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

Sixty years of oceanography and marine biology: An annual review (Ombar) - A brief retrospective and prospective

Publisher PD

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

Satellite-based emergency mapping using optical imagery: experience and reflections from the 2015 Nepal earthquakes

Landslides triggered by large earthquakes in mountainous regions contribute significantly to overall earthquake losses and pose a major secondary hazard that can persist for months or years. While scientific investigations of coseismic landsliding are increasingly common, there is no protocol for rapid (hours-to-days) humanitarian-facing landslide assessment and no published recognition of what is possible and what is useful to compile immediately after the event. Drawing on the 2015 Mw 7.8 Gorkha earthquake in Nepal, we consider how quickly a landslide assessment based upon manual satellite-based emergency mapping (SEM) can be realistically achieved and review the decisions taken by analysts to ascertain the timeliness and type of useful information that can be generated. We find that, at present, many forms of landslide assessment are too slow to generate relative to the speed of a humanitarian response, despite increasingly rapid access to high-quality imagery. Importantly, the value of information on landslides evolves rapidly as a disaster response develops, so identifying the purpose, timescales, and end users of a post-earthquake landslide assessment is essential to inform the approach taken. It is clear that discussions are needed on the form and timing of landslide assessments, and how best to present and share this information, before rather than after an earthquake strikes. In this paper, we share the lessons learned from the Gorkha earthquake, with the aim of informing the approach taken by scientists to understand the evolving landslide hazard in future events and the expectations of the humanitarian community involved in disaster response. Please read the corrigendum first before accessing the articl

A genetic contribution from the Far East into Ashkenazi Jews via the ancient Silk Road

Contemporary Jews retain a genetic imprint from their Near Eastern ancestry, but obtained substantial genetic components from their neighboring populations during their history. Whether they received any genetic contribution from the Far East remains unknown, but frequent communication with the Chinese has been observed since the Silk Road period. To address this issue, mitochondrial DNA (mtDNA) variation from 55,595 Eurasians are analyzed. The existence of some eastern Eurasian haplotypes in eastern Ashkenazi Jews supports an East Asian genetic contribution, likely from Chinese. Further evidence indicates that this connection can be attributed to a gene flow event that occurred less than 1.4 kilo-years ago (kya), which falls within the time frame of the Silk Road scenario and fits well with historical records and archaeological discoveries. This observed genetic contribution from Chinese to Ashkenazi Jews demonstrates that the historical exchange between Ashkenazim and the Far East was not confined to the cultural sphere but also extended to an exchange of genes

National-Scale Rainfall-Triggered Landslide Susceptibility and Exposure in Nepal

Nepal is one of the most landslide-prone countries in the world, with year-on-year impacts resulting in loss of life and imposing a chronic impediment to sustainable livelihoods. Living with landslides is a daily reality for an increasing number of people, so establishing the nature of landslide hazard and risk is essential. Here we develop a model of landslide susceptibility for Nepal and use this to generate a nationwide geographical profile of exposure to rainfall-triggered landslides. We model landslide susceptibility using a fuzzy overlay approach based on freely-available topographic data, trained on an inventory of mapped landslides, and combine this with high resolution population and building data to describe the spatial distribution of exposure to landslides. We find that whilst landslide susceptibility is highest in the High Himalaya, exposure is highest within the Middle Hills, but this is highly spatially variable and skewed to on average relatively low values. Around 4 × 106 Nepalis (∼15\% of the population) live in areas considered to be at moderate or higher degree of exposure to landsliding (>0.25 of the maximum), and critically this number is highly sensitive to even small variations in landslide susceptibility. Our results show a complex relationship between landslides and buildings, that implies wider complexity in the association between physical exposure to landslides and poverty. This analysis for the first time brings into focus the geography of the landslide exposure and risk case load in Nepal, and demonstrates limitations of assessing future risk based on limited records of previous events

Complete mitochondrial DNA sequences provide new insights into the Polynesian motif and the peopling of Madagascar

More than a decade of mitochondrial DNA (mtDNA) studies have given the 'Polynesian motif' renowned status as a marker for tracing the late-Holocene expansion of Austronesian speaking populations. Despite considerable research on the Polynesian motif in Oceania, there has been little equivalent work on the western edge of its expansion - leaving major issues unresolved regarding the motif's evolutionary history. This has also led to considerable uncertainty regarding the settlement of Madagascar. In this study, we assess mtDNA variation in 266 individuals from three Malagasy ethnic groups: the Mikea, Vezo, and Merina. Complete mtDNA genome sequencing reveals a new variant of the Polynesian motif in Madagascar; two coding region mutations define a Malagasy-specific sub-branch. This newly defined 'Malagasy motif' occurs at high frequency in all three ethnic groups (13-50%), and its phylogenetic position, geographic distribution, and estimated age all support a recent origin, but without conclusively identifying a specific source region. Nevertheless, the haplotype's limited diversity, similar to those of other mtDNA haplogroups found in our Malagasy groups, best supports a small number of initial settlers arriving to Madagascar through the same migratory process. Finally, the discovery of this lineage provides a set of new polymorphic positions to help localize the Austronesian ancestors of the Malagasy, as well as uncover the origin and evolution of the Polynesian motif itself

Potential pitfalls in MitoChip detected tumor-specific somatic mutations: a call for caution when interpreting patient data

<p>Abstract</p> <p>Background</p> <p>Several investigators have employed high throughput mitochondrial sequencing array (MitoChip) in clinical studies to search mtDNA for markers linked to cancers. In consequence, a host of somatic mtDNA mutations have been identified as linked to different types of cancers. However, closer examination of these data show that there are a number of potential pitfalls in the detection tumor-specific somatic mutations in clinical case studies, thus urging caution in the interpretation of mtDNA data to the patients. This study examined mitochondrial sequence variants demonstrated in cancer patients, and assessed the reliability of using detected patterns of polymorphisms in the early diagnosis of cancer.</p> <p>Methods</p> <p>Published entire mitochondrial genomes from head and neck, adenoid cystic carcinoma, sessile serrated adenoma, and lung primary tumor from clinical patients were examined in a phylogenetic context and compared with known, naturally occurring mutations which characterize different populations.</p> <p>Results</p> <p>The phylogenetic linkage analysis of whole arrays of mtDNA mutations from patient cancerous and non-cancerous tissue confirmed that artificial recombination events occurred in studies of head and neck, adenoid cystic carcinoma, sessile serrated adenoma, and lung primary tumor. Our phylogenetic analysis of these tumor and control leukocyte mtDNA haplotype sequences shows clear cut evidence of mixed ancestries found in single individuals.</p> <p>Conclusions</p> <p>Our study makes two prescriptions: both in the clinical situation and in research 1. more care should be taken in maintaining sample identity and 2. analysis should always be undertaken with respect to all the data available and within an evolutionary framework to eliminate artifacts and mix-ups.</p