Preprints
Filtering by Subject: Genetics and Genomics
Genome-wide strengthening of evolutionary constraint across the volvocine multicellularity gradient
Published: 2026-07-03
Subjects: Computational Biology, Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics
The evolutionary cost of maintaining somatic cell populations has been hypothesised to drive proteome-wide strengthening of constraint on coding sequence at the origin of multicellularity. Prior work on the volvocine clade has reported lower d_N/d_S in colonial than in unicellular relatives on 55 chloroplast genes (Hu et al. 2019) and on 105 nuclear single-copy orthogroups across colonial species [...]
Taming the dragon: genetic variation in wild and domesticated Antirrhinum majus
Published: 2026-06-30
Subjects: Botany, Genetics, Genetics and Genomics, Horticulture, Life Sciences, Plant Sciences
Domesticated species and their wild relatives provide powerful case studies for examining the processes that shape rapid diversification. Here, we conduct a population genetic analysis of 31 domesticated varieties and 33 natural populations of the common snapdragon, Antirrhinum majus, a species in which closely related flower colour varieties form hybrid zones and display extensive variation in [...]
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 [...]
Avian Population Genomics: Latest Findings and Future Prospects
Published: 2026-06-25
Subjects: Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
Birds are one of the most recognizable and diverse groups of organisms on Earth. This group has played an important role in many fields, including the development of methods in behavioral ecology and evolutionary theory. The use of population genomics took off following the increased accessibility of high-throughput sequencing across taxa. Several features of bird genomes make them particularly [...]
EarthChirp: a global reference library for insect acoustic recognition and discovery across the audible and ultrasonic spectrum
Published: 2026-06-18
Subjects: Computational Biology, Ecology and Evolutionary Biology, Entomology, Genetics and Genomics
1. Passive acoustic monitoring (PAM) is scaling rapidly, but automated recognition for insects lags far behind birds. The dominant recogniser (BirdNET) classifies only ~35 insect species and building bespoke insect classifiers requires labelled training data that does not exist for most taxa. 2. We present EarthChirp, a training-free recogniser for singing insects (Orthoptera and Cicadidae) [...]
Choices that matter: the impact of substitution models on machine learning-based species delimitation inference
Published: 2026-06-16
Subjects: Bioinformatics, Computational Biology, Genetics and Genomics, Life Sciences, Molecular Genetics
The choice of nucleotide substitution models is a cornerstone of phylogenetic inference, influencing the accuracy of the estimated evolutionary parameters and, by extension, demographic and species delimitation model selection. With the growing adoption of machine learning methods trained on simulated data, it remains unclear how the substitution model used during simulation training influences [...]
Inferring genomic landscapes with the integrative sequentially Markov coalescent (iSMC)
Published: 2026-05-27
Subjects: Bioinformatics, Biology, Computational Biology, Genetics and Genomics, Genomics, Life Sciences
The integrative Sequentially Markovian Coalescent (iSMC) is an extension of the sequentially Markovian Coalescent (SMC) model allowing for parameter heterogeneity along the genome, such as recombination and mutation rates. Heterogeneous parameters follow an autocorrelation process that modulates the genealogical process, extending the hidden state space and adding as few as two extra parameters [...]
Representational limits in detecting ecological change
Published: 2026-04-28
Subjects: Agriculture, Animal Sciences, Biochemistry, Biophysics, and Structural Biology, Biodiversity, Bioinformatics, Biology, Biotechnology, Cell and Developmental Biology, Ecology and Evolutionary Biology, Entomology, Food Science, Forest Sciences, Genetics and Genomics, Immunology and Infectious Disease, Laboratory and Basic Science Research Life Sciences, Life Sciences, Marine Biology, Microbiology, Neuroscience and Neurobiology, Other Life Sciences, Pharmacology, Toxicology and Environmental Health, Physiology, Plant Sciences, Research Methods in Life Sciences, Systems Biology
Detecting ecological change remains a persistent challenge, even in systems with extensive monitoring data and increasingly sophisticated analytical tools. Uncertainty is usually attributed to stochasticity, limited observations, or imperfect models. Here, I argue that an additional and largely overlooked constraint arises from representational limits: systematic ways in which graphs, indicators, [...]
