SEARCH · bioRxiv Science

Results for “genetics”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,387 records · Page 77Linked to original sources

bioRxiv2026

Genetic Diversity and Population Structure of the Black-Footed Cat: Insights into Felis's Deadliest Predator

BackgroundBlack-footed cats (Felis nigripes) are one of Africas least studied felines. The population dynamics and demographic history of this solitary species have not been well-described. Reports of ongoing decline of present-day populations resulted in the IUCN Red List categorizing the species as vulnerable to extinction. As populations decline and become isolated from each other, they become susceptible to strong genetic drift and inbreeding, which can lead to the accumulation of deleterious alleles and increased sextinction risk. However, the IUCN cited data deficiencies across the species range as a limitation in this categorization for black-footed cats. In cases where ecological surveys are lacking, range-wide population genomic surveys can improve our understanding of population dynamics. ResultsIn the first genomic study of free-roaming individuals, we sequenced whole genomes of black-footed cats (N=44) from across their distribution. To do so, we incorporated whole genome sequences generated from both modern biological samples and century-old museum specimens. We assembled a highly contiguous reference genome using a combination of PacBio HiFi data and publicly available Hi-C data and investigated the demographic history, population structure, and genetic diversity of wild black-footed cats. We found evidence of historical effective population sizes of [~]11,500 individuals, which is lower than estimates reported in other felid species. Consistent with modest historical population sizes, we found that present-day genome-wide diversity was low ({pi} {approx} 0.0004). However, despite low genetic diversity, we find that black-footed cat genomes do not harbor long runs of homozygosity. Simulation results indicate that low present-day genetic diversity may simply result from modest historical population size. However, other analyses point to evidence of a population contraction in the last 50 generations, which could contribute to future genomic erosion. We also compared genomic variation in populations across the range to evaluate patterns of population structure, finding evidence of higher genetic similarity between individuals in closer geographic proximity. ConclusionOverall, these results provide range-wide information about the demographic history and present-day genetic diversity of an understudied species. Together with analyses of population structure, we speculate that there may be greater connectivity between populations of black-footed cats than previously assumed. Our study underscores the utility of genomic data in providing insights into population dynamics for better conservation management.

evolutionary biology↗

bioRxiv2026

A Low-Cost, High-Throughput Design-Build-Test Pipeline for Engineering Genetic Systems: Stress Testing with Complex Structural Proteins

Genetic systems engineering is constrained by high DNA synthesis costs, assembly inefficiencies, and challenges in expressing complex proteins. To address these limitations, we developed a highly parallel, low-cost pipeline for the design, assembly, and functional screening of genetic systems, which we stress-tested on highly repetitive structural proteins, including spider silk, biocements, reflectins, and talins. The integrated pipeline combines computational genetic systems design, low-cost many-plasmid DNA assembly from oligopools, automated many-to-many mapping using nanopore sequencing data, and a label-free biosensor to measure single-cell protein expression levels. We applied this pipeline to build 240 plasmids, achieving an 88% success rate (up to 2000 bp) using standard clonal isolation and 58% assembly efficiency (up to 5600 bp) without selective DNA purification, while lowering material costs by up to 24-fold. We applied the biosensor to identify genetic factors that create distinct cellular subpopulations with varying protein expression levels. Overall, the integrated pipeline will dramatically lower the cost of high-throughput synthetic biology, while demonstrating how designing genetic systems to improve build efficiency ("design for build") and directly incorporating biosensors into genetic systems ("design for test") will greatly accelerate design-build-test workflows.

