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.     

A mathematical approach to multiple genetic relationships

A fundamental concept in the treatment of genetic relationships is that of gene identity which first was introduced by Cotterman (1940). Based on this notion several measures of relationship evolved such as the inbreeding coefficient, the coefficient of kinship, and the identity coefficients; by means of these quantities joint and conditional phenotype probabilities could be derived. This paper is an attempt at a general mathematical treatment of genetic relationships: Identity states are defined for any number of individuals, a method is given for the calculation of the corresponding identity coefficients by means of generalized coefficients of kinship, and applications are emphasized.     

Analyse des pedigrees et calcul des coefficients d'identité par les arbres géniques

Two genes in a pedigree are identical by descent if they are two copies of a common ancestor gene. To obtain an unambiguous definition of the set of genes, at some autosomal locus, any gene is defined as an ordered pair of zygotes: the zygote who carries the gene, and the parent who transmitted it. The natural ordered structure on the set of zygotes yields an ordered structure upon the set of genes. Any event of the mendelian segregation splits down the set of genes into non-overlaping classes of identical genes: when considered as an ordered sub-set of genes, each class is shown to have the algebraic properties of a tree. Given a sub-set ?? of genes, a family of exclusive events ensuring identity between all genes of ?? is identified as a family of genic trees with some property. This relationship between segregational events and genic trees is extended to the case where two sub-sets ?? and ??′ of genes are considered together. As a consequence, a general method is obtained to compute either identity coefficients involving any number of genes splitted into one or two identity classes, or the fifteen coefficients defined among four genes, whichever the relationships between zygotes and genes might be. Using this approach to deal with the allelic structure in a set of genes carried by related zygotes is suggested.     

“We are not simply ‘multicultural’”: intersecting ethnic and religious identities of Japanese-Korean young adults in South Korea

The present study explores the ethnic and religious identities of 21 multicultural young adults with a Japanese mother and a Korean father, all residing in South Korea where the “myth” of a mono-ethnic nation still lingers. In the study, one is considered multicultural provided they are born to both one foreign-born parent and one Korean-born parent. All interviewees are members of the Family Federation for World Peace Unification religion established in South Korea in the 1950s. Interviews with these young adults showed (a) that there was an intersectionality between their ethnic identity and religious identity; (b) that the influence of the interaction between the Church and the mother on the ethnic and religious identities of the interviewees was substantial; and (c) that they distinguished themselves from other multicultural individuals and even from non-multicultural individuals concerning their socio-economic background and transcending religious mission.     

Population genetics of autopolyploids under a mixed mating model and the estimation of selfing rate

Nowadays, the population genetics analysis of autopolyploid species faces many difficulties due to (i) limited development of population genetics tools under polysomic inheritance, (ii) difficulties to assess allelic dosage when genotyping individuals and (iii) a form of inbreeding resulting from the mechanism of ‘double reduction’. Consequently, few data analysis computer programs are applicable to autopolyploids. To contribute bridging this gap, this article first derives theoretical expectations for the inbreeding and identity disequilibrium coefficients under polysomic inheritance in a mixed mating model. Moment estimators of these coefficients are proposed when exact genotypes or just markers phenotypes (i.e. allelic dosage unknown) are available. This led to the development of estimators of the selfing rate based on adult genotypes or phenotypes and applicable to any even‐ploidy level. Their statistical performances and robustness were assessed by numerical simulations. Contrary to inbreeding‐based estimators, the identity disequilibrium‐based estimator using phenotypes is robust (absolute bias generally < 0.05), even in the presence of double reduction, null alleles or biparental inbreeding due to isolation by distance. A fairly good precision of the selfing rate estimates (root mean squared error < 0.1) is already achievable using a sample of 30–50 individuals phenotyped at 10 loci bearing 5–10 alleles each, conditions reachable using microsatellite markers. Diallelic markers (e.g. SNP) can also perform satisfactorily in diploids and tetraploids but more polymorphic markers are necessary for higher ploidy levels. The method is implemented in the software SPAGeDi and should contribute to reduce the lack of population genetics tools applicable to autopolyploids.     

