The Persistent Maladaptation of \u3cem\u3ePieris macdunnoughii\u3c/em\u3e: Constraints on Adaptation to an Evolutionary Trap

Evolutionary traps arise when organisms use novel, low-quality or even lethal resources based on previously reliable cues. Persistence of such maladaptive interactions depends not only on how individuals locate important resources, such as host plants, but also the mechanisms underlying poor performance. Pieris macdunnoughii (Remington) (Lepidoptera: Pieridae) lays eggs on a non-native mustard, Thlaspi arvense (L.) (Brassicaceae), which is lethal to its larvae. However, in the 150 years since T. arvense invaded this butterfly continues to recognize and oviposit on the invasive mustard. I evaluated two possible constraints on the evolution of decreased preference within an invaded population. First, an evolutionary response to selection may be constrained by low heritable genetic variation for preference. Second, evolutionary traps are expected to persist when overlapping cue sets (cue similarity) link decreased preference for the novel, unsuitable plant with decreased preference for the historical, high-quality resources. I determined that while preference for the nonnative host over the native host is heritable, sex-linked, and varies considerably in the population, it is unlikely that this preference is correlated with preference for native hosts with similar defensive chemical profiles. Thus, neither a lack of heritable genetic variation nor an increased risk of excluding good host plants when avoiding T. arvense are likely to be constraining escape from this evolutionary trap. Instead, our results suggest behavioral plasticity may buffer populations from innate preference for the lethal host. Finally, I tested the mechanisms underlying poor performance of neonate larvae on the novel host. Larvae were less likely to start eating T. arvense and starvation was a primary cause of mortality, indicating a pre-ingestive feeding deterrent. A primary oviposition stimulant, the glucosinolate sinigrin, increased this deterrent effect and mortality when added to T. arvense and native host plant leaves. Pre-ingestive deterrents, even those familiar to herbivorous insects, may significantly contribute to the persistence of evolutionary traps

Chromosome Level Assembly of the Comma Butterfly (Polygonia c-album)

The comma butterfly (Polygonia c-album, Nymphalidae, Lepidoptera) is a model insect species, most notably in the study of phenotypic plasticity and plant-insect coevolutionary interactions. In order to facilitate the integration of genomic tools with a diverse body of ecological and evolutionary research, we assembled the genome of a Swedish comma using 10X sequencing, scaffolding with matepair data, genome polishing, and assignment to linkage groups using a high-density linkage map. The resulting genome is 373 Mb in size, with a scaffold N50 of 11.7 Mb and contig N50 of 11,2Mb. The genome contained 90.1% of single-copy Lepidopteran orthologs in a BUSCO analysis of 5,286 genes. A total of 21,004 gene-models were annotated on the genome using RNA-Seq data from larval and adult tissue in combination with proteins from the Arthropoda database, resulting in a high-quality annotation for which functional annotations were generated. We further documented the quality of the chromosomal assembly via synteny assessment with Melitaea cinxia. The resulting annotated, chromosome-level genome will provide an important resource for investigating coevolutionary dynamics and comparative analyses in Lepidoptera.Peer reviewe

Chronic Supplementation With a Mitochondrial Antioxidant (MitoQ) Improves Vascular Function in Healthy Older Adults.

UNLABELLED: Excess reactive oxygen species production by mitochondria is a key mechanism of age-related vascular dysfunction. Our laboratory has shown that supplementation with the mitochondrial-targeted antioxidant MitoQ improves vascular endothelial function by reducing mitochondrial reactive oxygen species and ameliorates arterial stiffening in old mice, but the effects in humans are unknown. Here, we sought to translate our preclinical findings to humans and determine the safety and efficacy of MitoQ. Twenty healthy older adults (60-79 years) with impaired endothelial function (brachial artery flow-mediated dilation 7.60 m/s; n=11). Plasma oxidized LDL (low-density lipoprotein), a marker of oxidative stress, also was lower after MitoQ versus placebo (P0.1). These findings in humans extend earlier preclinical observations and suggest that MitoQ and other therapeutic strategies targeting mitochondrial reactive oxygen species may hold promise for treating age-related vascular dysfunction. CLINICAL TRIAL REGISTRATION: URL: http://www.clinicaltrials.gov. Unique identifier: NCT02597023.This work was supported by National Institutes of Health (NIH) awards AG049451, AG000279, AG053009, Colorado CTSA UL1 TR001082, and an industry contract with MitoQ Limited (MitoQ Limited provided MitoQ and some financial support). M.P. Murphy is supported by UK MRC MC_U105663142 and as a Wellcome Trust Investigator (110159/Z/15/Z)

Exploring the relationship between plural values of nature, human well‐being, and conservation and development intervention: Why it matters and how to do it?