synthetic biology↗

bioRxiv2026

Genetic manipulation of a giant virus-associated virophage

Virophages are double-stranded DNA viruses that hyperparasitize giant viruses infecting unicellular eukaryotes. Parasitization by virophages often reduces the replication of giant viruses, thereby modulating microbial communities in the environment. However, the molecular mechanisms underlying the tripartite relationship are largely unknown due to methodological limitations. In the present study, we developed a reverse-genetics system for a Sputnik virophage that parasitizes the amoeba-infecting giant virus, mimivirus. We demonstrated that transfection of genomic DNA could recover infectious virophage particles. Transfection of genomic DNA synthesized by circular polymerase extension reaction (CPER) also resulted in the recovery of infectious viruses. As a proof of concept, we successfully modified two Sputnik genes by transfecting CPER-assembled mutant genomic DNA. Collectively, our reverse-genetics system provides a framework for assessing the functional importance of Sputnik genes and should facilitate future genetic studies of virophages. Significance statementVirophages are viruses that hyperparasitize giant viruses, which infect unicellular eukaryotes and have extremely large particles and genomes. Giant viruses modulate microbial communities not only by killing their hosts but also by altering host cellular functions. Virophages modulate the replication of giant viruses, thereby driving ecosystem dynamics. Previous studies have demonstrated their widespread distribution through isolation and metagenomic analyses. However, the functions of most virophage genes remain unknown. Due to the lack of genetic tools, the molecular mechanisms underlying the interactions between virophages and giant viruses remain largely elusive. Here, we established a virophage reverse-genetics system based on circular polymerase extension reaction. Our results demonstrate that the system can dissect virophage gene functions and will accelerate virophage genetics.

microbiology↗

bioRxiv2026

The shape of evolution: persistent homology of genetic-distancedata as an observable of reticulate processes in pathogen andplant genomes

Evolutionary biology has long theorized processes--recombination, lineage divergence, drug-resistance sweeps, introgression, refugial persistence--whose signatures in genomic data are incompatible with tree structure. We argue that the shape of genetic-distance data, formalized through simplicial complexes and quantified through persistent homology, is a direct observable of these processes. The Vietoris--Rips filtration of a genetic-distance matrix yields the Betti numbers {beta}0 (connected components), {beta}1 (loops), and {beta}2 (cavities); we read {beta}1 not as a literal count of recombination events but as a quantity that is monotone in effective recombination above a sampling-dependent geometric baseline, and we organise the resulting shapes into a four-letter alphabet of topological primitives (K1 clonal, K2 divergence, K3 reticulation, K4 higher-order reticulation). Coalescent and Wright--Fisher simulations establish the two load-bearing claims: {beta}1 rises monotonically with the recombination rate over six orders of magnitude, and persistent-homology features separate reticulate from non-reticulate histories with 98--100% recall (the residual confusion falls entirely within the non-reticulate K1/K2 pair, which {beta}1 does not distinguish). We then apply the pipeline to four empirical systems. (i) On the MalariaGEN Pf7 Plasmodium falciparum dataset (n = 20,864, 33 countries), per-population {beta}1 spans two orders of magnitude and diverges significantly from a label--shuffle null (median 20.5, range 8-32); the ordering runs opposite to recombination rate-freely-recombining African populations sit lowest and clonal/swept Southeast Asian and Papuan populations highest--because at the population scale {beta}1 is dominated by demographic structure rather than recombination rate, a point we reconcile explicitly with the controlled dose-response. (ii) Colombian Cauca SP-resistant samples carry {beta}1 = 12 against a near-clonal SP-sensitive baseline of {beta}1 = 5 (and two orders of magnitude more total persistence), the high-{beta}1, multi-origin band of K3 consistent with resistance carried on several genomic backgrounds. (iii) The Cambodia artemisinin sweep (2008-2018) traces a K3 [->] K1 trajectory, {beta}1 rising to a mid-sweep peak of 45 and collapsing to 13 at fixation--to our knowledge the first direct observation of a selective-sweep transient in topological coordinates, with the caveat that the per-bin values are medians of three subsamples with wide bars. (iv) On Arabidopsis thaliana 1001 Genomes data, Iberian relict populations (Spain, {beta}1/n = 0.64) exceed post-glacial-expansion populations (Sweden 0.54; United Kingdom 0), generalising the framework beyond pathogens. A P. falciparum mitochondrial negative control recovers {beta}1 = 0 across all subsamples, establishing pipeline specificity. Moving above the 1-skeleton, {beta}2 is zero at the clonal/expansion limits and positive across the reticulate systems; a controlled two-vs-three-way admixture simulation confirms that {beta}2 separates regimes that share a {beta}1 profile, while the further suggestion that the ratio = {beta}2/{beta}1 separates microevolutionary from macroevolutionary timescales is presented, given the small number of systems and the absence of a {beta}2 null, as a hypothesis for future testing. Together these results demonstrate that the topology of genetic-distance data is an evolutionary observable, with immediate implications for drug-resistance surveillance in P. falciparum. Author summaryBiologists usually picture the history of life as a tree, in which lineages split and never rejoin. Many of the most consequential evolutionary events break that picture: malaria parasites recombine in the mosquito gut, drug-resistant strains arise repeatedly on different genetic backgrounds, and plant populations that survived the Ice Age in southern refuges carry tangled ancestry that no tree can represent. We ask a different question of genetic data--not "what tree fits?" but "what shape does the data make?" --and answer it with topological data analysis, which measures shape through three counts (the Betti numbers) of clusters, loops, and higher-order cavities. Loops appear when lineages recombine and rejoin. We show, in simulations and in real Plasmodium falciparum and Arabidopsis thaliana genomes, that the loop count rises with recombination above a baseline set by finite sampling, cleanly separates recombining from clonal histories, and tracks a real artemisinin-resistance sweep in Cambodia as it rises and collapses over a decade. A non-recombining mitochondrial control correctly shows no loops. The shape of genetic data is thus a direct, tree-free readout of evolutionary process, with immediate value for drug-resistance surveillance.

