Preprints
Filtering by Subject: Evolution
Plant sex chromosome evolution in the phylogenomic era
Published: 2026-08-13
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Life Sciences, Plant Sciences
Plants harbor a tremendous diversity of sexual systems, including various forms of chromosomal sex determination that have arisen repeatedly across major clades, especially in angiosperms. The causes and consequences of sex chromosome evolution are far-reaching, with implications for sexual system, mating system, and life history evolution, genome architecture, and speciation, extinction, and [...]
Chromosomal speciation through holocentric lenses
Published: 2026-08-11
Subjects: Ecology and Evolutionary Biology, Evolution, Life Sciences
Chromosomal rearrangements (CRs) can trigger speciation by acting as barriers to gene flow. Two main theoretical frameworks were developed on how they contribute to speciation: causing infertility in heterokaryotypes (hybrid dysfunction) or creating islands of divergence through recombination suppression. However, these theories were developed with monocentric chromosomes in mind. Species with [...]
Beyond the mammalian nucleolus—a comparative perspective on nucleolar dynamics in stress and through the life cycle
Published: 2026-08-11
Subjects: Cell and Developmental Biology, Cell Biology, Ecology and Evolutionary Biology, Evolution, Microbiology, Organismal Biological Physiology
Classically the site of ribosomal RNA transcription, processing and early ribosome assembly, the nucleolus is increasingly understood as a dynamic multiphase condensate reshaped by cell state. Most reviews of this plasticity are mammal-centred. Here we set mammals alongside fungi, plants and animal germlines, following the nucleolus through the life cycle under environmental change and through [...]
The series of genetic codes that preceded our own
Published: 2026-07-31
Subjects: Evolution, Genetics, Paleobiology
We produce a working hypothesis for the steps by which the canonical genetic code might have been constructed. We assume amino acids were added in the order inferred from their enrichment or depletion in ancestrally reconstructed sequences dating back to the Last Universal Common Ancestor (LUCA) relative to that in ancient but post-LUCA controls. To convert this ordering into a time series of [...]
Nervous system centralization as the evolutionary scaffold for body segmentation: A review of the evidence
Published: 2026-07-28
Subjects: Developmental Biology, Ecology and Evolutionary Biology, Evolution, Integrative Biology, Life Sciences, Molecular Genetics
The evolutionary origins of two major bilaterian innovations, the centralized nervous system and the segmented body plan, have both been debated as cases of homology versus convergence, often using strikingly similar arguments. Here we review the comparative developmental genetics of both processes across the three segmented animal phyla (arthropods, annelids, and chordates) focusing on the [...]
Lactate Dehydrogenase as a Candidate Genomic Marker of Climate Change in Mammals?
Published: 2026-07-13
Subjects: Bioinformatics, Comparative and Evolutionary Physiology, Evolution, Genetics, Genomics, Molecular Genetics, Other Ecology and Evolutionary Biology, Population Biology
Climate change imposes metabolic and thermal stress on mammals, yet genomic markers that track lineage specific adaptation remain limited. Lactate dehydrogenase (LDH), a central enzyme in lactate metabolism and anaerobic stress response, has not previously been evaluated for its evolutionary association with climate change induced selection. Here, comparative genomics across 14 mammalian species [...]
RSV G selection analyses support constraint of the CX3C/cystine-noose core and diversification in mucin-like regions
Published: 2026-07-07
Subjects: Evolution
The RSV attachment (G) glycoprotein is a highly variable surface antigen and an important target of humoral immunity, yet it contains a short central conserved region (CCR; RSV-A2 residues 157-198) with a CX3C chemokine-mimic motif and disulfide-bonded cystine noose. A pre-specified hypothesis was tested: FEL-positive diversifying sites are enriched in the CCR and/or the CX3C motif. Using a [...]
Reassessment of coding-sequence constraint across the volvocine multicellularity gradient: correction of versions 1 and 2
Published: 2026-07-03
Subjects: Computational Biology, Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics
Versions 1 and 2 of this preprint interpreted lower dN/dS and shorter amino-acid terminal branches as evidence that coding-sequence constraint strengthens across the volvocine multicellularity gradient. Re-examination of the models and comparisons does not support that interpretation. The original rooted branch-model fits often reached boundary estimates. An unrooted specification, which is a [...]
