We investigate the consequences of adopting the criteria used by the state of California, as described by Myers et al. (2011), for conducting familial searches. We carried out a simulation study of randomly generated profiles of related and unrelated individuals with 13-locus CODIS genotypes and YFiler® Y-chromosome haplotypes, on which the Myers protocol for relative identification was carried out. For Y-chromosome sharing first degree relatives, the Myers protocol has a high probability ([Formula: see text]) of identifying their relationship. For unrelated individuals, there is a low probability that an unrelated person in the database will be identified as a first-degree relative. For more distant Y-haplotype sharing relatives (half-siblings, first cousins, half-first cousins or second cousins) there is a substantial probability that the more distant relative will be incorrectly identified as a first-degree relative. For example, there is a [Formula: see text] probability that a first cousin will be identified as a full sibling, with the probability depending on the population background. Although the California familial search policy is likely to identify a first degree relative if his profile is in the database, and it poses little risk of falsely identifying an unrelated individual in a database as a first-degree relative, there is a substantial risk of falsely identifying a more distant Y-haplotype sharing relative in the database as a first-degree relative, with the consequence that their immediate family may become the target for further investigation. This risk falls disproportionately on those ethnic groups that are currently overrepresented in state and federal databases.
Summary A total of 3961 married couples from six major geographical areas representing the South Sinai governorates in Egypt were studied to assess the rate of consanguineous marriage. The population of six selected areas (St Catherines, Nuweiba, Abu Rudeis, Ras Sudr, El Tor and Abu Zenima) were subdivided into Bedouin, urban and mixed populations. A questionnaire-based interview was conducted showing that the consanguinity rate in this region is 37.5%, with the highest rate recorded in Abu Rudeis (52.3%) and lowest rate in Nuweiba (24.1%). Consanguinity was significantly higher among the Bedouin population compared with the urban population in Abu Rudeis, Ras Sudr, El Tor and Abu Zenima, while in St Catherines and Nuweiba there was no statistically significant difference. Among consanguineous couples, 5%, 60% and 35% were double first cousins, first cousins and second cousins respectively. The mean inbreeding coefficient α of the studied population was 0.01845.
- Proceedings of the National Academy of Sciences of the United States of America
- Published almost 6 years ago
Ancestral environmental exposures have previously been shown to promote epigenetic transgenerational inheritance and influence all aspects of an individual’s life history. In addition, proximate life events such as chronic stress have documented effects on the development of physiological, neural, and behavioral phenotypes in adulthood. We used a systems biology approach to investigate in male rats the interaction of the ancestral modifications carried transgenerationally in the germ line and the proximate modifications involving chronic restraint stress during adolescence. We find that a single exposure to a common-use fungicide (vinclozolin) three generations removed alters the physiology, behavior, metabolic activity, and transcriptome in discrete brain nuclei in descendant males, causing them to respond differently to chronic restraint stress. This alteration of baseline brain development promotes a change in neural genomic activity that correlates with changes in physiology and behavior, revealing the interaction of genetics, environment, and epigenetic transgenerational inheritance in the shaping of the adult phenotype. This is an important demonstration in an animal that ancestral exposure to an environmental compound modifies how descendants of these progenitor individuals perceive and respond to a stress challenge experienced during their own life history.
Close relatives can share large segments of their genome identical by descent (IBD) that can be identified in genome-wide polymorphism datasets. There are a range of methods to use these IBD segments to identify relatives and estimate their relationship. These methods have focused on sharing on the autosomes, as they provide a rich source of information about genealogical relationships. We can hope to learn additional information about recent ancestry through shared IBD segments on the X chromosome, but currently lack the theoretical framework to use this information fully. Here, we fill this gap by developing probability distributions for the number and length of X chromosome segments shared IBD between an individual and an ancestor k generations back, as well as between half- and full-cousin relationships. Due to the inheritance pattern of the X and the fact that X homologous recombination only occurs in females (outside of the pseudoautosomal regions), the number of females along a genealogical lineage is a key quantity for understanding the number and length of the IBD segments shared amongst relatives. When inferring relationships among individuals, the number of female ancestors along a genealogical lineage will often be unknown. Therefore, our IBD segment length and number distributions marginalize over this unknown number of recombinational meioses through a distribution of recombinational meioses we derive. By using Bayes theorem to invert these distributions, we can estimate the number of female ancestors between two relatives, giving us details about the genealogical relations between individuals not possible with autosomal data alone.
- Proceedings of the National Academy of Sciences of the United States of America
- Published over 2 years ago
Nonrandom mating in human populations has important implications for genetics and medicine as well as for economics and sociology. In this study, we performed an integrative analysis of a large cohort of Mexican and Puerto Rican couples using detailed socioeconomic attributes and genotypes. We found that in ethnically homogeneous Latino communities, partners are significantly more similar in their genomic ancestries than expected by chance. Consistent with this, we also found that partners are more closely related-equivalent to between third and fourth cousins in Mexicans and Puerto Ricans-than matched random male-female pairs. Our analysis showed that this genomic ancestry similarity cannot be explained by the standard socioeconomic measurables alone. Strikingly, the assortment of genomic ancestry in couples was consistently stronger than even the assortment of education. We found enriched correlation of partners' genotypes at genes known to be involved in facial development. We replicated our results across multiple geographic locations. We discuss the implications of assortment and assortment-specific loci on disease dynamics and disease mapping methods in Latinos.
The classification of kin into structured groups is a diverse phenomenon which is ubiquitous in human culture. For populations which are organized into large agropastoral groupings of sedentary residence but not governed within the context of a centralised state, such as our study sample of 83 historical Bantu-speaking groups of sub-Saharan Africa, cultural kinship norms guide all aspects of everyday life and social organization. Such rules operate in part through the use of differing terminological referential systems of familial organization. Although the cross-cultural study of kinship terminology was foundational in Anthropology, few modern studies have made use of statistical advances to further our sparse understanding of the structuring and diversification of terminological systems of kinship over time. In this study we use Bayesian Markov Chain Monte Carlo methods of phylogenetic comparison to investigate the evolution of Bantu kinship terminology and reconstruct the ancestral state and diversification of cousin terminology in this family of sub-Saharan ethnolinguistic groups. Using a phylogenetic tree of Bantu languages, we then test the prominent hypothesis that structured variation in systems of cousin terminology has co-evolved alongside adaptive change in patterns of descent organization, as well as rules of residence. We find limited support for this hypothesis, and argue that the shaping of systems of kinship terminology is a multifactorial process, concluding with possible avenues of future research.
BACKGROUND: Characterising genetic diversity through the analysis of massively parallel sequencing (MPS) data offers enormous potential to significantly improve our understanding of the genetic basis for observed phenotypes, including predisposition to and progression of complex human disease. Great challenges remain in resolving which genetic variants are genuinely associated with disease from the millions of ‘bystanders’ and artefactual signals. RESULTS: FAVR is a suite of new methods designed to work with commonly used MPS analysis pipelines to assist in the resolution of some of these issues with a focus on relatively rare genetic variants. To the best of our knowledge, no equivalent has previously been described. The most important and novel aspect of FAVR is the use of signatures in comparator sequence alignment files during variant filtering, and annotation of variants potentially shared between individuals. The FAVR methods use these signatures to facilitate filtering of (i) platform-specific artefacts, (ii) common genetic variants, and, where relevant, (iii) artefacts derived from imbalanced paired-end sequencing, as well as annotation of genetic variants based on evidence of co-occurrence in individuals. By comparing conventional variant calling with or without downstream processing by FAVR methods applied to whole-exome sequencing datasets, we demonstrate a 3-fold smaller rare single nucleotide variant shortlist with no detected reduction in sensitivity. This analysis included Sanger sequencing of rare variant signals not evident in dbSNP131, assessment of known variant signal preservation, and comparison of observed and expected rare variant numbers across a range of first cousin pairs. The principles described herein were applied in our recent publication identifying XRCC2 as a new breast cancer risk gene and have been made publically available as a suite of software tools. CONCLUSIONS: FAVR is a platform-agnostic suite of methods that significantly enhances the analysis of large volumes of sequencing data for the study of rare genetic variants and their influence on phenotypes.
Motivated by the cooperative breeding hypothesis, we investigate the effect of having kin on the mortality of reproductive women based on family reconstitutions for the Krummhörn region (East Frisia, Germany, 1720-1874). We rely on a combination of Cox clustered hazard models and hazard models stratified at the family level. In order to study behavior-related effects, we run a series of models in which only kin who lived in the same parish are considered. To investigate structural, non-behavior-related effects, we run a different model series that include all living kin, regardless their spatial proximity. We find that women of reproductive age who had a living mother had a reduced mortality risk. It appears that having living sisters had an ambivalent impact on women’s mortality: i.e., depending on the socioeconomic status of the family, the effect of having living sisters ranged between representing a source of competition and representing a source of support. Models which are clustered at the family level suggest that the presence of a living mother-in-law was associated with reduced mortality among her daughters-in-law especially among larger-scale farm families. We interpret this finding as a consequence of augmented consanguineous marriages among individuals of higher social strata. For instance, in first cousin marriages, the mother-in-law could also be a biological aunt. Thus, it appears that among the wealthy elite, the genetic in-law conflict was neutralized to some extent by family solidarity. This result further suggests that the tipping point of the female trade-off between staying with the natal family and leaving the natal family to join an economically well-established in-law family might have been reached very quickly among women living under the socioeconomic conditions of the Krummhörn region.
- International journal of aging & human development
- Published 11 months ago
The aim of this study was to examine the later-life preparation pattern of Korean baby boomers and its effect on depression. Using the fourth wave of Korean Retirement and Income Study, later-life preparation was measured by economic, physical, and psychological preparation, and leisure, and family relationship satisfaction. The data analysis included latent class analysis, correlations, multiple logistic regression, and analysis of variance. Later-life patterns of Korean baby boomers were classified as high-level (35.7%), low-level (31.1%), and health and family relationship (33.2%) preparation patterns. For depression, the low-level pattern was associated with significantly higher level of depression; however, no differences were found in other two patterns. Researchers recommended a postretirement program to reflect the unique characteristics of Korean baby boomers. Moreover, findings regarding the importance of health and family relationships can be applied to other countries that have historical and cultural backgrounds similar to Korea.
Children have the right to be brought up in safe environments. However, this right is often infringed by people who are supposed to provide love, care, and protection to children. These people can include biological fathers, step-fathers, brothers, cousins, aunts, mothers, and uncles. Violation of children takes place in a variety of ways, however, for the purpose of this paper, the focus is on child sexual abuse within the family system. A literature review is adopted as the methodology for the discussions in this paper. The purpose of this paper is firstly to demonstrate that child sexual abuse happens within the family system in South Africa, and secondly, to argue that the prevention of child sexual abuse should start within the family system and this can be achieved by conducting educational social group work sessions on child sexual abuse with the family members.