Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems

Summary 1. Significant advances in both mathematical and molecular approaches in ecology offer unprecedented opportunities to describe and understand ecosystem functioning. Ecological networks describe interactions between species, the underlying structure of communities and the function and stability of ecosystems. They provide the ability to assess the robustness of complex ecological communities to species loss, as well as a novel way of guiding restoration. However, empirically quantifying the interactions between entire communities remains a significant challenge. 2. Concomitantly, advances in DNA sequencing technologies are resolving previously intractable questions in functional and taxonomic biodiversity and provide enormous potential to determine hitherto difficult to observe species interactions. Combining DNA metabarcoding approaches with ecological network analysis presents important new opportunities for understanding large-scale ecological and evolutionary processes, as well as providing powerful tools for building ecosystems that are resilient to environmental change. 3. We propose a novel ‘nested tagging’ metabarcoding approach for the rapid construction of large, phylogenetically structured species-interaction networks. Taking tree–insect–parasitoid ecological networks as an illustration, we show how measures of network robustness, constructed using DNA metabarcoding, can be used to determine the consequences of tree species loss within forests, and forest habitat loss within wider landscapes. By determining which species and habitats are important to network integrity, we propose new directions for forest management. 4. Merging metabarcoding with ecological network analysis provides a revolutionary opportunity to construct some of the largest, phylogenetically structured species-interaction networks to date, providing new ways to: (i) monitor biodiversity and ecosystem functioning; (ii) assess the robustness of interacting communities to species loss; and (iii) build ecosystems that are more resilient to environmental change

Sexual selection protects against extinction

Reproduction through sex carries substantial costs, mainly because only half of sexual adults produce offspring1. It has been theorized that these costs could be countered if sex allows sexual selection to clear the universal fitness constraint of mutation load2,3,4. Under sexual selection, competition between (usually) males and mate choice by (usually) females create important intraspecific filters for reproductive success, so that only a subset of males gains paternity. If reproductive success under sexual selection is dependent on individual condition, which is contingent to mutation load, then sexually selected filtering through ‘genic capture’5 could offset the costs of sex because it provides genetic benefits to populations. Here we test this theory experimentally by comparing whether populations with histories of strong versus weak sexual selection purge mutation load and resist extinction differently. After evolving replicate populations of the flour beetle Tribolium castaneum for 6 to 7 years under conditions that differed solely in the strengths of sexual selection, we revealed mutation load using inbreeding. Lineages from populations that had previously experienced strong sexual selection were resilient to extinction and maintained fitness under inbreeding, with some families continuing to survive after 20 generations of sib × sib mating. By contrast, lineages derived from populations that experienced weak or non-existent sexual selection showed rapid fitness declines under inbreeding, and all were extinct after generation 10. Multiple mutations across the genome with individually small effects can be difficult to clear, yet sum to a significant fitness load; our findings reveal that sexual selection reduces this load, improving population viability in the face of genetic stress.We thank the Natural Environment Research Council and the Leverhulme Trust for financial support, D. Edward for statistical advice and colleagues at the 2013 Biology of Sperm meeting for comments that improved analytical design and interpretation.Peer reviewedPeer Reviewe

Overcoming the pitfalls of merging dietary metabarcoding into ecological networks

The construction of increasingly detailed species interaction networks is extending the potential applications of network ecology, providing an opportunity to understand complex eco-evolutionary interactions, ecosystem service provision and the impacts of environmental change on ecosystem functioning. Dietary metabarcoding is a rapidly growing tool increasingly used to construct ecological networks of trophic interactions, enabling the determination of individual animal diets including difficult-to-distinguish prey taxa and even for species where traditional dietary analyses are unsuitable (e.g. fluid feeders and small invertebrates). Several challenges, however, surround the use of dietary metabarcoding, especially when metabarcoding-based interactions are merged with observation-based species interaction data. We describe the difficulties surrounding the quantification of species interactions, sampling perspective discrepancy (i.e. zoocentric vs. phytocentric sampling), experimental biases, reference database omissions and assumptions regarding direct and indirect consumption events. These problems are not, however, insurmountable. Effective experimental design and data curation with appropriate attention paid to these problems renders the incorporation of dietary metabarcoding into ecological network analysis a powerful tool for the construction of highly resolved networks. Throughout, we discuss how these problems should be addressed when merging data to construct ecological networks

The predator problem and PCR primers in molecular dietary analysis: Swamped or silenced; depth or breadth?

Dietary metabarcoding has vastly improved our ability to analyse the diets of animals, but it is hampered by a plethora of technical limitations including potentially reduced data output due to the disproportionate amplification of the DNA of the focal predator, here termed “the predator problem”. We review the various methods commonly used to overcome this problem, from deeper sequencing to exclusion of predator DNA during PCR, and how they may interfere with increasingly common multipredator‐taxon studies. We suggest that multiprimer approaches with an emphasis on achieving both depth and breadth of prey detections may overcome the issue to some extent, although multitaxon studies require further consideration, as highlighted by an empirical example. We also review several alternative methods for reducing the prevalence of predator DNA that are conceptually promising but require additional empirical examination. The predator problem is a key constraint on molecular dietary analyses but, through this synthesis, we hope to guide researchers in overcoming this in an effective and pragmatic way

Assessment of variation in the alberta context tool: the contribution of unit level contextual factors and specialty in Canadian pediatric acute care settings

