Distant Relatives Research Articles

Detailed kinship estimation for detecting bias among breeding families in a reintroduced population of the endangered bagrid catfish Tachysurus ichikawai

AbstractIn the context of initiatives focused on captive breeding and reintroduction of endangered animal species, it is crucial to minimize any bias in reproductive success during the reintroduction phase in order to preserve genetic diversity. One population of Tachysurus ichikawai, a critically endangered bagrid catfish endemic to Japan, faces a threat from the construction of a dam. To address this, a captive breeding program followed by translocation is being implemented. Multiple breeding families are involved in this process; however, if there is a bias in reproductive success among them after release, it will result in a decline in genetic diversity. To ascertain potential biases of reproductive success among released individuals, we attempted to identify the familial lineage of individuals born at the release site. Due to the unavailability of samples from the released individuals themselves, we reconstructed the pedigree of three generations using distant kinship relationships, such as grandparent–grandchild and uncle–aunt–nephew–niece relationships, with data of 2230–5674 single‐nucleotide polymorphisms obtained from whole genome re‐sequence, and three different software. Our findings indicate no bias between lineages in the first year after reintroduction, but a significant bias in the second year, emphasizing the need for continuous management and monitoring of reintroduced populations. This study demonstrates that monitoring kinship after reintroduction can correct lineage bias, which is critical for the prompt restoration of genetic diversity.

Young Chinese’s Modern Arranged Marriage and Mosaic Familialism in Shanghai

Abstract With rapid socio-economic development over the past four decades, a unique tapestry of Chinese society has unfolded into a mosaic of rapid modernization and resurgent patriarchal tradition. Within this complex temporality, parents still remain salient in young Chinese’ love and marital life. This study uses data from semi-structured interviews with recently married young people and their parents to investigate how young adults and their parents are involved in the marriage formation process. We found that in this joint process of intergenerational cooperative marriage arrangement, young people and their parents play different roles, as accommodating decision-makers and respectful advisers, respectively. They agreed that a modern marriage based on individual, romantic love was also a union between two families and welcomed their parents’ involvement. Moreover, they considered getting married and taking their parents’ opinions and preferences into account in their marriage decision as part of their filial piety towards their parents. We have also found that mothers played a salient and significant role in facilitating the transformation of the traditional and distant patriarchal intergenerational relationship into a warm and supportive family union. There are two sides to the mother’s role: the entrenchment of the traditional gender roles and the elevation of women’s status in the family.

Cryo-EM structure of rotavirus B NSP2 reveals its unique tertiary architecture.

Rotavirus (RV) NSP2 is a multifunctional RNA chaperone that exhibits numerous activities that are essential for replication and viral genome packaging. We performed an in silico analysis that highlighted a distant relationship of NSP2 from rotavirus B (RVB) to proteins from other human RVs. We solved a cryo-electron microscopy structure of RVB NSP2 that shows structural differences with corresponding proteins from other human RVs. Based on the structure, we identified amino acid residues that are involved in RNA interactions. Anisotropy titration experiments showed that these residues are important for nucleic acid binding. We also identified structural motifs that are conserved in all RV species. Collectively, our data complete the structural characterization of rotaviral NSP2 protein and demonstrate its structural diversity among RV species.IMPORTANCERotavirus B (RVB), also known as adult diarrhea rotavirus, has caused epidemics of severe diarrhea in China, India, and Bangladesh. Thousands of people are infected in a single RVB epidemic. However, information on this group of rotaviruses remains limited. As NSP2 is an essential protein in the viral life cycle, including its role in the formation of replication factories, it may be a target for future antiviral strategy against viruses with similar mechanisms.

Unveiling the Genetic Secrets of Chinese Indigenous Pigs from Guizhou Province: Diversity, Evolution and Candidate Genes Affecting Pig Coat Color.