Gender Identity and Autism Spectrum Disorders

In this review, we briefly summarize much of the existing literature on gender-related concerns and autism spectrum disorders (ASD), drawing attention to critical shortcomings in our current understanding and potential clinical implications. Some authors have concluded that gender identity disorder (GID), or gender dysphoria (GD), is more common in individuals with ASD, providing a range of potential explanations. However, existing literature is quantitatively limited, and our capacity to draw conclusions is further complicated by conceptual challenges regarding how gender identity is best understood. Discourses that emphasize gender as a component of identity formation are gaining prominence and seem particularly salient when applied to ASD. Individuals with ASD should enjoy equal rights with regard to treatment for gender dysphoria. Clinicians may be able to assist individuals in understanding this aspect of their identity by broadening the social frame and facilitating an exploration of gender roles.     

An indirect approach to the extensive calculation of relationship coefficients

A method was described for calculating population statistics on relationship coefficients without using corresponding individual data. It relied on the structure of the inverse of the numerator relationship matrix between individuals under investigation and ancestors. Computation times were observed on simulated populations and were compared to those incurred with a conventional direct approach. The indirect approach turned out to be very efficient for multiplying the relationship matrix corresponding to planned matings (full design) by any vector. Efficiency was generally still good or very good for calculating statistics on these simulated populations. An extreme implementation of the method is the calculation of inbreeding coefficients themselves. Relative performances of the indirect method were good except when many full-sibs during many generations existed in the population.     

Genetic similarity of polyploids: a new version of the computer program POPDIST (version 1.2.0) considers intraspecific genetic differentiation

For evolutionary studies of polyploid species estimates of the genetic identity between species with different degrees of ploidy are particularly required because gene counting in samples of polyploid individuals often cannot be done, e.g., in triploids the phenotype AB can be genotypically either ABB or AAB. We recently suggested a genetic distance measure that is based on phenotype counting and made available the computer program POPDIST. The program provides maximum-likelihood estimates of the genetic identities and distances between polyploid populations, but this approach is not informative for populations within species that only differ in their allele frequencies. We now close this gap by applying the frequencies of shared 'bands' in both populations to Nei's identity measure. Our simulation study demonstrates the close correlation between the band-sharing identity and the genetic identity calculated on the basis of gene frequencies for any degree of ploidy. The new extended version of POPDIST (version 1.2.0) provides the option of choosing either the maximum-likelihood estimator or the band-sharing measure.     

Computation of identity by descent probabilities conditional on DNA markers via a Monte Carlo Markov Chain method

The accurate estimation of the probability of identity by descent (IBD) at loci or genome positions of interest is paramount to the genetic study of quantitative and disease resistance traits. We present a Monte Carlo Markov Chain method to compute IBD probabilities between individuals conditional on DNA markers and on pedigree information. The IBDs can be obtained in a completely general pedigree at any genome position of interest, and all marker and pedigree information available is used. The method can be split into two steps at each iteration. First, phases are sampled using current genotypic configurations of relatives and second, crossover events are simulated conditional on phases. Internal track is kept of all founder origins and crossovers such that the IBD probabilities averaged over replicates are rapidly obtained. We illustrate the method with some examples. First, we show that all pedigree information should be used to obtain line origin probabilities in F2 crosses. Second, the distribution of genetic relationships between half and full sibs is analysed in both simulated data and in real data from an F2 cross in pigs.     

Affiliative ethnic identity: a more elastic link between ethnic ancestry and culture

This paper explains the development of affiliative ethnic identity: an individual identity rooted in knowledge, regular consumption and deployment of an ethnic culture that is unconnected to an individual's ethnic ancestry until that individual regards herself, and may be regarded by others, as an affiliate of a particular ethnic group. While ethnic culture remains identifiably linked to a particular ethnic ancestry, ideological, institutional and demographic changes have elasticized the link between ancestry and culture, making the formation of affiliative ethnic identity possible. Multiculturalism and its accompanying value of diversity have become institutionalized such that individuals regard ethnic difference as something to be recognized and celebrated. The prevalence of ethnic culture in schools, ethnically infused products of popular culture, demographic changes and growing interethnic contact allow individuals, regardless of ethnic ancestry, ready access to multiple ethnic cultures, providing the basis for the formation of affiliative ethnic identity.     

Postcolonial France: race,Islam, and the future of the republic

Abstract

The study explored feelings of European identity and attitudes towards Europe manifested in two groups within the British population: the indigenous white British population (N?=?58) and the South-Asian ethnic minority (N?=?44). A social survey approach was used with scales to evaluate British, European and ethnic identities and also attitudes towards Europe. Perceived compatibility of identities was also assessed using a visual representation of identities task. Previous research findings were confirmed with the indigenous white British respondents, who displayed a strong sense of national identity negatively correlated with European identity. In contrast, the South Asian respondents displayed positive feelings of identification on all three levels, and a British identity that correlated positively with European identification.     

