Preprints

Filtering by Subject: Genetics and Genomics

The contributions of Dr. Nettie Stevens to the field of sex chromosome biology

Sarah Carey, Laramie Aközbek, Alex Harkess

Published: 2021-10-05
Subjects: Genetics and Genomics, Life Sciences

The early 1900s delivered many foundational discoveries in genetics, including re-discovery of Mendel’s research and the chromosomal theory of inheritance. Following these insights, many focused their research on whether the development of separate sexes had a chromosomal basis or if instead it was caused by environmental factors. It is Dr. Nettie M. Stevens’ Studies in Spermatogenesis (1905) [...]

Misinterpretation of genomic data matters for endangered species listing: the subspecific status of the Peñasco least chipmunk (Neotamias minimus atristriatus)

Andrew G Hope, Jennifer K. Frey

Published: 2021-10-01
Subjects: Genetics and Genomics, Genomics, Life Sciences

Puckett et al. (2021. Ecology and Evolution, 11, 12114-12128) evaluated the subspecies status of the Peñasco least chipmunk (Neotamias minimus atristriatus) using genomic approaches and concluded that their results did not support the distinction of this taxon as a subspecies and recommended it be synonymized with N. m. operarius. We refute the interpretations, conclusions, and taxonomic [...]

Learning from your mistakes: a novel method to predict the response to directional selection

Lisandro Milocco, Isaac Salazar-Ciudad

Published: 2021-09-27
Subjects: Animal Sciences, