Preprints
Filtering by Subject: Molecular Genetics
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 [...]
Epigenetic changes associated with reproductive investment and life-history trade-offs in lekking male black grouse (Lyrurus tetrix)
Published: 2025-10-05
Subjects: Genomics, Molecular Genetics, Other Ecology and Evolutionary Biology
Life-history trade-offs are a central concept in evolutionary biology, yet their underlying molecular mechanisms are not yet fully understood. Whilst much research has focused on genetic variation, epigenetic mechanisms, which regulate gene regulation, may be equally important. To investigate this, we collected blood samples from 50 male black grouse (Lyrurus tetrix) before and after the [...]
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 [...]
Genomic data confirms that mutation cannot restore genetic diversity lost through population bottlenecks
Published: 2025-06-13
Subjects: Ecology and Evolutionary Biology, Genomics, Life Sciences, Molecular Genetics, Population Biology
Maintaining within-species genetic diversity is a critical goal of biodiversity conservation as it determines a species’ ability to adapt to environmental change. Without human intervention, isolated populations can only recover genetic diversity post-bottleneck through the accumulation of new mutations over evolutionary timescales. Using recent estimates of mutation rates from major genomic [...]
Cellular Innovations and Diversity in the Lepidopteran Compound Eye
Published: 2025-05-28
Subjects: Behavior and Ethology, Ecology and Evolutionary Biology, Entomology, Evolution, Life Sciences, Molecular Genetics
Lepidoptera, having co-diversified with flowering plants and adapted to various diel niches, present a remarkable system for studying compound eye cell type diversity. Here we synthesize the latest research regarding lepidopteran eye evolution across different timescales, from species-level variation to family-level changes, and mechanistic levels, from broad anatomical variation to molecular [...]
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 [...]
Conservation macrogenetics reveals the potential hidden consequences of the 2019-2020 Black Summer fires on Australian biodiversity
Published: 2025-03-17
Subjects: Biodiversity, Genetics, Genomics, Life Sciences, Molecular Genetics, Other Ecology and Evolutionary Biology, Population Biology
The use of genetic analyses has become ubiquitous in conservation planning and management. Typically, such analyses are employed at the species-level, though as genetic data accrue, it is now possible to consider the genetic composition of multiple species across landscapes. Such macrogenetic perspectives can reveal the potential genetic ramifications of extreme disturbance events, such as [...]
Transferable approaches to CRISPR-Cas9 induced genome editing in non-model insects: a brief guide
Published: 2025-02-27
Subjects: Animal Experimentation and Research, Animal Sciences, Entomology, Genetics, Life Sciences, Molecular Genetics, Other Genetics and Genomics, Zoology
Despite the large variety of insect species with divergent morphological, developmental and physiological features questions on gene function could for a long time only be addressed in few model species. The adoption of the bacterial CRISPR-Cas system for genome editing in eukaryotic cells widened the scope of the field of functional genetics: for the first time the creation of heritable genetic [...]
On the feasibility of nonadaptive, nonsequential abiogenesis. An alternative to the Oparin-Haldane model
Published: 2025-02-18
Subjects: Biochemistry, Biochemistry, Biophysics, and Structural Biology, Cellular and Molecular Physiology, Comparative and Evolutionary Physiology, Computational Biology, Evolution, Molecular Biology, Molecular Genetics, Other Ecology and Evolutionary Biology, Population Biology, Systems and Integrative Physiology Life Sciences, Systems Biology
The emergence of life from non-living matter remains one of the most profound unresolved questions in natural philosophy. The Oparin-Haldane model assumes a gradualist evolution, where adaptive precursors are obligated. Yet, for more than a century, all experimental efforts have failed to achieve abiogenesis. May it be that this view is paradoxical in explaining how living matter arises without [...]
When the microbiome shapes the host: immune evolution implications for infectious disease
Published: 2023-10-24
Subjects: Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Evolution, Immunity, Immunology and Infectious Disease, Immunology of Infectious Disease, Life Sciences, Molecular Genetics, Pathogenic Microbiology
The microbiome includes both “mutualist” and “pathogen” microbes, regulated by the same innate immune architecture. A major question has therefore been: how do hosts prevent pathogenic infections while maintaining beneficial microbes? One idea suggests hosts can selectively activate innate immunity upon pathogenic infection, but not mutualist colonisation. Another idea posits that hosts can [...]
STRyper: a macOS application for microsatellite genotyping and chromatogram management
Published: 2023-07-29
Subjects: Biodiversity, Bioinformatics, Molecular Genetics, Other Ecology and Evolutionary Biology
Microsatellite markers analyzed by capillary sequencing remain useful tools for rapid genotyping and low-cost studies. This contrasts with the lack of a free application to analyze chromatograms for microsatellite genotyping that is not restricted to human genotyping. To fill this gap, I have developed STRyper, a macOS application whose source code is published under the General Public License. [...]
How do monomorphic bacteria evolve? The Mycobacterium tuberculosis complex and the awkward population genetics of extreme clonality
Published: 2022-12-15
Subjects: Evolution, Genetics and Genomics, Genomics, Life Sciences, Molecular Genetics, Pathogenic Microbiology, Population Biology
Exchange of genetic material through sexual reproduction or horizontal gene transfer is ubiquitous in nature. Among the few outliers that rarely recombine and mainly evolve by de novo mutation are a group of deadly bacterial pathogens, including the causative agents of leprosy, plague, typhoid, and tuberculosis. The interplay of evolutionary processes is poorly understood in these organisms. [...]
Incompatibility and interchangeability in molecular evolution
Published: 2022-11-02
Subjects: Evolution, Life Sciences, Molecular Genetics
There is remarkable variation in the rate at which genetic incompatibilities in molecular interactions accumulate. In some cases, minor changes – even single nucleotide substitutions – create major epistatic incompatibilities when hybridization forces new variants to function in a novel genetic background from an isolated population. In other cases, genes or even entire functional pathways can be [...]
Genomic architecture of resistance and tolerance to Swiss needle cast and Rhabdocline needle cast diseases in Douglas-fir
Published: 2022-08-10
Subjects: Genetics and Genomics, Life Sciences, Molecular Genetics
Understanding the genetic architecture of tolerance and resistance to pathogens is important to monitor and maintain resilient tree populations. Here we investigate the genetic basis of tolerance and resistance and to needle cast disease in Douglas-fir (Pseudotsuga menziesii) caused by two fungal pathogens: Swiss needle cast (SNC) caused by Nothophaeocryptopus gaeumannii, and Rhabdocline needle [...]