An equivalence between models of restricted selection and genetic groups

Summary An equivalence between a model of restricted selection and a model of genetic groups is presented. This correspondence leads to a realization of how genetic groups account for selection. Specifically, genetic groups act to remove the covariance between predictions of sire merit and functions of the true selection differentials. Further results illustrate a correspondence between models of selection on random effects and models of selection on residuals. Application of the results is useful, not in establishing concrete definitions for the structure of genetic groups, but in the analysis of how groups account for selection.     

Bayes factor for testing between different structures of random genetic groups: A case study using weaning weight in Bruna dels Pirineus beef cattle

The implementation of genetic groups in BLUP evaluations accounts for different expectations of breeding values in base animals. Notwithstanding, many feasible structures of genetic groups exist and there are no analytical tools described to compare them easily. In this sense, the recent development of a simple and stable procedure to calculate the Bayes factor between nested competing models allowed us to develop a new approach of that method focused on compared models with different structures of random genetic groups. The procedure is based on a reparameterization of the model in terms of intraclass correlation of genetic groups. The Bayes factor can be easily calculated from the output of a Markov chain Monte Carlo sampling by averaging conditional densities at the null intraclass correlation. It compares two nested models, a model with a given structure of genetic groups against a model without genetic groups. The calculation of the Bayes factor between different structures of genetic groups can be quickly and easily obtained from the Bayes factor between the nested models. We applied this approach to a weaning weight data set of the Bruna dels Pirineus beef cattle, comparing several structures of genetic groups, and the final results showed that the preferable structure was an only group for unknown dams and different groups for unknown sires for each year of calving.     

Fine-scale population genetic structure in a fission-fusion society

Nonrandom patterns of mating and dispersal create fine-scale genetic structure in natural populations — especially of social mammals — with important evolutionary and conservation genetic consequences. Such structure is well-characterized for typical mammalian societies; that is, societies where social group composition is stable, dispersal is male-biased, and males form permanent breeding associations in just one or a few social groups over the course of their lives. However, genetic structure is not well understood for social mammals that differ from this pattern, including elephants. In elephant societies, social groups fission and fuse, and males never form permanent breeding associations with female groups. Here, we combine 33 years of behavioural observations with genetic information for 545 African elephants ( Loxodonta africana ), to investigate how mating and dispersal behaviours structure genetic variation between social groups and across age classes. We found that, like most social mammals, female matrilocality in elephants creates co-ancestry within core social groups and significant genetic differentiation between groups (Φ_ST = 0.058). However, unlike typical social mammals, male elephants do not bias reproduction towards a limited subset of social groups, and instead breed randomly across the population. As a result, reproductively dominant males mediate gene flow between core groups, which creates cohorts of similar-aged paternal relatives across the population. Because poaching tends to eliminate the oldest elephants from populations, illegal hunting and poaching are likely to erode fine-scale genetic structure. We discuss our results and their evolutionary and conservation genetic implications in the context of other social mammals.     

Should genetic groups be fitted in BLUP evaluation? Practical answer for the French AI beef sire evaluation

Some analytical and simulated criteria were used to determine whether a priori genetic differences among groups, which are not accounted for by the relationship matrix, ought to be fitted in models for genetic evaluation, depending on the data structure and the accuracy of the evaluation. These criteria were the mean square error of some extreme contrasts between animals, the true genetic superiority of animals selected across groups, i.e. the selection response, and the magnitude of selection bias (difference between true and predicted selection responses). The different statistical models studied considered either fixed or random genetic groups (based on six different years of birth) versus ignoring the genetic group effects in a sire model. Including fixed genetic groups led to an overestimation of selection response under BLUP selection across groups despite the unbiasedness of the estimation, i.e. despite the correct estimation of differences between genetic groups. This overestimation was extremely important in numerical applications which considered two kinds of within-station progeny test designs for French purebred beef cattle AI sire evaluation across years: the reference sire design and the repeater sire design. When assuming a priori genetic differences due to the existence of a genetic trend of around 20% of genetic standard deviation for a trait with h² = 0.4, in a repeater sire design, the overestimation of the genetic superiority of bulls selected across groups varied from about 10% for an across-year selection rate p = 1/6 and an accurate selection index (100 progeny records per sire) to 75% for p = 1/2 and a less accurate selection index (20 progeny records per sire). This overestimation decreased when the genetic trend, the heritability of the trait, the accuracy of the evaluation or the connectedness of the design increased. Whatever the data design, a model of genetic evaluation without groups was preferred to a model with genetic groups when the genetic trend was in the range of likely values in cattle breeding programs (0 to 20% of genetic standard deviation). In such a case, including random groups was pointless and including fixed groups led to a large overestimation of selection response, smaller true selection response across groups and larger variance of estimation of the differences between groups. Although the genetic trend was correctly predicted by a model fitting fixed genetic groups, important errors in predicting individual breeding values led to incorrect ranking of animals across groups and, consequently, led to lower selection response.     