evolutionary biology↗

bioRxiv2026

Mapping the genetic architecture of human cortical expansion and its links to neuropsychiatric disorders

Cortical expansion is a defining feature of human evolution and neurodevelopment, involving the tangential growth and gyrification of the cerebral cortex. Although disruptions to the expansion of the cortex are implicated in diverse brain-based disorders, the genetic architecture underlying this process remains undercharacterized. Here, we integrated GWAS data for five neuroanatomical phenotypes measured in up to 73,800 individuals to model a latent genomic factor capturing the shared genetic basis of cortical surface area, folding, curvature, gyrification, and intracranial volume. Using a multivariate framework, we mapped this pleiotropic architecture across biological scales, identifying novel effector genes, neural cell types, and developmental pathways involved in cortical expansion. Functional genomic evidence indicated that a diverse cellular ensemble contributes to the tangential growth and gyrification of the cortex during prenatal neurodevelopment, with progenitor cell lineages prominently involved. Regional analyses further revealed that genetic influences are spatially heterogeneous and organized along canonical anatomical, functional, and developmental gradients. Finally, cortical expansion exhibited substantial genetic overlap with neurodevelopmental, psychiatric, and neurological disorders, with shared genetic influences often concentrated in prefrontal cortical regions. Together, these findings map the genetic architecture of human cortical expansion and implicate it as a common etiological axis linking evolution, neurodevelopment, and health and disease.

genomics↗

bioRxiv2026

Asymmetric migration shapes genetic structure of the invasive avian vampire fly (Philornis downsi) across the Galapagos Islands.

Biological invasions on islands provide a natural framework to study how dispersal and connectivity influence evolutionary and ecological processes. The avian nest parasitic fly, Philornis downsi - first recorded in Darwins finch nests in 1997 - causes high mortality in endemic land birds, yet its inter-island and sex-specific patterns of dispersal and genetic structure remain poorly understood. We use low-coverage whole genome sequencing to investigate genome-wide patterns of genetic diversity, directional migration and effective population size in P. downsi across five major Galapagos Islands and its native range in mainland Ecuador. We find evidence for a genetic bottleneck in the Galapagos, isolation by distance, and evidence that the island closest to the Ecuadorian mainland, San Cristobal, is genetically divergent from the other four islands sampled, despite retaining the highest genetic diversity. No evidence was found for sex-biased dispersal; however, sex-biased genetic structure was detected using only markers from inferred autosomal scaffolds. We found asymmetric gene flow with higher migration rates from San Cristobal westward to the other islands, matching the direction of both southeast trade winds and major cargo shipping routes. Our results suggest both natural and human-mediated colonisation of P. downsi from the mainland through San Cristobal to the other islands, followed by high inter-island dispersal among closely situated sink islands. Our findings are critical for prioritising islands for control strategies that will reduce P. downsi impacts on vulnerable endemic birds and underscore the value of understanding directional migration patterns for managing invasive species in metapopulations.

