Biology subjects

Murray, C. S.

Publications and source records attributed to Murray, C. S..

11 recordsLinked to original sources

bioRxiv2026

DNA 6mA marks transcriptionally active chromatin in malaria parasites

DNA N6-methyladenine (6mA) has emerged as a significant epigenetic modification across a broad range of eukaryotes, from unicellular protists to metazoa. However, its role in unicellular eukaryotic parasites with highly AT-rich genomes, such as malaria-causing Plasmodium falciparum, remains unclear. Using mass spectrometry, South-western blotting, and Single Molecule Real-Time sequencing (Pacific Biosciences) across four stages of P. falciparum intra-erythrocytic development (IED), we confirmed that 0.02-0.04% of genomic adenines are modified to 6mA, with over 60% of the sites being stably maintained during the IED cycle. Notably, 6mA is enriched at transcription start sites, with genes bearing 6mA marks within their 5 and 3 untranslated regions exhibiting significantly elevated steady-state transcript levels. Consistent with this, 6mA loci show a strong positive correlation with activating histone post-translational modifications, while showing no significant association with repressive histone marks. Furthermore, in contrast to unicellular ciliates such as Oxytricha and Tetrahymena - organisms that share ancestry with Plasmodium - 6mA-marked genomic regions do not occlude nucleosomes. Lastly, we identified a putative 6mA methyltransferase belonging to the METTL4 family in P. falciparum, PfN6AMT encoded by the PF3D7_1303100 gene, and demonstrate that recombinant PfN6AMT exhibits robust methyltransferase activity in vitro, with mutation of its active site residues abolishing catalytic activity. Collectively, our findings demonstrate that 6mA is a low-abundance, yet reproducible, feature of the P. falciparum epigenome that is associated with transcriptionally active chromatin, and that the molecular mechanisms governing DNA adenine methylation may have undergone substantial evolutionary divergence, even among closely related eukaryotic lineages.

genomics↗

bioRxiv2026

The effects of elevated seawater pH and total alkalinity following dosing of sodium hydroxide in Calanus finmarchicus

Ocean Alkalinity Enhancement (OAE) is a marine carbon dioxide removal (mCDR) strategy that involves adding alkaline substances to surface waters to enhance CO2 uptake and storage. The dispersal of alkaline materials such as sodium hydroxide (NaOH) into seawater can cause rapid increases in pH and total alkalinity (TA) that substantially exceeds natural variability in marine environments. Such fluctuations may negatively affect marine life, especially small animals like copepods who cannot avoid OAE plumes and whose physiological processes could be disrupted by large and rapid shifts in seawater pH. To address knowledge gaps regarding potential biological impacts of OAE, we studied these effects in Calanus finmarchicus, a keystone copepod species in the Northwest Atlantic Ocean. We exposed C. finmarchicus from the late juvenile copepodite stages and adult females to NaOH-dosed seawater at pH 10.5 ([~]5,000 {micro}mol kg-1 TA) and pH 9.0 ([~]3,150 {micro}mol kg-1 TA) for durations that reflect expected short-term exposure times during field OAE deployments (pH 10.5: 1, 5, 10 minutes; pH 9.0: 1, 15, 30 minutes). None of the treatment combinations resulted in mortality immediately after the initial exposure. Individuals were monitored for survival for 72 hours post-exposure (hpe), and only one treatment group (juveniles exposed to pH 10.5 for 10 minutes) showed a significant reduction in final survival; no other pH-duration combination showed increased mortality. Effects on the ability to initiate an escape response were more substantial. Adult females treated with pH 10.5 for 5 or 10 minutes showed a significant reduction in escape response immediately after exposure. In contrast, juveniles showed no immediate change in escape response following exposure to pH 10.5 or pH 9.0, although juveniles exposed to pH 10.5 for 10 minutes exhibited reduced escape response at 24 hpe. Using microrespirometry, we measured oxygen consumption following a 10-minute exposure to pH 10.5 and detected no effect on routine metabolic rate immediately post-exposure or at 12 hpe. Overall, our results suggest that C. finmarchicus is relatively tolerant to short-term exposures to very high pH and alkalinity. Future work should prioritize longer-term exposure under more moderate ocean OAE conditions.

