An Analysis of Heterosis VS. Inbreeding Effects with an Autotetraploid Cross-Fertilized Plant: MEDICAGO SATIVA L

Self-fertilization and crossing were combined to produce a large number of levels of inbreeding and of degrees of kinship. The inbreeding effect increases with the complexity of the character and with its supposed relationship with fitness. A certain amount of heterozygosity appears to be necessary for the expression of variability. With crossing of unrelated noninbred plants, genetic variance is mainly additive, but with inbreeding its major part is nonadditive. High additivity in crossing, therefore, coexists with strong inbreeding depression. However, even in inbreeding the genetic coefficient of covariation among relatives appears to be strongly and linearly related to the classical coefficient of kinship. This means that deviations from the additive model with inbreeding could be partly due to an effect of inbreeding on variances through an effect on means. An attempt to analyze genetic effects from a theoretical model, based upon the identity by descent relationship at the level of means and of covariances between relatives, tends to show that allelic interactions are more important and nonallelic interactions are less important for a character closely related to fitness. For a complex character, these results lead to the conception of a genome organized in polygenic complementary blocks integrating epistasis and dominance. Some consequences for plant breeding are also discussed.     

Assessment of relationships between pigs based on pedigree and genomic information

Relationships play a very important role in studies on quantitative genetics. In traditional breeding, pedigree records are used to establish relationships between animals; while this kind of relationship actually represents one kind of relatedness, it cannot distinguish individual specificity, capture the variation between individuals or determine the actual genetic superiority of an animal. However, with the popularization of high-throughput genotypes, assessments of relationships among animals based on genomic information could be a better option. In this study, we compared the relationships between animals based on pedigree and genomic information from two pig breeding herds with different genetic backgrounds and a simulated dataset. Two different methods were implemented to calculate genomic relationship coefficients and genomic kinship coefficients, respectively. Our results show that, for the same kind of relative, the average genomic relationship coefficients (G matrix) were very close to the pedigree relationship coefficients (A matrix), and on average, the corresponding values were halved in genomic kinship coefficients (K matrix). However, the genomic relationship yielded a larger variation than the pedigree relationship, and the latter was similar to that expected for one relative with no or little variation. Two genomic relationship coefficients were highly correlated, for farm1, farm2 and simulated data, and the correlations for the parent-offspring, full-sib and half-sib were 0.95, 0.90 and 0.85; 0.93, 0.96 and 0.89; and 0.52, 0.85 and 0.77, respectively. When the inbreeding coefficient was measured, the genomic information also yielded a higher inbreeding coefficient and a larger variation than that yielded by the pedigree information. For the two genetically divergent Large White populations, the pedigree relationship coefficients between the individuals were 0, and 62 310 and 175 271 animal pairs in the G matrix and K matrix were greater than 0. Our results demonstrated that genomic information outperformed the pedigree information; it can more accurately reflect the relationships and capture the variation that is not detected by pedigree. This information is very helpful in the estimation of genomic breeding values or gene mapping. In addition, genomic information is useful for pedigree correction. Further, our findings also indicate that genomic information can establish the genetic connection between different groups with different genetic background. In addition, it can be used to provide a more accurate measurement of the inbreeding of an animal, which is very important for the assessment of a population structure and breeding plan. However, the approaches for measuring genomic relationships need further investigation.     

Genetic and Cultural Kinship among the Lamaleran Whale Hunters

The human ability to form large, coordinated groups is among our most impressive social adaptations. Larger groups facilitate synergistic economies of scale for cooperative breeding, such economic tasks as group hunting, and success in conflict with other groups. In many organisms, genetic relationships provide the structure for sociality to evolve via the process of kin selection, and this is the case, to a certain extent, for humans. But assortment by genetic affiliation is not the only mechanism that can bring people together. Affinity based on symbolically mediated and socially constructed identity, or cultural kinship, structures much of human ultrasociality. This paper examines how genetic kinship and two kinds of cultural kinship--affinal kinship and descent--structure the network of cooperating whale hunters in the village of Lamalera, Indonesia. Social network analyses show that each mechanism of assortment produces characteristic networks of different sizes, each more or less conducive to the task of hunting whales. Assortment via close genetic kin relationships (r?=?0.5) produces a smaller, denser network. Assortment via less-close kin relations (r?=?0.125) produces a larger but less dense network. Affinal networks are small and diffuse; lineage networks are larger, discrete, and very dense. The roles that genetic and cultural kinship play for structuring human sociality is discussed in the context of these results.     

