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bioRxiv2025

From Orphan Genes to Cryptogenic Gene Candidates: Reassessing Uniqueness

BackgroundOrphan genes lack recognizable homologues outside a given taxonomic unit; thus, they have elusive evolutionary origins. They have long been invoked to explain lineage specific traits in medicine and evolutionary biology. Here, we re-analyzed a 2023 repository of putative orphan genes compiled from over 80,000 bacterial species. Using iterative homology-based analyses, we reassessed each genes taxonomic distribution across a broader genomic landscape. ResultsThese results challenge the long-held assertion that species truly harbor large numbers of orphan genes and instead demonstrate that their prevalence has been overestimated. Many "orphan genes" from 2023 now match homologues in other bacterial taxa (2025), demonstrating that sparse sampling had inflated earlier orphan counts. To better reflect these findings, we propose the term Cryptogenic Gene Candidates (CGCs). This offers a more precise alternative to orphan genes, as it more accurately reflects the provisional and potentially temporary nature of these genes apparent uniqueness. This revised terminology acknowledges that many genes identified as having a unique origin may lose this status as more genomes are sequenced. Although our analyses substantially reduced the number of false-positive CGCs, it cannot determine whether a given CGC truly encodes a functional protein or is an artifact of bioinformatic analysis. To minimize annotation artifacts, we then applied additional computational filters to prioritize candidates most likely to encode bona fide proteins. ConclusionsThis work revises the understanding of orphan gene prevalence, establishes CGCs as a more accurate classification, and provides a prioritized set of candidates to guide future experimental studies.

bioinformatics↗

bioRxiv2025

Diagnosability to inform species delimitation for the genus Emydura (Testudines: Chelidae) from northern Australia

Understanding the evolutionary history of diversifying lineages and the delineation of species remain major challenges for evolutionary biology. Here we use single nucleotide polymorphisms (SNPs) and sequence fragment presence-absence (SilicoDArT) data to combine phylogenetics and population genetics to assess species boundaries with a focus on diagnosability. We challenge current and proposed taxonomies in a genus of Australian freshwater turtles (Chelidae: Emydura) from northern Australia and southern New Guinea. In a six-step process, we combine phylogeny with the concept of diagnosability based on fixed allelic differences to select diagnosable lineages as candidate species. Four taxa are supported as diagnosable lineages, two of which we elevate to species status. The nuclear and mitochondrial phylogenies differed in important respects, which we attribute to recent or contemporary lateral transfer of mitochondria during hybridization events, deeper historical hybridization or possibly incomplete lineage sorting of the mitochondrial genome. Taxonomic decisions in cases of allopatry require subjective judgement. Our six-step strategy and the necessary (but not sufficient) criterion of diagnosability adds an additional level of objectivity before that subjectivity is applied, and so reduces the risk of taxonomic inflation that can accompany lineage approaches to species delimitation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/664252v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1b89bc8org.highwire.dtl.DTLVardef@fb892dorg.highwire.dtl.DTLVardef@1eb09a8org.highwire.dtl.DTLVardef@1c7300c_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2025

A decision matrix to better identify repeatable physiological variation within individuals

The performance of an individual has remained at the heart of evolutionary biology since the time of Darwin. Physiologists are equally drawn to the implications of individual variation for health and sporting endeavours, and specifically, whether or not a physiological trait is repeatable within an individual. Experimental biologists are especially interested in temporally stable physiological traits that are relevant to an individuals lifetime fitness for natural selection to act upon. Experimental noise, however, confounds the measurement of such repeatability, even though validated protocols exist for measuring many meaningful physiological performance traits. Missing is a decision matrix that helps distinguish individual variation from experimental noise. We propose a precision-&-repeatability assessment matrix (PRAM) that integrates established assessments of individual variability and repeatability. This matrix places metrics that are more repeatable and precise in the quadrant closest to the origins of Cartesian coordinates; those farthest away are less acceptable in terms of both repeatability and precision. As a case study, PRAM is applied to whole-organism aerobic and non-aerobic metabolic performance metrics from fish that were measured with the same protocols. The analysis illustrates that aerobic metabolic metrics can be more repeatable and precise than non-aerobic ones. Consequently, PRAM helps physiologists to better understand whether the observed variability is due to non-repeatable metrics or true individual variation.