ecology↗

bioRxiv2025

Patterns of gene family evolution and selection across Daphnia

Gene family expansion underlies a host of biological innovations across the tree of life. Understanding why specific gene families expand or contract requires comparative genomic investigations clarifying further how species adapt in the wild. This study investigates the gene family change dynamics within several species of Daphnia, a group of freshwater microcrustaceans that are useful model systems for evolutionary genetics. We employ comparative genomics approaches to understand the forces driving gene evolution and draw upon candidate gene families that change gene numbers across Daphnia. Our results suggest that genes related to stress responses and glycoproteins generally expand across taxa, and we investigate evolutionary hypotheses of adaptation that may underpin expansions. Through these analyses, we shed light on the interplay between gene expansions and selection within other ecologically relevant stress response gene families. While we show generalities in gene family turnover in genes related to stress response (i.e., DNA repair mechanisms), most gene family evolution is driven in a species-specific manner. Additionally, while we show general trends towards positive selection within some expanding gene families, many genes are not undergoing selection, highlighting the complex nature of diversification and evolution within Daphnia. Our research enhances the understanding of individual gene family evolution within Daphnia and provides a case study of ecologically relevant genes prone to change.

evolutionary biology↗

bioRxiv2025

Appendometer: A system for simultaneous, high-throughput morphometry of Drosophila legs and wings

O_LIThe inheritance of many different organismal features is correlated, as is their evolution, sug-gesting that we need to understand the pattern and causes of those correlations to understand evolution. Unfortunately, we generally lack the ability to rapidly and accurately measure large numbers of traits, making it difficult to describe the patterns of trait relationships or for-mulate hypothesis about the causes of their entanglement. We have previously developed a system to make high-dimensional measurements of Drosophilid fly wings in live specimens. Here, we report the extension of this approach to rapidly assess the dimensions of the distal leg segments, femur, tibia, and tarsi. Using the system, we describe the covariance of the wing and leg morphology and evaluate the relative rates of evolution of legs and wings. C_LIO_LIWe use two simple suction devices to immobilize and position legs and wings of an anaes-thetized fly for imaging, then take a single image incorporating both appendages. We em-ployed a machine learning method to measure leg segment lengths, which should be broadly applicable across diverse taxa. Experienced users can image the legs and wings of a fly every two minutes, with outlier detection and correction taking approximately 40 seconds. To demonstrate the usefulness of these methods, we measured the legs and wings of over 4,000 specimens from 43 different Drosophilid taxa. We estimated the rate of wing and leg evolu-tion using a phylogenetic mixed model. C_LIO_LIRepeatabilities of leg segments lengths averaged over 80%. The rate of evolution of wing and leg sizes are similar, but the rate of wing proportion evolution is 1.6 times as high as that of leg proportions due to strong allometric changes in wing shape. Within-species variation in leg proportions is highly correlated with the rate of leg proportion evolution, as is true for wings. Relative lengths of leg segments showed a strong pattern of negative correlations be-tween the lengths of the tarsal segments and of the femurs and tibias, while all other segment correlations were positive. This pattern was repeated in the rate estimates, suggesting that se-lection favors tradeoffs between tarsi and the remainder of the leg. C_LIO_LIOur simple system for imaging and measuring legs and wings simultaneously has high throughput and repeatability. It is readily applicable to a wide variety of winged insects and other traits, including wings, that could be imaged. Applied to Drosophila, our morphometric system enlarges the ability to study inheritance, pleiotropy, and evolution in this important model taxon. C_LI

evolutionary biology↗

bioRxiv2024

Gene expression and DNA methylation changes in response to hypoxia in toxicant-adapted Atlantic killifish (Fundulus heteroclitus)