evolutionary biology↗

bioRxiv2026

Population Genetics of Native Red Mulberry at Its Northwestern Boundary Suggests Postglacial Founder Effects

Morus rubra is native to the eastern United States, with its range extending into the Upper Midwest and southern Ontario, Canada. Its present distribution suggests that past glacial events in North America may have influenced the genetic structure of populations at the species northwestern range boundary. This study assessed genetic variation among six M. rubra populations believed to have experienced postglacial colonization using published nuclear microsatellite markers and sequences from the chloroplast trnL-trnF region. Five nuclear microsatellite markers previously developed for M. alba were successfully transferred to M. rubra, while the chloroplast trnL-trnF region provided an additional marker for evaluating chlorotype diversity. Nuclear microsatellite diversity was higher in southern unglaciated populations than in northern glaciated populations, a pattern consistent with the observed distribution of chlorotype diversity. Together, these results support ancient founder effects associated with leading-edge expansion following glacial recession and suggest that postglacial colonization contributed to the present-day genetic structure of M. rubra at its northwestern range boundary. Because M. rubra hybridizes with the naturalized invasive M. alba, reduced genetic diversity in marginal populations may increase their vulnerability to genetic swamping. The markers characterized in this study provide useful tools for population genetic research in Morus, and the findings have important implications for the conservation and management of marginal and threatened M. rubra populations in the Upper Midwest.

evolutionary biology↗

bioRxiv2026

Metabolome genome-wide association study reveals hierarchical and epistatic genetic control of flavonoid metabolism in soybean

Metabolic phenotypes are often governed by complex genetic architectures involving both additive and non-additive effects. However, the extent to which epistatic interactions contribute to the pathway-level regulation of plant metabolism remains unclear. In this study, we investigated the genetic architecture of flavonoid-related metabolites using metabolomic and genomic data from 200 soybean accessions cultivated under multiple environmental conditions. Broad-sense heritability estimates revealed that many metabolites were under strong genetic control, particularly flavonoid-related metabolites. Principal component analysis-based metabolome-wide genome-wide association studies identified four major loci associated with flavonoid metabolic variation, including a locus corresponding to flavonoid 3'-hydroxylase. Conditional analyses based on multilocus genetic backgrounds demonstrated that the effects of downstream loci were highly dependent on upstream genotypes. In particular, single-nucleotide polymorphism effects were frequently detectable only in specific allelic backgrounds defined by the major flavonoid 3'-hydroxylase locus, consistent with strong epistatic interactions among loci. Bayesian network analyses further supported a hierarchical genetic structure consistent with upstream regulation of downstream loci across the flavonoid biosynthetic pathway. These results demonstrate that highly heritable metabolic phenotypes can be controlled by a few loci exhibiting both additive and context-dependent non-additive effects. Our findings provide evidence that pathway-level metabolic diversity in soybean is generated through hierarchical and epistatic genetic control involving a limited set of key loci.

plant biology↗

bioRxiv2026

Host genetics and social relationships jointly shape fitness-associated microbiome variation in a population of feral horses