Genetic support groups in the delivery of comprehensive genetic services.

This research sought information about the services provided by genetic support groups, their members' experiences in obtaining genetic and related services, and members' recommendations for improving services. Results from a survey of 43 directors of genetic support groups showed that these organizations not only provide their members with a wide range of informational and supportive services but also address the need for education of both the public and health professionals about genetic disorders. A second survey of 931 members of genetic support groups found that, although they obtained genetic information from a variety of professional and informal sources, many of them experienced barriers to obtaining sufficient genetic information. Respondents called for professionals to improve their interpersonal skills in working with clients and to assist families in obtaining a wider variety of services. On the basis of these findings, a service model and priorities are proposed to bring together genetic specialists, community professionals, and genetic support groups for the delivery of comprehensive services to individuals and families with genetic disorders.     

Molecular ecology of social behaviour: analyses of breeding systems and genetic structure

Molecular genetic studies of group kin composition and local genetic structure in social organisms are becoming increasingly common. A conceptual and mathematical framework that links attributes of the breeding system to group composition and genetic structure is presented here, and recent empirical studies are reviewed in the context of this framework. Breeding system properties, including the number of breeders in a social group, their genetic relatedness, and skew in their parentage, determine group composition and the distribution of genetic variation within and between social units. This group genetic structure in turn influences the opportunities for conflict and cooperation to evolve within groups and for selection to occur among groups or clusters of groups. Thus, molecular studies of social groups provide the starting point for analyses of the selective forces involved in social evolution, as well as for analyses of other fundamental evolutionary problems related to sex allocation, reproductive skew, life history evolution, and the nature of selection in hierarchically structured populations. The framework presented here provides a standard system for interpreting and integrating genetic and natural history data from social organisms for application to a broad range of evolutionary questions.     

Theory of nucleus breeding schemes with overlapping generations

Summary Explicit methods are derived for estimating steady-state genetic responses and genetic differences between nucleus and base progeny crops in open nucleus breeding schemes which utilize genetic differences between progeny groups with parents of different ages or between age groups. Explicit methods are also given for estimating proportions which should be selected from the different nucleus and base selection groups so as to maximise genetic responses under each of a range of selection methods. Some basic differences between selection programmes utilizing genetic differences between progeny groups with parents of different ages and those utilizing genetic differences between age groups in nucleus breeding schemes are summarized.     

Fuzzy classification of phantom parent groups in an animal model

Background

Genetic evaluation models often include genetic groups to account for unequal genetic level of animals with unknown parentage. The definition of phantom parent groups usually includes a time component (e.g. years). Combining several time periods to ensure sufficiently large groups may create problems since all phantom parents in a group are considered contemporaries.

Methods

To avoid the downside of such distinct classification, a fuzzy logic approach is suggested. A phantom parent can be assigned to several genetic groups, with proportions between zero and one that sum to one. Rules were presented for assigning coefficients to the inverse of the relationship matrix for fuzzy-classified genetic groups. This approach was illustrated with simulated data from ten generations of mass selection. Observations and pedigree records were randomly deleted. Phantom parent groups were defined on the basis of gender and generation number. In one scenario, uncertainty about generation of birth was simulated for some animals with unknown parents. In the distinct classification, one of the two possible generations of birth was randomly chosen to assign phantom parents to genetic groups for animals with simulated uncertainty, whereas the phantom parents were assigned to both possible genetic groups in the fuzzy classification.

