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Results for “Evolutionary Biology”

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bioRxiv2020

A single nucleotide change underlies the genetic assimilation of a plastic trait

Genetic assimilation - the evolutionary process by which an ancestral environmentally sensitive phenotype is made constitutive - is a fundamental concept in biology. Its evolutionary relevance is debated, and our understanding of its prevalence, and underlying genetics and molecular mechanisms, is poor. Matricidal hatching is an extreme form of maternal provisioning induced by adverse conditions, which varies among Caenorhabditis elegans populations. We identified wild isolates, sampled from natural populations across multiple years and locations, that express a derived state of near-constitutive matricidal hatching. A single amino acid change in kcnl-1, encoding a small-conductance calcium-activated potassium channel subunit, explains most of this variation. A gain-of-function mutation altering the S6 transmembrane domain causes inappropriate activation of the K+ channel, leading to reduced vulval muscle excitability, and thus reduced expulsion of embryos, irrespective of environment. Using reciprocal allelic replacements, we show that this amino acid change is sufficient to induce constitutive matricidal hatching whilst re-establishing the ancestral protein abolishes matricidal hatching and restores egg-laying, thereby doubling lifetime reproductive fitness under benign conditions. While highly deleterious in the laboratory, experimental evolution showed that KNCL-1(V530L) is maintained under fluctuating resource availability. Selection on a single point mutation can therefore underlie the genetic assimilation of an ancestrally plastic trait with drastic life-history consequences.

evolutionary biology↗

bioRxiv2014

Inference of evolutionary forces acting on human biological pathways

Because natural selection is likely to act on multiple genes underlying a given phenotypic trait, we study here the potential effect of ongoing and past selection on the genetic diversity of human biological pathways. We first show that genes included in gene sets are generally under stronger selective constraints than other genes and that their evolutionary response is correlated. We then introduce a new procedure to detect selection at the pathway level based on a decomposition of the classical McDonald-Kreitman test extended to multiple genes. This new test, called 2DNS, detects outlier gene sets and takes into account past demographic effects as well as evolutionary constraints specific to gene sets. Selective forces acting on gene sets can be easily identified by a mere visual inspection of the position of the gene sets relative to their 2D null distribution. We thus find several outlier gene sets that show signals of positive, balancing, or purifying selection, but also others showing an ancient relaxation of selective constraints. The principle of the 2DNS test can also be applied to other genomic contrasts. For instance, the comparison of patterns of polymorphisms private to African and non-African populations reveals that most pathways show a higher proportion of non-synonymous mutations in non-Africans than in Africans, potentially due to different demographic histories and selective pressures.

Evolutionary Biology↗

bioRxiv2023

The amino acid sequence determines protein abundance through its conformational stability and reduced synthesis cost.

Understanding what drives protein abundance is essential to biology, medicine, and biotechnology. Driven by evolutionary selection, the amino acid sequence is tailored to meet the required abundance of proteomes, underscoring the intricate relationship between sequence and functional demand. Yet, the specific role of amino acid sequences in determining proteome abundance remains elusive. Here, we demonstrate that the amino acid sequence predicts abundance by shaping a proteins conformational stability. We show that increasing the abundance provides metabolic cost benefits, underscoring the evolutionary advantage of maintaining a highly abundant and stable proteome. Specifically, using a deep learning model (BERT), we predict 56% of protein abundance variation in Saccharomyces cerevisiae solely based on amino acid sequence. The model reveals latent factors linking sequence features to protein stability. To probe these relationships, we introduce MGEM (Mutation Guided by an Embedded Manifold), a methodology for guiding protein abundance through sequence modifications. We find that mutations increasing abundance significantly alter protein polarity and hydrophobicity, underscoring a connection between protein stability and abundance. Through molecular dynamics simulations and in vivo experiments in yeast, we confirm that abundance-enhancing mutations result in longer-lasting and more stable protein expression. Importantly, these sequence changes also reduce metabolic costs of protein synthesis, elucidating the evolutionary advantage of cost-effective, high-abundance, stable proteomes. Our findings support the role of amino acid sequence as a pivotal determinant of protein abundance and stability, revealing an evolutionary optimization for metabolic efficiency.