Relatedness coefficients in pedigrees with inbred founders

We study an extension of the standard framework for pedigree analysis, in which we allow pedigree founders to be inbred. This solves a number of practical challenges in calculating coefficients of relatedness, including condensed identity coefficients. As a consequence we expand considerably the class of pedigrees for which such coefficients may be efficiently computed. An application of this is the modelling of background inbreeding as a continuous effect. We also use inbred founders to shed new light on constructibility of relatedness coefficients, i.e., the problem of finding a genealogy yielding a given set of coefficients. In particular, we show that any theoretically admissible coefficients for a pair of noninbred individuals can be produced by a finite pedigree with inbred founders. Coupled with our computational methods, implemented in the R package ribd, this allows for the first time computer analysis of general constructibility solutions, thus making them accessible for practical use.

     

Between global racial and bounded identity: choice of destigmatization strategies among Ethiopian Jews in Israel

Abstract

Our research explores how Ethiopian Jews in Israel apply local and global cultural resources when forming their reactive strategies to stigmatization. Drawing on 40 in-depth interviews with adult men and women, we examine class variations in the destigmatization strategies of working-class and middle-class Ethiopian Jews. Working-class Ethiopian Jews rely on their local bounded identity, that of Jews, rather than identity politics, which stresses phenotype in formulating destigmatization strategies. The former provide is Ethiopians of all classes with the network of meaning necessary for active participation in the broader society, whereas the latter is primarily the province of a small number of highly educated middle-class individuals, those who had access to social networks of highly educated liberals and could mobilize valued global black cultural resources (e.g. music, art) to their advantage in the local context.     

Similarity in the begging calls of nestling Red‐winged Blackbirds

ABSTRACT Although individually distinct begging calls may permit parents to recognize their offspring, birds nesting in dense breeding colonies where fledglings intermingle might benefit from additional adaptations. For example, if the calls of all nestlings in a brood were similar, parents would need to recognize only one brood call instead of the identity calls of each nestling. We recorded nestling Red‐winged Blackbirds (Agelaius phoeniceus) to determine whether their calls function to identify individuals (identity call hypothesis) or broods (brood call hypothesis). We used spectrogram cross‐correlation and dynamic time warping as well as call duration, peak frequency, and frequency range to estimate the similarity of begging calls of nestling Red‐winged Blackbirds. We recorded individual nestlings on day 5 and on day 9 of the nestling period to determine whether calls of individuals were more similar than calls of different nestlings, and whether calls of broodmates were more similar than calls of nestlings from different broods. We found that calls of 8‐d‐old individuals were more similar than calls of different nestlings, but the calls of broodmates were not more similar than those of nestlings from different broods. These results were consistent with the identity call hypothesis. We then compared begging calls of pairs of nestlings recorded separately and together on day 9. We found that the calls of 8‐d‐old nestlings recorded together were more similar than when they were recorded separately. In addition, using playback of begging calls from normal broods and artificial “broods” constructed from the calls of single nestlings, we found that females returned with food sooner in response to the calls of single nestlings (with enhanced call similarity) than to those of normal broods. Our results suggest that similar begging calls may be beneficial for both nestlings and parents, with broodmates fed at higher rates when their calls are more similar and, after fledging, parents needing to recognize only one brood call instead of the identity calls of each fledgling.     

Random marginal agreement coefficients: rethinking the adjustment for chance when measuring agreement

Agreement coefficients quantify how well a set of instruments agree in measuring some response on a population of interest. Many standard agreement coefficients (e.g. kappa for nominal, weighted kappa for ordinal, and the concordance correlation coefficient (CCC) for continuous responses) may indicate increasing agreement as the marginal distributions of the two instruments become more different even as the true cost of disagreement stays the same or increases. This problem has been described for the kappa coefficients; here we describe it for the CCC. We propose a solution for all types of responses in the form of random marginal agreement coefficients (RMACs), which use a different adjustment for chance than the standard agreement coefficients. Standard agreement coefficients model chance agreement using expected agreement between two independent random variables each distributed according to the marginal distribution of one of the instruments. RMACs adjust for chance by modeling two independent readings both from the mixture distribution that averages the two marginal distributions. In other words, both independent readings represent first a random choice of instrument, then a random draw from the marginal distribution of the chosen instrument. The advantage of the resulting RMAC is that differences between the two marginal distributions will not induce greater apparent agreement. As with the standard agreement coefficients, the RMACs do not require any assumptions about the bivariate distribution of the random variables associated with the two instruments. We describe the RMAC for nominal, ordinal and continuous data, and show through the delta method how to approximate the variances of some important special cases.     

