Genetic-demographic structure of the Adyg population]

The results of comparative analysis of series of genetical and demographical parameters in two ethnically distinct populations coexisting in Adyg autonomous region of the Krasnodar district are presented. The parameters of population structure in Russians and Adygs were determined, such as sex and age distribution, ethnical marital assortativity, vital statistics and selection pressure. The analysis revealed that the populations only differ in the level of ethnical marital assortment: the coefficient of assortativity H is 2.54 and 1.55 for Adygs and Russians, respectively.     

Characterization of the marriage structure and migration in Chuvash population]

Parameters of the marriage structure and migration were analyzed on the basis of marriage records in the Kanash, Cheboksary, and Morgaushi raions of the Chuvash Republic. Ethnic assortiveness was not detected in Chuvashes and was 4.16-18.05 in Russians. Gene flow between Chuvashes and Russians was 5.1-8.3%; the degree of endogamy was 0.61-0.70.     

The population structure and inbreeding coefficient in the Yerkes Chimpanzee Colony

This paper describes the establishment and expansion of the Yerkes Chimpanzee Colony over its first half-century of existence. Particular attention is given to the patterns of matings in the population and resultant distribution and levels of inbreeding. Over the period encompassed by this investigation the population mean inbreeding coefficient is 0.0045; the mean inbreeding coefficient for all inbred sibships (20 out of 264) is 0.0990. The mean inbreeding coefficient for all chimpanzees born in the colony is 0.0079, and the highest inbreeding coefficient for any individual is 0.125.     

Genetic demographic characteristics of the rural population of the Tuva Republic: marriage structure and inbreeding]

Marriage structure was studied in three rural populations of the Tuva Republic: the Shinaan population and the populations of Todzhinskii and Bai-Taiginskii raions (districts). The Shinaan and Bai-Taiginskii populations had high levels of endogamy (0.6704 and 0.6050, respectively). In the Todzhinskii population, which was characterized by a mixed ethnic composition, endogamy was 0.3779 for the total population and 0.4626 for Tuvinians; interethnic marriages in this population were rare. The values of marriage assortativeness with respect to birthplace were 19.38, 40.75, 75.87, and 41.87% in the Shinaan, Bai-Taiginskii, all the Todzhinskii populations, and Tuvinian monoethnic marriages in the Todzhinskii raion, respectively. High marriage assortativeness with respect to ethnicity was found. Its values (A') were 91.85 and 93.49% in Tuvinians and Russians, respectively. Tuvinian populations were characterized by high inbreeding. The total (F(it)), random (Fst), and nonrandom inbreeding (Fis) estimated by isonymy were 0.004237, 0.002298, and 0.001944 in the Shinaan population, 0.007292, 0.009448, and -0.002177 in the Bai-Taiginskii population, and 0.003846, 0.004152, and -0.000307 in the Todzhinskii population, respectively (in the latter populations, the F(it), Fst, and Fis values for Tuvinian marriages alone were 0.005000, 0.007222, and -0.002238, respectively). The results obtained indicate that individual territorial groups of Tuvinians retain a high degree of genetic isolation from one another.     

Population structure in the Connecticut Valley. I. Marital migration

This study reports on an analysis of marital migration among 12 communities in the Connecticut River Valley of Massachusetts during the years 1790-1849. Genetic inferences are drawn, and the requisite assumptions considered. The effect of geographic distance on genetic kinship is predicted using Malécot's isolation-by-distance model. The resulting estimates are discussed in terms of geographic and historical factors. The configuration of communities as predicted by kinship values approximates closely their actual geographic locations. Estimated genetic heterogeneity was low for the historical Connecticut Valley population, and community isolation breaks down rapidly over time. The region thus assumes its place among a number of sedentary, agricultural populations for which the isolation-by-distance model provides an adequate representation. A regression analysis which includes variables in addition to distance indicates that historical and economic factors contribute some additional explanatory power to the distribution of mating frequencies.     

