Using exclusion rate to unify niche and neutral perspectives on coexistence

The competitive exclusion principle is one of the most influential concepts in ecology. The classical formulation suggests a correlation between competitor species similarity and competition severity, leading to rapid competitive exclusion where species are very similar; yet neutral models show that identical species can persist in competition for long periods. Here, we resolve the conflict by examining two components of similarity – niche overlap and competitive similarity – and modeling the effects of each on exclusion rate (defined as the inverse of time to exclusion). Studying exclusion rate, rather than the traditional focus on binary outcomes (coexistence vs exclusion), allows us to examine classical niche and neutral perspectives using the same currency. High niche overlap speeds exclusion, but high similarity in competitive ability slows it. These predictions are confirmed by a well-known model of two species competing for two resources. Under ecologically plausible scenarios of correlation between these two factors, the strongest exclusion rates may be among moderately similar species, while very similar and highly dissimilar competitors have very low exclusion rates. Adding even small amounts of demographic stochasticity to the model blurs the line between deterministic and probabilistic coexistence still further. Thus, focusing on exclusion rate, instead of on the binary outcome of coexistence versus exclusion, allows a variety of outcomes to result from competitive interactions. This approach may help explain species coexistence in diverse competitive communities and raises novel issues for future work

Is oxygen limitation in warming waters a valid mechanism to explain decreased body sizes in aquatic ectotherms?

The authors would like to acknowledge funding from Australian Research Council (grant No. DP170104240) and the Kone Foundation (to AA), Horizon 2020 European research projects ClimeFish (grant No. 677039) (to ARB) and Australian Academy of Science (to JRM)Peer reviewedPostprintPostprin

Contrasting changes in the abundance and diversity of North American bird assemblages from 1971 to 2010

This article is based upon work from COST Action ES1101 "Harmonising Global Biodiversity Modelling" (Harmbio), supported by COST (European Cooperation in Science and Technology).Although it is generally recognized that global biodiversity is declining, few studies have examined long-term changes in multiple biodiversity dimensions simultaneously. In this study we quantified and compared temporal changes in the abundance, taxonomic diversity, functional diversity and phylogenetic diversity of bird assemblages, using roadside monitoring data of the North American Breeding Bird Survey from 1971 to 2010. We calculated 12 abundance and diversity metrics based on five year average abundances of 519 species for each of 768 monitoring routes. We did this for all bird species together as well as for four sub-groups based on breeding habitat affinity (grassland, woodland, wetland and shrubland breeders). The majority of the biodiversity metrics increased or remained constant over the study period, whereas the overall abundance of birds showed a pronounced decrease, primarily driven by declines of the most abundant species. These results highlight how stable or even increasing metrics of taxonomic, functional or phylogenetic diversity may occur in parallel with substantial losses of individuals. We further found that patterns of change differed among the species sub-groups, with both abundance and diversity increasing for woodland birds and decreasing for grassland breeders. The contrasting changes between abundance and diversity and among the breeding habitat groups underscore the relevance of a multi-faceted approach to measuring biodiversity change. Our findings further stress the importance of monitoring the overall abundance of individuals in addition to metrics of taxonomic, functional or phylogenetic diversity, thus confirming the importance of population abundance as an essential biodiversity variable.Publisher PDFPeer reviewe

Full lifetime perspectives on the costs and benefits of lay date variation in tree swallows

Animals must balance various costs and benefits when deciding when to breed. The costs and benefits of breeding at different times have received much attention, but most studies have been limited to investigating short-term season-to-season fitness effects. However, breeding early, versus late, in a season may influence lifetime fitness over many years, trading off in complex ways across the breeder?s lifepan. In this study, we examined the complete life histories of 867 female tree swallows (Tachycineta bicolor) breeding in Ithaca, New York, between 2002 and 2016. Earlier breeders outperformed later breeders in short-term measures of reproductive output and offspring quality. Though there were weak indications that females paid long-term future survival costs for breeding early, lifetime fledgling output was markedly higher overall in early-breeding birds. Importantly, older females breeding later in the season did not experience compensating life-history advantages that suggested an alternative equal-fitness breeding strategy. Rather, most or all of the swallows appear to be breeding as early as they can, and differences in lay dates appear to be determined primarily by differences in individual quality or condition. Lay date had a significant repeatability across breeding attempts by the same female, and the first lay date of females fledged in our population was strongly influenced by the first lay date of their mothers, indicating the potential for ongoing selection on lay date. By examining performance over the entire lifespan of a large number of individuals, we were able to clarify the relationship between timing of breeding and fitness and gain new insight into the sources of variability in this important life history trait.Fil: Winkler, David Ward. Cornell University; Estados UnidosFil: Hallinger, Kelly K.. Cornell University; Estados UnidosFil: Pegan, Teresa M.. University of Michigan; Estados UnidosFil: Taff, Conor C.. Cornell University; Estados UnidosFil: Verhoeven, Mo A.. University of Groningen; Países BajosFil: Van Oordt, David Chang. Cornell University; Estados UnidosFil: Stager, Maria. University of Montana; Estados UnidosFil: Uehling, Jennifer J.. Cornell University; Estados UnidosFil: Vitousek, Maren N.. Cornell University; Estados UnidosFil: Andersen, Michael J.. University of New Mexico; Estados UnidosFil: Ardia, Daniel R.. Franklin & Marshall College; Estados UnidosFil: Belmaker, Amos. Tel Aviv University; IsraelFil: Ferretti, Valentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; ArgentinaFil: Forsman, Anna M.. University Of Central Florida; Estados UnidosFil: Gaul, Jennifer R.. International High School at La Guardia Community College; Estados UnidosFil: Llambias, Paulo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; ArgentinaFil: Orzechowski, Sophia C.. Harvard University; Estados UnidosFil: Shipley, Ryan. Max Planck Institute For Animal Behavior; AlemaniaFil: Wilson, Maya. Virginia Polytechnic Institute. Department Of Geological Sciences; Estados UnidosFil: Yoon, Hyun Seok. University of Tennessee; Estados Unido