Susceptibility genes and the question of embodied identity

Drawing on an assumption of the co-construction of the material and the social, late-onset Alzheimer's disease (AD) is used as an illustrative example to assess claims for an emergent figure of the "individual genetically at risk." Current medical understanding of the genetics of AD is discussed, followed by a summary of media and AD society materials that reveal an absence of gene hype in connection with this disease. Excerpts from interviews with first-degree relatives of patients diagnosed with AD follow. Interviewees hold complex theories of causation. After genetic testing they exhibit few if any subjective changes in embodied identity or lifestyle. Family history is regarded by interviewees as a better indicator of future disease than is genetic testing. We argue that, even when molecular genetics are better understood, predictions about complex disease based on genotyping will be fraught with uncertainty, making problematic the concept of individuals as genetically at risk when applied to late-onset complex disease.     

Variance and Covariance of Actual Relationships between Relatives at One Locus

The relationship between pairs of individuals is an important topic in many areas of population and quantitative genetics. It is usually measured as the proportion of thegenome identical by descent shared by the pair and it can be inferred from pedigree information. But there is a variance in actual relationships as a consequence of Mendelian sampling, whose general formula has not been developed. The goal of this work is to develop this general formula for the one-locus situation,. We provide simple expressions for the variances and covariances of all actual relationships in an arbitrary complex pedigree. The proposed method relies on the use of the nine identity coefficients and the generalized relationship coefficients; formulas have been checked by computer simulation. Finally two examples for a short pedigree of dogs and a long pedigree of sheep are given.     

Becoming American by becoming Muslim: strategic assimilation among second-generation Muslim American parents

ABSTRACT

Strategic assimilation describes how individuals use boundary work to construct identities which allow them to selectively maintain ties to a minority community while assimilating into the mainstream. However, scholarship that accounts for the role that minority religious identity plays in these processes is warranted. The current study fills a theoretical and empirical niche by exploring boundary work among not only racial, but religious minorities in their processes of identity construction and assimilation. Based on two years of ethnographic fieldwork as well as 72 in-depth interviews with Muslim Americans in Metro-Detroit, I demonstrate how upper-middle-class suburban second-generation parents actively deconstructed class, racial, and ethnic boundaries to construct boundaries around religious identity and generational identity. In so doing, they consciously crafted a de-ethnicized interpretation of Islam and hence a Muslim American identity that they saw as integral in promoting upward assimilation for themselves and their third-generation children.     

South African Museums and the Creation of a New National Identity

Museums are important sites of national cultural production, collective memory making, and the construction of national narratives. Contemporary South Africa is a particularly interesting place to study these processes. With the demise of apartheid, South Africa faces the difficult challenge of creating a new national identity that incorporates an examination of past oppression yet leaves the way open for building a national identity that incorporates all its diverse groups. The museums reviewed below, the Robben Island Prison Museum, the District Six Museum in Capetown, and the Kwa Muhle local history museum in Durban all make important contributions to this process.     

Intersectionality and trauma analysis in bioarchaeology

Intersectionality, the theory named by Kimberlé Crenshaw, outlines how multiple elements of an individual's social identity overlap to create and preserve societal inequalities and discrimination. Recently bioarchaeology's engagement with intersectionality has become increasingly explicit, as the field recognizes the lived experience of multiple axes of an individual's identity. Evidence of trauma can remain observable in an individual's skeleton for years, making it an ideal subject of study for intersectional analyses in bioarchaeology. Using contrasting case studies of two individuals who died in hospitals and were unclaimed after death, we explore the theoretical and methodological application of intersectionality to investigations of accidental and interpersonal trauma. Differences in identities and structural inequalities affect bone quality and health outcomes. As we demonstrate, a broken bone is the intersecting result of biological, histomorphological, sociocultural, and behavioral factors. This approach allows for a better acknowledgement of the inherent complexity of past lives, elevating and amplifying previously silenced voices. In this way, intersectionality in bioarchaeology demands social justice.