Fine-scale population structure, inbreeding risk and avoidance in a wild insect population

The ecological and evolutionary importance of fine-scale genetic structure within populations is increasingly appreciated. However, available data are largely restricted to wild vertebrates and eusocial insects. In addition, there is the expectation that most insects tend to have such large- and high-density populations and are so mobile that they are unlikely to face inbreeding risks through fine-scale population structuring. This has made the growing body of evidence for inbreeding avoidance in insects and its implication in mating systems evolution somewhat enigmatic. We present a 4-year study of a natural population of field crickets. Using detailed video monitoring combined with genotyping, we track the movement of all adults within the population and investigate genetic structure at a fine scale. We find some evidence for relatives being found in closer proximity, both across generations and within a single breeding season. Whilst incestuous matings are not avoided, population inbreeding is low, suggesting that mating is close to random and the limited fine-scale structure does not create significant inbreeding risk. Hence, there is little evidence for selective pressures associated with the evolution of inbreeding avoidance mechanisms in a closely related species.     

The structure of the inbreeding coefficient in a rural Asian population

The population-genetic study of an elementary rural population located in the Urgut district of Samarcand province was carried out. The pedigree for the whole population starting from the founders was evaluated. From 208 marriages presented in the population, 148 (71.2%) were consanguineous. The mean coefficient of inbreeding calculated from the pedigree was 0.028. A new approach to the evaluation of marital assortativity in a rural Uzbek population without tribial differentiation and inherited surnames was proposed. It consists in awarding artificial surnames to the founders of the population. Applying this approach to the population under study gives following values of F-statistics: FIT = 0.031, FIS = 0.01841, FST = 0.01282.     

Density-dependent migration and human population structure in historical Massachusetts

Studies of population structure often focus on the effects of population size and migration rates on genetic variation. Few studies, however, have investigated the relationship between these two factors. The purpose of this paper is to determine the extent to which migration (and gene flow) is density-dependent (that is, affected by population size) for populations in historical Massachusetts. Data from 4,859 marriage records were analyzed from four populations in north-central Massachusetts during the time period 1741 to 1849. These data were placed into 29 samples defined in terms of population and time cohort. Within each cohort the overall exogamy rate was computed along with three estimates of gene flow based on marital migration: local migration (k), long-distance migration (m), and effective migration rate (me). Three samples show unusually low rates that reflect the history of settlement. Regression analyses were used with the remaining samples, and they show nonlinear density-dependent migration that is unrelated to temporal trends. Migration is highest in samples with small population sizes (less than 800) and large population sizes (greater than 1,600). Migration is lowest in medium-sized populations. Two processes are suggested to explain this curvilinear relationship of migration and population size. In small populations, the lack of suitable potential mates and/or availability of settled land leads to an increase in migration into the population. As population size increases, this migration decreases. After populations reach a certain size, migration increases again, most likely reflecting the economic pull of larger populations. These patterns could act to enhance, or counter, genetic drift, depending on the direction of density dependence.     

Marital structure and genetic isolation in a rural Hispanic population in Northern New Mexico

An investigation of the mating structure of the rural Hispanic population of the village of Abiquiu in northern New Mexico was carried out using village marriage registers. Marital movement and departure from random mating were analyzed by the distribution of birth places of marriage partners and by surname isonymy. The time periods studied were 1882 to 1910 and 1947 to 1977. The results of these analyses show marked marital isolation (median marital distances by birthplace of 11.5 and 20.0 miles, respectively) and a significant departure from random mating (F = 0.0556 and F = 0.0495, respectively). In each case the non-random component of the isonymy coefficient (F_n) greatly exceeds the random, or expected, component. Assortative mating for culture and proximity governed by the historical settlement pattern is indicated as the process producing these results. Isolation has begun to break down in recent years but as yet has had no great effect on the genetic structure of the Abiquiu population.     

