Preprints
Filtering by Subject: Genetics and Genomics
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 [...]
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
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 Nanopore [...]
Genetic evidence for the rediscovery in the wild of the critically endangered Sahara killifish Apricaphanius saourensis (Cyprinodontiformes: Aphaniidae)
Published: 2025-07-21
Subjects: Biodiversity, Biology, Genetics and Genomics, Life Sciences, Other Life Sciences, Zoology
Apricaphanius saourensis was described in 2006 from the Saoura River in western Algeria, and is currently listed as possibly extinct in the wild. We recently discovered an aphaniid population in a very isolated secondary wadi of the Guir River about 115 Km northwest of A. saourensis’ type locality, which we hypothesized could belong to A. saourensis based on images taken from living individuals. [...]
Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions
Published: 2025-06-03
Subjects: Evolution, Genetics and Genomics, Life Sciences
Genes that don't have identifiable homologs in other species have been an intriguing and interesting topic of research for many years. These so-called orphan genes were first studied in yeast and since then, they have been found in many other species. This has fostered a whole field of research aiming at tracing back their evolutionary origin and functional significance. Orphan genes represent an [...]
IQ2MC: A New Framework to Infer Phylogenetic Time Trees Using IQ-TREE 3 and MCMCTree with Mixture Models
Published: 2025-05-06
Subjects: Bioinformatics, Computational Biology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Genomics, Life Sciences
IQ-TREE and MCMCTree are two widely used phylogenetic tools to infer phylogenetic trees and estimate divergence times, respectively. As MCMCTree performs fast approximate Markov Chain Monte Carlo sampling to obtain the times along a fixed tree topology, it would be natural to use IQ-TREE to obtain the tree. However, it is currently not possible to integrate these tools seamlessly, as MCMCTree [...]
A practical framework for identifying genetic subpopulations and ESUs: insights for IUCN assessments and broader management
Published: 2025-05-05
Subjects: Biodiversity, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
Species conservation assessments, such as the International Union for Conservation of Nature (IUCN) Red List and Green Status of Species, guide global conservation priorities by evaluating species’ extinction risk and recovery status. Although such frameworks provide scope to include genetic information, this aspect of biodiversity, which is critical for species’ fitness and adaptive [...]
Genetic load in Evolutionarily Significant Units (ESUs): conservation and management implications
Published: 2025-05-05
Subjects: Biodiversity, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
The Conservation Genetics Specialist Group of the International Union for Conservation of Nature (IUCN) proposes introducing Evolutionarily Significant Units (ESUs) as an additional new assessment unit in the IUCN Red List and Green Status. This proposal is made because ESUs possess unique evolutionary trajectories present within species and harbour genetic diversity that requires safeguarding. [...]