Globally, land and seascapes across the bioculturally diverse tropics are in transition. Impacted by the demands of distant consumers, the processes of global environmental change and numerous interventions seeking climate, conservation and development goals, these transitions have the potential to impact the relationships and plurality of values held between people and place. This paper is a Synthesis of seven empirical studies within the Special Feature (SF): ‘What is lost in transition? Capturing the impacts of conservation and development interventions on relational values and human wellbeing in the tropics’. Through two Open Forum workshops, and critical review, contributing authors explored emergent properties across the papers of the SF. Six core themes were identified and are subsumed within broad categories of: (i) the problem of reconciling scale and complexity, (ii) key challenges to be overcome for more plural understanding of social dimensions of landscape change and (iii) ways forward: the potential of an environmental justice framework, and a practical overview of methods available to do so. The Synthesis interprets disparate fields and complex academic work on relational values, human well-being and de-colonial approaches in impact appraisal. It offers a practical and actionable catalogue of methods for plural valuation in the field, and reflects on their combinations, strengths and weaknesses. The research contribution is policy relevant because it builds the case for why a more plural approach in intervention design and evaluation is essential for achieving more just and sustainable futures, and highlights some of the key actions points deemed necessary to achieve such a transition to conventional practice

Nintedanib for non-IPF progressive pulmonary fibrosis: 12-month outcome data from a real-world multicentre observational study

Background Nintedanib slows lung function decline for patients with non-idiopathic pulmonary fibrosis progressive pulmonary fibrosis (PPF) in clinical trials, but the real-world safety and efficacy are not known. Methods In this retrospective cohort study, standardised data were collected from patients in whom nintedanib was initiated for PPF between 2019 and 2020 through an early-access programme across eight centres in the United Kingdom. Rate of lung function change in the 12 months pre- and post-nintedanib initiation was the primary analysis. Symptoms, drug safety, tolerability and stratification by interstitial lung disease subtype and computed tomography pattern were secondary analyses. Results 126 patients were included; 67 (53%) females; mean±sd age 60±13 years. At initiation of nintedanib, mean forced vital capacity (FVC) was 1.87 L (58% predicted) and diffusing capacity of the lung for carbon monoxide (DLCO) was 32.7% predicted. 68% of patients were prescribed prednisolone (median dose 10 mg) and 69% were prescribed a steroid-sparing agent. In the 12 months after nintedanib initiation, lung function decline was significantly lower than in the preceding 12 months: FVC −88.8 mL versus −239.9 mL (p=0.004), and absolute decline in DLCO −2.1% versus −6.1% (p=0.004). Response to nintedanib was consistent in sensitivity and secondary analyses. 89 (71%) out of 126 patients reported side-effects, but 86 (80%) of the surviving 108 patients were still taking nintedanib at 12 months with patients reporting a reduced perception of symptom decline. There were no serious adverse events. Conclusion In PPF, the real-world efficacy of nintedanib replicated that of clinical trials, significantly attenuating lung function decline. Despite the severity of disease, nintedanib was safe and well tolerated in this real-world multicentre study

The Marine Viromes of Four Oceanic Regions

Viruses are the most common biological entities in the marine environment. There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed. Metagenomic analyses of 184 viral assemblages collected over a decade and representing 68 sites in four major oceanic regions showed that most of the viral sequences were not similar to those in the current databases. There was a distinct “marine-ness” quality to the viral assemblages. Global diversity was very high, presumably several hundred thousand of species, and regional richness varied on a North-South latitudinal gradient. The marine regions had different assemblages of viruses. Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic. However most viral species were found to be widespread. With a majority of shared species between oceanic regions, most of the differences between viral assemblages seemed to be explained by variation in the occurrence of the most common viral species and not by exclusion of different viral genomes. These results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure

The Consensus Coding Sequence (Ccds) Project: Identifying a Common Protein-Coding Gene Set for the Human and Mouse Genomes

Effective use of the human and mouse genomes requires reliable identification of genes and their products. Although multiple public resources provide annotation, different methods are used that can result in similar but not identical representation of genes, transcripts, and proteins. The collaborative consensus coding sequence (CCDS) project tracks identical protein annotations on the reference mouse and human genomes with a stable identifier (CCDS ID), and ensures that they are consistently represented on the NCBI, Ensembl, and UCSC Genome Browsers. Importantly, the project coordinates on manually reviewing inconsistent protein annotations between sites, as well as annotations for which new evidence suggests a revision is needed, to progressively converge on a complete protein-coding set for the human and mouse reference genomes, while maintaining a high standard of reliability and biological accuracy. To date, the project has identified 20,159 human and 17,707 mouse consensus coding regions from 17,052 human and 16,893 mouse genes. Three evaluation methods indicate that the entries in the CCDS set are highly likely to represent real proteins, more so than annotations from contributing groups not included in CCDS. The CCDS database thus centralizes the function of identifying well-supported, identically-annotated, protein-coding regions.National Human Genome Research Institute (U.S.) (Grant number 1U54HG004555-01)Wellcome Trust (London, England) (Grant number WT062023)Wellcome Trust (London, England) (Grant number WT077198

Exploring the relationship between plural values of nature, human well-being, and conservation and development intervention: Why it matters and how to do it?