Gut microbiome variation is consequential for host fitness, but its contribution to adaptive evolution in host populations remains unclear. Although gut microbiome heritability has been demonstrated in humans, domesticated animals, and wildlife, no study has simultaneously assessed heritability of, and natural selection on, microbiome traits. Moreover, prior studies have not investigated whether non-genetic inheritance mechanisms (e.g., maternal and social transmission) could also contribute to microbiome-mediated adaptation. Using quantitative genetic animal models and shotgun metagenomic data from the long-term, individual-based study of feral Sable Island horses (2394 samples, 794 known-fate individuals), we estimated additive genetic, maternal, and social contributions to fitness-associated dimensions of the microbiome identified using canonical analyses of principal coordinates. Combined, additive genetic, permanent environment, and social effects explained 47% and 38% of the variance in fitness-associated dimensions of microbiota or microbial gene family profiles, respectively, with social effects being 2-4 times stronger than additive genetic effects on average. Contrary to our predictions, we observed no evidence for maternal effects. We provide the first evidence that fitness-associated microbiome traits are heritable, and so, theoretically capable of evolution in response to selection. Strong social effects further indicate the possible concurrent importance of non-genetic inheritance to microbiome-mediated adaptive evolution.

ecology↗

bioRxiv2026

Milankovic cycles and Cultural Evolution as Important Catalysts for Hominin Genetic Diversification

Climate variability is widely considered a key driver of human evolution, yet the mechanisms linking long-term climate change driven by Milankovi[c] cycles to hominin demography and genetic diversity remain elusive. Here we couple an agent-based demographic model, incorporating an idealized genetic marker, cultural dynamics, and a realistic Pleistocene climate framework, to quantify how astronomically forced climate and vegetation variability shaped the genetic structure of African hominins over the past 1.9 Myr. We show that warm early Pleistocene climates sustained a continent-wide network of genetically diverse demes until ~900 ka. The subsequent decline in atmospheric CO2, associated cooling, and reduced vegetation during the Mid-Pleistocene Transition triggered widespread demographic collapse, with populations surviving only in southern and eastern Africa. This reorganization in population structure leads to a decline in simulated genetic diversity, consistent in timing with genomic and archeological evidence. Introducing cultural innovations in the model, represented as enhanced carrying capacity, enables hominin populations to recover from this diversity bottleneck, adapt to increasingly harsh late Pleistocene environments and long glacial periods, rapidly expand across Africa during interglacials, and ultimately disperse into Eurasia. Our results identify Milankovi[c]-scale climate forcing and cultural growth as important catalysts of hominin population structure and genetic diversification.

evolutionary biology↗

bioRxiv2026

A panel of Diversity Outbred mouse embryonic stem cells: enabling the functional characterization of natural genetic variation in vitro

Phenotypic variation in pluripotent stem cells arises largely from genetic variants that impact stability of the pluripotent state, response to differentiation cues, and cell fate diversification. Panels derived from genetic reference populations leverage genetic diversity to map the loci influencing these molecular and cellular traits. Here we describe the first publicly available resource for in vitro systems genetics in Mus musculus: 299 genetically diverse, highly heterozygous embryonic stem cell lines derived from Diversity Outbred mice, with minimal kinship across the panel. We characterize genomic integrity and allelic variation across the panel and describe differences in pluripotency and differentiation networks in embryoid bodies. Mapping the genetic determinants of gene expression differences in response to cadmium exposure in embryoid bodies identified 13 regulatory hotspots, the largest acting on ribosome biogenesis genes. This panel enables mapping of loci and gene-by-environment interactions that influence molecular identity in pluripotent cells and their derived cell types.

systems biology↗

bioRxiv2026

Mapping tsetse fly connectivity in Uganda with machine learning landscape genetics

