Biology subjects

Yates, M. C.

Publications and source records attributed to Yates, M. C..

7 recordsLinked to original sources

bioRxiv2025

A strong relationship between environmental DNA metabarcoding and rank-based abundance of fish

O_LIIncreasingly, molecular methods of species monitoring are integrated into freshwater biodiversity surveys and fisheries management. Inferring organism abundance or biomass from sequence counts derived from metabarcoding data has been an exciting but contentious concept in the biomonitoring community for some time. Although demonstrating a strong correlation with abundance has proven difficult, many researchers have assumed that quantitative metabarcoding data can at least provide broad-scale ranking of abundance. However, robust field validations of this widely-held assumption remain scarce. C_LIO_LIHere, we analyse metabarcoding read counts of fish eDNA data derived from 20 lakes and use betabinomial mixed effects models to compare this to rank abundance generated from long-term fish survey data. Rank abundance data for 18 species was generated within-species across-sites, meaning that ranks compare the abundance of the same species in different lakes. We also investigated a possible allometric effect on eDNA production by analysing a subset of data for effects of fish body mass on the amount of eDNA sequences. C_LIO_LIWe found a good relationship between species-specific eDNA sequences and within-species rank abundance categories for fishes, with rare fish producing 3% of sequences in a library, moderately abundant producing 7% and abundant fish producing 29%, according to model predictions. C_LIO_LIWe found a small negative effect of body mass on the amount of eDNA sequences, where the proportion of reads recovered significantly decreased with increased mean body mass of the population. C_LIO_LISynthesis and applications: The benefit of this approach is the potential for rapid assessment of rank abundance for multiple species, including smaller species which are often missed by conventional methods such as gillnetting, with relatively low amounts of additional effort. This approach will assist practitioners taking a species-based approach to freshwater habitat management in lakes worldwide. C_LI

ecology↗

bioRxiv2024

eDNA provides accurate and precise estimates of abundance by integrating bioenergetics and particle mass-balance

Anthropogenic activities have led to an unprecedented crisis in freshwater biodiversity loss. The capacity to monitor the abundance of wild populations is critical to conserving biodiversity, but conventional physical specimen collection methods are invasive, costly, and labour-intensive. Environmental DNA (eDNA) offers a promising alternative, being easy to sample, with studies under controlled laboratory conditions showing consistent correlations between eDNA concentration and abundance. However, applying eDNA to monitor abundance remains contentious, as eDNA particle dynamics and the ecology of eDNA production can decouple this relationship in natural ecosystems. To address this, we provide a novel modeling method to produce population estimates from eDNA. We integrated bioenergetics and mass-balance frameworks to relate eDNA concentrations to freshwater fish population abundance estimated through conventional mark-recapture in Brook Trout (Salvelinus fontinalis) across nine Rocky Mountains lakes, five of which underwent size-selective harvesting over two years. Our integrated framework improved the variance explained in eDNA concentrations from 24% to 71%. The integrated model accurately distinguished most (94%) abundance estimates across populations and sampling periods, detecting both natural and harvest-induced reductions in abundance within several populations. This study is the first to empirically integrate the DNA production mechanism and particle dynamics and provide a new methodological approach enabling rapid and accurate abundance quantification. We also discuss how this new tool can be integrated in existing monitoring programs.

ecology↗

bioRxiv2022

A general framework to unify the estimation of numerical abundance and biomass from quantitative eDNA data

Does environmental DNA (eDNA) correlate more closely with numerical abundance (N) or biomass in aquatic organisms? We hypothesize that the answer is neither: eDNA production likely scales allometrically, reflecting key physiological rates and surface area-to-body mass relationships. Building on individual-level frameworks developed from the Metabolic Theory of Ecology, we derive a framework through which quantitative eDNA data can be transformed to simultaneously reflect both population-level N and biomass. We then validated our framework using data from two previously published studies: (i) a marine eDNA metabarcoding dataset; and (ii) a freshwater single-species qPCR dataset. Using a Bayesian modeling approach, we estimated the value of the allometric scaling coefficient that jointly optimized the relationship between N, biomass, and corrected eDNA data to be 0.82 and 0.77 in Case Studies (i) and (ii), respectively. These estimates closely match expected scaling coefficients estimated in previous work on Teleost fish metabolic rates. We also demonstrate that correcting quantitative eDNA can significantly improve correspondence between eDNA- and traditionally-derived quantitative community biodiversity metrics (e.g., Shannon index and Bray-Curtis dissimilarity) under some circumstances. Collectively, we show that quantitative eDNA data is unlikely to correspond exactly to either N or biomass, but can be corrected to reflect both through our unifying joint modelling framework. This framework can also be further expanded to include other variables that might impact eDNA pseudo-steady-state concentrations in natural ecosystems (e.g., temperature, pH, and phenology), and is flexible enough to model these relationships across trophic levels. Significance StatementAquatic animals release DNA (from shed cells, mucous, faeces, etc.) into water, which can be detected via environmental DNA (eDNA) sampling. What is less clear is whether we can estimate numerical abundance (N) or biomass from eDNA concentrations. We hypothesize that eDNA production scales allometrically; that is, large animals release less DNA per unit mass than smaller animals. Building from the Metabolic Theory of Ecology, we derived a framework through which eDNA data can be transformed to simultaneously reflect both N and biomass. We then validated the framework using two case studies in marine and freshwater systems. This framework unifies discrepancies between eDNA, N, and biomass data, unlocking the potential of eDNA to monitor population abundance/biomass and quantify biodiversity.

ecology↗

bioRxiv2022

Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms?

To safeguard biodiversity in a changing climate, we require taxonomic information about species turnover and insights into the health of organisms. Environmental DNA approaches are increasingly used for species identification, but cannot provide functional insights. Transcriptomic methods reveal the physiological states of macroorganisms, but are currently species specific and require tissue sampling or animal sacrifice, making community-wide assessments challenging. Here, we test if broad functional information (expression level of the transcribed genes) can be harnessed from environmental RNA (eRNA), which includes extra-organismal RNA from macroorganisms along with whole microorganisms. We exposed Daphnia pulex as well as phytoplankton prey and microorganism colonizers to control (20 {degrees}C) and heat stress (28 {degrees}C) conditions for seven days. We sequenced eRNA from tank water (after complete removal of Daphnia) as well as RNA from Daphnia tissue, enabling comparisons of extra-organismal and organismal RNA based gene expression profiles. Both RNA types detected similar heat stress responses of Daphnia. Using eRNA, we identified 32 Daphnia genes to be differentially expressed following heat stress. Of these, 17 were also differentially expressed and exhibited similar levels of relative expression in organismal RNA. In addition to the extra-organismal Daphnia response, eRNA detected community-wide heat stress responses consisting of distinct functional profiles and 121 differentially expressed genes across 8 taxa. Our study demonstrates that environmental transcriptomics based on eRNA can non-invasively reveal gene expression responses of macroorganisms following environmental changes, with broad potential implications for the biomonitoring of ecological health across the trophic chain.

ecology↗

bioRxiv2022

Interspecific allometric scaling in eDNA production in fishes reflects physiological and surface area allometry

Relating environmental DNA (eDNA) signal strength to organism abundance requires a fundamental understanding of eDNA production. A number of studies have demonstrated that eDNA production may scale allometrically - that is, larger organisms tend to exhibit lower mass-specific eDNA production rates, likely due to allometric scaling in key processes related to eDNA production (e.g. surface area, excretion/egestion). While most previous studies have examined intra-specific allometry, physiological rates and organism surface area also scale allometrically across species. We therefore hypothesize that eDNA production will similarly exhibit inter-specific allometric scaling. To evaluate this hypothesis, we reanalyzed previously published eDNA data from Stoeckle et al. (2021) which compared metabarcoding read count to organism count and biomass data obtained from trawl surveys. Using a Bayesian model we empirically estimated the value of the allometric scaling coefficient ( b) for bony fishes to be 0.67 (credible interval = 0.58 - 0.77), although our model failed to converge for chondrichthyan species. We found that integrating allometry significantly improved correlations between organism abundance and metabarcoding read count relative to traditional metrics of abundance (density and biomass) for bony fishes. Although substantial unexplained variation remains in the relationship between read count and organism abundance, our study provides evidence that eDNA production tends to scale allometrically across species. Future studies investigating the relationship between eDNA signal strength and metrics of fish abundance could potentially be improved by accounting for allometry - a scaling coefficient value of [~]2/3 appears to be both theoretically and empirically justified.

ecology↗

bioRxiv2020

Single generation exposure to a captive diet: a primer for domestication selection in a salmonid fish?

Millions of wild animals in captivity are reared on diets that differ in their uptake and composition from natural conditions. Few studies have investigated whether such novel diets elicit unintentional domestication selection in captive rearing and supplementation programs. In highly fecund salmonid fishes, natural and captive mortality is highest in the first few months of exogenous feeding. This high early mortality might be a potent driver of unintentional selection because wild fish normally forage on live prey whereas they are fed almost exclusively pellet feed in captivity: fish that do not adapt pellet feed well under captive conditions experience reduced growth and/or die. We tested this hypothesis by generating a large number of families from F1 captive and wild fish originating from the same three populations and then rearing them each on pellet and natural, live, drifting feed for three months at the beginning of exogenous feeding. We found that captive fish of every population grew faster than wild fish in all diet treatments. Populations exhibited an idiosyncratic response to diet treatment, with two populations exhibiting faster growth on a pellet diet versus the natural diet but another population exhibiting similar growth in both diet treatments. Fish exposed to a natural diet also exhibited higher survival relative to those given a pellet diet. Captive and wild fish did not differ in survival, regardless of population of origin. Overall, we found evidence that rapid domestication selection associated with a single generation exposure to a novel captive diet generates genetically-based changes to individual fitness (e.g., growth and survival) in a wild fish.

evolutionary biology↗

bioRxiv2020

Allometric scaling strengthens the relationship between eDNA particle concentration and organism abundance in nature

Organism abundance is a critical parameter in ecology, but its estimation is often challenging. Approaches utilizing eDNA to indirectly estimate abundance have recently generated substantial interest. However, preliminary correlations observed between eDNA concentration and abundance in nature are typically moderate in strength with significant unexplained variation. Here we apply a novel approach to integrate allometric scaling coefficients into models of eDNA concentration and organism abundance. We hypothesize that eDNA particle production scales non-linearly with mass, with scaling coefficients < 1. Wild populations often exhibit substantial variation in individual body size distributions; we therefore predict that the distribution of mass across individuals within a population will influence population-level eDNA production rates. To test our hypothesis, we collected standardized body size distribution and mark-recapture abundance data using whole-lake experiments involving nine populations of brook trout. We correlated eDNA concentration with three metrics of abundance: density (individuals/ha), biomass (kg/ha), and allometrically scaled mass (ASM) ({sum}(individual mass0.73)/ha). Density and biomass were both significantly positively correlated with eDNA concentration (adj. R2 = 0.59 and 0.63, respectively), but ASM exhibited improved model fit (adj. R2 = 0.78). We also demonstrate how estimates of ASM derived from eDNA samples in unknown systems can be converted to biomass or density estimates with additional size structure data. Future experiments should empirically validate allometric scaling coefficients for eDNA production, particularly where substantial intraspecific size distribution variation exists. Incorporating allometric scaling may improve predictive models to the extent that eDNA concentration may become a reliable indicator of abundance in nature.

ecology↗