Pedigree analysis of the Turkish Arab horse population: structure,inbreeding and genetic variability

The aim of this study was to evaluate genetic variability in the Turkish Arab horse population using pedigree information. This study is the first detailed pedigree analysis of the breed in Turkey. Pedigree data were collected from the National Studbook. The pedigree data for 23 668 horses, born between 1904 and 2014, were used in the analysis. From this data set, a reference population (RP) of 14 838 animals symbolising the last generation was defined. Demographic parameters, the inbreeding level (F), the average relatedness (AR), the effective population size (N_e), the effective number of founders (f_e), the effective number of ancestors (f_a) and the number of founder genome equivalents (f_g) were calculated for the population. The average generation interval for the RP was 12.2±4.6 years, whereas the calculated pedigree completeness levels were 98.2%, 96.6% and 95.0% for the first, second and third known generations. The mean equivalent generations (t), the average complete generations and the mean maximum generations for the RP were 7.8, 5.4 and 12.2, respectively, whereas the meanFand AR were 4.6% and 9.5% for the RP. The rate of inbred animals was 94.2% for the RP, whereas the number of founders, the number of ancestors and thef_e,f_aandf_gwere 342, 223, 40, 22 and 9.6 for the RP. The large differences observed betweenf_e, and the number of founders demonstrates that genetic diversity decreased between the founder and the RP. Contribution of the 14 most influential founder to the RP was 50.0%, whereas just eight ancestral horses can account for 50% of the genetic variability.N_eestimated via an individual increase in inbreeding per generation (${\overline{N}}_{\text{e}}$), and paired increase in coancestry$\left(\text{}{\overline{N}}_{eC}\right)$, were 74.4±3.9 and 73.5±0.58, respectively. The inbreeding increases with the pedigree knowledge. In addition, the decrease in inbreeding in last years is more noticeable.     

Examination of the relationship between inbreeding and population size

This chapter presents a method for examining the relationship between effective population size and accumulated random inbreeding in human populations. Using a linear regression model on 9 Irish isolates, results show that this method is very useful in assessing differential influences on population structure. Inbreeding refers to the level expected at random due to finite population size, offset by migration into the population. The data used consist of effective population size estimates and kinship estimates derived from surnames for 9 isolates on, or near, the west coast of Ireland. Based on the non-parametric correlation results, there is no monotonic relationship between effective population size and the inverse of kinship. The demographic data available show that, with the exception of Garumna, Lettermullen, and the Aran Islands, the other populations changed little in population size during the latter part of the 19th century. The fact that observed kinship is higher than predicted kinship suggests an increse in population size. These analyses suggest that there is little, if any, relationship between population size and inbreeding among these populations, using 1891 effective population size estimates. Given the range of demogrphic, ecological, and cultural environments of human populations, perhaps it is unexpected to see a set of populations adhering strongly to a given theoretical model. The more important aspect of such model fitting is not whether or not a given model shows a significant fit, but rather the analysis of deviations from an expected relationship.     

Joint effects of self-fertilization and population structure on mutation load, inbreeding depression and heterosis

Both the spatial distribution of organisms and their mode of reproduction have important effects on the change in allele frequencies within populations. In this article, we study the combined effect of population structure and the rate of partial selfing of organisms on the efficiency of selection against recurrent deleterious mutations. Assuming an island model of population structure and weak selection, we express the mutation load, the within- and between-deme inbreeding depression, and heterosis as functions of the frequency of deleterious mutants in the metapopulation; we then use a diffusion model to calculate an expression for the equilibrium probability distribution of this frequency of deleterious mutants. This allows us to derive approximations for the average mutant frequency, mutation load, inbreeding depression, and heterosis, the simplest ones being Equations 35-39 in the text. We find that population structure can help to purge recessive deleterious mutations and reduce the load for some parameter values (in particular when the dominance coefficient of these mutations is <0.2-0.3), but that this effect is reversed when the selfing rate is above a given value. Conversely, within-deme inbreeding depression always decreases, while heterosis always increases, with the degree of population subdivision, for all selfing rates.     

