Estimating FST and kinship for arbitrary population structures

F_ST and kinship are key parameters often estimated in modern population genetics studies in order to quantitatively characterize structure and relatedness. Kinship matrices have also become a fundamental quantity used in genome-wide association studies and heritability estimation. The most frequently-used estimators of F_ST and kinship are method-of-moments estimators whose accuracies depend strongly on the existence of simple underlying forms of structure, such as the independent subpopulations model of non-overlapping, independently evolving subpopulations. However, modern data sets have revealed that these simple models of structure likely do not hold in many populations, including humans. In this work, we analyze the behavior of these estimators in the presence of arbitrarily-complex population structures, which results in an improved estimation framework specifically designed for arbitrary population structures. After generalizing the definition of F_ST to arbitrary population structures and establishing a framework for assessing bias and consistency of genome-wide estimators, we calculate the accuracy of existing F_ST and kinship estimators under arbitrary population structures, characterizing biases and estimation challenges unobserved under their originally-assumed models of structure. We then present our new approach, which consistently estimates kinship and F_ST when the minimum kinship value in the dataset is estimated consistently. We illustrate our results using simulated genotypes from an admixture model, constructing a one-dimensional geographic scenario that departs nontrivially from the independent subpopulations model. Our simulations reveal the potential for severe biases in estimates of existing approaches that are overcome by our new framework. This work may significantly improve future analyses that rely on accurate kinship and F_ST estimates.     

Separation of common environment and dominance effects with classic kinship correlation models

Abstract

Common family environmental effect (γ²) and dominance effect (d² ) are usually confounded; either or both may make the sib‐sib correlation larger than the parent‐child correlation. The classic three kinship correlations (parent‐parent, parent‐offspring, sib‐sib) can accommodate either dominance (Model D) or common family environment effects (Model C), but not both. The relationship between the various components of the three correlations of Models D and C are given. In order to include both dominance and common family environment effects, a fourth correlation, that between half‐sibs, is added to the system which enables us to separate the dominance effects from the common family environments effects. Half‐sibs may constitute a potentially new source material for study of quantitative inheritance. The principle of the constant heredity/environment ratio is discussed.     

Gene-history correlation and population structure

Correlation of gene histories in the human genome determines the patterns of genetic variation (haplotype structure) and is crucial to understanding genetic factors in common diseases. We derive closed analytical expressions for the correlation of gene histories in established demographic models for genetic evolution and show how to extend the analysis to more realistic (but more complicated) models of demographic structure. We identify two contributions to the correlation of gene histories in divergent populations: linkage disequilibrium, and differences in the demographic history of individuals in the sample. These two factors contribute to correlations at different length scales: the former at small, and the latter at large scales. We show that recent mixing events in divergent populations limit the range of correlations and compare our findings to empirical results on the correlation of gene histories in the human genome.     

Dispersal,kinship and inbreeding in an island population of the Great Tit

We investigated the kinship structure of an island population of the Great Tit (Parus major). Kinship of birds could be inferred by comparing their family trees. Dispersal was also studied to explain the observed pattern of kinship. On the island of Vlieland the tits breed in several wooded areas. Both males and females preferred to breed in their natal area; males did so more strongly than females. Hence gene flow between the areas is restricted. However, within the largest wooded area females showed random dispersal, while males showed a slight tendency to breed near their natal site. The degree of kinship of neighbouring birds is a suitable control group for the relatedness of partners that takes into account the effects of dispersal. In the largest wooded area, birds were on average equally related to their partner and to their neighbours. Moreover, the mean coefficient of kinship between male and female neighbours was equal to the average kinship in this part of the population. We conclude that mating is random with respect to kinship. There is no evidence for avoidance of inbreeding. It is unlikely that kin recognition plays an important role in the process of mate choice in this population of Great Tits. We suggest that ecological factors are the main causes for the observed patterns of dispersal and mating. On the island more female than male immigrants enter the population each year. Incidental data indicate an exchange of birds between the population studied and surrounding populations. Ancestries of immigrants are not known, and indeed a first analysis of all birds, including immigrants, showed that males were more closely related than females. However, differential immigration could not fully explain the observed difference in kinship. The presence of local adaptation in males is suggested as a possible additional cause.     

