A complex speciation-richness relationship in a simple neutral model

Speciation is the "elephant in the room" of community ecology. As the ultimate source of biodiversity, its integration in ecology's theoretical corpus is necessary to understand community assembly. Yet, speciation is often completely ignored or stripped of its spatial dimension. Recent approaches based on network theory have allowed ecologists to effectively model complex landscapes. In this study, we use this framework to model allopatric and parapatric speciation in networks of communities and focus on the relationship between speciation, richness, and the spatial structure of communities. We find a strong opposition between speciation and local richness, with speciation being more common in isolated communities and local richness being higher in more connected communities. Unlike previous models, we also find a transition to a positive relationship between speciation and local richness when dispersal is low and the number of communities is small. Also, we use several measures of centrality to characterize the effect of network structure on diversity. The degree, the simplest measure of centrality, is found to be the best predictor of local richness and speciation, although it loses some of its predictive power as connectivity grows. Our framework shows how a simple neutral model can be combined with network theory to reveal complex relationships between speciation, richness, and the spatial organization of populations.Comment: 9 pages, 5 figures, 1 table, 50 reference

Primary Postnatal Dorsal Root Ganglion Culture from Conventionally Slaughtered Calves

Neurological disorders in ruminants have an important impact on veterinary health, but very few host-specific in vitro models have been established to study diseases affecting the nervous system. Here we describe a primary neuronal dorsal root ganglia (DRG) culture derived from calves after being conventionally slaughtered for food consumption. The study focuses on the in vitro characterization of bovine DRG cell populations by immunofluorescence analysis. The effects of various growth factors on neuron viability, neurite outgrowth and arborisation were evaluated by morphological analysis. Bovine DRG neurons are able to survive for more than 4 weeks in culture. GF supplementation is not required for neuronal survival and neurite outgrowth. However, exogenously added growth factors promote neurite outgrowth. DRG cultures from regularly slaughtered calves represent a promising and sustainable host specific model for the investigation of pain and neurological diseases in bovines

Long-distance migratory shorebirds travel faster towards their breeding grounds, but fly faster post-breeding

Long-distance migrants are assumed to be more time-limited during the pre-breeding season compared to the post-breeding season. Although breeding-related time constraints may be absent post-breeding, additional factors such as predation risk could lead to time constraints that were previously underestimated. By using an automated radio telemetry system, we compared pre- and post-breeding movements of long-distance migrant shorebirds on a continent-wide scale. From 2014 to 2016, we deployed radio transmitters on 1,937 individuals of 4 shorebird species at 13 sites distributed across North America. Following theoretical predictions, all species migrated faster during the pre-breeding season, compared to the post-breeding season. These differences in migration speed between seasons were attributable primarily to longer stopover durations in the post-breeding season. In contrast, and counter to our expectations, all species had higher airspeeds during the post-breeding season, even after accounting for seasonal differences in wind. Arriving at the breeding grounds in good body condition is beneficial for survival and reproductive success and this energetic constraint might explain why airspeeds are not maximised in the pre-breeding season. We show that the higher airspeeds in the post-breeding season precede a wave of avian predators, which could suggest that migrant shorebirds show predation-minimizing behaviour during the post-breeding season. Our results reaffirm the important role of time constraints during northward migration and suggest that both energy and predation-risk constrain migratory behaviour during the post-breeding season

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits

Human and mouse essentiality screens as a resource for disease gene discovery

The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery. Discovery of causal variants for monogenic disorders has been facilitated by whole exome and genome sequencing, but does not provide a diagnosis for all patients. Here, the authors propose a Full Spectrum of Intolerance to Loss-of-Function (FUSIL) categorization that integrates gene essentiality information to aid disease gene discovery

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.