Factors Associated to Duration of Hepatitis A Outbreaks: Implications for Control

Even though hepatitis A mass vaccination effectiveness is high, outbreaks continue to occur. The aim of this study was to investigate the association between duration and characteristics of hepatitis A outbreaks. Hepatitis A (HA) outbreaks reported between 1991 and 2007 were studied. An outbreak was defined as ≥2 epidemiologically-linked cases with ≥1 case laboratory-confirmed by detection of HA immunoglobulin M (IgM) antibodies. Relationships between explanatory variables and outbreak duration were assessed by logistic regression. During the study period, 268 outbreaks (rate 2.45 per million persons-year) and 1396 cases (rate 1.28 per 105 persons-year) were reported. Factors associated with shorter duration were time to intervention (OR = 0.96; 95% CI: 0.94–0.98) and school setting (OR = 0.39; 95% CI: 0.16–0.92). In person-to-person transmission outbreaks only time to intervention was associated with shorter outbreak duration (OR = 0.96; 95% CI: 0.95–0.98). The only variables associated with shorter outbreak duration were early administration of IG or vaccine and a school setting. Timely reporting HA outbreaks was associated with outbreak duration. Making confirmed HA infections statutory reportable for clinical laboratories could diminish outbreak duration

BioTIME: A database of biodiversity time series for the Anthropocene.

MotivationThe BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables includedThe database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grainBioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).Time period and grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.Software format.csv and .SQL

Optical Drug Monitoring: Photoacoustic Imaging of Nanosensors to Monitor Therapeutic Lithium in Vivo

Personalized medicine could revolutionize how primary care physicians treat chronic disease and how researchers study fundamental biological questions. To realize this goal, we need to develop more robust, modular tools and imaging approaches for in vivo monitoring of analytes. In this report, we demonstrate that synthetic nanosensors can measure physiologic parameters with photoacoustic contrast, and we apply that platform to continuously track lithium levels in vivo. Photoacoustic imaging achieves imaging depths that are unattainable with fluorescence or multiphoton microscopy. We validated the photoacoustic results that illustrate the superior imaging depth and quality of photoacoustic imaging with optical measurements. This powerful combination of techniques will unlock the ability to measure analyte changes in deep tissue and will open up photoacoustic imaging as a diagnostic tool for continuous physiological tracking of a wide range of analytes

Altered Gene Synchrony Suggests a Combined Hormone-Mediated Dysregulated State in Major Depression

Coordinated gene transcript levels across tissues (denoted “gene synchrony”) reflect converging influences of genetic, biochemical and environmental factors; hence they are informative of the biological state of an individual. So could brain gene synchrony also integrate the multiple factors engaged in neuropsychiatric disorders and reveal underlying pathologies? Using bootstrapped Pearson correlation for transcript levels for the same genes across distinct brain areas, we report robust gene transcript synchrony between the amygdala and cingulate cortex in the human postmortem brain of normal control subjects (n = 14; Control/Permutated data, p<0.000001). Coordinated expression was confirmed across distinct prefrontal cortex areas in a separate cohort (n = 19 subjects) and affected different gene sets, potentially reflecting regional network- and function-dependent transcriptional programs. Genewise regional transcript coordination was independent of age-related changes and array technical parameters. Robust shifts in amygdala-cingulate gene synchrony were observed in subjects with major depressive disorder (MDD, denoted here “depression”) (n = 14; MDD/Permutated data, p<0.000001), significantly affecting between 100 and 250 individual genes (10–30% false discovery rate). Biological networks and signal transduction pathways corresponding to the identified gene set suggested putative dysregulated functions for several hormone-type factors previously implicated in depression (insulin, interleukin-1, thyroid hormone, estradiol and glucocorticoids; p<0.01 for association with depression-related networks). In summary, we showed that coordinated gene expression across brain areas may represent a novel molecular probe for brain structure/function that is sensitive to disease condition, suggesting the presence of a distinct and integrated hormone-mediated corticolimbic homeostatic, although maladaptive and pathological, state in major depression