Background: There are few validated measures of organizational context and none that we located are parsimonious and address modifiable characteristics of context. The Alberta Context Tool (ACT) was developed to meet this need. The instrument assesses 8 dimensions of context, which comprise 10 concepts. The purpose of this paper is to report evidence to further the validity argument for ACT. The specific objectives of this paper are to: (1) examine the extent to which the 10 ACT concepts discriminate between patient care units and (2) identify variables that significantly contribute to between-unit variation for each of the 10 concepts. Methods: 859 professional nurses (844 valid responses) working in medical, surgical and critical care units of 8 Canadian pediatric hospitals completed the ACT. A random intercept, fixed effects hierarchical linear modeling (HLM) strategy was used to quantify and explain variance in the 10 ACT concepts to establish the ACT’s ability to discriminate between units. We ran 40 models (a series of 4 models for each of the 10 concepts) in which we systematically assessed the unique contribution (i.e., error variance reduction) of different variables to between-unit variation. First, we constructed a null model in which we quantified the variance overall, in each of the concepts. Then we controlled for the contribution of individual level variables (Model 1). In Model 2, we assessed the contribution of practice specialty (medical, surgical, critical care) to variation since it was central to construction of the sampling frame for the study. Finally, we assessed the contribution of additional unit level variables (Model 3). Results: The null model (unadjusted baseline HLM model) established that there was significant variation between units in each of the 10 ACT concepts (i.e., discrimination between units). When we controlled for individual characteristics, significant variation in the 10 concepts remained. Assessment of the contribution of specialty to between-unit variation enabled us to explain more variance (1.19% to 16.73%) in 6 of the 10 ACT concepts. Finally, when we assessed the unique contribution of the unit level variables available to us, we were able to explain additional variance (15.91% to 73.25%) in 7 of the 10 ACT concepts. Conclusion: The findings reported here represent the third published argument for validity of the ACT and adds to the evidence supporting its use to discriminate patient care units by all 10 contextual factors. We found evidence of relationships between a variety of individual and unit-level variables that explained much of this between-unit variation for each of the 10 ACT concepts. Future research will include examination of the relationships between the ACT’s contextual factors and research utilization by nurses and ultimately the relationships between context, research utilization, and outcomes for patients

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Differential predictors for alcohol use in adolescents as a function of familial risk

Abstract: Traditional models of future alcohol use in adolescents have used variable-centered approaches, predicting alcohol use from a set of variables across entire samples or populations. Following the proposition that predictive factors may vary in adolescents as a function of family history, we used a two-pronged approach by first defining clusters of familial risk, followed by prediction analyses within each cluster. Thus, for the first time in adolescents, we tested whether adolescents with a family history of drug abuse exhibit a set of predictors different from adolescents without a family history. We apply this approach to a genetic risk score and individual differences in personality, cognition, behavior (risk-taking and discounting) substance use behavior at age 14, life events, and functional brain imaging, to predict scores on the alcohol use disorders identification test (AUDIT) at age 14 and 16 in a sample of adolescents (N = 1659 at baseline, N = 1327 at follow-up) from the IMAGEN cohort, a longitudinal community-based cohort of adolescents. In the absence of familial risk (n = 616), individual differences in baseline drinking, personality measures (extraversion, negative thinking), discounting behaviors, life events, and ventral striatal activation during reward anticipation were significantly associated with future AUDIT scores, while the overall model explained 22% of the variance in future AUDIT. In the presence of familial risk (n = 711), drinking behavior at age 14, personality measures (extraversion, impulsivity), behavioral risk-taking, and life events were significantly associated with future AUDIT scores, explaining 20.1% of the overall variance. Results suggest that individual differences in personality, cognition, life events, brain function, and drinking behavior contribute differentially to the prediction of future alcohol misuse. This approach may inform more individualized preventive interventions

Interventions for weight reduction in obesity to improve survival in women with endometrial cancer

To determine the impact of weight loss interventions, in addition to standard management of endometrial cancer, on overall survival and the frequency of adverse events. Secondary objectives include an assessment of weight loss interventions on endometrial cancer-specific survival, cardiovascular event frequency, and QoL, stratified according to patient BMI, and patient and tumour characteristics

Community assembly and diversification in a species-rich radiation of island weevils (Coleoptera: Cratopini)

[Aim] To test a prediction derived from island biogeographical theory that in situ speciation should make an increasingly important contribution to community assembly as islands age. This prediction is tested on estimated biogeographical histories from Mauritius (approximately 9 Myr) and Reunion (approximately 5 Myr). We additionally investigate the evolutionary dynamics of insect flight loss, as the loss of flight in island lineages can influence patterns of diversification. [Location] Mascarene Islands; Southwest Indian Ocean. [Taxon] Weevils. [Methods] Up to five individuals of each taxonomically described species sampled within each sampling site were sequenced for the mitochondrial gene Cytochrome Oxidase II to delimit operational taxonomic units (OTUs). OTUs were further sequenced for the nuclear genes Arginine Kinase, Histone 3 and ribosomal 28s, to reconstruct the phylogenetic history of the group. Timings of colonization and in situ speciation events were estimated with beast2. [Results] Our results support the hypothesis that present-day species richness on the older island of Mauritius is largely the result of in situ speciation, with few colonization events, of which all but the most basal are recent. In contrast, Reunion presents a more uniform temporal spectrum of colonization times. Flight loss has evolved convergently at least five times, and speciation events associated with flight loss are significantly younger than speciation events that have not resulted in flight loss. [Main conclusions] Patterns of community assembly on the islands of Mauritius and Reunion fit a model where the addition of new species and species turnover is increasingly dominated by in situ speciation as an island community matures. Repeated flight loss indicates selection for flightlessness, with the young age of flightless lineages suggesting higher extinction rates over longer evolutionary time-scales and little influence on present-day species richness.Fieldwork and laboratory work were supported by funding from the ANR, France (ANR‐2006‐BDIV002), and a NERC‐funded PhD studentship to JJNK.Peer Reviewe