Preprints
Filtering by Subject: Genetics and Genomics
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
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 [...]
Practical genetic diversity protection: an accessible framework for IUCN subpopulation and Evolutionarily Significant Unit identification
Published: 2025-05-05
Subjects: Biodiversity, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
The International Union for Conservation of Nature (IUCN) sets global conservation standards, including the Red List of Threatened Species and the Green Status of Species. Recent analyses showed that genetic diversity has not been effectively considered by IUCN species assessments, despite being fundamental to species’ fitness and adaptive potential. Incorporation of genetic diversity into IUCN [...]
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. [...]
Plant genomic variation and its implications for proposed EU NGT legislation
Published: 2025-04-09
Subjects: Biotechnology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Genomics, Life Sciences, Molecular Genetics, Plant Breeding and Genetics Life Sciences, Plant Sciences
The European Commission proposal for New Genomic Techniques (NGTs) of July 2023 specifies that NGT1 plants, which are considered equivalent to conventional plants, may differ from the recipient or parental plant by no more than 20 insertions, which cannot be longer than 20 bp; deletions can be of any size and number. Here, we examine the proposed 20/20 NGT1 limit against the background of the [...]
The molecular evolutionary basis of species formation revisited
Published: 2025-04-09
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Life Sciences
How do new species arise? This is among the most fundamental questions in evolutionary biology. The first genetic model for how reproductive barriers leads to the origin of new species was proposed nearly 90 years ago. However, empirical evidence for the genetic mechanisms that cause reproductive barriers took many decades to accumulate. In 2010, Presgraves presented a comprehensive review of the [...]
Variability, drivers, and utility of genetic diversity-area relationships in terrestrial vertebrates
Published: 2025-04-03
Subjects: Biodiversity, Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Life Sciences
Maintaining genetic diversity within and among populations is critical for conservation and a prominent goal of the Kunming-Montreal Global Biodiversity Framework. However, direct estimates of genetic diversity are unavailable for most species, and time and resources are insufficient to fill these substantial data gaps and meet conservation target timelines. Robust, proxy-based predictions of [...]
MYB regulator of ‘colorless’ flavonols underlies the evolution of red flowers in Iochroma (Solanaceae)
Published: 2025-03-13
Subjects: Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences, Plant Sciences
Anthocyanins, the pigments that give rise to blue, purple, red and pink colors in many flowers and fruits, are produced by the deeply conserved flavonoid biosynthesis pathway. The regulation of this pathway is thus fundamental for species differences in color across flowering plants, and a growing body of evidence implicates MYB transcription factors as key players activating or suppressing the [...]
Genetic diversity is key to a nature-positive future
Published: 2025-02-21
Subjects: Biodiversity, Genetics and Genomics, Life Sciences
1. Nature-positive describes the concept of halting and then reversing the loss of biodiversity in a manner that is equitable to all, particularly indigenous peoples and local communities. 2. Genetic diversity is the foundational component of biodiversity, underpinning species and ecosystem diversity. Genetic diversity is vital to resilience and ecosystem services. While genetic diversity was [...]
Repeated mitochondrial capture with limited genomic introgression in a lizard group
Published: 2025-02-19
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Life Sciences
Mitochondrial introgression is common among animals and is often first identified through mitonuclear discordance — discrepancies between evolutionary relationships inferred from mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA). Over recent decades, genomic data have also revealed extensive nuclear introgression in many animal groups, with implications for genetic and phenotypic diversity. [...]
A curated benchmark dataset for molecular identification based on genome skimming
Published: 2024-12-19
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
Genome skimming is a promising sequencing strategy for DNA-based taxonomic identification. However, the lack of standardized datasets for benchmarking genome skimming tools presents a challenge in comparing new methods to existing ones. As part of the development of varKoder, a new tool for DNA-based identification, we curated four datasets designed for comparing molecular identification tools [...]
Altered phenotypic responses of asexual Arctic Daphnia after 10 years of rapid climate change
Published: 2024-11-05
Subjects: Comparative and Evolutionary Physiology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences, Terrestrial and Aquatic Ecology
Understanding the fates of organisms and ecosystems under global change requires consideration of the organisms’ rapid adaptation potential. In the Arctic, the recent temperature increase strongly impacts freshwater ecosystems which are important sentinels for climate change. However, a mechanistic understanding on the adaptive capacity of their key zooplankton grazers, among them polyploid, [...]