Preprints

Filtering by Subject: Genomics

Environmental RNA mitigates fish ghosts related to fish feeds for aquaculture in molecular ecological survey in a bay.

Kaede Miyata, Yasuaki Inoue, Natsumi Kitazaki, et al.

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

Marina Brasó-Vives, Diego Andrés Hartasánchez, Julien F. Ayroles, et al.

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

Michael L Yuan, Rayna C Bell, Edward A Myers

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

Michael L Yuan, Joost Merjenburgh, Timothy P. van Wagensveld, et al.

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 [...]

Gene-culture coevolution: A broader evolutionary perspective

Sven Michael Kasser, Laura Fortunato, Kevin N. Lala

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 [...]

The Genomics for Australian Plants (GAP) framework initiative – developing genomic resources for understanding the evolution and conservation of the Australian flora.

Lalita Simpson, David Cantrill, Margaret Byrne, et al.

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

Shibani Veeraragavan, Maria Johansen, Iain Johnston

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

Iain Johnston

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

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

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)

Pedro Henrique Pezzi, Lucas C Wheeler, Loreta Brandão Freitas, et al.

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

Cynthia Riginos, Iva Popovic, Zoe Meziere, et al.

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 universal DNA signature for the Tree of Life

Bruno A S de Medeiros, Liming Cai, Peter J Flynn, et al.

Published: 2024-01-18
Subjects: Bioinformatics, Computational Biology, Genomics, Other Ecology and Evolutionary Biology

Species identification using DNA barcodes has revolutionized biodiversity sciences and society at large. However, conventional barcoding methods may lack power and universal applicability across the Tree of Life. Alternative methods based on whole genome sequencing are hard to scale due to large data requirements. Here, we develop a novel DNA-based identification method, varKoding, using [...]

otb: Creating a HiC/HiFi Pipeline to Assemble the Prosapia bicincta Genome

David Molik, Amanda R Stahlke, Sharu P Sharma, et al.

Published: 2023-12-05
Subjects: Agriculture, Bioinformatics, Computational Biology, Genomics, Other Animal Sciences

The implementation of a new genomic assembly pipeline named only the best [Genome Assembly Tools] (otb) has effectively addressed various challenges associated with data management during the development and storage of genome assemblies. otb, which incorporates a comprehensive pipeline involving a setup layer, quality checks, templating, and the integration of Nextflow and Singularity. The [...]

Withdrawn: Datathons: fostering equitability in data reuse in ecology

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

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

Building a Portuguese Coalition for Biodiversity Genomics

João Pedro Marques, Paulo Célio Alves, Isabel R. Amorim, et al.

Published: 2023-07-10
Subjects: Genomics

The diverse physiography of the Portuguese land and marine territory, spanning from continental Europe to the Atlantic archipelagos, has made it an important repository of biodiversity throughout the Pleistocene glacial cycles, leading to a remarkable diversity of species and ecosystems. This rich biodiversity is under threat from anthropogenic drivers, such as climate change, invasive species, [...]

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