Biology subjects

Diaz, R. M.

Publications and source records attributed to Diaz, R. M..

5 recordsLinked to original sources

bioRxiv2022

Temporal changes in the individual size distribution decouple long-term trends in abundance, biomass, and energy use of North American breeding bird communities

AimA core objective of contemporary biodiversity science is to understand long-term trends in the structure and function of ecological communities. Different currencies of ecological function - specifically, total abundance, total standing biomass, and total metabolic flux - are naturally linked, but may become decoupled if the underlying size structure of a system changes. Here, we seek to establish how changes in community size composition modulate long-term relationships between different currencies of ecological function for North American birds. LocationNorth America, north of Mexico. Time period1988-2018. Major taxa studiedBreeding birds. MethodsWe used species traits and allometric scaling to estimate individual size measurements and basal metabolic rate for birds observed in the North American Breeding Bird Survey. We compared the long-term trajectories for community-wide standing biomass and energy use to the long-term trends driven by changes in individual abundance alone. Finally, we used dissimilarity metrics to evaluate the link between changes in species and size composition and changes in the relationship between abundance- and size-driven dynamics. ResultsFor a substantial minority of communities, shifts in community size composition have decoupled the long-term dynamics of biomass, energy use, and individual abundance. While trends in abundance were dominated by decreases, trends in biomass were evenly divided between decreases and increases, and trends in energy use featured more increases than expected given changes in abundance alone. Communities with decoupled dynamics showed greater increases in community-wide mean body size than other communities, but did not differ from other communities in overall turnover in species or size composition. Main conclusionsSize- and abundance-based currencies of ecological function are linked, but not necessarily equivalent. For North American breeding birds, shifts in species composition favoring larger-bodied species may have partially offset declines in standing biomass driven by losses of individuals over the past 30 years.

ecology↗

bioRxiv2021

Maintenance of community function through compensation breaks down over time in a desert rodent community

Understanding the ecological processes that maintain community function in systems experiencing species loss, and how these processes change over time, is key to understanding the relationship between community structure and function and predicting how communities may respond to perturbations in the Anthropocene. Using a 30-year experiment on desert rodents, we show that the impact of species loss on community-level energy use has changed repeatedly and dramatically over time, due to 1) the addition of new species to the community, and 2) a reduction in functional redundancy among the same set of species. Although strong compensation, initially driven by the dispersal of functionally redundant species to the local community, occurred in this system from 1997-2010, since 2010, compensation has broken down due to decreasing functional overlap within the same set of species. Simultaneously, long-term changes in sitewide community composition due to niche complementarity have decoupled the dynamics of compensation from the overall impact of species loss on community-level energy use. Shifting, context-dependent compensatory dynamics, such as those demonstrated here, highlight the importance of explicitly long-term, metacommunity, and eco-evolutionary perspectives on the link between species-level fluctuations and community function in a changing world.

ecology↗

bioRxiv2021

Empirical abundance distributions are more uneven than expected given their statistical baseline

Exploring and accounting for the emergent properties of ecosystems as complex systems is a promising horizon in the search for general processes to explain common ecological patterns. For example, the ubiquitous hollow-curve form of the species abundance distribution is frequently assumed to reflect ecological processes structuring communities, but can also emerge as a statistical phenomenon from the mathematical definition of an abundance distribution. Although the hollow curve may be a statistical artefact, ecological processes may induce subtle deviations between empirical species abundance distributions and their statistically most probable forms. These deviations may reflect biological processes operating on top of mathematical constraints and provide new avenues for advancing ecological theory. Examining [~]22,000 communities, we found that empirical SADs are highly uneven and dominated by rare species compared to their statistical baselines. Efforts to detect deviations may be less informative in small communities - those with few species or individuals - because these communities have poorly-resolved statistical baselines. The uneven nature of many empirical SADs demonstrates a path forward for leveraging complexity to understand ecological processes governing the distribution of abundance, while the issues posed by small communities illustrate the limitations of using this approach to study ecological patterns in small samples.

ecology↗

bioRxiv2020

Development and validation of IMMUNO-COV: a high-throughput clinical assay for detecting antibodies that neutralize SARS-CoV-2

We here describe the development and validation of IMMUNO-COV, a high-throughput clinical test to quantitatively measure SARS-CoV-2-neutralizing antibodies, the specific subset of anti-SARS-CoV-2 antibodies that block viral infection. The test measures the capacity of serum or purified antibodies to neutralize a recombinant Vesicular Stomatitis Virus (VSV) encoding the SARS-CoV-2 spike glycoprotein. This recombinant virus (VSV-SARS-CoV-2-S-{Delta}19CT) induces fusion in Vero cell monolayers, which is detected as luciferase signal using a dual split protein (DSP) reporter system. VSV-SARS-CoV-2-S-{Delta}19CT infection was blocked by monoclonal -SARS-CoV-2-spike antibodies and by plasma or serum from SARS-CoV-2 convalescing individuals. The assay exhibited 100% specificity in validation tests, and across all tests zero false positives were detected. In blinded analyses of 230 serum samples, only two unexpected results were observed based on available clinical data. We observed a perfect correlation between results from our assay and 80 samples that were also assayed using a commercially available ELISA. To quantify the magnitude of the anti-viral response, we generated a calibration curve by adding stepped concentrations of -SARS-CoV-2-spike monoclonal antibody to pooled SARS-CoV-2 seronegative serum. Using the calibration curve and a single optimal 1:100 serum test dilution, we reliably measured neutralizing antibody levels in each test sample. Virus neutralization units (VNUs) calculated from the assay correlated closely (p < 0.0001) with PRNTEC50 values determined by plaque reduction neutralization test against a clinical isolate of SARS-CoV-2. Taken together, these results demonstrate that the IMMUNO-COV assay accurately quantitates SARS-CoV-2 neutralizing antibodies in human sera and therefore is a potentially valuable addition to the currently available serological tests. The assay can provide vital information for comparing immune responses to the various SARS-CoV-2 vaccines that are currently in development, or for evaluating donor eligibility in convalescent plasma therapy studies.

immunology↗

bioRxiv2018

Developing a modern data workflow for living data

Data management and publication are core components of the research process. An emerging challenge that has received limited attention in biology is managing, working with, and providing access to data under continual active collection. \"Evolving data\" present unique challenges in quality assurance and control, data publication, archiving, and reproducibility. We developed a evolving data workflow for a long-term ecological study that addresses many of the challenges associated with managing this type of data. We do this by leveraging existing tools to: 1) perform quality assurance and control; 2) import, restructure, version, and archive data; 3) rapidly publish new data in ways that ensure appropriate credit to all contributors; and 4) automate most steps in the data pipeline to reduce the time and effort required by researchers. The workflow uses two tools from software development, version control and continuous integration, to create a modern data management system that automates the pipeline.

ecology↗