evolutionary biology↗

bioRxiv2024

TreeFormer: A transformer-based tree rearrangement operation for phylogenetic reconstruction

Phylogenetic inference is a fundamental problem in biology, which studies the origins and evolutionary relationships among species. Popular phylogenetic inference methods, such as IQ-TREE, RAxML, and PHYML, typically utilize heuristic tree search algorithms to seek a phylogenetic tree that maximizes the likelihood of the observed genetic data. However, tree search is time-consuming and often prone to local optima. To address these issues, we introduce TreeFormer, a new Transformer-based tree rearrangement operation for tree search. Experimental results show that TreeFormer achieves higher accuracy than FastTree 2 when reconstructing trees from real alignments with fewer than 1000 sites.

evolutionary biology↗

bioRxiv2024

Automatic Discovery of Optimal Discrete Character Models

Modeling discrete character evolution in a Markovian framework has become common practice in phylogenetic comparative methods. The increasing size and complexity of these models reflects a trend of analyses to include more taxa and more discrete characters. However, as complexity of the models increase, so do the number of potential model structures and number of estimable parameters, making it nearly impossible to consider all modeling options for a given dataset. To overcome this issue, I apply a combination of regularization and simulated annealing to models of discrete character evolution. This allows for the automatic searching and optimization across different model structures without user specification. I test this framework under several simulation scenarios including hidden rates and multiple discrete characters. The results indicate that regularized models significantly outperform traditional approaches, yielding a far lower variance and a nearly tenfold reduction in the overall error of parameter estimates in the most extreme scenarios. I illustrate the power of automatic model selection by revisiting the ancestral state estimation of concealed ovulation and mating systems in Old World monkeys. Using the dredge algorithm, I discover a previously unexamined model structure which has both better statistical performance and a differing ancestral state reconstruction when compared to default model sets. In general, these results highlight the dangers of an over-reliance on default model sets. The combination of automatic model selection and regularization help overcome problems of over-parameterization, and these results demonstrate that when inferences are drawn from a larger model space, they can be both more statistically robust and biologically realistic.

evolutionary biology↗

bioRxiv2026

A pleiotropic hitchhiking model recapitulates alignments between fly wing divergence and variation

The alignment among mutational variance (M), standing genetic variance (G), and macroevolutionary divergence (R) in Drosophila wing shape poses a rate paradox under a simple constraint hypothesis: evolution follows mutational lines of least resistance, yet proceeds orders of magnitude slower than the abundant genetic variation would permit. This is difficult to reconcile with a simple constraint view in which long-term evolution merely tracks the amount of available variation in each direction. Previous explanations invoke deleterious pleiotropy on unmeasured traits or correlational selection on trait combinations, but recent empirical work finds little evidence of fitness costs beyond flight performance. Here, by reanalyzing published data, I show that wing size shows the hallmark of the primary selection target: among all wing traits, size exhibits the lowest ratio of standing genetic to mutational variance, indicating the strongest selective depletion. Based on this empirical observation, I develop a single-axis selection model in which natural selection targets only a single trait while all other traits evolve as correlated byproducts via within-module pleiotropy. This minimal model reproduces both the observed M -G-R alignment and slower-than-neutral divergence rates, explaining micro- and macroevolutionary patterns in fly wings without invoking complex adaptive landscapes. Significance StatementA fundamental question in biology is whether large-scale evolutionary patterns arise from the same processes that drive change within populations. Fly wing shape offers a striking test case: the directions of genetic variation and species divergence are closely aligned, yet wing shape evolves far more slowly than expected -- a rate paradox under a simple constraint hypothesis. I show that this paradox can be explained by a simple mechanism: natural selection on one trait indirectly constrains the evolution of other non-selected traits through within-module pleiotropy. This single-axis selection model reproduces observed evolutionary patterns without requiring complex multivariate selection, and its prediction that wing size is the primary target of selection is supported by reanalysis of published data. The framework applies broadly to any trait that shares mutations with correlated characters.

