Preprints
Filtering by Subject: Genomics
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 [...]
De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods
Published: 2025-04-07
Subjects: Bioinformatics, Genomics
A novel mechanism of de novo gene origination from non-genic sequences was first proposed in the early 2000s. Subsequent studies have since provided evidence of de novo gene emergence across all domains of life, revealing its occurrence to be more frequent than initially anticipated. While studies mainly agree on the general concept of de novo emergence from non-genic DNA, the exact methods and [...]
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 as biodiversity is increasingly threatened globally. 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 [...]
Environmental RNA mitigates fish ghosts related to fish feeds for aquaculture in molecular ecological survey in a bay.
Published: 2024-12-19
Subjects: Aquaculture and Fisheries Life Sciences, Biodiversity, Genomics, Terrestrial and Aquatic Ecology
The use of environmental DNA for molecular ecological surveys has become widely utilized in ecological assessments of various water environments, from rivers to coastal and marine areas. However, it is important to consider the scenarios of potential contamination of environmental nucleic acids in interpreting the results. In this study, we analyzed the fish species present in the feed that may [...]
Unlocking the hidden dimensions of genomic diversity within species
Published: 2024-12-16
Subjects: Evolution, Genomics, Molecular Biology
The missing heritability problem, defined as the failure of genetic variants to explain variance in phenotypes, has been an unsolved issue in genetics for the past two decades. A potential solution to this problem stems from the idea that single nucleotide polymorphisms and copy-number variants, the most commonly studied forms of genomic diversity, do not represent the totality of the information [...]
Reassessing a Holocene extinction: multiple lines of evidence do not support the historical presence and recent extirpation of a protected anole on the island of Anguilla
Published: 2024-09-20
Subjects: Biodiversity, Genomics, Integrative Biology, Other Ecology and Evolutionary Biology, Zoology
Accurate assessment of historical species ranges is important for conservation science and management. Inaccurate historical species ranges can lead to incorrect assumptions about local extinctions, population trends, and potential sites for reintroductions. Yet, historical knowledge is often lacking for many species. Here, we examine the case of the bearded anole, Anolis pogus, which has long [...]
Demographic expansion and panmixia in a St. Martin endemic, Anolis pogus, coincides with the decline of a competitor
Published: 2024-09-19
Subjects: Biodiversity, Ecology and Evolutionary Biology, Evolution, Genomics, Population Biology, Zoology
Understanding patterns of differentiation at microgeographic scales can enhance our understanding of evolutionary dynamics and lead to the development of effective conservation strategies. In particular, high levels of landscape heterogeneity can strongly influence species abundances, genetic structure, and demographic trends. The bearded anole, Anolis pogus, is endemic to the topographically [...]
Not by selection alone: expanding the scope of gene-culture coevolution
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) - 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 [...]
The Genomics for Australian Plants (GAP) framework initiative – developing genomic resources for understanding the evolution and conservation of the Australian flora.
Published: 2024-07-08
Subjects: Biodiversity, Botany, Genomics
The generation and analysis of genome-scale data—genomics—is driving a rapid increase in plant biodiversity knowledge. However, the speed and complexity of technological advance in genomics presents challenges for its widescale use in evolutionary and conservation biology. Here, we introduce and describe a national-scale collaboration conceived to build genomic resources and capability for [...]
Evolution and maintenance of mtDNA gene content across eukaryotes
Published: 2024-04-22
Subjects: Evolution, Genetics, Genomics
Across eukaryotes, most genes required for mitochondrial function have been transferred to, or otherwise acquired by, the nucleus. Encoding genes in the nucleus has many advantages. So why do mitochondria retain any genes at all? Why does the set of mtDNA genes vary so much across different species? And how do species maintain functionality in the mtDNA genes they do retain? In this review we [...]
The nitroplast and its relatives support a universal model of features predicting gene retention in endosymbiont and organelle genomes
Published: 2024-04-22
Subjects: Evolution, Genomics
Endosymbiotic relationships have shaped eukaryotic life. As endosymbionts coevolve with their host, towards full integration as organelles, their genomes tend to shrink, with genes being completely lost or transferred to the host nucleus. Modern endosymbionts and organelles show diverse patterns of gene retention, and why some genes and not others are retained in these genomes is not fully [...]
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 [...]
Incomplete lineage sorting and hybridization underlie of tree discordance in Petunia and related genera (Petunieae, Solanaceae)
Published: 2024-03-29
Subjects: Biodiversity, Bioinformatics, Botany, Genomics
Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies [...]
Cryptic species and hybridisation in corals: challenges and opportunities for conservation and restoration
Published: 2024-02-14
Subjects: Genomics, Marine Biology, Other Ecology and Evolutionary Biology
The conservation and management of coral reef ecosystems will benefit from accurate assessments of reef-building coral species diversity. However, the true diversity of corals may be obfuscated by cryptic yet genetically distinct groups, which are likely more pervasive than currently recognised. Here, we investigate the prevalence of cryptic coral groups and assess evidence for their permeability [...]
A composite universal DNA signature for the Tree of Life
Published: 2024-01-18
Subjects: Bioinformatics, Computational Biology, Genomics, Other Ecology and Evolutionary Biology
Species identification using DNA barcodes has revolutionized biodiversity sciences.However, conventional barcoding methods may lack power and universal applicabilityacross the Tree of Life. Alternative methods based on whole genome sequencing are hardto scale due to large data requirements. Here, we develop a novel DNA-based identificationmethod, varKoding, using exceptionally low-coverage genome [...]