The local pig breeds in Guizhou possess exceptional meat quality, robust adaptability, and resilience to harsh feeding conditions, making them ideal for producing high-quality pork. With over 10 local pig breeds in the region, we focused on 7 specific breeds: Baixi pigs (BX), Congjiang Xiang pigs (CJX), Guanling pigs (GL), Jianhe White Xiang pigs (JHBX), Jiangkou Luobo pigs (JKLB), Kele pigs (KL), and Qiandong Hua pigs (QDH). Unfortunately, these breeds face threats such as introduced species and inbreeding, resulting in a decline in population size and numbers. To better protect and utilize these breeds, we employed genome-wide single-nucleotide polymorphism (SNP) markers to investigate the population structure, genetic diversity, and selection characteristics of 283 pigs across these seven breeds. Our findings revealed distinct ancestral sources between Chinese and Western pig breeds, as demonstrated by principal component analysis, adjacent tree analysis, and ADMIXTURE analysis. Notably, JHBX exhibited a distant genetic relationship from the other six local pig breeds in Guizhou province, showcasing unique genetic characteristics. While the genetic diversity of the six Chinese native pig populations, excluding JHBX, was generally moderate in Guizhou province, the JHBX population displayed low genetic diversity. Therefore, it is imperative to intensify selection efforts to prevent inbreeding decline in JHBX while further enhancing the protection measures for the other six pig populations. Additionally, we identified candidate genes influencing the size disparity among pigs in Guizhou province through signal selection. Our study outcomes serve as a reference for developing effective conservation and utilization plans for pig breeds in Guizhou province and deepen our understanding of the genetic mechanisms underlying pig body size.

Two New Species of Freshwater Planarian (Platyhelminthes, Tricladida, Dugesiidae, Dugesia) from Southern China Exhibit Unusual Karyotypes, with a Discussion on Reproduction in Aneuploid Species

Two new species of the genus Dugesia from Southern China are described by applying an integrative approach, including morphological, karyological, histological, and molecular information. In the molecular phylogenetic tree, the two new species, Dugesia pendula Chen & Dong, sp. nov. and Dugesia musculosa Chen & Dong, sp. nov., fall into an Eastern Palearctic/Oriental clade and an Oriental/Australasian clade, respectively, while sharing only a rather distant relationship. The separate specific status of the two new species is supported also by their genetic distances. Dugesia pendula is characterized by the following features: symmetrical openings of the oviducts into the bursal canal, a duct between seminal vesicle and diaphragm, small diaphragm, dorsally located seminal vesicle, a penis papilla suspended from the dorsal wall of the male atrium, and mixoploid karyotype with diploid complements of 2n=2x=14+0−1 B-chromosome and triploid complements of 2n=3x=21+0−1 B-chromosome, with all chromosomes being metacentric. Dugesia musculosa is characterized by the following features: asymmetrical openings of the oviducts into the bursal canal; a ventrally displaced ejaculatory duct with a terminal opening; two diaphragms; a bursal canal provided with a strong, thick layer of circular muscle, which extends from the copulatory bursa to the common atrium and gonoduct; the left vas deferens opening at the midlateral wall of the seminal vesicle, while the right sperm duct opens at the dorsolateral wall of the seminal vesicle; and karyotype consisting of complicated diploid and aneuploid mosaicism, with diploid complements of 2n=2x=16 and 2n=2x=16−17th-18th, with all chromosomes being metacentric. The uncommon karyotypes, combined with the asexual reproduction of aneuploid animals, are evaluated in the context of the relationship between ploidy levels and reproductive modalities in the genus Dugesia.

Paternal Orphanhood, Parental Illness, and Child’s Biological Relationship to Household Head: Their Impact on Child Health in Nigeria

Abstract This research fills a hole in the literature by investigating whether, in Nigeria, differences exist in the health of paternal orphans or vulnerable children depending on whether they have a close biological relationship with the household head compared to a distant relationship when health is measured through diarrhea, fever, and cough. The research analyzes the 2013 Nigeria Demographic and Health Survey Data and employs a multi-level logistic regression as the model estimation technique. The results show that, regardless of the measure of child health, among paternal orphans or vulnerable children there is no significant difference in the health of grandchildren or children who are relatives/non-relatives of their household head in contrast to biological children of the household head. Further, results indicate that, among non-orphans or non-vulnerable children, there is a positive and statistically significant difference only in the odds of diarrhea for grandchildren compared to biological children. The devotion of foreign aid in social and health services in 2011–2013 from the United States Agency for International Development (USAID) for only orphans and vulnerable children, alongside contributions from the Nigeria government and other organizations, alleviated poor health status among said children.