evolutionary biology↗

bioRxiv2026

The Stochastic Pacemaker: Cumulative Behavioral Noise Drives Morphological Plasticity in Pea Aphids

Phenotypic variation within a single genotype under the same environment (intragenetic variation), the biologically meaningful part of Verror, is frequently treated as a statistical nuisance rather than a biological reality, yet it represents an evolutionary driver of fitness that remains poorly integrated into evolutionary theory. The mechanism that translates such stochasticity into deterministic developmental phenotypic outcomes is not well understood. Here, we test a cumulative stochasticity model using wing polyphenism of the pea aphid (Acyrthosiphon pisum), where asexual mothers produce winged instead of wingless offspring in response to tactile cues. The model predicts that stochastic variation in maternal locomotor behavior alters the rate of tactile cue accumulation and thereby influences the probability of producing winged offspring. We demonstrate that maternal locomotor activity acts as a "stochastic pacemaker", where an individuals movement determines the rate at which it actively constructs its environment and accumulates environmental cues. Our results reveal that genotypes differ significantly in both mobility and the temporal pattern of wing induction, with behavioral variation explaining approximately 20% of the total phenotypic variance across genotypes. Crucially, we show that maternal mobility increases progressively during crowding, accompanied by significant temporal heteroscedasticity. This expanding variance and increase in mean suggest that initial, trivial stochasticity is magnified into systematic behavioral divergence through the integration of environmental signals. By demonstrating that total accumulated locomotor activity predicts offspring phenotype, we provide a mechanistic bridge between transient behavioral noise and stable morphological shifts. More broadly, our work reveals that Verror is a dynamic product of behavioral history, suggesting a fundamental role for individual-level niche construction in generating macro-phenotypic diversity.

evolutionary biology↗

bioRxiv2026

A hierarchical Bayesian framework accommodates intraspecific and interspecific variation in multivariate traits

Phylogenetic comparative methods are a critical tool in biology, providing the framework to test evolutionary hypotheses of phenotypic diversification. Accommodating intraspecific variation in multivariate analyses is critical for accurate evolutionary inference, but current methods that incorporate intraspecific variation either 1) assume that traits evolve independently or 2) that all taxa share the same intraspecific covariance structure. Violations of these assumptions can produce biased estimates of evolutionary parameters. Here, we introduce a hierarchical Bayesian framework for multivariate traits that jointly estimates taxon-specific intraspecific covariance structures alongside the underlying evolutionary process. This framework propagates uncertainty from sample size discrepancies and missing data, enabling the incorporation of highly variable morphological traits into phylogenetic analyses. Analysis of simulated data confirms that the model and implementation are well calibrated under the assumed generative model, including challenging datasets with more traits than individuals and substantial missing observations. Applied to perikymata spacing across the great ape clade, including modern humans and Neandertals, the framework recovers intraspecific covariance structures that differ among taxa and yields evolutionary rate estimates markedly more uniform across the tooth crown than those obtained when taxon means are fixed. Our method, which is applicable to other multivariate traits, provide a flexible, tractable approach to joint estimation of intraspecific variation and evolutionary process in multivariate traits.

evolutionary biology↗

bioRxiv2026

Sequence-structured fitness landscapes predict influenza evolution

Seasonal influenza viruses continually evolve to evade host immunity. Vaccines must be regularly updated to protect against new circulating strains, motivating efforts to forecast viral evolution. Recent experimental and computational methods have made progress on this problem, but learning the fitness landscape driving viral evolution remains challenging because genomic surveillance samples only a small fraction of the possible sequence space. Here, we developed a generative framework that shares information across genetically related variants, inferring effective mutation-level contributions to viral fitness from temporal sequence data. Applied to hemagglutinin and neuraminidase from A/H3N2 and A/H1N1 viruses, the inferred fitness landscapes recovers known determinants of antigenicity and reveals convergent spatial organization across subtypes consistent with common antibody-mediated selection. Forward simulations from these landscapes predicted both the fixation or loss of circulating mutations and the future composition of viral populations, outperforming models based on neutral evolution or multinomial-logistic growth. Collectively, our results show that interpretable representations of pathogen fitness landscapes can reveal biologically important features and improve prospective evolutionary forecasting.

evolutionary biology↗

bioRxiv2022

Phylogeographic analysis reveals an ancient East African origin of the human herpes simplexvirus 2 dispersal out-of-Africa.