Results

The empirical prediction error variance (PEV) was somewhat lower for fuzzy-classified genetic groups. The ranking of animals with unknown parents was more correct and less variable across replicates in comparison with distinct genetic groups. In another scenario, each phantom parent was assigned to three groups, one pertaining to its gender, and two pertaining to the first and last generation, with proportion depending on the (true) generation of birth. Due to the lower number of groups, the empirical PEV of breeding values was smaller when genetic groups were fuzzy-classified.

Conclusion

Fuzzy-classification provides the potential to describe the genetic level of unknown parents in a more parsimonious and structured manner, and thereby increases the precision of predicted breeding values.     

Genetic groups in the common plant species Castanopsis chinensis and their associations with topographic habitats

In general, even within a local area, many common plant species are found in different types of environment. We propose that if the association of a common plant species with different types of environment is investigated, by analysing all individuals in a given population as a single entity, the results might be misleading or incomplete owing to intraspecific variation. To test this hypothesis, we used molecular markers to classify mature Castanopsis chinensis individuals with a diameter at breast height ≥ 40 cm into different genetic groups and analysed the associations of these groups with topographic features and habitats within a 20‐ha Dinghushan forest plot, South China. Our results indicated that the different groups had different topographical associations, and that the spatial distributions and genetic structures of individuals varied among the groups. Therefore, if significant genetic structure exists in the population of a common species within a community, to understand the relationship between the spatial distributions of individuals in the population and the environment, it is necessary to classify the individuals into genetic groups and analyse the data for these groups, rather than for a combined group of all individuals.     

Anchoring of canine linkage groups with chromosome-specific markers

A high-resolution genetic map with polymorphic markers spaced frequently throughout the genome is a key resource for identifying genes that control specific traits or diseases. The lack of rigorous selection against genetic disorders has resulted in many breeds of dog suffering from a very high frequency of genetic diseases, which tend to be breed-specific and usually inherited as autosomal recessive or apparently complex genetic traits. Many of these closely resemble human genetic disorders in their clinical and pathologic features and are likely to be caused by mutations in homologous genes. To identify loci important in canine disease genes, as well as traits associated with morphological and behavioral variation, we are developing a genetic map of the canine genome. Here we report on an updated version of the canine linkage map, which includes 341 mapped markers distributed over the X and 37 autosomal linkage groups. The average distance between markers on the map is 9.0 cM, and the linkage groups provide estimated coverage of over 95% of the genome. Fourteen linkage groups contain either gene-associated or anonymous markers localized to cosmids that have been assigned to specific canine chromosomes by FISH. These 14 linkage groups contain 150 microsatellite markers and allow us to assign 40% of the linkage groups to specific canine chromosomes. This new version of the map is of sufficient density and characterization to initiate mapping of traits of interest. Received: 23 February 1999 / Accepted: 28 April 1999     

Genetic consequences of group living in Mongolian gerbils

Social behavior can shape the local population genetic structure of mammals. Group living can increase pairwise genetic relatedness of mammals at a local level but differentiate the genetic structure at a population level through offspring philopatry and nonrandom mating. Our study aimed to test the hypothesis that social groups of Mongolian gerbils (Meriones unguiculatus) would consist of genetically related individuals due to offspring philopatry and would have distinct genetic structures because of restricted gene flow among social groups and nonrandom mating. We genotyped 327 wild gerbils, live captured from 28 social groups in Inner Mongolia, China, using nine microsatellite loci. The within-group pairwise genetic relatedness coefficient averaged 0.28 ± 0.14 (standard deviation), whereas the average pairwise genetic relatedness coefficient of the whole gerbil population was 0.0 ± 0.2. Additionally, the value of the global F statistic (F(st)) was 0.21, suggesting a substantial genetic differentiation among social groups of Mongolian gerbils. The Bayesian clustering divided the 327 gerbils into 23 distinct genetic clusters. Therefore, our results show that high within-group genetic relatedness and among-group genetic differentiation are the genetic consequences of group living in social mammals because of restricted gene flow, female philopatry, and nonrandom mating within social groups.     

