Preprints
Filtering by Subject: Genetics and Genomics
A dataset for benchmarking molecular identification tools based on genome skimming
Published: 2024-12-19
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
Genome skimming is an emerging tool allowing for scalable DNA barcoding efforts for numerous biodiversity science applications. Despite its growing importance, there are few standardized datasets for benchmarking genome skimming tools, making it challenging to evaluate new methods (e.g., using machine learning), and comparing to existing ones (e.g., conventional barcoding loci derived from [...]
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, [...]
Mapeando Necessidades: Oportunidades para a Utilização de Ferramentas Genéticas e Genômicas na Conservação da Biodiversidade Brasileira
Published: 2024-09-12
Subjects: Biodiversity, Genetics and Genomics
Biodiversity conservation, especially in megadiverse regions like Brazil, faces challenges that demand the implementation of innovative approaches. In this context, a partnership agreement was signed between the Chico Mendes Institute for Biodiversity Conservation (ICMBio) and the Vale Institute ofTechnology (ITV), named GBB (Genomics of the Brazilian Biodiversity), aiming to develop genetic and [...]
Gene-culture coevolution: A broader evolutionary perspective
Published: 2024-09-05
Subjects: Anthropology, Biological and Physical Anthropology, Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics, Social and Behavioral Sciences
Gene-culture coevolution (GCC) stands out among approaches to human evolution for its ambitious synthesis of biological and social sciences. Combining insights from cultural evolution and human genetics, it has been invoked to explain the evolution of many "species-defining" human traits, from language to large-scale cooperation. However, despite its broad conceptual appeal, empirical evidence [...]
Strong small-scale differentiation but no cryptic species within the two isopod species Asellus aquaticus and Proasellus coxalis in a restored urban river system (Emscher, Germany)
Published: 2024-07-04
Subjects: Biodiversity, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences, Zoology
Worldwide, humans have strongly altered river networks. Key changes resulted in modified hydromorphology, poor habitat quality and availability, migration barriers, and pollution. Restoration measures aim at mitigating anthropogenic stressors and to restore connectivity, but the biological success of the measures is not guaranteed. Analyzing genetic diversity and population structure of target [...]
Range size variably predicts genetic diversity in Gehyra geckos
Published: 2024-06-25
Subjects: Biodiversity, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
Genetic diversity is a fundamental population genetic parameter, and predicts adaptive capacity. Neutral theory predicts a positive correlation between population (or range) size and genetic diversity, but this can be confounded by other demographic processes. To investigate the role of range size, population fluctuation and introgression in determining genetic diversity, we generate and analyse [...]
Why there are so many definitions of fitness in models
Published: 2024-04-11
Subjects: Biology, Computational Biology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Life Sciences, Population Biology
“Fitness” quantifies the ability to survive and reproduce, but is operationalized in many different ways. Generally, short-term fitness (e.g., expected number of surviving offspring) is assigned to genotypes or phenotypes, and used to non-trivially derive longer-term operationalizations of fitness (e.g. fixation probability or sojourn time), providing insight as to which organismal strategies [...]
Datathons: fostering equitability in data reuse in ecology
Published: 2024-04-04
Subjects: Biodiversity, Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Genetics, Genetics and Genomics, Genomics, Life Sciences, Microbiology
Approaches to rapidly collect global biodiversity data are increasingly important, but biodiversity blindspots persist. We organized a three-day Datathon event to improve the openness of local biodiversity data, and facilitate data reuse by local researchers. The first Datathon, organized among microbial ecologists in Uruguay and Argentina assembled the largest microbiome dataset in the region to [...]
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, whether based on morphological, molecular, or other types of data. In the case of methods based on DNA sequences, most of them are rooted in the coalescent theory. However, coalescence-based [...]
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 [...]
Withdrawn: 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
Duplicate of https://doi.org/10.32942/X2389Q
Best practices for genetic and genomic data archiving
Published: 2023-09-25
Subjects: Bioinformatics, Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of [...]