A novel recursive algorithm for the calculation of the detailed identity coefficients

Background

A recursive algorithm to calculate the fifteen detailed coefficients of identity is introduced. Previous recursive procedures based on the generalized coefficients of kinship provided the detailed coefficients of identity under the assumption that the two individuals were not an ancestor of each other.

Findings

By using gametic relationships to include three, four or two pairs of gametes, we can obtain these coefficients for any pair of individuals. We have developed a novel linear transformation that allows for the calculation of pairwise detailed identity coefficients for any pedigree given the gametic relationships. We illustrate the procedure using the well-known pedigree of Julio and Mencha, which contains 20 Jicaque Indians of Honduras, to calculate their detailed coefficients.

Conclusions

The proposed algorithm can be used to calculate the detailed identity coefficients of two or more individuals with any pedigree relationship.     

Inference of kinship coefficients from Korean SNP genotyping data

The determination of relatedness between individuals in a family is crucial in analysis of common complex diseases. We present a method to infer close inter-familial relationships based on SNP genotyping data and provide the relationship coefficient of kinship in Korean families. We obtained blood samples from 43 Korean individuals in two families. SNP data was obtained using the Affymetrix Genome-wide Human SNP array 6.0 and the Illumina Human 1M-Duo chip. To measure the kinship coefficient with the SNP genotyping data, we considered all possible pairs of individuals in each family. The genetic distance between two individuals in a pair was determined using the allele sharing distance method. The results show that genetic distance is proportional to the kinship coefficient and that a close degree of kinship can be confirmed with SNP genotyping data. This study represents the first attempt to identify the genetic distance between very closely related individuals. [BMB Reports 2013; 46(6): 305-309]     

Rank-invariant estimation of inbreeding coefficients

The two alleles an individual carries at a locus are identical by descent (ibd) if they have descended from a single ancestral allele in a reference population, and the probability of such identity is the inbreeding coefficient of the individual. Inbreeding coefficients can be predicted from pedigrees with founders constituting the reference population, but estimation from genetic data is not possible without data from the reference population. Most inbreeding estimators that make explicit use of sample allele frequencies as estimates of allele probabilities in the reference population are confounded by average kinships with other individuals. This means that the ranking of those estimates depends on the scope of the study sample and we show the variation in rankings for common estimators applied to different subdivisions of 1000 Genomes data. Allele-sharing estimators of within-population inbreeding relative to average kinship in a study sample, however, do have invariant rankings across all studies including those individuals. They are unbiased with a large number of SNPs. We discuss how allele sharing estimates are the relevant quantities for a range of empirical applications.Subject terms: Population genetics, Evolutionary biology, Molecular ecology     

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.     

Applications of random amplified polymorphic DNA (RAPD) in molecular ecology

Molecular genetic markers have been developed into powerful tools to analyse genetic relationships and genetic diversity. As an extension to the variety of existing techniques using polymorphic DNA markers, the Random Amplified Polymorphic DNA (RAPD) technique may be used in molecular ecology to determine taxonomic identity, assess kinship relationships, analyse mixed genome samples, and create specific probes. Main advantages of the RAPD technology include (i) suitability for work on anonymous genomes, (ii) applicability to problems where only limited quantities of DNA are available, (iii) efficiency and low expense.     