Reconstructing the Human Genetic History of Mainland Southeast Asia: Insights from Genome-Wide Data from Thailand and Laos

Thailand and Laos, located in the center of Mainland Southeast Asia (MSEA), harbor diverse ethnolinguistic groups encompassing all five language families of MSEA: Tai-Kadai (TK), Austroasiatic (AA), Sino-Tibetan (ST), Hmong-Mien (HM), and Austronesian (AN). Previous genetic studies of Thai/Lao populations have focused almost exclusively on uniparental markers and there is a paucity of genome-wide studies. We therefore generated genome-wide SNP data for 33 ethnolinguistic groups, belonging to the five MSEA language families from Thailand and Laos, and analyzed these together with data from modern Asian populations and SEA ancient samples. Overall, we find genetic structure according to language family, albeit with heterogeneity in the AA-, HM-, and ST-speaking groups, and in the hill tribes, that reflects both population interactions and genetic drift. For the TK speaking groups, we find localized genetic structure that is driven by different levels of interaction with other groups in the same geographic region. Several Thai groups exhibit admixture from South Asia, which we date to ∼600–1000 years ago, corresponding to a time of intensive international trade networks that had a major cultural impact on Thailand. An AN group from Southern Thailand shows both South Asian admixture as well as overall affinities with AA-speaking groups in the region, suggesting an impact of cultural diffusion. Overall, we provide the first detailed insights into the genetic profiles of Thai/Lao ethnolinguistic groups, which should be helpful for reconstructing human genetic history in MSEA and selecting populations for participation in ongoing whole genome sequence and biomedical studies.     

The peopling of sub-Saharan Africa: the case study of Cameroon.

This study analyzes the distribution of ten protein genetic polymorphisms in eighteen populations from the most densely inhabited areas of Cameroon. The languages spoken belong to three different linguistic families [Afro-Asiatic (AA), Nilo-Saharan (NS) and Niger-Kordofanian (NK)]. The analysis of variation of allele frequencies indicates that the level of genetic interpopulation differentiation is rather low (F(st) = 0.011 +/- 0.006) but statistically significant (p < 0.001). This result is not unexpected because of the relatively small geographic area covered by our survey. This value is also significantly lower than the one estimated for other groups of African populations. Among the factors responsible for this, we discuss the possible role of gene flow. There is a considerable genetic differentiation among the AA populations of north Cameroon as is to be expected because they all originated from the first agriculturists of the farming "savanna complex." The Podowko and Uldeme are considerably different from all the other AA groups, probably due to the combined effect of genetic drift and isolation. In the case of the Wandala and Massa, our analyses suggest that genetic admixture with allogeneous groups (especially with the Kanuri) played an important role in determining their genetic differentiation from other AA speaking groups. The Bantu speaking populations (Bakaka, Bamileke Bassa and Ewondo, NK family, Benué Congo subfamily) settled in western and southern Cameroon are more tightly clustered than AA speaking groups. This result shows that the linguistic affinity among these four populations coincides with a substantial genetic similarity despite their different origin. Finally, the Fulbe are genetically distinct from all the populations that belong to their same linguistic phylum (NK), and closer to the neighboring Fali and Tupuri, eastern Adamawa speaking groups of north Cameroon.     

