Preprints
Filtering by Subject: Genetics and Genomics
The genetic basis of a regionally isolated sexual dimorphism involves cortex
Published: 2024-01-29
Subjects: Biology, Evolution, Genetics and Genomics, Other Ecology and Evolutionary Biology, Population Biology
Sexual dimorphisms represent a source of phenotypic variation and result from differences in how natural and sexual selection act on males and females within a species. Identifying the genetic basis of dimorphism can be challenging, especially once it is fixed within a species. However, studying polymorphisms, even when fixed within a population, can provide insights into the genetic basis of [...]
Dense Sampling Phylogenomics Reveals Highly Dynamic Evolution of Batesian Mimicry Accuracy in Two Clades of Myrmecomorphic Spiders
Published: 2024-01-14
Subjects: Animal Sciences, Ecology and Evolutionary Biology, Genetics and Genomics
Batesian mimicry is an impressive example of convergent evolution driven by predation. However, the observation that many mimics only superficially resemble their models despite strong selective pressures is an apparent paradox. Here, we tested whether inaccurate mimicry represents an optimized or transitional stage at the macro-evolutionary scale by performing the hereto largest phylogenetic [...]
Towards the next generation of species delimitation methods: an overview of Machine Learning applications
Published: 2023-12-07
Subjects: Biology, Computational Biology, Ecology and Evolutionary Biology, Genetics and Genomics
Species delimitation is the process of distinguishing between populations of the same species and distinct species of a particular group of organisms. Various methods exist for inferring species limits, with most of them being rooted in Coalescent Theory. Their primary goal is to identify independently evolving lineages that should represent separate species. Coalescent models have improved [...]
Polyploid plants take cytonuclear perturbations in stride
Published: 2023-11-13
Subjects: Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences, Plant Biology
Hybridization in plants is often accompanied by nuclear genome doubling (allopolyploidy), which has been hypothesized to perturb interactions between nuclear and cytoplasmic (mitochondrial and plastid) genomes by creating imbalances in the relative copy number of these genomes and producing genetic incompatibilities between maternally derived cytoplasmic genomes and the half of the allopolyploid [...]
Multinational evaluation of genetic diversity indicators for the Kunming-Montreal Global Biodiversity Monitoring framework
Published: 2023-10-16
Subjects: Biodiversity, Genetics and Genomics, Life Sciences
In December 2022, the United Nations Convention on Biological Diversity (CBD) adopted the Kunming-Montreal Global Biodiversity Framework, in which 196 Parties, for the first time, committed to report on the status of genetic diversity for all species. To facilitate this reporting, three genetic diversity indicators were developed, two of which focus on the processes contributing to genetic [...]
Datathons: fostering equitability in data reuse in ecology
Published: 2023-10-06
Subjects: Biodiversity, Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Genetics, Genetics and Genomics, Genomics, Life Sciences, Microbiology
In the midst of a looming global biodiversity crisis, approaches to rapidly collect, curate, catalog, and integrate biodiversity data at global scales are more important than ever before1. Historically, data collection and reuse have been linked to local access to funding for scientific research and infrastructure, generating blind spots in the distribution of biodiversity data. At the same time, [...]
Don’t make genetic data disposable: Best practices for genetic and genomic data archiving
Published: 2023-09-25
Subjects: Bioinformatics, Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
In ecology and evolution, genetic and genomic data are commonly collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, such data are typically used only once by the data-generating authors. The repurposing of genetic and genomic datasets remains uncommon because it is often difficult, if not impossible, due to non-standard archiving practices and [...]
Plant mutations, beyond the clichés
Published: 2023-09-18
Subjects: Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences, Plant Sciences
The need of decoding life for taking care of biodiversity and the sustainable use of nature in the Anthropocene - a Faroese perspective
Published: 2023-07-29
Subjects: Biodiversity, Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
Biodiversity is under pressure, mainly due to human activities and climate change. At the international policy level, it is now recognised that genetic diversity is an important part of biodiversity. The availability of high-quality reference genomes gives the best basis for using genetics and genetic diversity towards the global aims of (i) protection of species, biodiversity, and nature, and [...]
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. [...]
Power and limitations of the mutations-area relationship to assess within-species genetic diversity targets for post-2020 Sustainable Development Goals
Published: 2022-12-09
Subjects: Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
To evaluate the United Nation’s preliminary post-2020 sustainable goals on protecting high levels of genetic diversity per species, Exposito-Alonso et al. (2022) proposed a new framework to predict a species’ loss of genetic diversity given its loss of habitat area. This method, called the mutations-area relationship (MAR), is analogous to the species-area relationship (SAR), often used to assess [...]
Alternative reading frames are an underappreciated source of protein sequence novelty
Published: 2022-12-05
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics, Life Sciences
Alternative reading frames of protein coding genes are a major contributor to the evolution of novel protein products. Recent studies demonstrating this include examples across the three domains of cellular life and in viruses. Alternative frame sequences both increase the number of trials available for the evolutionary invention of new genes and have unusual properties which may facilitate gene [...]
Understanding local plant extinctions before it’s too late: bridging evolutionary genomics with global ecology.
Published: 2022-12-01
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences, Plant Sciences
Understanding evolutionary genomic and population processes within a species range is key to anticipating the extinction of plant species before it is too late. However, most models of biodiversity risk projections under global change do not account for the genetic variation and local adaptation of different populations. Population diversity is critical to understanding extinction because [...]
Beyond genes-for-behaviour: the potential for genomics to resolve questions in avian brood parasitism
Published: 2022-10-27
Subjects: Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
Brood parasite-host interactions are among the most easily observable and amenable natural laboratories of antagonistic coevolution, and as such have intrigued evolutionary biologists for decades. It is therefore surprising they have not been at the forefront of genomic studies on evolutionary adaptation. Here we review state-of-the-art molecular methods in studying avian brood parasitism, a [...]
Maintenance and expansion of genetic and trait variation following domestication in a clonal crop
Published: 2022-09-01
Subjects: Agriculture, Bioinformatics, Biosecurity, Genetics and Genomics, Genomics, Life Sciences, Plant Sciences
Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterise the domestication and contemporary genetic [...]