physiology↗

bioRxiv2025

A model-free method for genealogical inference without phasing and its application for topology weighting

Recent advances in methods to infer and analyse ancestral recombination graphs (ARGs) are providing powerful new insights in evolutionary biology and beyond. Existing inference approaches tend to be designed for use with fully-phased datasets, and some rely on model assumptions about demography and recombination rate. Here I describe a simple model-free approach for genealogical inference along the genome from unphased genotype data called Sequential Tree Inference by Collecting Compatible Sites (sticcs). sticcs applies a heuristic algorithm based on the perfect phylogeny principle to reconstruct a local genealogy at each variant site in the genome, using a collecting procedure to import information from other nearby sites. Using simulations, I show that sticcs is accurate for ARG inference, but only when the sample size is small. However, I also describe how it can be applied for the purpose of topology weighting by stacking tree sequences inferred for multiple subsets of the data, removing the sample size restriction. Topology weights estimated in this way from unphased data tend to be more accurate than those computed with full ARGs inferred from perfectly phased data using several popular tools. The methods presented therefore have promise for analysis of relatedness and introgression in non-model species, including polyploids. The new methods are implemented in two Python packages, sticcs (for ARG inference) and twisst2 (for topology weighting using the stacking procedure), which both interface with the tskit library for analysis of tree sequence objects.

genomics↗

bioRxiv2025

Comparative transcriptomics of lateral hypothalamic cell types reveals conserved growth hormone-tachykinin dynamics in feeding

The lateral hypothalamus (LH) is a highly heterogeneous brain region regulating hunger and motivated behaviors. In zebrafish, the LH shows distinct neural activity across hunger, feeding, and satiety states. However, the functional and evolutionary conservation of relevant neural circuits remain unclear. Using integrative transcriptomics of zebrafish and mouse LH, we identify conserved cellular clusters with shared molecular markers, particularly within GABAergic neurons. We highlight a conserved GABAergic population expressing tachykinin and growth hormone receptors, which is responsive to food cues and modulated by hunger and feeding states. This cluster may mediate acute appetite-enhancing effects of growth hormone. In both species, feeding elevates growth hormone receptor and tachykinin expression and activates these neurons, while human growth hormone increases their activity and food intake in zebrafish. These findings suggest a conserved neural mechanism by which metabolic hormones influence feeding behavior. Our comparative LH atlas highlights the evolutionary biology of appetite regulation and the integration of hormonal and neural signals driving energy homeostasis.

neuroscience↗

bioRxiv2025

SwarmGenomics: A Unified Pipeline for Individual-Based Whole-Genome Analyses

Advances in sequencing technologies have made whole-genome data widely accessible, enabling research in population genetics, evolutionary biology, and conservation. However, analyzing whole-genome sequencing (WGS) data remains challenging, often requiring multiple specialized tools and substantial bioinformatics expertise. We present SwarmGenomics, a modular, user-friendly command-line pipeline for reference-based genome assembly and individual-based genetic analyses. The pipeline integrates seven modules: heterozygosity estimation, runs of homozygosity detection, Pairwise Sequentially Markovian Coalescent (PSMC) analysis, unmapped reads classification, repeat analysis, mitochondrial genome assembly, and nuclear mitochondrial DNA segment (NUMT) identification. Each module can be run independently or as part of a complete workflow. We demonstrate the pipelines utility with a case study on the giant panda (Ailuropoda melanoleuca), revealing insights into genetic diversity, inbreeding history, historical population size changes, transposable element activity, and microbial contamination. SwarmGenomics lowers the entry barrier for genomic analysis of diploid, non-model species, serving both as a research and teaching tool. The pipeline and documentation are available at https://github.com/AureKylmanen/Swarmgenomics.

genomics↗

bioRxiv2025

PlasmidFlow: A Web-based Platform for Interactive Visualization of Plasmid-Driven Traits

