Multiplex genotyping system for efficient inference of matrilineal genetic ancestry with continental resolution

Abstract Background: In recent years, phylogeographic studies have produced detailed knowledge on the worldwide distribution of mitochondrial DNA (mtDNA) variants, linking specific clades of the mtDNA phylogeny with certain geographic areas. However, a multiplex genotyping system for the detection of the mtDNA haplogroups of major continental distribution that would be desirable for efficient DNA-based bio-geographic ancestry testing in various applications is still missing. Results: Three multiplex genotyping assays, based on single-base primer extension technology, were developed targeting a total of 36 coding-region mtDNA variants that together differentiate 43 matrilineal haplo-/paragroups. These include the major diagnostic haplogroups for Africa, Western Eurasia, Eastern Eurasia and Native America. The assays show high sensitivity with respect to the amount of template DNA: successful amplification could still be obtained when using as little as 4 pg of genomic DNA and the technology is suitable for medium-throughput analyses. Conclusions: We introduce an efficient and sensitive multiplex genotyping system for bio-geographic ancestry inference from mtDNA that provides resolution on the continental level. The method can be applied in forensics, to aid tracing unknown suspects, as well as in population studies, genealogy and personal ancestry testing. For more complete inferences of overall bio-geographic ancestry from DNA, the mtDNA system provided here can be combined with multiplex systems for suitable autosomal and, in the case of males, Y-chromosomal ancestrysensitive DNA markers

Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine

Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylo

Belongingness challenged: Exploring the impact on older adults during the COVID-19 pandemic

Objectives The sense of belonging is a fundamental human need. Enacting it through face-to-face social activities was no longer possible during the COVID-19 pandemic. In this study, we investigate how the sense of belonging, and how it is enacted, changed longitudinally amongst older adults in the UK. In addition, we examine the interplay of the sense of belonging and resilience over time. Methods We employed a longitudinal qualitative research design to explore the experiences of older adults during one year of the COVID-19 pandemic (April 2020-April 2021). The analysis was undertaken with constructivist grounded theory. Findings Before the pandemic older adults were free to engage in social relationships with family and friends, often enacted within social activity groups where they felt valued and gained positive experiences. During the pandemic face to face enactment of belongingness was reduced; adjustments needed to be made to maintain the sense of belonging. The experience of older adults was heterogeneous. We examine three themes. First, how belongingness was enacted prior to the pandemic. Examples include: family holidays, visiting each other, sports activities, eating with friends and family, and visiting cultural events. Second, how participants adapted and maintained their social involvement. Examples include: distanced face-to-face activities; and learning new technology. Third, for some, a belongingness gap emerged and persisted. There was an irretrievable loss of family members or friends, the closure of social groups, or withdrawal from groups as priorities changed. As a consequence, of challenged belongingness, participants expressed increased loneliness, anxiety, social isolation, frustration and, feelings of depression. For many, the disrupted sense of belonging no longer fostered resilience, and some previously resilient participants were no longer resilient. </jats:sec

Older people's family relationships in disequilibrium during the COVID-19 pandemic. What really matters?

Abstract Inter- and intragenerational relationships are known to be important in maintaining the wellbeing of older people. A key aspect of these relationships is the exchange of both emotional and instrumental social support. However, relatively little is known about how this exchange of support changes in the context of widespread disruption. The COVID-19 pandemic provides an opportunity to examine how older people's family relationships are impacted by such social change. The present qualitative study explores how older people in the United Kingdom experienced changes in inter- and intragenerational support during the COVID-19 pandemic. Participants (N = 33) were recruited through a large-scale nationally representative survey (https://www.sheffield.ac.uk/psychology-consortium-covid19). We asked how life had been pre-pandemic, how they experienced the first national lockdown and what the future might hold in store. The data were analysed using constructivist grounded theory. This paper focuses on the importance of family relationships and how they changed as a consequence of the pandemic. We found that the family support system had been interrupted, that there were changes in the methods of support and that feelings of belonging were challenged. We argue that families were brought into disequilibrium through changes in the exchange of inter- and intragenerational support. The important role of grandchildren for older adults was striking and challenged by the pandemic. The significance of social connectedness and support within the family had not changed during the pandemic, but it could no longer be lived in the same way. The desire to be close to family members and to support them conflicted with the risk of pandemic infection. Our study found support for the COVID-19 Social Connectivity Paradox: the need for social connectedness whilst maintaining social distance. This challenged family equilibrium, wellbeing and quality of life in older people.</jats:p

An efficient multiplex genotyping approach for detecting the major worldwide human Y-chromosome haplogroups

The Y chromosome is paternally inherited and therefore serves as an evolutionary marker of patrilineal descent. Worldwide DNA variation within the non-recombining portion of the Y chromosome can be represented as a monophyletic phylogenetic tree in which the branches (haplogroups) are defined by at least one SNP. Previous human population genetics research has produced a wealth of knowledge about the worldwide distribution of Y-SNP haplogroups. Here, we apply previous and very recent knowledge on the Y-SNP phylogeny and Y-haplogroup distribution by introducing two multiplex genotyping assays that allow for the hierarchical detection of 28 Y-SNPs defining the major worldwide Y haplogroups. PCR amplicons were kept small to make the method sensitive and thereby applicable to DNA of limited amount and/or quality such as in forensic settings. These Y-SNP assays thus form a valuable tool for researchers in the fields of forensic genetics and genetic anthropology to infer a man's patrilineal bio-geographic ancestry from DNA

Lack of gene-language correlation due to reciprocal female but directional male admixture in Austronesians and non-Austronesians of East Timor

Nusa Tenggara, including East Timor, located at the crossroad between Island Southeast Asia, Near Oceania, and Australia, are characterized by a complex cultural structure harbouring speakers from two different major linguistic groups of different geographic origins (Austronesian (AN) and non-Austronesian (NAN)). This provides suitable possibilities to study gene-language relationship; however, previous studies from other parts of Nusa Tenggara reported conflicting evidence about gene-language correlation in this region. Aiming to investigate gene-language relationships including sex-mediated aspects in East Timor, we analysed the paternally inherited non-recombining part of the Y chromosome (NRY) and the maternally inherited mitochondrial (mt) DNA in a representative collection of AN-and NAN-speaking groups. Y-SNP (single-nucleotide polymorphism) data were newly generated for 273 samples and combined with previously established Y-STR (short tandem repeat) data of the same samples, and with previously established mtDNA data of 290 different samples with, however, very similar representation of geographic and linguistic coverage of the country. We found NRY and mtDNA haplogroups of previously described putative East/Southeast Asian (E/SEA) and Near Oceanian (NO) origins in both AN and NAN speakers of East Timor, albeit in different proportions, suggesting reciprocal genetic admixture between both linguistic groups for females, but directional admixture for males. Our data underline the dual genetic origin of East Timorese in E/SEA and NO, and highlight that substantial genetic admixtur