Global dung webs: high trophic generalism of dung beetles along the latitudinal diversity gradient

At the global scale, species diversity is known to strongly increase towards the equator for most taxa. According to theory, a higher resource specificity of consumers facilitates the coexistence of a larger number of species and has been suggested as an explanation for the latitudinal diversity gradient. However, only few studies support the predicted increase in specialisation or even showed opposite results. Surprisingly, analyses for detritivores are still missing. Therefore, we performed an analysis on the degree of trophic specialisation of dung beetles. We summarised 45 studies, covering the resource preferences of a total of 994503 individuals, to calculate the dung specificity in each study region. Our results highlighted a significant (4.3‐fold) increase in the diversity of beetles attracted to vertebrate dung towards the equator. However, their resource specificity was low, unrelated to diversity and revealed a highly generalistic use of dung resources that remained similar along the latitudinal gradient

Restoring understory and riparian areas in oil palm plantations does not increase greenhouse gas fluxes

Oil palm (OP) plantations have replaced large areas of forest in the tropical landscape of Southeast Asia and are major emitters of greenhouse gases (GHGs). To move towards more environmentally friendly plantation management, a hopeful approach is to implement strategies to increase vegetation complexity. These options include relaxed management of understory vegetation to increase complexity in productive plantations, passive restoration of forest areas around rivers by leaving mature oil palm during replanting, and active forest restoration along river margins with planting of forest trees. These practices have the potential to deliver a range of benefits such as soil protection, reduced erosion and sedimentation in rivers, pest control and support for biodiversity, but little is known about their impact on greenhouse gas fluxes. The aim of this study was to assess the impact of improved understory growth management and the use of riparian forestry on GHG fluxes in OP plantations, making use of two long-term experiments (the Biodiversity and Ecosystem Function in Tropical Agriculture Understory Vegetation (BEFTA UV) Project; the Riparian Ecosystem Restoration in Tropical Agriculture (RERTA) Project) in Riau Province, Sumatra, Indonesia. We measured nitrous oxide (N2O), methane (CH4) and ecosystem respiration (CO2) from mature OP sites with different levels of understory vegetation and different riparian buffer restoration treatments using the static chamber method. We used linear mixed effects models to test for treatment effects, whilst accounting for soil moisture and experimental design factors (time and space). The understory vegetation treatments (normal, reduced and enhanced complexity of understory) had no effect on N2O and CH4 flux. Regarding differences in ecosystem respiration, effects attributable to the understory vegetation treatments were not strong. For the riparian restoration treatments, the fixed effects variables in the models explained little variation in the fluxes of all GHGs. Therefore, given the proven benefits of more complex understory vegetation for supporting biodiversity and healthy ecosystem functioning, plus the potential for restored riparian buffers to support biodiversity and services and to reduce GHG emissions over time, our findings reinforce the concept that these features bring environmental benefits in OP landscapes, with no measurable effects on GHG emissions

Restoring understory and riparian areas in oil palm plantations does not increase greenhouse gas fluxes