A Purposeful Approach to LMX Differentiation: The Role of LMX With Key Members

A central idea in the leader-member exchange (LMX) literature is that leaders, due to the limited organizational and personal resources available to them, often struggle with developing and maintaining high-quality exchange relationships with all of their members. As a natural consequence, leaders typically form high-quality relationships with a select few members—often those who seem likable or are similar to the leader—while maintaining formal and distant relationships (i.e., low-quality LMX) with others. This form of differentiated treatment of members creates tensions in team dynamics. In this paper, we propose that leaders can mitigate the downsides of leader-member exchange differentiation (LMXD) for team dynamics by being more purposeful and strategic in how they differentiate in their treatment of members. Specifically, we posit that when leaders strategically develop high-quality LMX relationships with key members—individuals occupying influential positions in team social networks—such key members will engage in behaviors that buffer the negative impact of LMXD on team dynamics. Our framework integrates LMX theory with perspectives from social networks research to illustrate how strategic differentiation influences task and relational team dynamics. Finally, we discuss recommendations for empirically testing, theoretical extensions, and practical implications of this framework.

“Our Social Lives Were Kind of Ruined”: Challenges and Sources of Support During COVID-19 Distance Learning Among Latinx High School Students

The aim of this study was to better understand Latinx adolescents’ experiences during the pandemic and the transition to distance learning. Guided by the community cultural wealth framework, this study focuses on the key challenges and the sources of support that Latinx adolescents relied on during this unique period. Participants included 40 Latinx high school students from Southern California (28 female, 12 male; 75% Mexican or Mexican-American) between the ages of 14 and 17. A semi-structured interview was conducted with each participant; a thematic analysis approach was utilized to identify the key themes. Five themes emerged as the prominent challenges Latinx adolescents faced during the transition to distance learning. These challenges included disrupted peer relations, academic and motivation difficulties, home distractions, distant teacher relations, and poor mental health. In terms of the sources of support and coping resources to manage these challenges, the four key themes were supportive teacher relations, positive friend interactions, future aspirations and supportive family relations. The findings provide insights into Latinx adolescents’ experiences and sources of stress and support during distance learning. The findings have implications for how schools can best support Latinx youth with the transition to in-person schooling.

An approach to unified formulae for likelihood ratio calculation in pairwise kinship analysis.

Introduction: The likelihood ratio (LR) can be an efficient means of distinguishing various relationships in forensic fields. However, traditional list-based methods for derivation and presentation of LRs in distant or complex relationships hinder code editing and software programming. This paper proposes an approach for a unified formula for LRs, in which differences in participants' genotype combinations can be ignored for specific identification. This formula could reduce the difficulty of by-hand coding, as well as running time of large-sample-size simulation. Methods: The approach is first applied to a problem of kinship identification in which at least one of the participants is alleged to be inbred. This can be divided into two parts: i) the probability of different identical by descent (IBD) states according to the alleged kinship; and ii) the ratio of the probability that specific genotype combination can be detected assuming the alleged kinship exists between the two participants to the similar probability assuming that they are unrelated, for each state. For the probability, there are usually recognized results for common identification purposes. For the ratio, subscript letters representing IBD alleles of individual A's alleles are used to eliminate differences in genotype combinations between the two individuals and to obtain a unified formula for the ratio in each state. The unification is further simplified for identification cases in which it is alleged that both of the participants are outbred. Verification is performed to show that the results obtained with the unified and list-form formulae are equivalent. Results: A series of unified formulae are derived for different identification purposes, based on which an R package named KINSIMU has been developed and evaluated for use in large-size simulations for kinship analysis. Comparison between the package with two existing tools indicated that the unified approach presented here is more convenient and time-saving with respect to the coding process for computer applications compared with the list-based approach, despite appearing more complicated. Moreover, the method of derivation could be extended to other identification problems, such as those with different hypothesis sets or those involving multiple individuals. Conclusion: The unified approach of LR calculation can be beneficial in kinship identification field.