Ethnic genetics: relation between adaptive and neutral genetic differentiation of an ethnos

It is very important to be able to distinguish between selectively significant genetic variability and selectively-neutral one for quantitative analysis of genetic differentiation in human (and any other) populations. The key to the problem is to determine a start-point for detection of neutral genetic variability, which will help to establish alignment of adaptive and neutral forces operating in genetic differentiation. The purpose of this work is to adduce proofs in favour of mean Fst value for a sample of gene loci as of the start-point for measuring neutrality level of genetic differentiation. These proofs came from various demographic and onomastic characteristics of ethnic groups as well as from genetic chronology of ethnic history which is in good concordance with actual historical chronology of ethnic groups. Once the start-point for testing neutrality is determined, it becomes possible to reveal the selective pressure to which various human genes are undergone and to elucidate adaptive structure of mankind's genetic pool. It was shown that only 15 alleles from 49 belonging to 20 polymorphic loci can be considered selectively neutral.     

Ethnicity determination by names among the Aymara of Chile and Bolivia

The importance of surnames in genetic studies has been recognized for a century or so. While the ethnic affiliations of individuals are ordinarily established in genetic studies by admixture analysis based on gene frequencies, often there are implicit assumptions in these attempts that are difficult to validate in the absence of detailed ethnohistories. In northern Chile and western Bolivia, where genetic admixture has been known to occur among the Aymara Indians and Spanish Caucasoids, the naming pattern (parental patriand matrinyms) allowed us to classify individuals on the basis of the frequency of Aymara names into 9 'ethnic' groups. From a sample of 2525 individuals it is shown that admixture occurred in lineages nonrandomly, implying assortative mating of surnames. Admixture and genetic distance analysis on the basis of 31 genetic markers on approximately 1700 of these individuals reveals that there is a reasonable agreement of ethnic classification of individuals by name and phenotype data on genetic markers. The Aymara-named groups are shown to be predominantly Amerindian (89%) in their genetic profiles. Individuals whose current naming pattern is basically Spanish also exhibit a substantial fraction of genes of Amerindian origin (67%). Presence of some rare alleles not found in Amerindian or Spanish Caucasoids in the admixed groups suggest infiltration of Negroid genes in the past.     

Analysis of the genetic structure and morphology of Polygonatum cyrtonema in Anhui Province,eastern China revealed three distinct genetic groups

Polygonatum cyrtonema Hua, a rhizome-propagating herb endemic to China, is used in many traditional Chinese medicines and foods. The hilly mountains in western and southern Anhui province is one of its main natural distribution and artificial cultivation areas. We assessed the genetic diversity and structure of P. cyrtonema germplasm resources in Anhui by nine pairs of SSR primers and selected morphological characters. The results showed that the 13 sampled populations of P. cyrtonema possessed normal levels of genetic diversity but could be clustered into three distinct genetic groups. The levels of within-group genetic diversity was similar among the three groups, but their distribution areas and morphological characters were remarkably different. Group I was confined to the Tianmu (including Jiuhua) Mountains, group II was distributed in the Huangshan Mountains, and group III was restricted to the Dabie Mountains. Furthermore, the leaf length:width ratio significantly differed among groups, and the peduncle length of group I was significantly shorter than that of the other two groups. Levels of genetic differentiation among the three groups was close to that between different species within the genus. Thus, the three genetic groups of P. cyrtonema should be considered as independent units for conservation and breeding management in the Anhui region.     

Genetic differentiation among morphological variants of Acacia saligna (Mimosaceae)

This study investigated the pattern of genetic variation in Acacia saligna (Labill.) H.L. Wendl. to facilitate its development as a crop species for dryland salinity management. A. saligna is a morphologically variable species and four main variants are recognized. The genetic structure within A. saligna was investigated in populations across the geographic range of the species using nuclear restriction fragment length polymorphism loci. The analysis identified considerable genetic variation within A. saligna that was genetically structured into three groups. Two of the three groups corresponded to variants recognized in the field study; the third group encompassed the other two variants which, though morphologically different, were not genetically differentiated. The level of genetic differentiation between the groups suggests they may represent different taxa and a taxonomic revision of the species may be required. Identification of different taxa within A. saligna will have implications for the utilization and domestication of the species, as the taxa will need to be evaluated separately to determine their suitability for agroforestry. The high genetic variation between and within groups suggests there is a large genetic base available for breeding improved cultivars.     