Oil palm (OP) plantations have replaced large areas of forest in the tropical landscape of Southeast Asia and are major emitters of greenhouse gases (GHGs). To move towards more environmentally friendly plantation management, a hopeful approach is to implement strategies to increase vegetation complexity. These options include relaxed management of understory vegetation to increase complexity in productive plantations, passive restoration of forest areas around rivers by leaving mature oil palm during replanting, and active forest restoration along river margins with planting of forest trees. These practices have the potential to deliver a range of benefits such as soil protection, reduced erosion and sedimentation in rivers, pest control and support for biodiversity, but little is known about their impact on greenhouse gas fluxes. The aim of this study was to assess the impact of improved understory growth management and the use of riparian forestry on GHG fluxes in OP plantations, making use of two long-term experiments (the Biodiversity and Ecosystem Function in Tropical Agriculture Understory Vegetation (BEFTA UV) Project; the Riparian Ecosystem Restoration in Tropical Agriculture (RERTA) Project) in Riau Province, Sumatra, Indonesia. We measured nitrous oxide (N 2 O), methane (CH 4) and ecosystem respiration (CO 2) from mature OP sites with different levels of understory vegetation and different riparian buffer restoration treatments using the static chamber method. We used linear mixed effects models to test for treatment effects, whilst accounting for soil moisture and experimental design factors (time and space). The understory vegetation treatments (normal, reduced and enhanced complexity of understory) had no effect on N 2 O and CH 4 flux. Regarding differences in ecosystem respiration, effects attributable to the understory vegetation treatments were not strong. For the riparian restoration treatments, the fixed effects variables in the models explained little variation in the fluxes of all GHGs. Therefore, given the proven benefits of more complex understory vegetation for supporting biodiversity and healthy ecosystem functioning, plus the potential for restored riparian buffers to support biodiversity and services and to reduce GHG emissions over time, our findings reinforce the concept that these features bring environmental benefits in OP landscapes, with no measurable effects on GHG emissions

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue.

Genome-wide DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men. Mutations were present at high levels in morphologically normal tissue distant from the cancer, reflecting clonal expansions, and the underlying mutational processes at work in morphologically normal tissue were also at work in cancer. Our observations demonstrate the existence of ongoing abnormal mutational processes, consistent with field effects, underlying carcinogenesis. This mechanism gives rise to extensive branching evolution and cancer clone mixing, as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule. Subsets of mutations were shared either by morphologically normal and malignant tissues or between different ERG lineages, indicating earlier or separate clonal cell expansions. Our observations inform on the origin of multifocal disease and have implications for prostate cancer therapy in individual cases

Global assessment of marine plastic exposure risk for oceanic birds

Plastic pollution is distributed patchily around the world’s oceans. Likewise, marine organisms that are vulnerable to plastic ingestion or entanglement have uneven distributions. Understanding where wildlife encounters plastic is crucial for targeting research and mitigation. Oceanic seabirds, particularly petrels, frequently ingest plastic, are highly threatened, and cover vast distances during foraging and migration. However, the spatial overlap between petrels and plastics is poorly understood. Here we combine marine plastic density estimates with individual movement data for 7137 birds of 77 petrel species to estimate relative exposure risk. We identify high exposure risk areas in the Mediterranean and Black seas, and the northeast Pacific, northwest Pacific, South Atlantic and southwest Indian oceans. Plastic exposure risk varies greatly among species and populations, and between breeding and non-breeding seasons. Exposure risk is disproportionately high for Threatened species. Outside the Mediterranean and Black seas, exposure risk is highest in the high seas and Exclusive Economic Zones (EEZs) of the USA, Japan, and the UK. Birds generally had higher plastic exposure risk outside the EEZ of the country where they breed. We identify conservation and research priorities, and highlight that international collaboration is key to addressing the impacts of marine plastic on wide-ranging species

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets

Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutations. Through the temporal dissection of aberrations, we identified driver mutations specifically associated with steps in the progression of prostate cancer, establishing, for example, loss of CHD1 and BRCA2 as early events in cancer development of ETS fusion-negative cancers. Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and should be considered candidates for future clinical trials