Five Species of Wild Freshwater Sport Fish in Wisconsin, USA, Reveal Highly Diverse Viromes.

Studies of marine fish have revealed distant relatives of viruses important to global fish and animal health, but few such studies exist for freshwater fish. To investigate whether freshwater fish also host such viruses, we characterized the viromes of five wild species of freshwater fish in Wisconsin, USA: bluegill (Lepomis macrochirus), brown trout (Salmo trutta), lake sturgeon (Acipenser fulvescens), northern pike (Esox lucius), and walleye (Sander vitreus). We analyzed 103 blood serum samples collected during a state-wide survey from 2016 to 2020 and used a metagenomic approach for virus detection to identify known and previously uncharacterized virus sequences. We then characterized viruses phylogenetically and quantified prevalence, richness, and relative abundance for each virus. Within these viromes, we identified 19 viruses from 11 viral families: Amnoonviridae, Circoviridae, Coronaviridae, Hepadnaviridae, Peribunyaviridae, Picobirnaviridae, Picornaviridae, Matonaviridae, Narnaviridae, Nudnaviridae, and Spinareoviridae, 17 of which were previously undescribed. Among these viruses was the first fish-associated coronavirus from the Gammacoronavirus genus, which was present in 11/15 (73%) of S. vitreus. These results demonstrate that, similar to marine fish, freshwater fish also harbor diverse relatives of viruses important to the health of fish and other animals, although it currently remains unknown what effect, if any, the viruses we identified may have on fish health.

Investigative genetic genealogy for human remains identification.

Investigative genetic genealogy (IGG) has emerged as a highly effective tool for tying a forensic DNA sample to an identity. While much of the attention paid to IGG has focused on cases where the DNA is from an unknown suspect, IGG has also been used to help close hundreds of unidentified human remains (UHR) cases. Genome-wide single-nucleotide polymorphism (SNP) genotype data can be obtained from forensic samples using microarray genotyping or whole-genome sequencing (WGS) with protocols optimized for degraded DNA. After bioinformatic processing, the SNP data can be uploaded to public GG databases that allow law enforcement usage, where it can be compared with other users' data to find distant relatives. A genetic genealogist can then build the family trees of the relatives to narrow down the identity of the source of the forensic DNA sample. To date, 367 UHR identifications using IGG have been publicly announced. The same IGG techniques developed and refined for UHR cases have significant potential for disaster victim identification, where DNA is often extremely compromised, and close family references may not be available. This paper reviews the laboratory, bioinformatic, and genealogical techniques used in IGG for UHR cases and presents three case studies that demonstrate how IGG is assisting with remains identification.

Patients’ perceptions and practices of informing relatives: a qualitative study within a randomised trial on healthcare-assisted risk disclosure

In a multicentre randomised controlled trial (DIRECT), we evaluate whether an intervention of providing direct letters from healthcare professionals to at-risk relatives (ARRs) affects the proportion of ARRs contacting a cancer genetics clinic, compared with patient-mediated disclosure alone (control). With the aim to explore how the patients included in the trial perceived and performed risk communication with their ARRs we analysed 17 semi-structured interviews with reflexive thematic analysis. All patients described that they disclosed risk information to all close relatives themselves. No integrity-related issues were reported by patients offered the intervention, and all of them accepted direct letters to all their ARRs. Patients’ approaches to informing distant relatives were unpredictable and varied from contacting all distant ARRs, sharing the burden with the family, utilising the offer of sending direct letters, vaguely relying on others to inform, or postponing disclosure. Most patients limited their responsibility to the disclosure, although others wanted relatives to get genetic counselling or felt a need to provide additional information to the ARRs before ending their mission. We also identified confusion about the implication of test results, who needed risk information, and who was responsible for informing ARRs. These misunderstandings possibly also affected risk disclosure. This study revealed that despite accepting the direct letters to be sent to all relatives, the patients also contributed to risk disclosure in other ways. It was only in some situations to distant relatives that the healthcare-assisted letter was the only means of communication to the ARRs.

