Preprints
Filtering by Subject: Genetics and Genomics
Representational limits in detecting ecological change
Published: 2026-04-29
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: 2026-04-02
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: 2026-04-01
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: 2026-01-29
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 [...]
The interplay between epigenetic mechanisms and deleterious mutations: implications for fitness, evolution and conservation
Published: 2026-01-14
Subjects: Biology, Ecology and Evolutionary Biology, Genetics, Genetics and Genomics, Genomics, Life Sciences, Molecular Genetics
Understanding the causal effects of genetic mutations is essential for explaining fitness variation, forecasting evolutionary trajectories and assessing extinction risk, yet remains a fundamental challenge, particularly in natural populations. While amino acid substitutions can alter protein structure and function, mutations affecting gene regulation can also have significant fitness [...]
Business as usual will commit biodiversity to genetic erosion: parallels from climate change for proactive conservation
Published: 2025-12-15
Subjects: Biodiversity, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
Biodiversity and climate resilience are tightly linked. Genetic diversity enables species to adapt in a rapidly changing world, yet its loss (genetic erosion) remains the least visible dimension of the biodiversity crisis. Although climate science has long recognised that past emissions can lock in future climate impacts (“committed climate change”), the idea that biodiversity also faces future, [...]
Adaptive introgression in the context of climate adaptation
Published: 2025-11-28
Subjects: Ecology and Evolutionary Biology, Genetics and Genomics
As the biosphere faces accelerating environmental disruption, including climate change, and the prospect of an anthropogenically-driven mass extinction, understanding the mechanisms that enable species to adapt has become increasingly urgent. One mechanism attracting growing attention is adaptive introgression, the transfer of beneficial genetic variation between closely related species. Although [...]
Response to “Radiolarian evolution: Analytical challenges in estimating the diversity and origin of Nature’s stars”
Published: 2025-11-15
Subjects: Biodiversity, Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Genetics and Genomics, Marine Biology
We appreciate Daniel Lahr’s concern (Lahr, 2025) on the interpretation and conclusions of our study “Extant diversity, biogeography, and evolutionary history of Radiolaria” (Sandin et al., 2025). Given that some of these comments were already addressed in our original study following reviewers comments and that such issues are well known in the molecular diversity and evolution fields we [...]
TwisstNTern 2: Ternary analysis of topology weights from tree sequences
Published: 2025-11-07
Subjects: Bioinformatics, Genetics and Genomics, Life Sciences
Recent advances in genealogical inference now allow the reconstruction of genome-wide sequences of trees for large sets of samples, providing detailed records of how evolutionary relationships vary along the genome. Tree sequences encode a vast amount of information, but new approaches are needed to extract relevant patterns and make inferences. TwisstNtern is a program for visualising and [...]
What fraction of the genomic basis of local adaptation are we missing?
Published: 2025-10-05
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Life Sciences
How will species adapt to changing environments? To what extent does adaptation to previous conditions maintain the variation needed to adapt to future conditions? To answer these kinds of questions, we need to identify locally adaptive alleles and quantify their effects. Theory shows that the architecture of adaptation can depend upon the nature of mutation and on how ecology shapes the [...]
CartograPlant: Bridging genomic, phenotypic, and environmental data to advance plant resilience and eco-evolutionary insight
Published: 2025-09-30
Subjects: Agriculture, Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Genetics and Genomics, Integrative Biology, Life Sciences, Plant Biology, Plant Breeding and Genetics Life Sciences, Plant Pathology, Systems Biology
Climate change is threatening plant health and productivity at all spatial scales, and these impacts are further compounded by the rising incidence of invasive pests and pathogens. Effectively addressing these challenges requires a comprehensive understanding of plant demography as well as the mechanisms and drivers of adaptation. Achieving this understanding requires the integration of [...]