Human herpes simplex virus 2 (HSV-2) is a globally ubiquitous, slow evolving DNA virus. HSV-2 genomic diversity can be divided into two main groups: an African lineage and worldwide lineage. Competing hypotheses have been put forth to explain the history of HSV-2. HSV-2 may have originated in Africa and then followed the first wave of human migration out of Africa between 50-100 kya. Alternatively, HSV-2 may have migrated out of Africa via the trans-Atlantic slave trade within the last 150-500 years. The lack of HSV-2 genomes from West and Central Africa, combined with a lack of molecular clock signal in HSV-2 has precluded robust testing of these competing hypotheses. Here, we expand the geographic sampling of HSV-2 genomes in order to resolve the geography and timing of divergence events within HSV-2. We analyze 65 newly sequenced HSV-2 genomes collected from primarily West and Central Africa along with 330 previously published genomes sampled over a 47-year period. Evolutionary simulations confirm that the molecular clock in HSV-2 is too slow to be detected using available data. However, phylogeographic analysis indicates that all biologically plausible evolutionary rates would place the ancestor of the worldwide lineage in East Africa, arguing against the trans-Atlantic slave trade as the source of worldwide diversity. The best supported evolutionary rates between 4.2x10-8 and 5.6x10-8 substitutions/site/year suggest a most recent common ancestor for HSV-2 around 90-120 kya and initial dispersal around 21.9-29.3 kya. These dates suggest HSV-2 left Africa during subsequent waves of human migration out of East Africa.

evolutionary biology↗

bioRxiv2025

Associations between reproduction-focused life strategy, sex and Borderline Personality Disorder symptom expression: Evidence from the NESARC national study.

IntroductionBorderline personality disorder (BPD) features span internalizing and externalizing dimensions of psychopathology, and their expression varies across biological sexes. Despite substantial research efforts, major gaps remain in our understanding of this heterogeneity, particularly regarding its developmental underpinnings. Life history theory, a leading framework in evolutionary developmental biology, can help make sense of this heterogeneity. MethodsIn a large nationally representative prospective survey (n = 34 653), the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC), we used Multi-group MIMIC models to investigate whether and how the degree to which individuals trade off somatic maintenance against short-term reproductive goals relates to severity of BPD at a general and a single symptom level, and whether these associations differ between men and women in the general adult population. ResultsMen and women prioritizing short-term reproductive goals over somatic maintenance were more likely to endorse each of the 9 DSM-IV BPD symptoms through higher BPD severity, and were more likely to express impulsivity (b=0.11; SE, 0.018; p<.001) and suicidal/self-mutilation behavior (b =0.24; SE, 0.026; p< .001) and less likely to endorse stress-related paranoid ideation (b=-0.066; SE, 0.023; p=.004). Finally, females with a reproduction-oriented life history strategy were more likely to endorse affective instability than males (Females: b=0.12; SE, 0.025; p<.001; Males: b=-0.015; SE, 0.044; p=0.73). ConclusionsAn evolutionary-developmental framework, rooted in human life history theory can help make sense of the heterogeneous manifestations of BPD. Our work also opens the door for future research on the interplay of the reproduction/maintenance trade-off with other genetic and environmental factors and developmental processes in explaining the occurrence of BPD symptoms.

evolutionary biology↗

bioRxiv2021

What are housekeeping genes?