Introduction - Tsetse flies (genus Glossina) are biting insects that transmit human and animal trypanosomiases across sub-Saharan Africa, and sustainable vector control depends on understanding dispersal barriers and reinvasion routes. Despite major progress toward elimination, Uganda remains at risk for both human forms of the disease (Trypanosoma brucei gambiense and T. b. rhodesiense) and planners still lack reliable maps of tsetse movement and reinvasion risk. Methods and Results - We address this gap with machine-learning landscape genetics and species distribution models, integrating estimates of population genetic distance and geospatial environmental data to predict and map Glossina fuscipes fuscipes connectivity across Uganda and western Kenya. Inputs included microsatellite genotypes from 11 loci genotyped in 2,736 flies sampled from 87 localities and remotely sensed environmental predictors summarized along least-cost paths. Random forest models predicted patterns of genetic differentiation better than distance-only models, supporting the use of a machine-learning framework for connectivity inference across complex heterogeneous landscapes, and identified variables related to temperature and water availability as the strongest predictors of genetic connectivity. Conclusions - Combining landscape genetics predictions of connectivity with a species distribution model revealed regions with high habitat suitability but low connectivity that represent priority zones for area-wide integrated pest management strategies, including established riverine control tools such as tiny targets and other targeted interventions aimed at reducing reinvasion risk. These results provide biologically interpretable maps and quantitative uncertainty metrics that can guide targeted tsetse control, while providing a transferable analytical pipeline for modeling and mapping genetic connectivity across other species and landscapes.

evolutionary biology↗

bioRxiv2026

A Variational Modeling Framework for Population Genetic Dynamics

Population genetic dynamics are shaped by multiple evolutionary processes, including mutation, recombination, selection, and genetic drift. With the rapid growth of genomic data, modeling multilocus evolutionary dynamics and the resulting patterns of genetic variation has become increasingly important. Existing approaches often face challenges in jointly describing multiple evolutionary processes and modeling multilocus systems, motivating the development of more flexible and extensible frameworks. Here, we develop a variational framework for population genetic dynamics based on generalized gradient-flow theory, drawing on nonequilibrium thermodynamics. In our model, mutation, recombination, and selection are represented as modular variational components, with different life-cycle stages connected through a gamete-individual two-state system. Mutation and recombination act on the gamete state, selection acts on the individual state, and finite-population genetic drift is represented by a stochastic extension. Our model represents multilocus genetic variation directly in the full haplotype-frequency space, recovers classical mutation, recombination, and selection dynamics in the corresponding limits and provides a natural stochastic extension for finite populations. Numerical experiments and SLiM forward simulations show that our model captures the dynamics of allele frequencies, haplotype frequencies, and linkage disequilibrium in multilocus systems. The variational formulation opens avenues for future extensions to additional evolutionary processes and more complex multilocus systems, as well as for developing differentiable computational methods for gradient-based parameter inference and scalable genomic modeling.

evolutionary biology↗

bioRxiv2026

Challenges and opportunities for integrating genetic diversity monitoring in megadiverse countries: reflections from Mexico

Megadiverse countries concentrate most of the World's biodiversity. These countries encompass different levels of research infrastructure, and nearly all of them have been historically committed to the Convention of Biological Diversity, often setting precedents and leading new approaches. Here, we ask whether the assessment of genetic diversity indicators provide novel insights for biodiversity management and conservation in one of those countries, Mexico. We evaluated the first national application of the Kunming-Montreal Global Biodiversity Framework (GBF), genetic diversity indicators in Mexico. The data covered 97 taxa across diverse ecosystem types and taxonomic groups, including crop wild relatives, to assess the capacity of genetic diversity indicators to provide novel insights, as well as their relevance for strengthening national conservation strategies. We calculated two indicators: the proportion of populations with an effective population size greater than 500 (Ne 500) and the proportion of populations maintained (PM). Data were sufficient to estimate the Ne 500 indicator for 47 taxa and the PM for 28 taxa, with mean indicator values of 0.217 and 0.936, respectively. Species' geographic range was positively associated with Ne 500, whereas national endemicity had no significant effect. Comparisons with the IUCN Red List and Mexico's national extinction-risk legislation revealed that genetic vulnerability occurs even among taxa not currently recognized as threatened. Our findings highlight a gap in legal recognition of genetic diversity protection that could be strengthened by incorporating population-level assessments focused on maintaining adaptive potential in the long-term. Additionally, the indicators allowed to highlight conservation concerns within crop wild relatives, though fully realizing their potential requires integrating the entire wild-to-domesticated complex. The Mexican experience highlights that the main challenge for scaling the monitoring of genetic diversity is not only generating new data, but integrating existing information into systems that strengthen collaboration and communication among researchers, local communities, and government institutions.

