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Gold, Z. J.

Publications and source records attributed to Gold, Z. J..

3 recordsLinked to original sources

Spatial clustering reveals the impact of higher-order interactions in a diverse annual plant community

Spatial patterns are widespread in ecology, but their effects on species interactions remain unresolved, especially in diverse communities. In principle, the degree of spatial clustering could alter the concentration of higher-order interactions, which occur when one (or more) species modifies competition between two others. When species are well mixed, heterospecific neighbors have ample opportunity to modify a competitors interactions with other species. In contrast, species clustering can reduce the concentration of interspecific higher-order interactions. In a field experiment with annual grassland plants in California, we manipulated the spatial arrangement -- but not the number or identity -- of two competitors and measured how they jointly affected a focal individual. We found that focal plants produced more seeds when their competitors were clustered than when they were mixed. These results suggest that interspecific higher-order interactions generally had a stronger competitive (or weaker facilitative) effect than intraspecific ones. However, the effect of clustering varied across species. Larger differences in focal fecundity were correlated with competitors that had greater differences in size and/or functional traits between the spatial arrangements. Additionally, a competitive hierarchy among our study species predicted the effects of clustered versus mixed competitors on focal seed production. Altogether, our work suggests that the spatial arrangement of competitors changes the realized strength of competition in diverse plant communities by modifying the concentration of higher-order interactions. Given the extensive variation in spatial aggregation in plant communities, this mechanism is likely to be a powerful but underappreciated force shaping competition in nature. Significance StatementPlant species coexist in remarkably diverse assemblages throughout the world. Spatial patterns, including aggregation and intermixing, are also widespread in these communities. One potentially underappreciated mechanism that may structure the spatial dynamics of plant communities is interactions that uniquely occur in diverse systems, often called higher-order interactions. Here, we experimentally demonstrated that spatially mediated higher-order interactions operate among annual plants. These higher-order interactions, and their associated changes in competitor size and functional traits, were correlated with the competitive imbalance between competitors. Because both spatial aggregation and competitive hierarchies are widespread in nature, higher-order interactions emerging from their combination may be a more common driver of biodiversity patterns in plant communities than previously thought.

ecology↗

Toward Quantitative Metabarcoding

Amplicon-sequence data from environmental DNA (eDNA) and microbiome studies provides important information for ecology, conservation, management, and health. At present, amplicon-sequencing studies - known also as metabarcoding studies, in which the primary data consist of targeted, amplified fragments of DNA sequenced from many taxa in a mixture - struggle to link genetic observations to underlying biology in a quantitative way, but many applications require quantitative information about the taxa or systems under scrutiny. As metabarcoding studies proliferate in ecology following decades of microbial and microbiome work using similar techniques, it becomes more important to develop ways ot make them quantitative to ensure that their conclusions are adequately supported. Here we link previously disparate sets of techniques for making such data quantitative, showing that the underlying PCR mechanism explains observed patterns of amplicon data in a general way. By modeling the process through which amplicon-sequence data arises, rather than transforming the data post-hoc, we show how to estimate the starting DNA proportions from a mixture of many taxa. We illustrate how to calibrate the model using mock communities and apply the approach to simulated data and a series of empirical examples. Our approach opens the door to improve the use of metabarcoding data in a wide range of applications in ecology, public health, and related fields.

ecology↗

eDNA metabarcoding as a biomonitoring tool for marine protected areas

Monitoring of marine protected areas (MPAs) is critical for marine ecosystem management, yet current protocols rely on SCUBA-based visual surveys that are costly and time consuming, limiting their scope and effectiveness. Environmental DNA (eDNA) metabarcoding is a promising alternative for marine ecosystem monitoring, but more direct comparisons to visual surveys are needed to understand the strengths and limitations of each approach. This study compares fish communities inside and outside the Scorpion State Marine Reserve off Santa Cruz Island, CA using eDNA metabarcoding and underwater visual census surveys. Results from eDNA captured 76% (19/25) of fish species and 95% (19/20) of fish genera observed during pairwise underwater visual census. Species missed by eDNA were due to the inability of MiFish 12S barcodes to differentiate species of rockfishes (Sebastes, n=4) or low site occupancy rates of crevice-dwelling Lythrypnus gobies. However, eDNA detected an additional 30 fish species not recorded in paired visual surveys, but previously reported from prior visual surveys, highlighting the sensitivity of eDNA. Significant variation in eDNA signatures by location (50m) and site (~1000m) demonstrates the sensitivity of eDNA to address key questions such as community composition inside and outside MPAs. Interestingly, eDNA results recorded higher species richness outside the MPA while visual surveys observed the opposite pattern. This result is likely caused by swamping effects of high fish abundance in MPAs that reduce detection probabilities of pelagic and intertidal taxa. Results demonstrate the utility of eDNA metabarcoding for monitoring marine ecosystems, providing an important complementary tool to visual methods.

molecular biology↗