1. Globally, land and seascapes across the bioculturally diverse tropics are in transition. Impacted by the demands of distant consumers, the processes of global environmental change and numerous interventions seeking climate, conservation and development goals, these transitions have the potential to impact the relationships and plurality of values held between people and place. 2. This paper is a Synthesis of seven empirical studies within the Special Feature (SF): ‘What is lost in transition? Capturing the impacts of conservation and development interventions on relational values and human wellbeing in the tropics’. Through two Open Forum workshops, and critical review, contributing authors explored emergent properties across the papers of the SF. Six core themes were identified and are subsumed within broad categories of: (i) the problem of reconciling scale and complexity, (ii) key challenges to be overcome for more plural understanding of social dimensions of landscape change and (iii) ways forward: the potential of an environmental justice framework, and a practical overview of methods available to do so. 3. The Synthesis interprets disparate fields and complex academic work on relational values, human well-being and de-colonial approaches in impact appraisal. It offers a practical and actionable catalogue of methods for plural valuation in the field, and reflects on their combinations, strengths and weaknesses. 4. The research contribution is policy relevant because it builds the case for why a more plural approach in intervention design and evaluation is essential for achieving more just and sustainable futures, and highlights some of the key actions points deemed necessary to achieve such a transition to conventional practice

Simulating rewetting events in intermittent rivers and ephemeral streams: A global analysis of leached nutrients and organic matter

Climate change and human pressures are changing the global distribution and the ex‐ tent of intermittent rivers and ephemeral streams (IRES), which comprise half of the global river network area. IRES are characterized by periods of flow cessation, during which channel substrates accumulate and undergo physico‐chemical changes (precon‐ ditioning), and periods of flow resumption, when these substrates are rewetted and release pulses of dissolved nutrients and organic matter (OM). However, there are no estimates of the amounts and quality of leached substances, nor is there information on the underlying environmental constraints operating at the global scale. We experi‐ mentally simulated, under standard laboratory conditions, rewetting of leaves, river‐ bed sediments, and epilithic biofilms collected during the dry phase across 205 IRES from five major climate zones. We determined the amounts and qualitative character‐ istics of the leached nutrients and OM, and estimated their areal fluxes from riverbeds. In addition, we evaluated the variance in leachate characteristics in relation to selected environmental variables and substrate characteristics. We found that sediments, due to their large quantities within riverbeds, contribute most to the overall flux of dis‐ solved substances during rewetting events (56%–98%), and that flux rates distinctly differ among climate zones. Dissolved organic carbon, phenolics, and nitrate contrib‐ uted most to the areal fluxes. The largest amounts of leached substances were found in the continental climate zone, coinciding with the lowest potential bioavailability of the leached OM. The opposite pattern was found in the arid zone. Environmental vari‐ ables expected to be modified under climate change (i.e. potential evapotranspiration, aridity, dry period duration, land use) were correlated with the amount of leached sub‐ stances, with the strongest relationship found for sediments. These results show that the role of IRES should be accounted for in global biogeochemical cycles, especially because prevalence of IRES will increase due to increasing severity of drying event

Simulating rewetting events in intermittent rivers and ephemeral streams: a global analysis of leached nutrients and organic matter

Climate change and human pressures are changing the global distribution and extent of intermittent rivers and ephemeral streams (IRES), which comprise half of the global river network area. IRES are characterized by periods of flow cessation, during which channel substrates accumulate and undergo physico‐chemical changes (preconditioning), and periods of flow resumption, when these substrates are rewetted and release pulses of dissolved nutrients and organic matter (OM). However, there are no estimates of the amounts and quality of leached substances, nor is there information on the underlying environmental constraints operating at the global scale. We experimentally simulated, under standard laboratory conditions, rewetting of leaves, riverbed sediments, and epilithic biofilms collected during the dry phase across 205 IRES from five major climate zones. We determined the amounts and qualitative characteristics of the leached nutrients and OM, and estimated their areal fluxes from riverbeds. In addition, we evaluated the variance in leachate characteristics in relation to selected environmental variables and substrate characteristics. We found that sediments, due to their large quantities within riverbeds, contribute most to the overall flux of dissolved substances during rewetting events (56‐98%), and that flux rates distinctly differ among climate zones. Dissolved organic carbon, phenolics, and nitrate contributed most to the areal fluxes. The largest amounts of leached substances were found in the continental climate zone, coinciding with the lowest potential bioavailability of the leached organic matter. The opposite pattern was found in the arid zone. Environmental variables expected to be modified under climate change (i.e. potential evapotranspiration, aridity, dry period duration, land use) were correlated with the amount of leached substances, with the strongest relationship found for sediments. These results show that the role of IRES should be accounted for in global biogeochemical cycles, especially because prevalence of IRES will increase due to increasing severity of drying events