evolutionary biology↗

bioRxiv2026

Integrative genetic and transcriptomic analysis identifies candidate genes and compounds for Fragile X syndrome and autism spectrum disorder

Fragile X syndrome (FXS) is the most commonly known monogenic cause of autism spectrum disorder (ASD), yet how FXS biology relates to polygenic architecture of idiopathic ASD remains poorly defined. We integrated publicly available genetic data relevant to ASD and FXS, including population case-control risk, symptom discordance within monozygotic twin pairs, contrasts between ASD and other psychiatric disorders, and genetic variation associated with circulating plasma fragile X messenger ribonucleoprotein (FMRP) abundance. These data were used to identify associated genes and pathways across tissues and prioritize small molecules predicted to reverse genetically associated transcriptional signatures. Cross-tissue analysis identified XRN2 as the strongest association for population ASD risk and PPP3CA as the strongest association with FMRP abundance, providing distinct candidate links to ASD and FXS biology. We found no evidence that population ASD risk and symptom discordance within monozygotic twin pairs share common-variant architecture after accounting for linkage disequilibrium, suggesting that these phenotypes capture at least partially distinct sources of genetic signal. Connectivity mapping identified candidate compounds across eight genetic signatures, including several with biologically plausible mechanisms. Together, these findings provide a genetics-anchored framework for connecting FXS and ASD biology and for prioritizing candidate therapeutic mechanisms and compounds, while highlighting methodological safeguards needed for reliable integrative genomic drug repurposing.

bioinformatics↗

bioRxiv2026

Elevated genetic load is associated with reduced bite force in insular lizard populations

Demographic history can profoundly shape genomic variation by altering levels of inbreeding, the strength of genetic drift, and the efficacy of purifying selection, thereby influencing both the accumulation and expression of deleterious variation. Yet the extent to which these genomic consequences translate into organismal performance remains poorly understood. Here, we investigated how contrasting demographic histories shape genomic diversity, inbreeding, genetic load, and performance across mainland and insular populations of the Italian wall lizard, Podarcis siculus. Using whole-genome sequence data from 263 wild-caught individuals and field-based performance measurements from 134 lizards, we characterised population structure and demographic history, quantified genomic diversity, runs of homozygosity, and deleterious variation, and tested associations between genomic inbreeding and performance traits. Island populations showed reduced genetic diversity, increased autozygosity, and elevated genetic load relative to mainland populations, consistent with stronger genetic drift and reduced efficacy of purifying selection. Patterns of deleterious variation were consistent with purging of strongly, but not mildly, deleterious variants. Greater genomic autozygosity was associated with reduced bite force in island lizards, a pattern consistent with inbreeding depression, whereas sprint speed, sperm quality, immunocompetence, and spatial cognition showed no significant association with inbreeding. Genome-wide mapping of runs of homozygosity further identified multiple genomic regions associated with reduced bite performance. Together, these results show how demographic history shapes genomic diversity, homozygosity, and deleterious variation in wild vertebrate populations, while revealing that phenotypic consequences can be trait-specific, a pattern that may reflect differences in genetic architecture and the extent of environmental influence on trait variation.

evolutionary biology↗

bioRxiv2026

Impacts of different SETD1A mutations and genetic backgrounds on human induced pluripotent stem cell-derived hippocampal neurons