Plasmids are central mediators of horizontal gene transfer (HGT), facilitating the spread of antimicrobial resistance, virulence determinants, and adaptive functions across microbial communities. Despite the availability of extensive plasmid sequencing data, visualization of plasmid-mediated traits remains hindered by reliance on static figures or coding-intensive pipelines, limiting accessibility for microbiologists and epidemiologists. We present PlasmidFlow (https://plasmidflow.metabopotential.site), an interactive, web-based platform for the exploration of plasmid-host-trait associations across ecological and clinical contexts. The system integrates structured data parsing, relational storage, and modular visualization to support real-time exploration without requiring programming expertise. Users can upload plasmid-host-trait datasets, apply environment-or trait-specific filters, and generate publication-ready Sankey diagrams, plasmid-sharing network graphs, and binary trait heatmaps with full customization of visual properties. High-resolution export in SVG, PDF, and PNG formats, along with reproducible session storage, ensures compatibility with both research and publication workflows. By combining interactivity, scalability, and reproducibility, PlasmidFlow addresses a critical gap in microbial genomics, providing a user-friendly and extensible resource for investigating plasmid-driven traits in the context of antimicrobial resistance surveillance, microbial ecology, and evolutionary biology.

microbiology↗

bioRxiv2025

High-throughput Experimental Validation of Synonymous Mutation Neutrality in the Human Genome

The assumption that synonymous mutations are fitness-neutral is central to many foundational results in the fields of genetics, genomics, evolutionary biology, and medicine. However, recent results suggest synonymous mutations have pervasive and strong fitness effects. These vigorously debated studies in non-human model systems have even suggested that the proportion of synonymous mutations and their fitness effect sizes are similar to non-synonymous mutations. To systematically test synonymous neutrality across the human genome we utilize recent advances in base editing to probe the fitness effects of 8,558 potential synonymous mutations in 128 highly essential genes. Combined with novel base editing controls and extensive individual sgRNA guide-level validation experiments that quantify false positive rates, we find that synonymous mutations rarely have fitness effects on growth, occurring 165-fold (95% CI, 35-2929 fold) less frequently than non-synonymous fitness-altering mutations. Thus, despite a decade of high-profile controversies, the neutrality assumption for spontaneous synonymous mutations is valid.

genetics↗

bioRxiv2025

Genome-wide screening using TraDIS accelerates identification of key adaptive mutations of longer-term evolution experiment in Escherichia coli.

Long term laboratory-based evolution experiments are a powerful tool that are increasingly being used to study fundamental aspects of evolution and to identify genes that contribute to overall fitness under different conditions. However, even with automation, the time that they take to execute limits the extent to which evolution experiments can be used as part of a high throughput approach to understand the links between genotype and phenotype. Mutations that lead to genetic loss of function are frequently selected for in evolution experiments. Thus in principle these experiments could be done more rapidly by starting not with clonal isolates but with dense transposon libraries that will contain loss of function mutations in all non-essential genes. Here, we test this hypothesis by comparing the results of long term (5 month) evolution experiment, in which E. coli was grown with daily transfers in unbuffered LB starting at pH 4.5, with short term (5 and 10 day) experiments on a high density transposon library in the same strain and under the same conditions. We show that there is very significant overlap in the genes and pathways identified using the two methods. Use of this approach thus has the potential to significantly increase the throughput of laboratory-based evolution and enable rapid testing of a wide range of parameters that may have an impact on evolutionary trajectories. Author summaryUnderstanding how bacterial populations adapt to environmental stress is central to microbiology and evolutionary biology. Laboratory evolution experiments are commonly used to uncover the genetic changes that confer increased fitness, but these experiments are often slow and laborious. In this study, we asked whether the results of long-term adaptive laboratory evolution (ALE) could be predicted using a faster method: short-term selection of a dense transposon mutant library, analysed by transposon-directed insertion site sequencing (TraDIS). We evolved E. coli K-12 MG1655 in unbuffered LB at pH 4.5 for 5 months and compared the mutations that arose to those selected after just 10 days of evolution using a high-density transposon library in the same strain and conditions. We observed significant overlap in the genes identified by both approaches, including independent disruptions in shared regulatory pathways. This suggests that short-term selection on a diverse mutant population can uncover many of the same adaptive changes seen in long-term evolution experiments. We also identified and validated the fitness effects of several mutations uniquely found in the transposon approach. Rather than predicting specific mutations from first principles, this method offers a rapid, empirical means of anticipating which genes are likely to be involved in adaptation under defined conditions, helping to guide further mechanistic studies by offering a powerful shortcut for investigating microbial evolution.

