Biology subjects

Gilbert, B.

Publications and source records attributed to Gilbert, B..

3 recordsLinked to original sources

bioRxiv2018

The filtering metaphor revisited: competition and environment jointly structure invasibility and coexistence

Filtering, or the reduction in species diversity that occurs because not all species can persist in all locations, is thought to unfold hierarchically, at large scales due to the environment and at small scales due to competition. However, the ecological effects of competition and the environment are not independent, and observational approaches preclude investigation into their interplay. We use a demographic approach with 30 plant species to experimentally test (i) the effect of competition on species persistence in two soil moisture environments, and (ii) the effect of environmental conditions on the mechanisms underlying competitive coexistence. We find that competitors cause differential persistence of species across environments even when these effects are lacking in the absence of competition, and that the traits that determine persistence depend on the competitive environment. Changing environmental conditions generated idiosyncratic effects on coexistence outcomes, increasing competitive exclusion of some species while promoting coexistence of others. Our results highlight the importance of considering environmental filtering in light of, rather than in isolation from, competition, and challenge community assembly models and approaches to projecting future species distributions.

ecology↗

bioRxiv2017

IMPROVEMENTS TO BAYESIAN GENE ACTIVITY STATE ESTIMATION FROM GENOME-WIDE TRANSCRIPTOMICS DATA

An important question in many biological applications, is to estimate or classify gene activity states (active or inactive) based on genome-wide transcriptomics data. Recently, we proposed a Bayesian method, titled MultiMM, which showed superior results compared to existing methods. In short, MultiMM performed better than existing methods on both simulated and real gene expression data, confirming well-known biological results and yielding better agreement with fluxomics data. Despite these promising results, MultiMM has numerous limitations. First, MultiMM leverages co-regulatory models to improve activity state estimates, but information about co-regulation is incorporated in a manner that assumes that networks are known with certainty. Second, MultiMM assumes that genes that change states in the dataset can be distinguished with certainty from those that remain in one state. Third, the model can be sensitive to extreme measures (outliers) of gene expression. In this manuscript, we propose a modified Bayesian approach, which addresses these three limitations by improving outlier handling and by explicitly modeling network and other uncertainty yielding improved gene activity state estimates when compared to MultiMM.

genomics↗

bioRxiv2017

Frequency-dependent Maternal Effects across Species and Environments

O_LIMaternal provisioning of offspring in response to environmental conditions (\"maternal environmental effects\") has been argued as the missing link in plant life histories. Although empirical evidence suggests that maternal responses to abiotic conditions are common, there is little understanding of the prevalence of maternal provisioning in competitive environments.\nC_LIO_LIWe tested how competition in two soil moisture environments affects maternal provisioning of offspring seed mass. Specifically, we varied conspecific frequency from 90% (intraspecific competition) to 10% (interspecific competition) for 15 pairs of annual plant species that occur in California.\nC_LIO_LIWe found that conspecific frequency affected maternal provisioning (seed mass) in 48% of species, and that these responses included both increased (20%) and decreased (24%) seed mass. In contrast, 68% of species responded to competition through changes in per capita fecundity (seed number), which generally decreased as conspecific frequency increased. The direction and magnitude of frequency-dependent seed mass depended on the identity of the competitor, even among species in which fecundity was not affected by competitor identity.\nC_LIO_LISynthesis. Our research demonstrates how species responses to different competitive environments manifest through maternal provisioning, and that these responses alter previous estimates of environmental maternal effects and reproductive output; future study is needed to understand their combined effects on population and community dynamics.\nC_LI

ecology↗