A self tuning sliding window method for detecting phenotype linked regional poly-methylation architecture in sparse wildlife methylomes
Published: 2026-06-26
Subjects: Bioinformatics, Cellular and Molecular Physiology, Comparative and Evolutionary Physiology, Evolution, Genetics and Genomics, Marine Biology, Other Ecology and Evolutionary Biology
Despite featuring extreme physiological adaptations integration of wildlife species into the modern ‘omics’ frameworks are limited due to the sparsity in the data. To address the sparsity limitation a self-tuning sliding-window framework was developed for the identification of the regional poly-CpG methylation architecture associated with phenotypic traits. Under the framework the iteratively [...]
Beyond mistakes: same-sex partner acceptance and broad mating filters coexist in termite pairing
Published: 2026-06-24
Subjects: Behavior and Ethology, Ecology and Evolutionary Biology, Entomology, Evolution
Same-sex sexual behavior is often interpreted either as a mistake arising from indiscriminate attempts or as an adaptive behavior directed towards same-sex partners. These explanations are typically considered mutually exclusive. Here we challenge this assumption using an adaptive same-sex pairing system in Reticulitermes termites. Long-term male-male pairings originate from tandem running, in [...]
A mathematical foundation of modelling thermal injury and repair dynamics in ectotherms
Published: 2026-06-18
Subjects: Animal Experimentation and Research, Ecology and Evolutionary Biology, Environmental Indicators and Impact Assessment, Environmental Sciences, Evolution, Life Sciences, Physiology, Plant Sciences, Population Biology, Research Methods in Life Sciences, Statistical Models, Statistics and Probability, Survival Analysis
As global temperatures rise and extreme heat events impair ectotherm performance and survival, it is becoming increasingly important to predict how organisms accumulate and repair thermal injury under realistic benign and stressful temperatures. The thermal death time (TDT) model quantifies how heat events translate into thermal injury, but under natural temperature fluctuations the TDT model is [...]
Saved by the Symbiont: Environmental Stress Intensity and Endosymbiont-Mediated Stress Response Determine Evolved Host Complexity
Published: 2026-06-16
Subjects: Evolution, Life Sciences
Understanding how stress responses affect the trajectory of host–symbiont coevolution is central to predicting and managing species outcomes in the face of disturbances to ecosystems. Critically, it remains an open question how exactly we expect stressors to influence the coevolutionary dynamics of symbioses (on either end of the parasitism–mutualism continuum). In this work, we use in silico [...]
An integrated framework for unifying our understanding of nonconsumptive predation risk effects
Published: 2026-06-12
Subjects: Behavior and Ethology, Biology, Ecology and Evolutionary Biology, Evolution, Integrative Biology, Life Sciences, Other Ecology and Evolutionary Biology, Population Biology, Terrestrial and Aquatic Ecology
Predation risk can induce risk-induced trait responses (RITRs) – changes in prey defensive traits including behavior, morphology, life history, and physiology – thought to have profound effects on prey fitness and population dynamics (termed ‘nonconsumptive effects’). Yet, predicting the magnitude of RITRs and their fitness consequences remains difficult because outcomes depend heavily on [...]
Gradual development and chance beget individuality
Published: 2026-06-02
Subjects: Behavior and Ethology, Developmental Biology, Ecology and Evolutionary Biology, Evolution
Behaviors – and thus behavioral individuality – rarely emerge fully formed but are instead built gradually through development, shaped by processes involving learning, skill formation, and experience. Prevailing theory in behavioral ecology, however, has largely focused on static equilibrium outcomes where behaviors are analyzed only as fully formed traits, often neglecting development. Here, we [...]
The coevolution of cooperation and socially-mediated dispersal: a model
Published: 2026-06-01
Subjects: Behavior and Ethology, Evolution, Population Biology
Limited dispersal can promote the evolution of cooperation by increasing relatedness between social partners. However it also intensifies kin competition, potentially cancelling the benefits of helping. Here, we analyse a model in which individuals evolve both (i) the probability of cooperating within social groups as adults, and (ii) the dispersal probability of juveniles conditional on the [...]