Equivalent roles of marine subsidies and island characteristics in shaping island bird communities

AimSpecies distributions across islands are shaped by dispersal limitations, environmental filters and biotic interactions but the relative influence of each of these processes has rarely been assessed. Here, we examine the relative contributions of island characteristics, marine subsidies, species traits, and species interactions on avian community composition.LocationCentral Coast region of British Columbia, Canada.TaxonTerrestrial breeding birds.MethodsWe observed 3610 individuals of 32 bird species on 89 islands that spanned multiple orders of magnitude in area (0.0002–3 km$^{2}$). We fit a spatially explicit joint species distribution model to estimate the relative contributions of island physical characteristics, island‐specific inputs of marine subsidies, species' traits, and biotic interactions on species distributions. Biogeographic characteristics included island area, isolation, and habitat heterogeneity, while marine influence was represented by forest‐edge soil δ$^{15}$N, wrack biomass, shoreline substrate, and distance to shore. This approach also allowed us to estimate how much variation in distributions resulted from species' biological traits (i.e. body mass, feeding guild, feeding height, and nesting height).ResultsBird species distributions were determined almost equivalently by island biogeographic characteristics (23.5% of variation explained) and marine influence (24.8%). We detected variation in species‐specific responses to both island biogeographic characteristics and marine influence, but no significant effect of any biological trait examined. Additionally, we found evidence that habitat preferences were a more important driver than competitive interactions.Main ConclusionsAlthough most island biogeographic studies focus only on islands' physical characteristics, we found evidence for an equivalent role of marine subsidy in structuring island bird communities. Our study suggests that for small islands, disentangling the effects of island biogeographic characteristics, marine inputs, and biotic interactions is a useful next step in understanding species distributions

Biogeographic features mediate marine subsidies to island food webs

Although marine subsidies often enrich terrestrial ecosystems, their influence is known to be context-dependent. Additionally, the multitrophic impact of marine subsidies has not been traced through food webs across physically diverse islands. Here, we test predictions about how island characteristics can affect marine enrichment of food web constituents and how nutrients flow through island food webs. To evaluate enrichment and trace marine nutrients across food webs, we used stable isotopes of soil, flora, and fauna (n = 4752 samples) collected from 97 islands in British Columbia, Canada. Island area was the strongest predictor of enrichment across taxa; we found that samples were more 15N-rich on smaller islands. Enrichment declined with distance from shore but less so on small islands, implying a higher per-unit-area subsidy effect. These area and distance-to-shore effects were taxon-specific, and nearly twice as strong in basal food web groups. We also found that increases in δ15N correlated with increases in %N in basal trophic groups, as well as in songbirds, implying biologically relevant uptake of a potentially limiting nutrient. Path analysis demonstrated that subsidies in soil flow through plants and detritivores, and into upper-level consumers. Our results reveal an interplay between island biogeography and marine subsidies in shaping island food webs through bottom-up processes

Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda

Background International and global organisations advocate targeting interventions to areas of high HIV prevalence (ie, hotspots). To better understand the potential benefits of geo-targeted control, we assessed the extent to which HIV hotspots along Lake Victoria sustain transmission in neighbouring populations in south-central Uganda. Methods We did a population-based survey in Rakai, Uganda, using data from the Rakai Community Cohort Study. The study surveyed all individuals aged 15–49 years in four high-prevalence Lake Victoria fishing communities and 36 neighbouring inland communities. Viral RNA was deep sequenced from participants infected with HIV who were antiretroviral therapy-naive during the observation period. Phylogenetic analysis was used to infer partial HIV transmission networks, including direction of transmission. Reconstructed networks were interpreted through data for current residence and migration history. HIV transmission flows within and between high-prevalence and low-prevalence areas were quantified adjusting for incomplete sampling of the population. Findings Between Aug 10, 2011, and Jan 30, 2015, data were collected for the Rakai Community Cohort Study. 25 882 individuals participated, including an estimated 75·7% of the lakeside population and 16·2% of the inland population in the Rakai region of Uganda. 5142 participants were HIV-positive (2703 [13·7%] in inland and 2439 [40·1%] in fishing communities). 3878 (75·4%) people who were HIV-positive did not report antiretroviral therapy use, of whom 2652 (68·4%) had virus deep-sequenced at sufficient quality for phylogenetic analysis. 446 transmission networks were reconstructed, including 293 linked pairs with inferred direction of transmission. Adjusting for incomplete sampling, an estimated 5·7% (95% credibility interval 4·4–7·3) of transmissions occurred within lakeside areas, 89·2% (86·0–91·8) within inland areas, 1·3% (0·6–2·6) from lakeside to inland areas, and 3·7% (2·3–5·8) from inland to lakeside areas. Interpretation Cross-community HIV transmissions between Lake Victoria hotspots and surrounding inland populations are infrequent and when they occur, virus more commonly flows into rather than out of hotspots. This result suggests that targeted interventions to these hotspots will not alone control the epidemic in inland populations, where most transmissions occur. Thus, geographical targeting of high prevalence areas might not be effective for broader epidemic control depending on underlying epidemic dynamics. Funding The Bill & Melinda Gates Foundation, the National Institute of Allergy and Infectious Diseases, the National Institute of Mental Health, the National Institute of Child Health and Development, the Division of Intramural Research of the National Institute for Allergy and Infectious Diseases, the World Bank, the Doris Duke Charitable Foundation, the Johns Hopkins University Center for AIDS Research, and the President's Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

