Atlas: analysis tools for low-depth and ancient samples

Summary: Post-mortem damage (PMD) obstructs the proper analysis of ancient DNA samples and can currently only be addressed by removing or down-weighting potentially damaged data. Here we present ATLAS, a suite of methods to accurately genotype and estimate genetic diversity from ancient samples, while accounting for PMD. It works directly from raw BAM files and enables the building of complete and customized pipelines for the analysis of ancient and other low-depth samples in a very user-friendly way. Based on simulations we show that, in the presence of PMD, a dedicated pipeline of ATLAS calls genotypes more accurately than the state-of-the-art pipeline of GATK combined with mapDamage 2.0. Availability: ATLAS is an open- source C++ program freely available at https://bitbucket.org/phaentu/atlas

Give and take: Integrating the skills of critique into doctoral nursing curricula

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/89499/1/21453_ftp.pd

Student nurse mentoring : an evaluative study of the mentor's perspective

Our evaluative study aimed to capture the 'mentor voice' and provide an insight into the mentoring role from the perspective of the nurse mentor. Participants from each of the four fields of nursing practice were asked to comment on the satisfying and frustrating aspects of their mentoring role. The narrative data gleaned from the evaluation was evaluated utilising qualitative analysis and subsequently organised into key themes around the student-mentor relationship and the clinical environment. Given that the landscape of nurse education is set to change; in terms of new standards from the professional bodies and the political drivers, not to mention the changing profile of the student nurse; it is hoped that our findings may to help shape the relationship between the mentor, Organisation,student and the Higher Education Institution and possibly spark some debate around different models of mentoring

Midwives\u27 use of best available evidence in practice: An integrative review

Aims and objectives: To synthesise international research that relates to midwives\u27 use of best available evidence in practice settings and identify key issues relating to the translation of latest evidence into everyday maternity care. Background: Midwifery is a research‐informed profession. However, a gap persists in the translation of best available evidence into practice settings, compromising gold standard maternity care and delaying the translation of new knowledge into everyday practice. Design: A five‐step integrative review approach, based on a series of articles published by the Joanna Briggs Institute (JBI) for conducting systematic reviews, was used to facilitate development of a search strategy, selection criteria and quality appraisal process, and the extraction and synthesis of data to inform an integrative review. Methods: The databases CINAHL, MEDLINE, Web of Science, Implementation Science Journal and Scopus were searched for relevant articles. The screening and quality appraisal process complied with the PRISMA 2009 checklist. Narrative analysis was used to develop sub‐categories and dimensions from the data, which were then synthesised to form two major categories that together answer the review question. Results: The six articles reviewed report on midwives\u27 use of best available evidence in Australia, the UK and Asia. Two major categories emerged that confirm that although midwifery values evidence‐based practice (EBP), evidence‐informed maternity care is not always employed in clinical settings. Additionally, closure of the evidence‐to‐practice gap in maternity care requires a multidimensional approach. Conclusion: Collaborative partnerships between midwives and researchers are necessary to initiate strategies that support midwives\u27 efforts to facilitate the timely movement of best available evidence into practice. Relevance to clinical practice: Understanding midwives\u27 use of best available evidence in practice will direct future efforts towards the development of mechanisms that facilitate the timely uptake of latest evidence by all maternity care providers working in clinical settings

Extreme selective sweeps independently targeted the X chromosomes of the great apes

The unique inheritance pattern of the X chromosome exposes it to natural selection in a way that is different from that of the autosomes, potentially resulting in accelerated evolution. We perform a comparative analysis of X chromosome polymorphism in 10 great ape species, including humans. In most species, we identify striking megabase-wide regions, where nucleotide diversity is less than 20% of the chromosomal average. Such regions are found exclusively on the X chromosome. The regions overlap partially among species, suggesting that the underlying targets are partly shared among species. The regions have higher proportions of singleton SNPs, higher levels of population differentiation, and a higher nonsynonymous-to-synonymous substitution ratio than the rest of the X chromosome. We show that the extent to which diversity is reduced is incompatible with direct selection or the action of background selection and soft selective sweeps alone, and therefore, we suggest that very strong selective sweeps have independently targeted these specific regions in several species. The only genomic feature that we can identify as strongly associated with loss of diversity is the location of testis-expressed ampliconic genes, which also have reduced diversity around them. We hypothesize that these genes may be responsible for selective sweeps in the form of meiotic drive caused by an intragenomic conflict in male meiosis

Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs

Abstract Background Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. Mitochondrial DNA is more easily obtained from ancient samples than nuclear DNA and mitochondrial analyses have revealed important insights into the evolutionary history of canids. Utilizing a recently published dog Y-chromosome reference, we analyzed Y-chromosome sequence across a diverse collection of canids and determined the Y haplogroup of three ancient European dogs. Results We identified 1121 biallelic Y-chromosome SNVs using whole-genome sequences from 118 canids and defined variants diagnostic to distinct dog Y haplogroups. Similar to that of the mitochondria and previous more limited studies of Y diversity, we observe several deep splits in the Y-chromosome tree which may be the result of retained Y-chromosome diversity which predates dog domestication or post-domestication admixture with wolves. We find that Y-chromosomes from three ancient European dogs (4700–7000 years old) belong to distinct clades. Conclusions We estimate that the time to the most recent comment ancestor of dog Y haplogroups is 68–151 thousand years ago. Analysis of three Y-chromosomes from the Neolithic confirms long stranding population structure among European dogs.https://deepblue.lib.umich.edu/bitstream/2027.42/143535/1/12864_2018_Article_4749.pd

Ancient genomes provide insights into family structure and the heredity of social status in the early Bronze Age of southeastern Europe

Twenty-four palaeogenomes from Mokrin, a major Early Bronze Age necropolis in southeastern Europe, were sequenced to analyse kinship between individuals and to better understand prehistoric social organization. 15 investigated individuals were involved in genetic relationships of varying degrees. The Mokrin sample resembles a genetically unstructured population, suggesting that the community's social hierarchies were not accompanied by strict marriage barriers. We find evidence for female exogamy but no indications for strict patrilocality. Individual status differences at Mokrin, as indicated by grave goods, support the inference that females could inherit status, but could not transmit status to all their sons. We further show that sons had the possibility to acquire status during their lifetimes, but not necessarily to inherit it. Taken together, these findings suggest that Southeastern Europe in the Early Bronze Age had a significantly different family and social structure than Late Neolithic and Early Bronze Age societies of Central Europe

Little genetic differentiation as assessed by uniparental markers in the presence of substantial language variation in peoples of the Cross River region of Nigeria

<p>Abstract</p> <p>Background</p> <p>The Cross River region in Nigeria is an extremely diverse area linguistically with over 60 distinct languages still spoken today. It is also a region of great historical importance, being a) adjacent to the likely homeland from which Bantu-speaking people migrated across most of sub-Saharan Africa 3000-5000 years ago and b) the location of Calabar, one of the largest centres during the Atlantic slave trade. Over 1000 DNA samples from 24 clans representing speakers of the six most prominent languages in the region were collected and typed for Y-chromosome (SNPs and microsatellites) and mtDNA markers (Hypervariable Segment 1) in order to examine whether there has been substantial gene flow between groups speaking different languages in the region. In addition the Cross River region was analysed in the context of a larger geographical scale by comparison to bordering Igbo speaking groups as well as neighbouring Cameroon populations and more distant Ghanaian communities.</p> <p>Results</p> <p>The Cross River region was shown to be extremely homogenous for both Y-chromosome and mtDNA markers with language spoken having no noticeable effect on the genetic structure of the region, consistent with estimates of inter-language gene flow of 10% per generation based on sociological data. However the groups in the region could clearly be differentiated from others in Cameroon and Ghana (and to a lesser extent Igbo populations). Significant correlations between genetic distance and both geographic and linguistic distance were observed at this larger scale.</p> <p>Conclusions</p> <p>Previous studies have found significant correlations between genetic variation and language in Africa over large geographic distances, often across language families. However the broad sampling strategies of these datasets have limited their utility for understanding the relationship within language families. This is the first study to show that at very fine geographic/linguistic scales language differences can be maintained in the presence of substantial gene flow over an extended period of time and demonstrates the value of dense sampling strategies and having DNA of known and detailed provenance, a practice that is generally rare when investigating sub-Saharan African demographic processes using genetic data.</p