Tracing the close and distant evolutionary relationships of protein refoldability in firmicutes

Tracing the close and distant evolutionary relationships of protein refoldability in firmicutes

Racial/ethnic differences in living arrangements, distant relations, and later‐life mental health

AbstractObjectiveThis research investigates associations between living arrangements and older adults' depressive symptoms and whether these associations are moderated by extended family, friends, and neighborhoods for White, Black, and Hispanic older adults.BackgroundThe drastic marriage and kinship decline since the 1970s has raised growing concerns about aging alone in both the public and scholarship. This paper adopts critical race theory to examine the social convoy model which argues that distant networks will fill in to protect individuals from stressors in the absence of proximal relations.MethodsThis paper applies multilevel mixed‐effects linear models to 2006–2018 waves of Health and Retirement Study (N = 44,304 obs., with 32,599 White, 7028 Black, and 4677 Hispanics).ResultsWhile married couples living alone have the best mental health among Whites, co‐residing with both spouses/partners and children (the intergenerational coresidence) is associated with the lowest depressive symptoms for Black and Hispanic older adults. Moreover, strong social support from extended family and friends and a high level of neighborhood social cohesion can significantly mitigate increased depressive symptoms associated with living alone or with others only (people other than spouses/partners and children) for Whites, but not for Blacks and Hispanics.ConclusionThis research challenges the paradigm that considers “married couples living alone” as a normalized family structure. It also emphasizes the “double plight” of Black and Hispanic older adults, who show both a disproportionate decline in family ties and a lack of supportive distant relations serving as buffer zones in the absence of spouses and children.

Enrichment and Diversification of the Wheat Genome via Alien Introgression

Wheat, including durum and common wheat, respectively, is an allopolyploid with two or three homoeologous subgenomes originating from diploid wild ancestral species. The wheat genome’s polyploid origin consisting of just three diploid ancestors has constrained its genetic variation, which has bottlenecked improvement. However, wheat has a large number of relatives, including cultivated crop species (e.g., barley and rye), wild grass species, and ancestral species. Moreover, each ancestor and relative has many other related subspecies that have evolved to inhabit specific geographic areas. Cumulatively, they represent an invaluable source of genetic diversity and variation available to enrich and diversify the wheat genome. The ancestral species share one or more homologous genomes with wheat, which can be utilized in breeding efforts through typical meiotic homologous recombination. Additionally, genome introgressions of distant relatives can be moved into wheat using chromosome engineering-based approaches that feature induced meiotic homoeologous recombination. Recent advances in genomics have dramatically improved the efficacy and throughput of chromosome engineering for alien introgressions, which has served to boost the genetic potential of the wheat genome in breeding efforts. Here, we report research strategies and progress made using alien introgressions toward the enrichment and diversification of the wheat genome in the genomics era.

A comparative wordlist for investigating distant relations among languages in Lowland South America

The history of the language families in Lowland South America remains an understudied area of historical linguistics. Panoan and Tacanan, two language families from this area, have frequently been proposed to descend from the same ancestor. Despite ample evidence in favor of this hypothesis, not all scholars accept it as proven beyond doubt. We compiled a new lexical questionnaire with 501 basic concepts to investigate the genetic relation between Panoan and Tacanan languages. The dataset includes data from twelve Panoan, five Tacanan, and four other languages which have previously been suggested to be related to Pano-Tacanan. Through the transparent annotation of grammatical morphemes and partial cognates, our dataset provides the basis for testing language relationships both qualitatively and quantitatively. The data is not only relevant for the investigation of the ancestry of Panoan and Tacanan languages. Reflecting the state of the art in computer-assisted approaches for historical language comparison, it can serve as a role model for linguistic studies in other areas of the world.

Phylogenetic analysis of Eimeria tenella isolates from chicken of sub-tropical mountains of Meghalaya, India.