The concept of "housekeeping genes" has been used for four decades but remains loosely defined. Housekeeping genes are commonly described as "essential for cellular existence regardless of their specific function in the tissue or organism", and "stably expressed irrespective of tissue type, developmental stage, cell cycle state, or external signal". However, experimental support for the tenet that gene essentiality is linked to stable expression across cell types, conditions, and organisms has been limited. Here we use genome-scale functional genomic screens, bulk and single-cell sequencing technologies to test this link and optimize a quantitative and experimentally validated definition of housekeeping gene. Using the optimized definition, we identify, characterize, and provide as resources, housekeeping gene lists extracted from several human datasets, and 12 other animal species that include primates, chicken, and C. elegans. We find that stably expressed genes are not necessarily essential, and that the individual genes that are essential and stably expressed can considerably differ across organisms; yet the pathways enriched among these genes are conserved. Further, the level of conservation of housekeeping genes across the analyzed organisms captures their taxonomic groups, showing evolutionary relevance for our definition. Therefore, we here present a quantitative and experimentally validated definition of housekeeping genes that can contribute to better understanding of their unique biological and evolutionary characteristics.

evolutionary biology↗

bioRxiv2023

Evolutionary innovations in germline biology of placental mammals revealed by transcriptomics of first wave spermatogenesis in opossum

Mammalian spermatogenesis is a deeply conserved developmental program that is essential for fitness. Paradoxically, spermatogenic development also allows rapid divergence in gene expression and is thought to be a source of evolutionary novelty and gene birth. How mammalian spermatogenic cells protect a conserved developmental program while enabling exceptionally rapid divergence in gene expression and function is unknown. Here, we comprehensively profile the spermatogenic gene expression program in grey short-tailed opossum (Monodelphis domestica, a model marsupial) and compare it to equivalent data from the mouse (Mus musculus, a model placental mammal) to discover contrasting forces underlying the unique evolutionary dynamics of gene expression during mammalian spermatogenesis. For the first time, we describe the timing of the first wave of opossum spermatogenesis, and we combine bulk transcriptomic data from first-wave juvenile testes with single-cell transcriptomic data from adult testes to define conserved and divergent gene expression programs across the placental-marsupial split. We substantiate and extend our findings using genome-wide chromatin and multi-species transcriptome data and identify three classes of genes with different evolutionary trajectories: a deeply conserved central gene regulatory program governing spermatogenic progression; a separate class of spermatogenic genes exhibiting dynamic expression across placental mammals; and a third set of genes with evidence for directional selection in the placental mammal ancestor and constraint on expression levels within the placental mammalian lineage, representing placental innovations in germline gene expression and including biologically critical modules such as the DNA recombination and repair machinery.

genomics↗

bioRxiv2022

Genome size variation and evolution during invasive range expansion in an introduced plant

Plants demonstrate some of the greatest variation in genome size among eukaryotes, and their genome sizes can vary dramatically across individuals and populations within species. This genetic variation can have consequences for traits and fitness, but few studies have been able to attribute genome size differentiation to ecological and evolutionary processes. Biological invasions present particularly useful natural laboratories to infer selective agents that might drive genome size shifts across environments and population histories. Here, we test hypotheses for the evolutionary causes of genome size variation across 14 invading populations of yellow starthistle, Centaurea solstitialis, in California, USA. We use a survey of genome sizes and trait variation to ask: (1) Is variation in genome size associated with developmental trait variation? (2) Are genome sizes smaller toward the leading edge of the expansion, consistent with selection for colonizer traits? Or alternatively, does genome size increase toward the leading edge of the expansion, consistent with predicted consequences of founder effects and drift? (3) Finally, are genome sizes smaller at higher elevations, consistent with selection for shorter development times? We found that 2C DNA content varied 1.21-fold among all samples, and was associated with flowering time variation, such that plants with larger genomes reproduced later, with lower lifetime capitula production. Genome sizes increased toward the leading edge of the invasion, but tended to decrease at higher elevations, consistent with genetic drift during range expansion but potentially strong selection for smaller genomes and faster development time at higher elevations.

evolutionary biology↗

bioRxiv2026

An open-access CT-based 3D anatomical dataset of extant sharks across all major lineages