microbiology↗

bioRxiv2025

Effect of cellular nutrient economy on the evolution of genome size in phytoplankton

The origin of genome size variation remains a central question in evolutionary biology. Previous analyses suggest that the energetic costs of small insertions and deletions (indels) influence genome size by altering the cellular energy budget. Here, we present a theoretical framework for genome evolution in phytoplankton--the main producers of the sunlit ocean--whose growth depends on nutrient availability. We derive an expression for the selection coefficient on indels as a function of the minimum amount of nutrient inside the cell. Parameter estimates indicate that 1-bp indels can be counterselected in phytoplankton with minimal nutrient requirements. We then test three predictions of nutrient-driven selection on genome evolution. Altogether, this model provides a quantitative and mathematical basis for the genome streamlining hypothesis.

ecology↗

bioRxiv2025

Genome dynamics across the radiation of a mega-diverse genus

Understanding the drivers of species diversity and rapid radiations is a major goal in evolutionary biology. Begonia is one of the most species-rich angiosperm genera with 2,164 species currently identified. This genus exhibits considerable variation in chromosome number and a wide range of genome sizes, allowing us to associate genome dynamics with divergence and speciation at a range of temporal scales. We investigate all main radiations within the Begoniaceae family using five previously published Begonia genomes and seven new genome assemblies. We show that Begonia species show more complex, repetitive and dynamic genomes overall than their close relative, the monotypic Hillebrandia sandwicensis. We identify families of repetitive elements that have recently expanded in species from two different highly speciose Southeast Asian sections and two large Neotropical radiations. Detailed characterisation of genomes from species belonging to two parallel radiations, one in Southeast Asia (Begonia section Coelocentrum) and the other in the Neotropics (Begonia section Gireoudia), revealed recent expansion in LTR retrotransposons (LTR-RTs) and satellite DNA, in contrast to more species-poor closely related clades. We further investigate variation in repetitive elements within species, finding that accessions from a population of the widespread Begonia heracleifolia with unusually large genomes show a markedly higher satellite repeat and Ty3/Gypsy LTR-RT content associated with the expansion of a few abundant repeat lineages. We find that accessions derived from this population show lower seed viability in crosses with other conspecific populations, and thus identify a direct link between expansions of repetitive DNA and the process of genetic isolation. These results show how genome dynamics may promote speciation in one of the most diverse flowering plant genera.

genomics↗

bioRxiv2025

Quantifying the effect of metal interactions on growth rate in Saccharomyces cerevisiae

Environmental stressors often co-occur, yet their combined effects on organisms remain poorly understood. As multifactorial anthropogenic changes intensify and alter environmental selection pressures, our understanding of stressor interactions is becoming increasingly important. However, established methods for characterizing the effects of stressor interactions can involve considerable experimental and computational labour. Here, we investigate how pairwise combinations of six divalent metal ions (Cd2+, Co2+, Cu2+, Mn2+, Ni2+, and Zn2+) affect the growth of Saccharomyces cerevisiae, using a high-throughput assay to generate concentration-response surfaces for all 15 combinations. We introduce{delta} , an easily calculable metric that quantifies the toxicity of a mixture relative to the toxicities of its individual components, and compare it to an established metric for synergism/antagonism, a, determined by calculating deviation from a null model of additivity, i.e., "concentration addition". Yeast growth rates reveal that metal mixture toxicity varies widely from the additive expectation with the effect of the combination ranging from greatly enhanced toxicity to greatly attenuated toxicity. Combinations with copper were more toxic than expected, and combinations with manganese or nickel were less. These trends correspond to known redox activities and metal-binding properties, pointing to possible mechanistic underpinnings rooted in oxidative stress and metal cofactor displacement. Furthermore, we find that a correlates with overlap in known metal resistance genes and similarity in redox potential, offering predictive insight into effects of metal interactions. While a provides a model-based measure of synergism or antagonism,{delta} serves as an intuitive, concentration-robust descriptor of ecological impact. Together, these metrics highlight the complexity of metal-metal interactions and the importance of accounting for nonadditive effects in ecotoxicological assessments. This framework provides a basis for evaluating mixture toxicity across diverse taxa and stressor types, with implications for both evolutionary biology and environmental risk assessment.