Genomic inbreeding and population structure of northern pike (Esox lucius) in Xinjiang,China

Northern pike (Esox lucius) was widely distributed in the high latitudes of the northern hemisphere. In China, northern pike was originally distributed only in the upper reaches of the Irtysh River in Xinjiang and has appeared in many water bodies outside the Irtysh River Basin in Northern Xinjiang. A total of four populations were collected from north to south in Xinjiang, including Irtysh River (RIR), Ulungu Lake (LUL), a small lake nearby Ulungu River (LJD), and Bosten Lake (LBO). We estimated population genomic parameters, performed gene flow analysis, and estimated the effective population size of each population. The proportion of individuals with high inbreeding coefficient (F ≥ 0.0625) accounted for 36.4% (44/121) of all sequenced individuals, approximately 4.5% (1/22) in LUL, 25.9% (7/27) in LBO, 42.9% (18/42) in RIR, and 60% (18/30) in LJD. RIR had the highest mean of genomic relatedness (coancestry coefficient = 0.025 ± 0.040, IBD = 0.036 ± 0.078). Gene flow results showed that the population spreading was from RIR into two branches, one was LBO, and the other continued to split into LUL and LJD, and migration signal from LBO to LUL was detected. Our results suggested that the extinction risk of northern pike was very low in Xinjiang of China, and the controlled capture fishery of northern pike could be developed reasonably.     

Evaluating the performance of likelihood methods for detecting population structure and migration

A plethora of statistical models have recently been developed to estimate components of population genetic history. Very few of these methods, however, have been adequately evaluated for their performance in accurately estimating population genetic parameters of interest. In this paper, we continue a research program of evaluation of population genetic methods through computer simulation. Specifically, we examine the software MIGRATEE-N 1.6.8 and test the accuracy of this software to estimate genetic diversity (Theta), migration rates, and confidence intervals. We simulated nucleotide sequence data under a neutral coalescent model with lengths of 500 bp and 1000 bp, and with three different per site Theta values of (0.00025, 0.0025, 0.025) crossed with four different migration rates (0.0000025, 0.025, 0.25, 2.5) to construct 1000 evolutionary trees per-combination per-sequence-length. We found that while MIGRATEE-N 1.6.8 performs reasonably well in estimating genetic diversity (Theta), it does poorly at estimating migration rates and the confidence intervals associated with them. We recommend researchers use this software with caution under conditions similar to those used in this evaluation.     

Evidence of inbreeding depression but not inbreeding avoidance in a natural house sparrow population

Inbreeding is common in small and threatened populations and often has a negative effect on individual fitness and genetic diversity. Thus, inbreeding can be an important factor affecting the persistence of small populations. In this study, we investigated the effects of inbreeding on fitness in a small, wild population of house sparrows (Passer domesticus) on the island of Aldra, Norway. The population was founded in 1998 by four individuals (one female and three males). After the founder event, the adult population rapidly increased to about 30 individuals in 2001. At the same time, the mean inbreeding coefficient among adults increased from 0 to 0.04 by 2001 and thereafter fluctuated between 0.06 and 0.10, indicating a highly inbred population. We found a negative effect of inbreeding on lifetime reproductive success, which seemed to be mainly due to an effect of inbreeding on annual reproductive success. This resulted in selection against inbred females. However, the negative effect of inbreeding was less strong in males, suggesting that selection against inbred individuals is at least partly sex specific. To examine whether individuals avoided breeding with close relatives, we compared observed inbreeding and kinship coefficients in the population with those obtained from simulations of random mating. We found no significant differences between the two, indicating weak or absent inbreeding avoidance. We conclude that there was inbreeding depression in our population. Despite this, birds did not seem to actively avoid mating with close relatives, perhaps as a consequence of constraints on mating possibilities in such a small population.     

Linkage and inbreeding coefficients in a finite random mating population

The notion of inbreeding coefficient associated with one single locus introduced by G. Malecot can be extended to two loci. For a panmictic model with separate generation the recurrence equations are given therein allowing to calculate the coefficients in the event of migration and mutation, or loss of kinship.Hence it is derived particularly that the limit genetic distance of two groups associated with two loci is, under specific hypotheses, little different from the sum of marginal genetic distances.For an isolat this paper studies, in terms of crossing over, mutations, and population size, the evolution of the inbreading coefficients of order 2 and especially the difference of this evolution from the evolution to independence of the two loci.