0Sharks exhibit extraordinary morphological diversity across a wide range of ecological niches, yet large-scale, high-resolution digital datasets of their internal anatomy remain limited. Here we present an open-access 3D shark anatomical repository derived from published X-ray computed tomography (CT) data, featuring manually segmented and systematically annotated models of the chondrocranium, visceral arches, axial skeleton, musculature, and viscera in standard STL format. The dataset comprises 117 individuals, representing 72 species across 25 families and all nine extant shark orders, with 115 full-body reconstructions and two head-only models. This open-access dataset offers a comprehensive resource for comparative anatomy, biomechanical simulations, evolutionary developmental biology and biomimetics research of extant sharks.

evolutionary biology↗

bioRxiv2019

Asymmetrical diversification of the receptor-ligand interaction controlling self-incompatibility in Arabidopsis

How two-components genetic systems accumulate evolutionary novelty and become diversified in the course of evolution is a fundamental problem in evolutionary systems biology. In the Brassicaceae, self-incompatibility (SI) is a spectacular example of a diversified allelic series in which numerous highly diverged receptor-ligand combinations are segregating in natural populations. However, the evolutionary mechanisms by which new SI specificities arise in the first place have remained elusive. Using in planta ancestral protein resurrection, we demonstrate that two allelic variants currently segregating as distinct receptor-ligand combinations diverged through an asymmetrical process whereby one variant has retained the same recognition specificity as the (now extinct) ancestor, while the other has functionally diverged and now represents a novel specificity no longer recognized by the ancestor. Examination of the structural determinants of the shift in binding specificity suggests that allosteric changes may be an important source of evolutionary novelty in this highly diversified receptor-ligand system.

evolutionary biology↗

bioRxiv2026

From genes to collective modes: biological constraints shape metabolic evolution

Population genetics has been successful in explaining how drift, selection, and mutation shape allele frequencies. However, we still lack an understanding of how biological and evolutionary constraints arising from genotype-phenotype maps shape evolutionary dynamics. To explore this question, we developed a new framework for simulating the evolution of an inherently polygenic and epistatic trait - metabolism - combining population genetics with flux balance analysis. We found that the evolution of metabolic networks exhibits surprisingly simple, reproducible dynamics. We identify evolutionary collective modes (EvCMs) - linear combinations of genes with high, constant selective pressure - as organizers of the long-term dynamics and the origin of this simplicity. EvCMs arise through the interaction of physical constraints, evolvability, and the requirements for growth. We developed a theoretical framework to predict EvCMs from large-scale metabolic models and found quantitative agreement between theory and simulation of E. coli central metabolism. Inspired by these results, we re-analyzed mutational data from Lenskis long-term evolution experiment and found compelling evidence for the existence of EvCMs. This work suggests that biological constraints encoded in genotype-phenotype maps play an important role in shaping evolutionary dynamics, offering a new perspective on complex trait evolution -- one that shifts focus from individual genes to collective modes.

evolutionary biology↗

bioRxiv2025

Genomic Resources for the Scuttle Fly Megaselia abdita: A Model Organism for Comparative Developmental Studies in Flies

The order Diptera (true flies) holds promise as a model taxon in evolutionary developmental biology due to the inclusion of the model organism, Drosophila melanogaster, and the ability to cost-effectively rear many species in laboratories. One of them, the scuttle fly Megaselia abdita (Phoridae) has been used in evolutionary developmental biology for 30 years and is an excellent phylogenetic intermediate between fruit flies and mosquitoes but remains underdeveloped in genomic resources. Here, we present a de novo chromosome-level assembly and annotation of M. abdita and transcriptomes of 9 embryonic and 4 postembryonic stages. We also compare 9 stage-matched embryonic transcriptomes between M. abdita and D. melanogaster. Our analysis of these resources reveals extensive chromosomal synteny with D. melanogaster, 28 orphan genes with embryo-specific expression including a novel F-box LRR gene in M. abdita, and conserved and diverged features of gene expression dynamics between M. abdita and D. melanogaster. Collectively, our results provide a new reference for studying the diversification of developmental processes in flies.

developmental biology↗