Efficient path-based computations on pedigree graphs with compact encodings

A pedigree is a diagram of family relationships, and it is often used to determine the mode of inheritance (dominant, recessive, etc.) of genetic diseases. Along with rapidly growing knowledge of genetics and accumulation of genealogy information, pedigree data is becoming increasingly important. In large pedigree graphs, path-based methods for efficiently computing genealogical measurements, such as inbreeding and kinship coefficients of individuals, depend on efficient identification and processing of paths. In this paper, we propose a new compact path encoding scheme on large pedigrees, accompanied by an efficient algorithm for identifying paths. We demonstrate the utilization of our proposed method by applying it to the inbreeding coefficient computation. We present time and space complexity analysis, and also manifest the efficiency of our method for evaluating inbreeding coefficients as compared to previous methods by experimental results using pedigree graphs with real and synthetic data. Both theoretical and experimental results demonstrate that our method is more scalable and efficient than previous methods in terms of time and space requirements.     

Kinship,lineage, and an evolutionary perspective on cooperative hunting groups in Indonesia

Work was conducted among traditional, subsistence whale hunters in Lamalera, Indonesia, in order to test if strict biological kinship or lineage membership is more important for explaining the organization of cooperative hunting parties ranging in size from 8 to 14 men. Crew identifications were collected for all 853 hunts that occurred between May 3 and August 5, 1999. Lineage identity and genetic relatedness were determined for a sample of 189 hunters. Results of matrix regression show that genetic kinship explains little of the hunters’ affiliations independent of lineage identity. Crew members are much more closely related to each other than expected by chance, but this is due to the correlation between lineage membership and genetic kinship. Lineage members are much more likely to affiliate in crews, but kin with r<0.5 are just as likely not to affiliate. The results are discussed vis-à-vis the evolution of cooperation and group identity.     

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.     

Genetic structure and heterozygosity in the kuru region,Eastern Highlands of New Guinea

Genetic structure of 20 of the 37 linguistic groups in the Eastern Highlands of New Guinea including the kuru region is analyzed using information on blood groups and serum protein polymorphisms. The average individual is heterozygous at 28.6% of loci and the average number of alleles per locus is 1.234. Coefficients of kinship for linguistic groups range from 0.005 for the sweet potato cultivating North Fore to 0.075 for the isolated Pawaians whose dietary staple is sago and who depend more on hunting and gathering. As one selects linguistic groups with smaller and smaller population size and increasing isolation, one finds that kinship coefficients rise as much as tenfold, but there is no concomitant loss of heterozygosity or trend toward fixation of alleles. Genetic relationships established by genetic distance trees and by principal components analysis are comparable and are consistent with other anthropological observations.     

Effects of competition on means,variances and covariances in quantitative genetics with an application to general combining ability selection

Summary General expressions are established for means, variances and covariances, taking into account the effect of interactions between individuals. For simplicity, only groups of size two are considered so that interactions are restricted to pairs of individuals; genetic effects are reduced to additivity and to additive × additive interaction between the direct effect of an allele and the associate effect of another. The effect of family structure is studied, and some consequences of interest to plant breeding are discussed by an application to general combining ability selection. From a population genetic point of view, this approach reveals a new application of coefficients of kinship.     

Kinship and Cooperation

Chagnon’s analysis of a well-known axe fight in the Yanomamö village of Mishimishiböwei-teri (Chagnon and Bugos 1979) is among the earliest empirical tests of kin selection theory for explaining cooperation in humans. Kin selection theory describes how cooperation can be organized around genetic kinship and is a fundamental tool for understanding cooperation within family groups. Previous analysis on groups of cooperative Lamaleran whale hunters suggests that the role of genetic kinship as a principle for organizing cooperative human groups could be less important in certain cases than previously thought (Alvard Human Nature 14:129–163, 2003b). Evidence that supports a strong role for genetic kinship—groups are found to be more related than expected by chance—may be spurious because of the correlation between social structure and genetic kinship. Reanalysis of Chagnon’s data using matrix regression techniques, however, confirms that genetic kinship was the primary organizing principle in the axe fight; affinal relations were also important, whereas lineage identity explained nothing.     

