↗

BB/O(ttawa)K(arlsburg) rats: features of a subline of diabetes-prone BB rats.

The development of incidence and age at onset of diabetes as well as the breeding performance and other phenotypic traits of the BB/O(ttawa)K(arlsburg) rat subline are assessed in relation to degree of inbreeding and mating system. With increasing inbreeding body weight decreased and striking changes were observed in incidence and age at onset of diabetes, whereas breeding performance remained largely unchanged. Because the rats were free of most of the relevant pathogens and the transfer of BB rats into a germ-poor environment with the aid of wet hysterectomy had no effect on incidence and age at onset of diabetes, a segregation of diabetogenic genes rather than an influence of environmental factors is supposed to be responsible for both the varying traits.

Aging↗

Frequency of first-cousin marriages from civil marriage certificates in Argentina.

In Argentina information concerning relatedness of mates, especially first cousins, was introduced into the legal marriage certificate, record, and statistical report in 1968. The 1980-1981 biennial data, including 212,320 legal marriage reports, were analyzed for all of Argentina, subdivided into 22 states and 494 counties. The registered 0.373% of first-cousin marriages allows an estimate of consanguineous marriages of 0.629% and a mean inbreeding coefficient of alpha = 0.00031. This estimate lies between the observed alpha = 0.00011 from hospital births and alpha = 0.00052 from Roman Catholic Church dispensations. These differences are not large, and they may be due to sampling variations, indicating a low rate of inbreeding in Argentina. The frequency of first-cousin marriages in the 22 Argentine states is heterogenous, and 9 counties, representing 5 different regions, were identified as having a high rate of first-cousin marriage. Three of these were previously known as genetic isolates. A second series of data, including all 32,690 legal marriages registered in the state of Buenos Aires during the first half of 1984, showed a frequency of first-cousin marriages of 0.677%. First-cousin mates, compared with non-first-cousin mates, had a higher frequency of both mates being born in the same state of Buenos Aires and similar frequency distributions for age at marriage, single previous marriage status, level of education, and rate of unemployment. It is concluded that legal marriage data on consanguinity is reliable, inexpensive, universal, and enduring. The last two characteristics make them suitable for the survey of geographic clusters and time trends.

Argentina↗

Heterozygosity and craniofacial dimensions of Zapotec school children from a subsistence community in the valley of Oaxaca, southern Mexico.

Gene flow is associated with differences in craniofacial and postcranial dimensions among indigenous populations of southern Mexico. This study compares four craniofacial dimensions in 322 children from families which have an average inbreeding coefficient of 0.01 and 36 children from families which have an inbreeding coefficient of zero (more heterozygous) in a Zapotec speaking community. In addition, two indices were computed. With sex and chronological age constant, there is a statistically significant difference between more and less heterozygous children in bizygomatic diameter. Differences in biparietal diameter and fronto-occipital length reflect the same tendency. The differences probably reflect more an effect of heterozygosity on these dimensions than facial dissimilarity of the populations from which the new genetic materials were drawn because gene flow was from related groups of Indians (e.g., Mixtec) in southern Mexico. Hence, midface growth and overall normal size appear to be affected by fluctuation in level of heterozygosity.

Analysis of Variance↗

[The relationship between kinship marriages and longevity in Azerbaijan].

In order to elucidate the role of inbreeding in human longevity, the individuals of both sexes aged 80-100 and more, all residents of the Azerbaijan SSR, were exposed to a genealogical examination. It was found that 22.46% of men and 12.92% of women were born in kinship marriages. The familial longevity indices appeared to be high in this examination. The inbreeding in the presence of favourable heredity does not reduce the level of longevity in the above region.

Aged↗