Genetic Analysis of Blue Marlin (Makaira nigricans) Stock Structure in the Atlantic Ocean

The genetic basis of stock structure of blue marlin (Makaira nigricans Lacepède 1802) in the Atlantic ocean was inferred from analyses of mitochondrial control region sequences. Blue marlin were collected in 1998 from 4 major geographic locations: western North Atlantic, Caribbean Sea, western South Atlantic and eastern Atlantic. Haplotype diversity (h) ranged from 0.99-1.0 and nucleotide sequence diversity (π) ranged from 0.11-0.13 within samples indicating that the control region harbors a significant amount of genetic variation. However, no significant differences were found in the spatial partitioning of genetic variation among the 4 collections; all pairwise ϕST values were negative and were therefore all taken as estimates around a true value of 0. As with previous studies of blue marlin, sequences were comprised of 2 distinct mitochondrial lineages separated by an average of 138 base pairs and ϕST between clades of 0.799 (P \u3c 0.0001). These 2 lineages were present in similar frequencies across sampling locations. Genetic data from this study support management of Atlantic blue marlin as a single, Atlantic-wide stock

Uncovering precision phenotype-biomarker associations in traumatic brain injury using topological data analysis

Background: Traumatic brain injury (TBI) is a complex disorder that is traditionally stratified based on clinical signs and symptoms. Recent imaging and molecular biomarker innovations provide unprecedented opportunities for improved TBI precision medicine, incorporating patho-anatomical and molecular mechanisms. Complete integration of these diverse data for TBI diagnosis and patient stratification remains an unmet challenge. Methods and findings: The Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Pilot multicenter study enrolled 586 acute TBI patients and collected diverse common data elements (TBI-CDEs) across the study population, including imaging, genetics, and clinical outcomes. We then applied topology-based data-driven discovery to identify natural subgroups of patients, based on the TBI-CDEs collected. Our hypothesis was two-fold: 1) A machine learning tool known as topological data analysis (TDA) would reveal data-driven patterns in patient outcomes to identify candidate biomarkers of recovery, and 2) TDA-identified biomarkers would significantly predict patient outcome recovery after TBI using more traditional methods of univariate statistical tests. TDA algorithms organized and mapped the data of TBI patients in multidimensional space, identifying a subset of mild TBI patients with a specific multivariate phenotype associated with unfavorable outcome at 3 and 6 months after injury. Further analyses revealed that this patient subset had high rates of post-traumatic stress disorder (PTSD), and enrichment in several distinct genetic polymorphisms associated with cellular responses to stress and DNA damage (PARP1), and in striatal dopamine processing (ANKK1, COMT, DRD2). Conclusions: TDA identified a unique diagnostic subgroup of patients with unfavorable outcome after mild TBI that were significantly predicted by the presence of specific genetic polymorphisms. Machine learning methods such as TDA may provide a robust method for patient stratification and treatment planning targeting identified biomarkers in future clinical trials in TBI patients

A century of trends in adult human height

Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.5-22.7) and 16.5 cm (13.3-19.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8-144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries

Rising rural body-mass index is the main driver of the global obesity epidemic in adults

Body-mass index (BMI) has increased steadily in most countries in parallel with a rise in the proportion of the population who live in cities 1,2 . This has led to a widely reported view that urbanization is one of the most important drivers of the global rise in obesity 3�6 . Here we use 2,009 population-based studies, with measurements of height and weight in more than 112 million adults, to report national, regional and global trends in mean BMI segregated by place of residence (a rural or urban area) from 1985 to 2017. We show that, contrary to the dominant paradigm, more than 55 of the global rise in mean BMI from 1985 to 2017�and more than 80 in some low- and middle-income regions�was due to increases in BMI in rural areas. This large contribution stems from the fact that, with the exception of women in sub-Saharan Africa, BMI is increasing at the same rate or faster in rural areas than in cities in low- and middle-income regions. These trends have in turn resulted in a closing�and in some countries reversal�of the gap in BMI between urban and rural areas in low- and middle-income countries, especially for women. In high-income and industrialized countries, we noted a persistently higher rural BMI, especially for women. There is an urgent need for an integrated approach to rural nutrition that enhances financial and physical access to healthy foods, to avoid replacing the rural undernutrition disadvantage in poor countries with a more general malnutrition disadvantage that entails excessive consumption of low-quality calories. © 2019, The Author(s)

Current genetic status, temporal stability and structure of the remnant wild European flat oyster populations : conservation and restoring implications

The flat oyster (Ostrea edulis) is one of the most appreciated molluscs in Europe, but natural beds have been greatly reduced due to harvesting and the effects of the parasite Bonamia ostreae. Characterization of current wild populations is required to develop long-term bed restoration programmes by enhancing genetic diversity and tolerance to bonamiosis. Oysters from different locations corresponding to the main natural beds from Denmark, The Netherlands, England, Ireland, France and Spain, including two different cohorts per location were sampled in 2011 and 2013. Sixteen microsatellite loci were used to study temporal and geographical genetic structure. Temporal variation was low, although sometimes significant probably due to high variance in reproductive success among individuals. Conversely, samples from different countries showed much higher genetic divergence, and Ireland and France presented differences among locations within country. Clustering analyses grouped samples into three main geographical regions, associated with oceanic fronts: one group constituted by The Netherlands and Denmark; another by France, Ireland and England; and a third one exclusively by Spain. Effective population sizes (Ne) within regions were high (>1000), which reflects population stability and low levels of genetic drift. The presence of regional genetic structure shows the potential for local adaptation of O. edulis and suggests caution when transplanting individuals, especially between distant geographical regions.</p