Coastal fish populations are threatened by multiple anthropogenic impacts, including the accumulation of industrial contaminants and the increasing frequency of hypoxia. Some populations of the Atlantic killifish (Fundulus heteroclitus), like those in New Bedford Harbor (NBH), Massachusetts, have evolved a resistance to dioxin-like polychlorinated biphenyls (PCBs) that may influence their ability to cope with secondary stressors. To address this question, we compared hepatic gene expression and DNA methylation patterns in response to mild or severe hypoxia in killifish from NBH and Scorton Creek (SC), a reference population from a relatively pristine environment. We hypothesized that NBH fish would show altered responses to hypoxia due to trade-offs linked to toxicant resistance. Our results revealed substantial differences between populations. SC fish demonstrated a dose-dependent changes in gene expression in response to hypoxia, while NBH fish exhibited a muted transcriptional response to severe hypoxia. Interestingly, NBH fish showed significant DNA methylation changes in response to hypoxia, while SC fish did not exhibit notable epigenetic alterations. These findings suggest that toxicant-adapted killifish may face trade-offs in their molecular response to environmental stress, potentially impacting their ability to survive severe hypoxia in coastal habitats. Further research is needed to elucidate the functional implications of these epigenetic modifications and their role in adaptive stress responses. Summary StatementThis study reveals how evolved resistance to toxicants in killifish may compromise their ability to respond to hypoxia, highlighting trade-offs that impact survival in stressed coastal environments.

physiology↗

bioRxiv2024

Cross-generational plasticity in Atlantic silversides (Menidia menidia) under the combined effects of hypoxia and acidification

We investigated the potential for cross-generational plasticity to influence how offspring respond to hypoxia and ocean acidification (hereafter HypOA) in the coastal forage fish Atlantic silverside (Menidia menidia). Mature wild silversides were treated with a control [dissolved oxygen (DO):100% air saturation (a.s.) / pCO2: 650 {micro}atm] or HypOA conditions [DO: 40% a.s. / pCO2: 2300 {micro}atm] for 10 days prior to spawning. Their offspring were reared under both treatments in factorial experimental design. Parental acclimation to HypOA altered several offspring traits, including increased embryo survival under HypOA and an overall reduction in post-hatch growth rate. Offspring from HypOA-treated parents that were reared under control conditions had larger eyes across the developmental period. When compared against the overall control group, larvae directly exposed to HypOA exhibited 2,416 differentially expressed transcripts (DETs). Although most of these DETs were specific to individual parental treatments, the most enriched Gene Ontology terms were conserved across parental treatments, including terms related to neurotransmitter secretion, nervous system development, axon pathfinding, calcium channel activity, proteolysis, and extracellular matrix organization. Larvae from HypOA-treated parents that were reared under control conditions exhibited a shift in constitutive gene expression similar to that seen in larvae directly exposed to HypOA. This highly consistent finding indicates that parental acclimation before fertilization promotes the transcriptional frontloading of genes in offspring. This effect may have primed regulatory functions in offspring that sense and respond to low DO and elevated pCO2 conditions. Though, our results suggest that this altered developmental phenotype may have some negative fitness consequences for offspring.

ecology↗

bioRxiv2024

Balancing selection and the functional effects of shared polymorphism in cryptic Daphnia species

The patterns of genetic variation within and between related taxa represent the genetic history of a species. Shared polymorphisms, loci with identical alleles across species, are of unique interest as they may represent cases of ancient selection maintaining functional variation post-speciation. In this study, we investigate the abundance of shared polymorphism in the Daphnia pulex species complex. We test whether shared mutations are consistent with the action of balancing selection or alternative hypotheses such as hybridization, incomplete lineage sorting, or convergent evolution. We analyzed over 2,000 genomes from North American and European D. pulex and several outgroup species to examine the prevalence and distribution of shared alleles between the focal species pair, North American and European D. pulex. We show that while North American and European D. pulex diverged over ten million years ago, they retained tens of thousands of shared alleles. We found that the number of shared polymorphisms between North American and European D. pulex cannot be explained by hybridization or incomplete lineage sorting alone. Instead, we show that most shared polymorphisms could be the product of convergent evolution, that a limited number appear to be old trans-specific polymorphisms, and that balancing selection is affecting young and ancient mutations alike. Finally, we provide evidence that a blue wavelength opsin gene with trans-specific polymorphisms has functional effects on behavior and fitness in the wild. Ultimately, our findings provide insights into the genetic basis of adaptation and the maintenance of genetic diversity between species.