Abstract Human induced pluripotent stem cells (hiPSCs) provide a translational platform to interrogate the impact of genetic risk factors for various disorders on human biology. It has been a common practice to engineer premature stop codons to model predicted loss-of-function mutations using isogenic hiPSCs, yet effects of mutation position for the same gene and genetic background have been rarely tested systematically and at multiple levels for comparison to those of patient-specific mutations. Ultra-rare, heterozygous, and predicted loss-of-function mutations in the SETD1A gene, which encodes a H3K4 methyltransferase, are highly penetrant genetic risk factors for schizophrenia. Here, we generated a large panel of isogenic heterozygous SETD1A mutant hiPSC lines, including premature stop-codon mutations in one early exon and one late exon in five genetic backgrounds and two patient-specific mutations, to gain insight into molecular, cellular, and functional changes in a disease-relevant and highly pure population of human hippocampal dentate granule cell-like neurons. Our multi-level analyses showed that different SETD1A mutations lead to divergent molecular and cellular phenotypes related to synapses, but convergent neuronal network deficits, while the genetic background influences gene expression with no substantial effects at cellular and network levels. Mechanistic analysis confirmed the early exon patient mutation as loss-of-function, but revealed that the predicted loss-of-function patient mutation in the late exon is likely gain-of-function. Consequently, while all mutations decreased global H3K4me3 levels, deficits were only partially rescued by inhibiting H3K4 demethylase LSD1 for early exon mutations, but not for late exon mutations. Together, these results suggest that highly penetrant mutations can lead to similar cellular and functional phenotypes across different genetic backgrounds, whereas different premature stop-codon mutations could have contrasting impacts due to distinct mechanisms. Our findings have practical implications for applying genome-editing in hiPSCs to model disorders, highlight the value of modeling patient-specific mutations and testing multiple mutations, and suggest the need for tailored mutation-dependent therapeutic strategies.

neuroscience↗

bioRxiv2026

Influenza A virus H5Nx genotypes assigned by genetic similarity are incongruent with global phylogenies

Influenza A virus H5N1 and other H5 subtypes (H5Nx) have broad host ranges and pose a pandemic risk. Since early 2022, H5 clade 2.3.4.4b has predominated globally, causing unprecedented mortality in wild birds, poultry, and mammals, with spillovers to humans. Accurate viral classification is essential for tracking H5Nx variant emergence and spread, but reassortment among genome segments with distinct evolutionary histories complicates genotyping. H5Nx genotype assignment tools, GenoFlu in North America and Genin2 in Europe, assign segments to clusters by genetic similarity to reference sequences and define genotypes as constellations of segment clusters. However, genetic similarity does not necessarily imply recent shared ancestry because mutations may occur multiple times across the tree and branches may exhibit variable evolutionary rates. Furthermore, similarity is defined relative to references that may inadequately represent diversity. We evaluated the congruence of genetic similarity-based H5Nx clusters and genotypes with phylogenies of global sequences across eight segments. Publicly available H5Nx nucleotide sequences from 41,366 samples were assigned genotypes using GenoFlu and Genin2, and maximum likelihood phylogenies were inferred for each segment. Phylogenetic clusters were identified using TreeCluster for a range of patristic distance thresholds and CD-HIT clusters were identified for a range of genetic similarity thresholds. Clustering methods were evaluated based on phylogenetic purity, monophyly, and diversity. Reassortment within predominant GenoFlu and Genin2 genotypes was evaluated based on their phylogenetic cluster spans. Expectedly, GenoFlu was largely unable to assign genomes from outside of North America, South America, and Antarctica from 2022 to 2025, whereas Genin2 assignments struggled outside of Europe, Africa, and Western Asia. Only 14.2% of GenoFlu clusters were monophyletic, while Genin2 clusters were more variable across segments (overall 49.3% monophyletic). Despite CD-HIT yielding genetic distance clusters of similar size to TreeCluster, they were less monophyletic (44%) and encompassed greater phylogenetic diversity. We identified several genotypes, such as GenoFlu B3.13, D1.1, and D1.3, with internal segments that had diversified into contiguous clusters. Similarly, the wide phylogenetic span of GenoFlu genotypes B3.5 and A3, and Genin2 genotypes EA-2020-C, EA-2021-AB, and EA-2022-CH suggest they may erroneously combine multiple reassortants. Genetic similarity-based H5Nx genotyping tools are rapid, stable, and sufficient for broad categorization, but may group viruses with distinct evolutionary histories and fail to assign divergent viruses, risking biased surveillance, modeling, and risk assessment.

bioinformatics↗