Microsatellites and kinship

Many evolutionary studies, particularly kinship studies, have been limited by the availability of segregating genetic marker loci. Microsatellites promise to alleviate these problems. Microsatellite loci are segments of DNA with very short sequence motifs repeated in tandem; their often numerous alleles differ in the number of these repeat units. They are very common in eukaryotic DNA and can be amplified by the polymerase chain reaction, which allows the use of minute or degraded DNA samples. The alleles can be scored consistently and compared unambiguously, even across different gels.     

Host-parasite kinship in a female-philopatric bird population: evidence from relatedness trend analysis

Conspecific brood parasitism (CBP), an alternative reproductive tactic where some females lay eggs in the nests of other females of the same species, occurs in many animals with egg care. It is particularly common in waterfowl, for reasons that are debated. Many waterfowl females nest near their birthplace, making it likely that some local females are relatives. We analyse brood parasitism in a Hudson Bay population of common eiders, testing predictions from two alternative hypotheses on the role of relatedness in CBP. Some models predict host-parasite relatedness, others predict that parasites avoid close relatives as hosts. To distinguish between the alternatives, we use a novel approach, where the relatedness of host-parasite pairs is tested against the spatial population trend in pairwise relatedness. We estimate parasitism, nest take-over and relatedness with protein fingerprinting and bandsharing analysis of egg albumen, nondestructively sampled from each new egg in the nest throughout the laying period. The results refute the hypothesis that parasites avoid laying eggs in the nests of related hosts, and corroborate the alternative of host-parasite relatedness. With an estimated r of 0.12-0.14, females laying eggs in the same nest are on average closer kin than nesting neighbour females. Absence of a population trend in female pairwise relatedness vs. distance implies that host-parasite relatedness is not only an effect of strong natal philopatry: some additional form of kin bias is also involved.     

Estimation of inbreeding,kinship and genetic distances from surnames--coastal population of middle Dalmatia,Croatia

This work was dedicated to the investigation of the population structure of the middle Dalmatia settlements: Jesenice, Mimice, Zivogos?e and Zaostrog by surname distribution study and applying the isonymous method. The surnames of males and females in marital pairs were analyzed as well as of their first and second-generation ancestors on the sample of a total of 3,024 examinees. The analyses of surnames pointed to the rates of inbreeding, kinship and genetic distances of the populations. Although the values of the inbreeding coefficient are high in all the four settlements, the inbreeding coefficient is exceptionally high in Mimice. A total kinship coefficient for the four settlements speaks also in favor of the high rate of kinship in the examined settlements, i.e. of the high rate of the reproductive isolation of the whole region during the analyzed period. The reasons for such high coefficients are natural features of the examined region (the mountains of Mosor, Biokovo and Rili?), poor traffic connection of this region in the past, the patrilineal mode of inheritance and the demographic specifics of the population. The matrix of genetic distances between examined settlement pairs reveals that Mimice, a settlement with the highest share of isonymous marriages, shows the greatest distances in comparison to the other settlements. On the other hand, Jesenice, Zivogos?e and Zaostrog are characterized by small genetic distances, which is the fact that speaks in favor of their genetic homogenization and "openness" toward interpopulational migrations, i.e. the gene flow.     

Microsatellite DNA markers for delineating population structure and kinship among the endangered Kirtland's warbler (Dendroica kirtlandii)

We document the isolation and characterization of 23 microsatellite DNA markers for the endangered Kirtland's warbler (Dendroica kirtlandii), a Nearctic/Neotropical migrant passerine. This suite of markers revealed moderate to high levels of allelic diversity (averaging 7.7 alleles per locus) and heterozygosity (averaging 72%). Genotypic frequencies at 22 of 23 (95%) markers conformed to Hardy–Weinberg equilibrium expectations, and no linkage disequilibrium was observed in blood samples taken from 14 warblers found on the wintering grounds in the Bahamas archipelago. Multilocus genotypes resulting from this suite of markers should reduce the amount of resources required for initiating new genetic studies assessing breeding structure, parentage, demographics, and individual‐level ecological interactions for D. kirtlandii.