Coccidiosis is the most common and pathogenic intestinal disease caused by different species of Eimeria is chicken. In this study, we describe the prevalence, molecular diagnosis and evolutionary insight of Eimeria tenella in chicken of Meghalaya's sub-tropical mountainous area. Faecal samples (337 no.) and dead chicks (298 no.) were collected every month from January to July' 2023 from poultry farms (4nos.) in and around Umiam, Ri-Bhoi, Meghalaya. The chicks were categorized into different age groups viz. < 3, 3-6 and > 6 weeks. Samples were examined by flotation techniques and post-mortem. The oocysts were sporulated in 2.5% potassium dichromate solution. Eimeria tenella's 18S rRNA gene genomic DNA was extracted, amplified, and sequenced. Fecal sample and postmortem examinations revealed 24.04% and 33.22% infections of Eimeria sp., respectively. Oocyst per gram (OPG) was recorded highest and lowest in July (26,500) and February (9800), respectively. Amplification of the 18S rRNA small subunit gene (SSU) by Polymerase Chain Reaction (PCR) revealed a 1790bp band size. The amplicon was sequenced and deposited in the NCBI database. BLAST analyses of the SSU rRNA gene of E. tenella, Umiam, Meghalaya isolate (OR458392.1) revealed sequence similarities of more than 99% with SSU rRNA gene sequences available in the NCBI database. Pair wise alignment exhibited nucleotide homology ranging from 71.59 to 100.0% with the maximum sequence homology (100.0%) shared with the E. tenella isolate from Turkey (HQ680474.1) and the lowest homology of 95.6% with UK (HG994972.1). Umiam isolate were found to have 97.08% and 100.0% nucleotide similarities with E. tenella from both the UK (AF026388.1) and the USA (U40264.1), respectively. However, nucleotide similarities of 98.24%, 85.33%, 84.75% and 81.35% were observed with E. tenella strain Bangalore (JX312808.1), E. tenella isolate Kerala-1 (JX093898.1), E. tenella isolate Kerala-3 (JX093900.1) and E. tenella isolate Kerala-2 (JX093899.1), respectively. Phylogenetic analysis of SSU rRNA sequences of E. tenella Umiam, Meghalaya isolate with cognate sequences throughout the world revealed these sequences are distinct but at the same time share a close phylogenetic relationship with Indian isolates from Bangalore and Andhra Pradesh. In addition, the distant phylogenetic relationship was observed with cognate gene sequences of United States of America, Canada, China. Phylogenetic analysis of SSU rRNA sequences of E. tenella Umiam, Meghalaya isolate with cognate sequences throughout the world revealed these sequences are distinct but at the same time share a close phylogenetic relationship with Indian isolates from Bangalore and Andhra Pradesh. Distant phylogenetic relationship was observed with cognate gene sequences of United States of America, Canada, China.

The Patterns of Impacted Third Molars and Their Associated Pathologies: A Retrospective Observational Study of 704 Patients.

Background: The study aims to investigate parameters in patients attending Fujairah Dental Center, including assessing the prevalence of impacted teeth, determining the frequency of associated pathological conditions, and evaluating the patterns and angulations of impacted third molars. Methods: It is a retrospective descriptive study of the panoramic radiographs of patients who attended Fujairah Dental Center for dental care between January 2011 and December 2017. The minimum age for inclusion was 17 years. Clinical records were used to obtain the demographic details of patients, such as age, gender, nationality, medical history, and smoking history. Seven hundred and four panoramic radiographs and clinical records of patients were analyzed. The age range was between 17 and 112 years old, with a mean age of 34 years (S.D 13.5). Results: Of the 704 panoramic radiographs evaluated, 236 (33.6%) X-rays showed teeth impaction with a total of 562 impacted teeth in the upper and lower jaws. Five hundred and twenty-five (93.4%) were impacted third molars, and 37 (6.5%) teeth were other kinds of impacted teeth. Females showed a higher frequency of impacted teeth (62.6%) compared to males (37.4%). The highest prevalence of impacted teeth was found in the 17-25 year age group (61%), and the prevalence declined with advancing age. Impacted third molars were more likely to occur in the mandible (57.3%) than in the maxilla (42.7%). Most of the impacted third molars were in the mesioangular position, followed by the vertical position. The evaluation of the depth of impacted third molars demonstrated that level C impaction was the most frequently seen, followed by level B impaction. Impacted third-molar teeth often presented with two roots (60.7%), followed by a single root (31.3%). An evaluation of the relationship between lower third molars and the inferior dental canal (IDC) revealed that the most frequently observed relation was interrupted (61.5%), followed by a distant relation to the ID canal, and 13% were superimposed. The most common morphological pattern of roots of the impacted third molars was either straight-type or curved and dilacerated roots (5.7%). Additionally, the most noticed pathological conditions associated with impacted teeth were carious second molars adjacent to impacted third molars (42%), which was more likely to be seen in the 17-25-year age group, with females having a higher prevalence than males.

