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Preprints

Filtering by Subject: Genetics and Genomics

Plant genomic variation and its implications for proposed EU NGT legislation

Alan H. Schulman, Frank Hartung, Marinus J.M. Smulders, et al.

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

Megan E Frayer, Nemo V Robles, María José Rodríguez Barrera, et al.

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

Chloé Schmidt, Sean M. Hoban, Deborah M. Leigh, et al.

Published: 2025-04-04
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)

Lucas C Wheeler, Maximilian Larter, Stacey D. Smith

Published: 2025-03-14
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

David O’Brien, Elana Bader, Jeanette Hall, et al.

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

Wesley Read, Rebecca J Laver, Ching Ching Lau, et al.

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

Renata Asprino, Liming Cai, Yujing Yan, et al.

Published: 2024-12-20
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

Athina Karapli-Petritsopoulou, Jasmin Josephine Heckelmann, Dörthe Becker, et al.

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

Cintia Povill, Silvia Britto Barreto, Izabela Santos Mendes, et al.

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 [...]

Not by selection alone: expanding the scope of gene-culture coevolution

Sven Michael Kasser, Kevin N. Lala, Laura Fortunato, et al.

Published: 2024-09-06
Subjects: Anthropology, Biological and Physical Anthropology, Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics, Social and Behavioral Sciences

Gene-culture coevolution (GCC) - an ambitious synthesis of biological and social sciences - is often used to explain the evolution of key human traits. Despite the framework’s broad conceptual appeal however, empirical evidence is often perceived as limited to a few key examples like lactase persistence. We argue this apparent gap between theoretical appeal and empirical evidence stems [...]

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)

Martina Weiss, Armin W. Lorenz, Christian K. Feld, et al.

Published: 2024-07-05
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

Ching Ching Lau, Keith Allen Christian, Jessica Fenker, et al.

Published: 2024-06-26
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

Daniel Jefferson Smith, Guilhem Doulcier, Pierrick Bourrat, et al.

Published: 2024-04-12
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

Stephanie Jurburg, Maria J. Alvarez Blanco, Antonis Chatzinotas, et al.

Published: 2024-04-05
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

Kalle Tunström, Ramprasad neethiraj, Naomi L.P. Keehnen, et al.

Published: 2024-01-30
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 [...]

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