ecology↗

bioRxiv2025

Demographic, behavioral, and ecological data from a long-term field study of wild baboons in Amboseli, Kenya

Long-term data sets on individually recognized animals and their environments are critical to understanding animal behavior, evolution, and ecology. However, they are resource- and time-intensive and seldom made publicly available. The Amboseli Baboon Research Project (ABRP) is one of the longest-running studies of a wild mammal population in the world and has collected extensive data on the baboon population of the Amboseli ecosystem in Kenya since 1971. Here, we describe four ABRP data sets newly available to the evolutionary biology, behavioral ecology, and primatology communities: (1) the sizes and demographic compositions of 21 social groups from 1971-2023; (2) the activity budgets of adult females and immatures from 1984-2023; (3) behavioral data on diet for adult females and immatures from 1984-2023; and (4) weather data, including precipitation from 1976-2023 and temperature from 1976-2022. Data are aggregated annually and monthly to enable cross-data set analyses. These data offer a rare longitudinal perspective on behavioral and ecological change in a wild mammal population.

animal behavior and cognition↗

bioRxiv2025

Simulating human foot mechanics during walking based on an anatomically detailed forward dynamic finite element model

PurposeForward dynamic musculoskeletal simulation is a powerful computational approach for investigating the biomechanics of human locomotion. However, existing models often oversimplify foot anatomy, thereby limiting our understanding of the role of detailed foot morphology in gait mechanics. In this study, we developed an anatomically accurate three-dimensional finite element (FE) model of the human foot to simulate its dynamic behavior during the stance phase of walking using an explicit forward dynamics approach. MethodsThe model incorporated detailed representations of bones, soft tissues, ligaments, and the plantar aponeurosis, and was driven by experimentally measured tibial kinematics and estimated muscle forces. ResultsSimulation results reasonably matched experimental data on ground reaction forces, plantar pressure distributions, and bone movements, confirming the models ability to replicate key aspects of foot-ground interactions during walking. Moreover, the model enabled the estimation of internal forces, stresses, and strains in foot structures that are not directly measurable in vivo, offering new insights into the biomechanics underlying foot pathologies. ConclusionsThis study potentially provides a robust framework for exploring the form-function relationship of the human foot, with applications in evolutionary biology, clinical interventions, and the study of locomotor disorders.

bioengineering↗

bioRxiv2025

Solving the gene classification problem with a novel Gene Space approach

Genomic organization and its comparative analysis throughout all major kingdoms of life are extensively studied across multiple scales, ranging from individual gene-level analyses to system-wide investigations. This work introduces a novel framework for characterizing genetic architecture through a new integral genomic parameter. We propose the concept of a multidimensional Gene Space to enable holistic quantification of genome organization principles. Gene Space -- a multidimensional space based on the frequencies of nucleotide tokens, such as individual nucleotides, codons, or codon pairs. We demonstrate that in this space, genes from each of the studied microorganism species occupy a limited region, and individual genes from different species can be effectively separated. Consequently, a specific Genome Subspace can be defined for each species, which constrains the organisms evolutionary pathways, thereby determining the constraints on gene optimization for these species. Further in-depth analysis is required to test if it is true for other organisms as well. The Gene Space framework offers a novel and powerful approach for genome analysis at the most basic levels, with promising applications in comparative genomics, evolutionary biology, and gene optimization.