CropPol: a dynamic, open and global database on crop pollination

Seventy five percent of the world's food crops benefit from insect pollination. Hence, there has been increased interest in how global change drivers impact this critical ecosystem service. Because standardized data on crop pollination are rarely available, we are limited in our capacity to understand the variation in pollination benefits to crop yield, as well as to anticipate changes in this service, develop predictions, and inform management actions. Here, we present CropPol, a dynamic, open and global database on crop pollination. It contains measurements recorded from 202 crop studies, covering 3,394 field observations, 2,552 yield measurements (i.e. berry weight, number of fruits and kg per hectare, among others), and 47,752 insect records from 48 commercial crops distributed around the globe. CropPol comprises 32 of the 87 leading global crops and commodities that are pollinator dependent. Malus domestica is the most represented crop (32 studies), followed by Brassica napus (22 studies), Vaccinium corymbosum (13 studies), and Citrullus lanatus (12 studies). The most abundant pollinator guilds recorded are honey bees (34.22% counts), bumblebees (19.19%), flies other than Syrphidae and Bombyliidae (13.18%), other wild bees (13.13%), beetles (10.97%), Syrphidae (4.87%), and Bombyliidae (0.05%). Locations comprise 34 countries distributed among Europe (76 studies), Northern America (60), Latin America and the Caribbean (29), Asia (20), Oceania (10), and Africa (7). Sampling spans three decades and is concentrated on 2001-05 (21 studies), 2006-10 (40), 2011-15 (88), and 2016-20 (50). This is the most comprehensive open global data set on measurements of crop flower visitors, crop pollinators and pollination to date, and we encourage researchers to add more datasets to this database in the future. This data set is released for non-commercial use only. Credits should be given to this paper (i.e., proper citation), and the products generated with this database should be shared under the same license terms (CC BY-NC-SA). This article is protected by copyright. All rights reserved

Global assessment of marine plastic exposure risk for oceanic birds

Plastic pollution is distributed patchily around the world's oceans. Likewise, marine organisms that are vulnerable to plastic ingestion or entanglement have uneven distributions. Understanding where wildlife encounters plastic is crucial for targeting research and mitigation. Oceanic seabirds, particularly petrels, frequently ingest plastic, are highly threatened, and cover vast distances during foraging and migration. However, the spatial overlap between petrels and plastics is poorly understood. Here we combine marine plastic density estimates with individual movement data for 7137 birds of 77 petrel species to estimate relative exposure risk. We identify high exposure risk areas in the Mediterranean and Black seas, and the northeast Pacific, northwest Pacific, South Atlantic and southwest Indian oceans. Plastic exposure risk varies greatly among species and populations, and between breeding and non-breeding seasons. Exposure risk is disproportionately high for Threatened species. Outside the Mediterranean and Black seas, exposure risk is highest in the high seas and Exclusive Economic Zones (EEZs) of the USA, Japan, and the UK. Birds generally had higher plastic exposure risk outside the EEZ of the country where they breed. We identify conservation and research priorities, and highlight that international collaboration is key to addressing the impacts of marine plastic on wide-ranging species.B.L.C., C.H., and A.M. were funded by the Cambridge Conservation Initiative’s Collaborative Fund sponsored by the Prince Albert II of Monaco Foundation. E.J.P. was supported by the Natural Environment Research Council C-CLEAR doctoral training programme (Grant no. NE/S007164/1). We are grateful to all those who assisted with the collection and curation of tracking data. Further details are provided in the Supplementary Acknowledgements. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.Peer reviewe

Global assessment of marine plastic exposure risk for oceanic birds

Plastic pollution is distributed patchily around the world’s oceans. Likewise, marine organisms that are vulnerable to plastic ingestion or entanglement have uneven distributions. Understanding where wildlife encounters plastic is crucial for targeting research and mitigation. Oceanic seabirds, particularly petrels, frequently ingest plastic, are highly threatened, and cover vast distances during foraging and migration. However, the spatial overlap between petrels and plastics is poorly understood. Here we combine marine plastic density estimates with individual movement data for 7137 birds of 77 petrel species to estimate relative exposure risk. We identify high exposure risk areas in the Mediterranean and Black seas, and the northeast Pacific, northwest Pacific, South Atlantic and southwest Indian oceans. Plastic exposure risk varies greatly among species and populations, and between breeding and non-breeding seasons. Exposure risk is disproportionately high for Threatened species. Outside the Mediterranean and Black seas, exposure risk is highest in the high seas and Exclusive Economic Zones (EEZs) of the USA, Japan, and the UK. Birds generally had higher plastic exposure risk outside the EEZ of the country where they breed. We identify conservation and research priorities, and highlight that international collaboration is key to addressing the impacts of marine plastic on wide-ranging species

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts