Biology subjects

Eaton, K. M.

Publications and source records attributed to Eaton, K. M..

5 recordsLinked to original sources

bioRxiv2026

Variation in hypoxia tolerance is driven by evolutionary changes in gene regulation in the eastern oyster

Understanding the genomic basis of stress tolerance is crucial for predicting biological responses to environmental change. Here, we investigated the genomic basis of divergence in hypoxia tolerance between two populations of eastern oyster (Crassostrea virginica) from Louisiana and Texas, USA. We combined low-coverage whole-genome sequencing data with previously generated transcriptomic evidence to understand the mechanisms underlying population-specific variation in hypoxia tolerance. Genome-wide analyses revealed substantial population differentiation (global FST = 0.21), indicative of a clear genetic break between our study populations. We combined estimates of genomic differentiation (FST) with diversity metrics to generate a set of exploratory candidate regions showing signatures consistent with recent selection. Several candidate genes identified through this approach were associated with the maintenance of homeostasis under environmental stress. We additionally tested whether genes previously identified as differentially expressed (DE) under hypoxia exhibit elevated genomic divergence between populations. While these hypoxia DEGs did show higher than expected between-population differentiation, this pattern also holds for other environmentally responsive genes. This suggests that transcriptomically responsive genes in general may generally show elevated divergence among populations, possibly due to a weaker effect of purifying selection. Furthermore, we found that hypoxia DEGs did not show an enrichment of nonsynonymous fixed differences (p = 0.9155, as compared to the genome-wide background), suggesting that the elevated divergence seen in these genes is not driven by rapid protein-coding evolution. Together, our results support a model in which population-scale differences in hypoxia tolerance occur primarily through evolution of gene regulation acting on environmentally responsive pathways.

genomics↗

bioRxiv2024

Broad thermal tolerance and high mitochondrial genetic connectivity in the pinfish (Lagodon rhomboides)

Pinfish (Lagodon rhomboides) are highly abundant in coastal ecosystems of the Gulf of Mexico and western Atlantic Ocean and serve as a crucial link in marine food webs. Despite their ecological relevance, little is known about this species susceptibility to anthropogenic climate change. Here, we characterized patterns of mitochondrial genetic divergence and examined the upper thermal tolerance of pinfish across a large portion of the species range. We found little evidence of population genetic differentiation among distant localities with divergent temperature regimes (e.g., Mexico and North Carolina), using two mitochondrial markers (CytB and COI). This suggests high genetic connectivity, which implies low potential for local adaptation of populations to different thermal conditions along a latitudinal gradient. To further examine population-scale differences in thermal tolerance, we assessed the critical thermal maxima (CTmax) of pinfish from four localities: North Carolina, Florida Keys, Alabama, and Texas. We found that CTmax was similar across sites, with all localities showing an average CTmax within a 1{degrees}C temperature range (34.5-35.5{degrees}C). This suggests that southern populations of pinfish may be more susceptible to the detrimental effects of ocean warming, as individuals in lower latitudes regularly experience temperatures within a few degrees of their CTmax. Finally, we examined the influence of varying salinity on the upper thermal limit of the pinfish and found that pinfish show no variation in CTmax under salinity conditions ranging from hypo-to hyper-saline (15-35 ppt). These results show that pinfish can tolerate a wide range of environmental parameters, but may rely on phenotypic plasticity rather than local adaptation to distinct conditions to cope with different environmental regimes.

evolutionary biology↗

bioRxiv2022

Does it pay to pay? A comparison of the benefits of open-access publishing across various sub-fields in Biology

Authors are often faced with the decision of whether to maximize impact or minimize costs when publishing the results of their research. For example, to potentially improve impact via increased accessibility, many subscription-based journals now offer the option of paying a fee to publish open access (i.e., hybrid journals), but this solution excludes authors who lack the capacity to pay to make their research accessible. Here, we tested if paying to publish open access in a subscriptionbased journal benefited authors by conferring more citations relative to closed access articles. We identified 146,415 articles published in 152 hybrid journals in the field of biology from 2013-2018 to compare the number of citations between various types of open access and closed access articles. In a simple generalized linear model analysis of our full dataset, we found that publishing open access in hybrid journals that offer the option confers an average citation advantage to authors of 17.8 citations compared to closed access articles in similar journals. After taking into account the number of authors, journal impact, year of publication, and subject area, we still found that open access generated significantly more citations than closed access (p < 0.0001). However, results were complex, with exact differences in citation rates among access types impacted by these other variables. This citation advantage based on access type was even similar when comparing open and closed access articles published in the same issue of a journal (p < 0.0001). However, by examining articles where the authors paid an article processing charge, we found that cost itself was not predictive of citation rates (p = 0.14). Based on our findings of access type and other model parameters, we suggest that, in most cases, paying for access does confer a citation advantage. For authors with limited budgets, we recommend pursuing open access alternatives that do not require paying a fee as they still yielded more citations than closed access. For authors who are considering where to submit their next article, we offer additional suggestions on how to balance exposure via citations with publishing costs.

scientific communication and education↗

bioRxiv2020

Thermally tolerant symbionts may explain Caribbean octocoral resilience to heat stress

Coral reef ecosystems are under threat from the frequent and severe impacts of anthropogenic climate change, particularly rising sea surface temperatures. The effects of thermal stress may be ameliorated by adaptation and/or acclimation of the host, symbiont, or holobiont (host + symbiont) to increased temperatures. We examined the role of the symbiont in promoting thermal tolerance of the holobiont, using Antillogorgia bipinnata (octocoral host) and Breviolum antillogorgium (symbiont) as a model system. We identified five distinct genotypes of B. antillogorgium from symbiont populations isolated from Antillogorgia colonies in the Florida Keys. Three symbiont genotypes were cultured and maintained at 26{degrees}C (ambient historical temperature) and two were cultured and maintained at 30{degrees}C (elevated historical temperature) for two years. Following culturing, we analyzed the growth rate and carrying capacity of each symbiont genotype at both ambient and elevated temperatures in culture (in vitro). All genotypes grew well at both temperatures, indicating thermal tolerance among these B. antillogorgium cultures. Prior culturing at the elevated temperature, however, did not result in increased thermal tolerance. We then inoculated juvenile A. bipinnata polyps with each of the five symbiont genotypes, and reared these polyps at both ambient and elevated temperatures (in hospite experiment). All genotypes were able to establish symbioses with polyps in both temperature treatments. Survivorship of polyps at 30{degrees}C was significantly lower than survivorship at 26{degrees}C, but all treatments had surviving polyps at 56 days post-infection, suggestive of broad thermal tolerance in B. antillogorgium, which may play a part in the increased resilience of Caribbean octocorals during heat stress events.

evolutionary biology↗

bioRxiv2020

Nanopore amplicon sequencing reveals molecular convergence and local adaptation of opsin genes

Local adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were amplified for individuals of C. artedi, C. hoyi, C. kiyi, and C. zenithicus. Comparisons revealed species-specific differences in the coding sequence of rhodopsin (Tyr261Phe substitution), suggesting local adaptation by C. kiyi to the blue-shifted depths of Lake Superior. Parallel evolution and "toggling" at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

evolutionary biology↗