Biology subjects

Holmes, A. E.

Publications and source records attributed to Holmes, A. E..

3 recordsLinked to original sources

bioRxiv2026

Community assembly dynamics in a regulated stream: Insights from environmental DNA

Degradation of freshwater habitats, including the alteration of natural flow regimes by impoundment, is a major threat to native fishes. When dam removal is not possible, management actions to recover natural flow regimes can benefit native species, but monitoring community responses is crucial to show efficacy. We used eDNA metabarcoding to quantify spatiotemporal trends in fish assemblages along the longitudinal profile of a regulated stream where a court-ratified environmental flows framework is used to benefit native fishes. At a subset of sites, we also compared eDNA results with concurrent surveys conducted using long-term standardized fisheries monitoring techniques to evaluate concordance. From 59 eDNA samples collected over approximately 2 years, we detected 26 fish taxa, including 8 native species, with 25 taxa resolving to species level using a custom reference sequence database; one taxon could not be resolved between closely related species. Fish assemblages varied predictably along the longitudinal profile of the stream and by season (fall and spring). Diversity indices were higher at downstream sites and in fall, reflecting greater richness of warm-water non-native species. Evenness was similar among sites but shifts in species ranks suggests reordering processes drive spatiotemporal variation in assembly. Gradient forest analysis identified thirteen species associated with spatiotemporal gradients, including both native cold-water species and non-native warm-water species. Overall, eDNA results were concordant with conventional fisheries monitoring but eDNA detected significantly greater species richness through increased detection of rare species. eDNA results align with long-term monitoring that demonstrated assemblage shifts in upper, but not lower stream reaches, and extends the insights into spatial responses, species reordering, and ecology of rare species. These findings demonstrate the value of eDNA as a complementary tool for understanding community assembly dynamics, including responses to stream rehabilitation and ecosystem management.

ecology↗

bioRxiv2022

Metadata preservation and stewardship for genomic data is possible, but must happen now

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species and population resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies of evolutionary biology, molecular ecology and conservation genetics produce large amounts of genome-scale genetic diversity data for wild populations. While open data policies have ensured an abundance of freely available genomic data stored in the databases of the International Nucleotide Sequence Database Collaboration (INSDC), only about 13% of current accessions have the associated spatial and temporal metadata in INSDC necessary to be reused in monitoring programs, macrogenetic studies, or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a "distributed datathon" to quantify the availability of these missing metadata in sources external to the INSDC and to test the hypothesis that these metadata decay with time. We also worked to remediate these missing metadata by extracting them, when present, from associated published papers, online repositories, and/or from direct communication with authors. Starting with 848 programmatically identified candidate datasets (INSDC BioProjects), we manually determined that 561 contained samples from wild populations. We successfully restored spatiotemporal metadata (locality name and/or geospatial coordinates and collection year) for 78% of these 561 datasets (N = 440 BioProjects comprising 45,105 individuals or BioSamples from 762 species in 17 phyla). We also quantified the availability of 33 additional categories of metadata in sources external to the INSDC. Information about associated publications and the type of habitat from which the samples were taken was the most easily found; information about sampling permits was the most challenging to locate. Looking at papers and online repositories was much more fruitful than contacting authors, who only replied to our email requests 45% of the time. Overall, 23% of our email queries to authors discovered useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declines significantly with the age of the dataset, with a 13.5% yearly decrease for metadata located in published papers or online repositories and up to a 22% yearly decrease for metadata that were only available from authors. This observable metadata decay, mirrored in studies of other types of biological data, should motivate swift updates to data sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost forever.

bioinformatics↗

bioRxiv2022

Experimental evaluation of environmental DNA methods for detection of a rare fish in turbid water

Environmental DNA (eDNA) approaches enable sensitive detection of rare aquatic species. However, water conditions like turbidity can limit sensitivity, resulting in false negative detections. The dynamics of eDNA detection in turbid conditions are poorly understood, but can be better characterized through experimental work. In this study, 1-L field-collected water samples were spiked with tank-sourced eDNA from a rare, endangered estuarine fish at concentrations similar to eDNA samples collected from the natural environment. Samples using non-turbid water (5 NTU), turbid water (50 NTU), and prefiltered turbid water were filtered using four filter types (pore size range 0.45 m-10 m). Detection success using a species-specific Taqman qPCR assay was assessed as both eDNA copy number and detection/non-detection. Glass fiber filters (nominal pore size 1.6 m) yielded the highest number of eDNA copies and detections in non-turbid water and the highest detection rate in turbid water when used without a prefilter. Detection was a more robust metric for evaluating species presence across turbidity conditions compared with eDNA copy number. Prefiltration improved detection rates for the other filters tested (polycarbonate and cartridge filters). Filter material and design appear to interact differently with the prefiltration step, and may be more important considerations than pore size for eDNA capture in turbid water. Interactions between eDNA particles, suspended particulate matter, and filters are important to consider for eDNA methods optimization and interpretation of rare species detections in turbid water.

molecular biology↗