Biology subjects

Lucas, G.

Publications and source records attributed to Lucas, G..

4 recordsLinked to original sources

bioRxiv2026

Expanded unbiased population-genomic summary statistics in pixy

Estimates of population-genetic summary statistics are often computed from variant-only VCFs, which commonly omit invariant sites (i.e. sites with only homozygous reference genotypes across all samples). However, these sites are critical for correctly estimating per site statistics such as nucleotide diversity ({pi}) and between population divergence (dxy). Our software pixy addressed this issue by providing support for computing statistics directly from "all-sites" VCFs that encode invariant positions explicitly (Korunes and Samuk 2021). pixy has since been widely adopted and used in a large variety of population genetic studies. Here we present a major update to pixy, which expands the original tool in four major areas. First, we provide implementations of new estimators of Wattersons {theta} and Tajimas D that are unbiased with respect to missing data. Secondly, we provide support for arbitrary ploidy and multiallelic sites. Third, we introduce a variety of optimizations, including multicore execution and a roughly order-of-magnitude reduction in per-worker memory footprint. Finally, we have broadly modernized our code base, test suite, and community contribution pathway. We validate these new features on simulated polyploid and multiallelic datasets, as well as two empirical datasets (one diploid and one autotetraploid), and benchmark the new multicore scaling. We position pixy relative to contemporary tools and discuss shared limitations of VCF-based estimators. By integrating support for diverse ploidies, allelic complexity, and genome-wide scale in one workflow, pixy provides the population genetics community with a straightforward tool for estimates of key summary statistics that are unbiased with respect to missing data. pixy remains completely open-source (MIT-licensed) and easily installable with the conda package management system.

bioinformatics↗

bioRxiv2025

Ketamine strengthens synaptic inputs to the dorsal raphe to boost serotonergic activity: pivotal for rapid antidepressant-like effects

Ketamine at subanaesthetic dose is known as a fast-acting antidepressant (AD), able to facilitate synaptic plasticity in the medial prefrontal cortex (mPFC) or the hippocampus. However, its influence on the serotonergic (5-HT) system is more confusing as it loses its behavioral effects in 5-HT-depleted animals, but does not modify 5-HT neuron function. We hypothesized that this discrepancy was due to the different temporal scales chosen in the related studies. We performed electrophysiological recordings of 5-HT neurons in the dorsal raphe nucleus (DRN) and microdialysis measurements of 5-HT release in the ventral hippocampus of male Sprague-Dawley rats. Experiments were designed to collect the results over a long duration, i.e. 4-5 hours after the injection. Levels of the pro-neuroplastic factors PSD-95 and Synapsin-1 in the DRN were also assessed, as was cell proliferation in the dentate gyrus (DG). 5-HT neuron mean firing rate was unmodified within the 2 h that followed ketamine (10 mg/kg, i.p.), but strongly (90%) increased in the 2-5 h time bin, an effect abolished by lesioning the mPFC or administering the mTOR inhibitor Torin-2. A similar kinetics was found for hippocampal 5-HT release. Synapsin-1 and PSD-95 mRNA transcriptions were enhanced at 2 h, and PSD-95 protein levels appeared to peak at 24 h. Finally, DG mitogenesis was enhanced 48 h post-injection, an augmentation suppressed in 5-HT-depleted animals. Low-dose ketamine provokes a "neuroplastic wave" originating in the mPFC and emerging in the hippocampus, a transfer in which the 5-HT system appears to act as an integrative hub of plasticity. SIGNIFICANCE STATEMENTThis study helps reconcile two theories, often opposed to explain antidepressant (AD) action: the "serotonergic hypothesis" proposing that AD efficacy primarily results from an increase of serotonin, and the "neuroplastic theory" whereby only significant changes in brain connectivity can explain mood improvement. Here we show that ketamine, a drug exerting AD effects much faster than classical molecules do, augments synaptic strength onto serotonergic neurons, which subsequently triggers an elevation of serotonin. In turn, this enhanced serotonergic neurotransmission leads to the production of new neurons in the hippocampus, therefore reshaping the circuitry of this brain area. The serotonergic system appears to transfer the neuroplastic changes induced by ketamine across the brain, thus behaving like an integrative hub for its AD action.

neuroscience↗

bioRxiv2025

Strong but diffuse genetic divergence underlies differentiation in an incipient species of marine stickleback

Understanding how lineages proceed along the "speciation continuum" and how species boundaries are maintained over time remain central questions in evolutionary biology. Populations early in the speciation process can give us detailed insight into the reproductive barriers that first initiate speciation. In this study, we explore the nature of genomic divergence between two sympatric marine stickleback ecotypes from Atlantic Canada, "whites" and "commons". Males of each ecotype exhibit distinct nuptial colorations, nesting habits, and parental care strategies. Using population genomic analyses of SNPs and copy number variants (CNVs; deletions and duplications) we show that whites and commons consistently form distinct populations. We uncover genomic differentiation in the white ecotype characteristic of an incipient species, showing extremely low genome-wide differentiation (FST) and very recent divergence ([~]1 kya). Demographic analysis detected very low levels of ongoing gene flow between populations. Our results and prior genomic studies suggest that reproductive isolation is being maintained between ecotypes despite recent evidence that hybridization in nature does occur. Contrary to other systems, we found many small, but dispersed regions of high differentiation throughout the genome rather than explicitly within chromosomal inversions or the sex chromosomes. On chromosomes VII and XVI, we identified CNVs overlapping genes enriched for olfaction, which may play a role in differences in reproductive strategies between ecotypes. Ultimately, our results demonstrate that genome-wide rather than localized differences can underlie the early stages of divergence, and that this pattern is corroborated by both SNPs and CNVs.

evolutionary biology↗

bioRxiv2025

Evidence of parental care as a novel reproductive isolating mechanism

Variation in behavior can contribute to reproductive isolation by preventing gene flow among populations. Here, we tested the novel hypothesis that parental care, when dysregulated, can function as a reproductive isolating mechanism in three-spined stickleback fish (Gasterosteus aculeatus). In the typical "common" stickleback ecotype, males provide care to their offspring by fanning with their pectoral fins and defending their nest. In contrast, a divergent "white" stickleback ecotype has evolutionarily lost care and disperses embryos into the surrounding environment. We examined how paternal care from common, white, and F1 hybrid fathers influenced offspring survival. We detected no intrinsic incompatibilities in embryos, but F1 hybrid fathers exhibited dysregulated parental care that coincided with decreased survival of parented offspring. The increased offspring mortality may be explained by further dysregulation of feeding and parenting circuitry, as F2 hybrids exhibited significantly higher rates of post-fertilization filial cannibalism than common or white fathers. Additionally, despite strong divergence in nesting-building and courtship behavior, F1 hybrids achieved mating success at a similar rate as male commons and whites, suggesting that prezygotic barriers against hybrids may be weak. The observed postzygotic isolation, and potentially weak prezygotic isolation in lab-based studies, suggest that hybridization is likely occurring at low rates in the wild. Population genetic analysis supported this, as low proportions of putative hybrids were detected in sympatric sites. Together, these results may help explain why genetic divergence between these phenotypically distinct ecotypes is low and provide evidence that dysregulated parental behavior can act as a newly discovered postzygotic reproductive isolating barrier.

evolutionary biology↗