A novel approach of kinship determination based on the physical length of genetically shared regions of chromosomes.

Determination of genetic relatedness between individuals plays a crucial role in resolving numerous civil cases involving familial relationships and in forensic investigation concerning missing persons. Short tandem repeats (STRs), known for their high degree of DNA polymorphism, have traditionally been the primary choice of DNA markers in genetic testing, but their application for kinships testing is limited to cases involving close kinship. SNPs have emerged as promising supplementary markers for kinship determination. Nevertheless, the challenging remains in discriminating between third-degree or more distant relatives, such as first cousins, using SNPs. To investigate a kinship analysis method for distant degree of familial relationships using high-density SNP data. A high-density SNP data from 337 individuals of Korean families using Affymetrix Axiom KORV1.0-96 Array was obtained for this study. SNPs were aligned by chromosomal positions, and identity-by-state (IBS) was determined, and then shared regions as consecutive SNPs with IBS of 1 or 2 were investigated. The physical lengths of these IBS segments were measured and summed them to create an Index, as a measure of kinship. The kinship was determined by the physical length of shared chromosomal regions that are distinguished by each kinship. Using this method, the relationship was able be distinguished up to the fourth degree of kinship, and non-relatives were clearly distinguished from true relatives. We also found a potential for this approach to be used universally, regardless of microarray platforms for SNP genotyping and populations. This method has a potential to determine the different degree of kinship between individuals and to distinguish non-relatives from true relatives, which can be of great help for practical applications in kinship determination.

GRUPS-rs, a high-performance ancient DNA genetic relatedness estimation software relying on pedigree simulations

Background: The study of fine-grain genetic kinship ties (parents, siblings, cousins, etc.) from ancient remains is now gaining significant interest within the field of paleogenetics, as a means of deciphering the social organization of past societies. However, kinship analyses are in practice often quite difficult to apply within paleogenetic studies, and may carry a high degree of uncertainty in the results they provide, especially when applied on low coverage and/or highly degraded samples, or when studying poorly characterized populations. To overcome these challenges, most of the available kinship estimation methods either refrain from inferring ties beyond the second degree (e.g., half-siblings), and/or rely on the use of a cohort of individuals to obtain a satisfactory statistical significance. Thus, the current state of the art remains intrinsically limited when attempting to estimate kinship on a small number of individuals, or when trying to detect more distant relationships (e.g., cousins). Methods:Here, we present GRUPS-rs:an update and complete reimplementation of GRUPS (Get Relatedness Using Pedigree Simulations), an ancient DNA kinship estimation software based on the methods originally developed in (Martin et al. 2017).GRUPS-rs both computes an estimate of relatedness from randomly sampled pseudo-haploidized variant calls, and leverages high-definition pedigree simulations to bypass the use of a cohort of individuals. Results: We highlight that GRUPS and GRUPS-rs are especially suitable to perform kinship analysis on a restricted number of ancient samples, and can provide a sufficient statistical significance to estimate genetic relatedness past the second degree, while taking into account user-defined contamination and sequencing error estimates. Importantly, GRUPS-rs offers an estimated 14000-fold speed-up in runtime performance compared to its predecessor — allowing the joint estimation of kinship between dozens of individuals in a matter of minutes — and is now bundled with a user-friendly Shiny interface, in which users can interactively visualize their results. Conclusions: The GRUPS kinship estimation method is now fully operational in its "GRUPS-rs" implementation, whose use is particularly recommended when analyzing a restricted number of low coverage DNA samples.