Estimation of inbreeding from ecclesiastical dispensations: application of three procedures to a Spanish case

The inbreeding coefficient of a population, estimated from ecclesiastical Roman Catholic dispensations, results from the relative contribution of different degrees of relationships (uncle-niece, first cousin, etc.). The interpopulation comparisons of consanguinity patterns may be obscured by the fact that in 1918 the Roman Catholic Church norm regulating the closest marriageable kinship was modified, limiting the application for an ecclesiastical dispensation to relatives of third degree (second cousins) or closer. Depending on the length of the period before or after the change of regulation, coefficients and rates may differ. Deviation of frequencies for multiple marriages may also occur. The aim of the present paper is to determine how the chosen procedure based on ecclesiastical dispensations may affect results, regarding the inbreeding coefficient, the consanguinity rate, the structure of consanguinity and the close/remote kinship ratio. As a sample case, information from the Gredos mountain range (central Spain) has been used.     

Unpedigreed populations and worst‐case scenarios

A population in which parentage information is not recorded is considered a pedigree “black hole” in terms of genetic management. Integration of animals from such an unpedigreed population into a genetically managed population is often accomplished by assuming a worst‐case scenario and recording all animals as highly interrelated (e.g., full siblings). The assumption that a worst‐case scenario is appropriate under a wide variety of circumstances is evaluated. It was determined that the genetic costs of overestimating relationships among animals from an unpedigreed population are always greater than the genetic costs of underestimating relationships by the same amount. This demonstrates that worst‐case scenarios, which are by definition intentional overestimates, are not generally appropriate. A method of obtaining an estimate that will yield the lowest overall genetic cost using the possible maximum and minimum levels of relatedness among animals from the unpedigreed population is presented along with two methods for implementation. Finally, for cases in which the estimated average relatedness among animals from an unpedigreed population is low, it is recommended that different analytical studbook datasets be used for calculation of inbreeding coefficients and mean kinship coefficients. This strategy would allow close estimation of average relatedness without risking inadvertent pairing of highly related animals from the unpedigreed population. Zoo Biol 20:305–314, 2001. © 2001 Wiley‐Liss, Inc.     

Quantitative analysis of connectivity in populations of a semi‐aquatic mammal using kinship categories and network assortativity

Analysing the impact of anthropogenic and natural river barriers on the dispersal of aquatic and semi‐aquatic species may be critical for their conservation. Knowledge of kinship relationships between individuals and reconstructions of pedigrees obtained using genomic data can be extremely useful, not only for studying the social organization of animals, but also inferring contemporary dispersal and quantifying the effect of specific barriers on current connectivity. In this study, we used kinship data to analyse connectivity patterns in a small semi‐aquatic mammal, the Pyrenean desman (Galemys pyrenaicus), in an area comprising two river systems with close headwaters and dams of various heights and types. Using a large SNP dataset from 70 specimens, we obtained kinship categories and reconstructed pedigrees. To quantify the barrier effect of specific obstacles, we built kinship networks and devised a method based on the assortativity coefficient, which measures the proportion between observed and expected kinship relationships across a barrier. The estimation of this parameter enabled us to infer that the most important barrier in the area was the watershed divide between the rivers, followed by a dam on one of the rivers. Other barriers did not significantly reduce the expected number of kinship relationships across them. This strategy and the information obtained with it may be crucial in determining the most important connectivity problems in an area and help develop conservation plans aimed at improving genetic exchange between populations of threatened species.     

Admissible Regions in a Simplex of Identity Coefficients

Genealogical relationships between any number of individuals are characterized, from the genetic point of view, by the probabilitiea of ell poeeible gene identity states occuning at an autosomel locus. However, only a eubepece of the apace of all probabilities ie in fact accemible to any relationehip. Badon a theorem of THOMPSON (1076). a characterization of the admissible region in the simplex of all condeneed identity coefficients of two non-inbred individuals is presented. Further s similar result in the caae of detailed coefficients is given.