Measuring connectedness among herds in mixed linear models: From theory to practice in large-sized genetic evaluations

A procedure to measure connectedness among groups in large-sized genetic evaluations is presented. It consists of two steps: (a) computing coefficients of determination (CD) of comparisons among groups of animals; and (b) building sets of connected groups. The CD of comparisons were estimated using a sampling-based method that estimates empirical variances of true and predicted breeding values from a simulated n-sample. A clustering method that may handle a large number of comparisons and build compact clusters of connected groups was developed. An aggregation criterion (Caco) that reflects the level of connectedness of each herd was computed. This procedure was validated using a small beef data set. It was applied to the French genetic evaluation of the beef breed with most records and to the genetic evaluation of goats. Caco was more related to the type of service of sires used in the herds than to herd size. It was very sensitive to the percentage of missing sires. Disconnected herds were reliably identified by low values of Caco. In France, this procedure is the reference method for evaluating connectedness among the herds involved in on-farm genetic evaluation of beef cattle (IBOVAL) since 2002 and for genetic evaluation of goats from 2007 onwards.     

Genetic Diversity,Population Genetic Structure and Protection Strategies for <Emphasis Type="Italic">Houpoëa officinalis</Emphasis> (Magnoliaceae), an Endangered Chinese Medical Plant

Houpoëa officinalis is a traditional Chinese medical plant, which has significantly declined in the past decades because of human influence and habitat fragmentation. Twelve expressed sequence tag SSR (EST-SSR) markers developed from the EST sequence of H. officinalis were used to analyse the genetic diversity and structure of fourteen natural populations. The results indicated that moderate genetic diversity and high genetic differentiation existed in this plant (Ho = 0.600, Fst = 0.327). STRUCTURE and UPGMA analyses showed that H. officinalis populations could be divided into 3 different groups, and the west group had higher genetic diversity than the central and east groups. The historical migration rates among the groups were low and unsymmetrical, and there was no significant correlation between Nei’s genetic distance and geographic distance. According to the genetic consequences, conservation strategies (in situ or ex situ, artificial pollination) should be carried out in all populations to preserve genetic diversity.     

The Interplay of Landscape Features and Social System on the Genetic Structure of a Primate Population: An Agent-Based Simulation Study Using “Tamarins”

Tamarins are small-bodied, forest-dwelling, callitrichines that live in groups containing one to a few adult individuals of each sex. Within these groups, reproduction is usually heavily skewed toward a single dominant male and dominant female, females commonly give birth to cooperatively reared twin offspring, and individuals of both sexes disperse, most often to adjacent groups. Throughout their geographic range, tamarin species are being subject to habitat loss and fragmentation, which may influence their ability to survive and disperse successfully. Here, we use a spatially explicit agent-based population genetics simulation toolkit (GENESYS) to explore the potential effects of social structure and landscape features on the population genetic structure of tamarin primates. We first model the population genetic consequences of tamarin social organization in a homogeneous landscape unconstrained by any barriers to gene flow. We then repeat our analyses using the same social system parameters but in different landscapes that either introduce a barrier to gene flow that restricts dispersal from one half of the model world to the other or divide the world into regions with differing “permeabilities” to dispersal. Our results demonstrate that, in our simulated populations, the social system of tamarins results in the clear and rapid genetic differentiation of social groups within a very short time frame. Over time, the limited dispersal of both males and females leads to a pattern of isolation by distance, as expected from a stepping-stone model of gene flow among groups. Introducing a barrier results in a somewhat more complex pattern: isolation by distance still obtains among social groups within regions on each side of the barrier, but the barrier has a much more significant effect on the structuring of genetic variation, leading to strong genetic differentiation among groups on opposite sides that becomes more pronounced over time. Introducing a region of limited dispersal permeability also results in strong differentiation of groups across that region, even though gene flow throughout the landscape is still possible. Our study demonstrates the utility of the GENESYS toolkit for modeling, in silico, the genetic consequences of many features of the social systems of primates and other group-living animals and for simultaneously exploring the effects of landscape features on spatial genetic structure.