The early detection of relapse following primary surgery for non-small-cell lung cancer and the characterization of emerging subclones, which seed metastatic sites, might offer new therapeutic approaches for limiting tumour recurrence. The ability to track the evolutionary dynamics of early-stage lung cancer non-invasively in circulating tumour DNA (ctDNA) has not yet been demonstrated. Here we use a tumour-specific phylogenetic approach to profile the ctDNA of the first 100 TRACERx (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy (Rx)) study participants, including one patient who was also recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and analyse the tumour-volume detection limit. Through blinded profiling of postoperative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients who are very likely to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastasis, providing a new approach for ctDNA-driven therapeutic studies

A Better Start: Protocol for a National Evaluation of an Area-based Intervention Programme on Early Life Outcomes

Introduction Pregnancy and the first few years of a child’s life are important windows of opportunity in which to equalize life chances. A Better Start (ABS) is an area-based intervention being delivered in five areas of socioeconomic disadvantage across England. This protocol describes an evaluation of the impact and cost-effectiveness of ABS. Methods and analysis The evaluation of ABS comprises a mixed-methods design including impact, cost effectiveness and process components. It involves a cohort study in the five ABS areas and 15 matched comparison sites (n=2885), beginning in pregnancy in 2017 and ending in 2024 when the child is age 7, with a separate cross-sectional baseline survey in 2016/17. Process data will include a profiling of the structure and services being provided in the five ABS sites at baseline and yearly thereafter, and data regarding the participating families and the services that they receive. Eligible participants will include pregnant women living within the designated sites, with recruitment beginning at 16 weeks of pregnancy. Data collection will involve interviewer-administered and self-completion surveys at eight time-points. Primary outcomes include nutrition, socio-emotional development, speech, language and learning. Data analysis will include the use of propensity score techniques to construct matched programme and comparison groups, and a range of statistical techniques to calculate the difference in differences between the intervention and comparison groups. The economic evaluation will involve a within-cohort study economic evaluation to compare individual-level costs and outcomes, and a decision analytic cost-effectiveness model to estimate the expected incremental cost per unit change in primary outcomes for ABS in comparison to usual care. Ethics and dissemination Ethical approval to conduct the study has been obtained. The learning and dissemination workstream involves working within and across the sites to generate learning via communities of practice and a range of learning and dissemination events. STRENGTHS AND LIMITATIONS OF STUDY • The study involves a large longitudinal design with matched comparison sites • The designation of ABS areas was not random, and statistical matching will be used to select comparison areas and propensity score techniques will be used to match individual in ABS areas to individuals in comparison areas • Concurrent implementation data will provide important information about systems level change • Recruitment in pregnancy of disadvantaged women will present many difficulties and uptake may be low • Loss to follow-up by 7 years may be high<br/

A Better Start: Protocol for a National Evaluation of an Area-based Intervention Programme on Early Life Outcomes

Introduction Pregnancy and the first few years of a child’s life are important windows of opportunity in which to equalize life chances. A Better Start (ABS) is an area-based intervention being delivered in five areas of socioeconomic disadvantage across England. This protocol describes an evaluation of the impact and cost-effectiveness of ABS. Methods and analysis The evaluation of ABS comprises a mixed-methods design including impact, cost effectiveness and process components. It involves a cohort study in the five ABS areas and 15 matched comparison sites (n=2885), beginning in pregnancy in 2017 and ending in 2024 when the child is age 7, with a separate cross-sectional baseline survey in 2016/17. Process data will include a profiling of the structure and services being provided in the five ABS sites at baseline and yearly thereafter, and data regarding the participating families and the services that they receive. Eligible participants will include pregnant women living within the designated sites, with recruitment beginning at 16 weeks of pregnancy. Data collection will involve interviewer-administered and self-completion surveys at eight time-points. Primary outcomes include nutrition, socio-emotional development, speech, language and learning. Data analysis will include the use of propensity score techniques to construct matched programme and comparison groups, and a range of statistical techniques to calculate the difference in differences between the intervention and comparison groups. The economic evaluation will involve a within-cohort study economic evaluation to compare individual-level costs and outcomes, and a decision analytic cost-effectiveness model to estimate the expected incremental cost per unit change in primary outcomes for ABS in comparison to usual care. Ethics and dissemination Ethical approval to conduct the study has been obtained. The learning and dissemination workstream involves working within and across the sites to generate learning via communities of practice and a range of learning and dissemination events. STRENGTHS AND LIMITATIONS OF STUDY • The study involves a large longitudinal design with matched comparison sites • The designation of ABS areas was not random, and statistical matching will be used to select comparison areas and propensity score techniques will be used to match individual in ABS areas to individuals in comparison areas • Concurrent implementation data will provide important information about systems level change • Recruitment in pregnancy of disadvantaged women will present many difficulties and uptake may be low • Loss to follow-up by 7 years may be high<br