The promise and challenge of environmental epigenomics in a rapidly changing world
Published: 2026-04-22
Subjects: Animal Sciences, Biology, Environmental Studies, Genetics and Genomics, Life Sciences, Research Methods in Life Sciences
There has been a fast-paced research effort on the role of epigenetic mechanisms in facilitating organisms’ capacity to cope with rapid environmental change, highlighted by several recent reviews and special issues on this topic. What is important, along with this momentum, is to pause and reflect on both the promises and challenges of linking detailed molecular mechanisms to broad patterns of [...]
The signal of admixture can decay rapidly when using clustering-based methods
Published: 2026-04-08
Subjects: Genetics and Genomics, Life Sciences, Molecular Genetics
Gene flow shapes evolutionary trajectories by introducing novel alleles, facilitating or retarding adaptation, or eroding divergence among populations. Studies commonly infer gene flow through estimates of genetic admixture from methods that cluster individuals by allele-frequency similarity. However, the ability of these methods to reliably detect historical admixture remains poorly understood, [...]
What is the human germline mutation rate? methodological innovations, challenges, and evolutionary implications
Published: 2026-04-08
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Life Sciences
Germline mutations are the ultimate source of heritable genetic variation, driving evolution, enabling adaptation, and underlying disease. Despite their fundamental importance, key questions remain unanswered: How frequently do germline mutations arise? Do mutation rates vary systematically across individuals, populations, and local genomic context? And what determines whether a mutation arising [...]
Harry Potter shows mirror to dire wolf de-extinction: perils of chasing ghosts of species’ past
Published: 2026-04-08
Subjects: Animal Sciences, Biology, Genetics and Genomics, Life Sciences, Other Life Sciences
Abstract 1. Conservation faces a paradox. As urban expansion and industrial-scale agriculture erode relational values between people and nature, a privileged minority dictates global biodiversity narratives. This shift is reinforced by media and technological interventions that frequently override lived, local experiences. For instance, gene editing tools like CRISPR are incorporated for [...]
Incorporating population genomic perspectives into kelp conservation and aquaculture in the Pacific Northwest
Published: 2026-04-01
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics, Life Sciences, Marine Biology
Recent kelp forest declines and growth in the kelp aquaculture industry have fueled increasing interest in ecological and evolutionary research on kelp forests, including kelp population genomics. While many kelp management activities have inherent genetic and evolutionary implications, kelp management in the Pacific Northwest (PNW) of North America has to date made only limited use of [...]
Range-wide pangenomics reveals vulnerability and adaptation in a sedentary bird
Published: 2026-03-31
Subjects: Biodiversity, Ecology and Evolutionary Biology, Genetics and Genomics
Structural genetic variants are known to underlie evolutionary adaptations, but have never been evaluated across the entire geographic range of a species. We constructed the first range-wide pangenome to evaluate how such variants may influence conservation efforts of the Montezuma quail (Cyrtonyx montezumae). Profiles of local adaptation, population structure, and genomic diversity all support a [...]
The overlooked small terrestrial mammal taxa (Rodentia, Eulipotyphla, and Lagomorpha) in the evolution of coronaviruses
Published: 2026-01-28
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Life Sciences, Molecular Genetics, Other Ecology and Evolutionary Biology
Coronaviruses have been extensively detected in bats over the past few decades. However, increasing evidence suggests that other taxa, such as Rodentia, Eulipotyphla, and Lagomorpha, may have played a significant role in the ecology and evolution of some coronaviruses. Here, we compile recent contributions illuminating these mammals' enigmatic role in coronavirus evolution. We highlight how [...]