Preprints
Filtering by Subject: Genetics and Genomics
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 [...]
The interplay between epigenetic mechanisms and deleterious mutations: implications for fitness, evolution and conservation
Published: 2026-01-13
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: 2025-11-27
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: 2025-11-14
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 [...]
Alternative Promoters Expand Transcriptional Complexity of Temperature Stress Responses in Cassava
Published: 2025-09-29
Subjects: Agriculture, Bioinformatics, Genetics and Genomics, Genomics, Plant Biology, Plant Sciences
Plant abiotic stress responses involve two major gene expression regulatory mechanisms: alternative promoter usage and differential expression. Although differentially expressed genes (DEGs) have been extensively studied, alternative promoter genes (APGs) remain poorly characterized despite their potential importance. We systematically compared APGs and DEGs in cassava (Manihot esculenta), a [...]
Mitochondrial genome evolution: the influence of partitioning, calibration, and gene heterogeneity on pleurodontan substitution rates
Published: 2025-09-15
Subjects: Ecology and Evolutionary Biology, Genetics and Genomics, Molecular Genetics
Substitution rate estimates are a key source of information in modern evolutionary biology, underpinning divergence time inference and other evolutionary analyses. Mitochondrial DNA nucleotide substitution rates, in particular, are commonly used for these purposes. However, these rates are typically derived from a small set of genes, closely related species, or from a limited number of model [...]
Project Psyche: Generating and utilising reference genomes for all Lepidoptera in Europe
Published: 2025-09-10
Subjects: Biodiversity, Genetics and Genomics, Genomics, Life Sciences
Project Psyche is a trans-national initiative to generate and study chromosome-level reference genomes of all ca. 11,000 described species of Lepidoptera (butterflies and moths) found in Europe. The Project Psyche community encompasses diverse researchers, amateur lepidopterists, practitioners, and industry experts united by a common vision of the importance of genomics for Lepidoptera. [...]
BPGA: an interactive Shiny application for basic population genetic analysis of genotype data
Published: 2025-08-31
Subjects: Bioinformatics, Education, Genetics and Genomics, Higher Education, Life Sciences
Background: Population structure and ancestry inference are routine in human genetics, yet remain inconvenient for non-experts because canonical tools (PLINK, GCTA, ADMIXTURE) require command-line expertise and careful data management. Results: BPGA (Basic Population Genetic Analysis) is an open‑source R/Shiny application that provides an interactive workflow for educational and exploratory [...]
Long-read sequencing for biodiversity analyses - a comprehensive guide
Published: 2025-08-26
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Environmental Monitoring, Genetics and Genomics, Life Sciences
1. DNA-based monitoring of biodiversity has revolutionised our ability to describe communities and rapidly assess anthropogenic impacts on biodiversity. Currently established molecular methods for biomonitoring rely heavily on classic metabarcoding utilising short reads, mostly through Illumina data. However, increasingly more studies use long-read sequencing technologies, such as Oxford [...]