evolutionary biology↗

bioRxiv2022

A cosmopolitan inversion drives seasonal adaptation in overwintering Drosophila

Drosophila melanogaster living in temperate regions evolve as they track seasonal fluctuations. Yet, we lack an understanding of the genetic architecture of seasonal adaptive tracking. By sequencing orchard populations collected across multiple years, we characterized the genomic signal of seasonal demography and identified that the cosmopolitan inversion In(2L)t drives seasonal adaptation. In(2L)t shows footprints of selection that are inconsistent with simple explanations of genetic drift, as well as signatures of partial selective sweeps. A meta-analysis of phenotypic studies shows that seasonal loci within In(2L)t are associated with behavior, life-history, physiology, and morphology traits. Our results identify candidate regions that underlie seasonal adaptive tracking and link them to phenotype. This work supports the general hypothesis that inversions are important drivers of rapid adaptation. One-Sentence SummaryA chromosomal inversion drives adaptive evolution between seasons in wild fruit flies.

evolutionary biology↗

bioRxiv2022

Sexual production is regulated by the brood in Bombus impatiens colonies

Sexual production in social insects marks the peak of colony development, yet the mechanisms regulating it remain unclear. We investigated the role of brood in colony development, worker reproduction, and sexual production in Bombus impatiens. While larvae are known to reduce worker egg-laying and enhance the queens reproductive inhibition, these effects were previously tested only in small groups. We manipulated brood size in full-sized, young colonies by doubling or removing brood and monitored development. Colonies with doubled brood produced significantly more gynes, independent of the number of workers, while reduced-brood colonies exhibited a non-significant increase in male production that was driven by colony size. Worker ovary activation was lower in double-brood colonies, with no change in aggression. A follow-up experiment directly testing the effect of colony size showed that higher worker density led to higher ovary activation in workers but did not affect sexual production. These results suggest that brood strongly influences colony development and sexual production, possibly reflecting an extended phenotype of the queen, whereas worker ovary activation appears to be a more flexible process influenced by either brood presence or colony size. Understanding brood dynamics may be key to understanding the evolution of female castes in social insects.

evolutionary biology↗

bioRxiv2021

Polygenic variation in sexual investment across an ephemerality gradient in Daphnia pulex

Species across the tree of life can switch between asexual and sexual reproduction. In facultatively sexual species, the ability to switch between reproductive modes is often environmentally dependent and subject to local adaptation. However, the ecological and evolutionary factors that influence the maintenance and turnover of polymorphism associated with facultative sex remain unclear. To address this basic question, we studied the ecological and evolutionary dynamics of polymorphism in reproductive strategy in a metapopulation of the model facultative sexual, Daphnia pulex, located in the southern United Kingdom. We found that patterns of clonal diversity, but not genetic diversity varied with ephemerality. Reconstruction of a multi-year pedigree demonstrated the co-existence of clones that were found to differ in their investment into male production. Mapping of quantitative variation in male production using lab-generated and field-collected individuals identified multiple putative QTL underlying this trait, and we identified a plausible candidate gene. The evolutionary history of these QTL suggests that they are relatively young, and male limitation in this system is a rapidly evolving trait. Our work highlights the dynamic nature of the genetic structure and composition of facultative sex across space and time and suggests that quantitative genetic variation in reproductive strategy can undergo rapid evolutionary turnover.

evolutionary biology↗

bioRxiv2020

There is no evidence of a universal genetic boundary among microbial species

A fundamental question in studying microbial diversity is whether there is a species boundary and if the boundary can be delineated by a universal genetic discontinuity. To address this question, Jain et al. computed the pairwise average nucleotide identity (ANI) of 91,761 microbial (bacterial and archaeal) genomes (the 90K genome dataset) and found that the ANI values from the 8 billion comparisons follow a strong bimodal distribution1. The authors concluded that a clear genetic discontinuum and species boundary were evident from the unprecedented large-scale ANI analysis. As a result, the researchers advocated that an ANI of 95% can be used to accurately demarcate all currently named microbial species. While the FastANI program described in the paper is useful, we argue that the papers conclusion of a universal genetic boundary is questionable and resulted from the substantial biased sampling in genome sequencing. We also caution against being overly confident in using 95% ANI for microbial species delineation as the high benchmarks reported in the paper were inflated by using highly redundant genomes.

microbiology↗