bioinformatics↗

bioRxiv2025

A non-invasive method to genotype cephalopod sex by quantitative PCR

Coleoid cephalopods (cuttlefish, octopus, and squid) are emerging model organisms in neuroscience, development, and evolutionary biology, and are of major economic importance in global fisheries. However, they are notoriously difficult and expensive to culture. The ability to determine sex early in development would enable more efficient and sustainable population management in both laboratory and wild settings. Here, we present a non-invasive method to genotype the sex of dwarf cuttlefish (Ascarosepion bandense) as young as three hours post-hatching using a skin swab and quantitative PCR assay, which detects a two-fold dosage difference between ZZ and Z0 sex chromosomes of males and females, respectively. Furthermore, we designed and validated primers for four additional cephalopod research species with assembled genomes (Octopus bimaculoides, Sepia officinalis, Euprymna berryi, Doryteuthis pealeii), and for a wild-caught species of economic value (Illex illecebrosus) using low-coverage whole genome sequencing data. This method enables accurate sex determination from hatchlings to adults across cephalopods, independent of genome quality or availability. HighlightsO_LIThe Z sex chromosome was identified in multiple cuttlefish, squid, and octopus species. C_LIO_LIA sensitive quantitative PCR assay can genotype ZZ/Z0 sex in each species. C_LIO_LILow-coverage short-read sequencing data is sufficient to design effective primers. C_LIO_LIqPCR on non-invasive skin swabs enables genotyping of living animals. C_LI

genetics↗

bioRxiv2025

A Comprehensive Catalog of Telomere Content Variation Across Human Populations

Quantifying telomere content across global human populations is critical to understanding the evolutionary biology of senescence and has implications for the field of biogerontology. Here, we analyzed 26 global human populations from Phase 3 of the 1000 Genomes Project and observed that differences in telomere content vary significantly across different human populations. Most notably, African-ancestry populations in the Americas: ACB (African Caribbean in Barbados) and ASW ((African Ancestry in Southwest USA) showed significantly different telomere content compared to both continental African populations and populations from other ancestries (p < 10-5) However, we did not observe significant differences (p > 0.05) in telomere content between sexes across and within different populations. We also report that out of the five superpopulations (separated by continental ancestry), humans of American ancestry show significant difference in telomere content with all other superpopulations (p < 0.001 for all comparisons), whereas humans of East Asian and South Asian ancestry show no significant differences with other superpopulations (p > 0.05). Our analysis suggests that the extent of telomere content variation is likely influenced by complex interactions between genomic and environmental factors. The pipeline to catalog telomere content variation is publicly available via: https://github.com/paribytes/TeloTales.

genomics↗

bioRxiv2025

RNA editing fine-tunes transcriptional plasticity and enhances the adaptability of Myzus persicae to diverse host plants

Parthenogenetic organisms can adapt to diverse and rapidly changing environments despite limited standing genetic variation, but the molecular mechanisms enabling such adaptability remain unclear. Here, we investigate this question in the green peach aphid (Myzus persicae, GPA), an asexual generalist herbivore capable of colonizing a wide range of host plants without underlying genetic change. By integrating RNA-seq and DNA-seq from genetically identical clones reared on different hosts, we identified 1,368 high-confidence RNA editing sites (RES), many of which exhibited strong host-dependent differences in editing levels. These RES encompassed all 12 possible nucleotide substitutions, with A-to-I, C-to-U, and U-to-C conversions being particularly prevalent. Editing at several sites shifted dynamically within 48 hours of host transfer and often coincided with changes in transcript abundance. Functional knockdown of the editing genes ADAR1 and ADAR2 reduced editing at specific sites, diminished fecundity, and abolished aphid survival on new hosts. Comparative analyses across aphid species reveal that although the biochemical signatures of A-to-I editing are deeply conserved, the genomic locations and functional roles of edited transcripts are species specific, reflecting lineage-specific adaptive strategies. Together, our findings demonstrate that RNA editing provides a rapid, reversible mechanism for environmental acclimation in GPA, enabling adaptive phenotypic plasticity even in the absence of genetic variation. This work establishes RNA editing as a key molecular basis for the remarkable ecological generalism of clonal organisms. Significance statementA major question in evolutionary biology is how clonal organisms with little genetic variation rapidly adapt to diverse, changing environments. Here we show that RNA editing provides a mechanism enabling the parthenogenetic green peach aphid (Myzus persicae) to colonize a wide range of host plants. RNA editing generates transcriptomic diversity, responds quickly to host shifts, and is essential for adaptation, as silencing ADAR genes disrupts A-to-I editing, reduces fitness, and prevents survival on new hosts. Comparative analyses across aphid species reveal that although the biochemical features of A-to-I editing are conserved, its genomic deployment and functional outcomes differ among species, reflecting lineage-specific strategies. These findings demonstrate that RNA editing creates a dynamic regulatory layer that offsets constraints of asexual reproduction.

molecular biology↗