Genomic Relationships, Novel Loci, and Pleiotropic Mechanisms across Eight Psychiatric Disorders

Genetic influences on psychiatric disorders transcend diagnostic boundaries, suggesting substantial pleiotropy of contributing loci. However, the nature and mechanisms of these pleiotropic effects remain unclear. We performed analyses of 232,964 cases and 494,162 controls from genome-wide studies of anorexia nervosa, attention-deficit/hyper-activity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, and Tourette syndrome. Genetic correlation analyses revealed a meaningful structure within the eight disorders, identifying three groups of inter-related disorders. Meta-analysis across these eight disorders detected 109 loci associated with at least two psychiatric disorders, including 23 loci with pleiotropic effects on four or more disorders and 11 loci with antagonistic effects on multiple disorders. The pleiotropic loci are located within genes that show heightened expression in the brain throughout the lifespan, beginning prenatally in the second trimester, and play prominent roles in neurodevelopmental processes. These findings have important implications for psychiatric nosology, drug development, and risk prediction.Peer reviewe

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

Migratory connectivity and annual cycle phenology of Rusty Blackbirds (Euphagus carolinus) revealed through archival GPS tags

Understanding spatial and temporal movement patterns of migratory birds throughout the annual cycle can help identify potential population threats. The behavior and habitat use of birds during migration and stopover periods is particularly understudied in many species. In this study, we used high spatial resolution archival GPS tags to track Rusty Blackbirds (Euphagus carolinus) from one eastern (New Hampshire) and two western (Alaska and Alberta) breeding populations across the annual cycle. We sought to determine: 1) migratory connectivity of the three distinct populations; 2) migratory phenology, behavior, and time spent during each phase of the annual cycle; and 3) habitat use of individuals throughout the nonbreeding period. We retrieved 7 tags from 30 tagged individuals following 1-year deployments. We found that four Alberta individuals overwintered in the Mississippi Alluvial Valley, two Alaska individuals overwintered in either the Great Plains or the Mississippi Alluvial Valley, and the single New Hampshire individual overwintered on the Southeastern Coastal Plain. Length of annual cycle stages varied among individuals, with the combined migratory periods occupying between 12% and 48% of the annual cycle. Stopover behavior was also widely variable, as minimum convex polygons of stopovers ranged from < 1 hectare to 505 km² and stopover durations ranged from 1 to 35 days (n = 40 stopovers). Birds predominantly used woody wetlands and emergent marsh during the nonbreeding period, but habitat use differed between roosting and foraging. Marshes were used more for nocturnal roosting, whereas woody wetlands were used for diurnal foraging. Our results can help efforts to conserve this declining species by targeting regions and habitats at specific times of year for management during the nonbreeding period. In particular, the large amount of time spent during migration periods suggests conservation efforts in stopover regions are just as important as those on the wintering grounds

Marine subsidies mediate patterns in avian island biogeography

The classical theory of island biogeography, which predicts species richness using island area and isolation, has been expanded to include contributions from marine subsidies, i.e. subsidized island biogeography (SIB) theory. We tested the effects of marine subsidies on species diversity and population density on productive temperate islands, evaluating SIB predictions previously untested at comparable scales and subsidy levels. We found that the diversity of terrestrial breeding bird communities on 91 small islands (approx. 0.0001-3 km2) along the Central Coast of British Columbia, Canada were correlated most strongly with island area, but also with marine subsidies. Species richness increased and population density decreased with island area, but isolation had no measurable influence. Species richness was negatively correlated with marine subsidy, measured as forest-edge soil δ15N. Density, however, was higher on islands with higher marine subsidy, and a negative interaction between area and subsidy indicates that this effect is stronger on smaller islands, offering some support for SIB. Our study emphasizes how subsidies from the sea can shape diversity patterns on islands and can even exceed the importance of isolation in determining species richness and densities of terrestrial biota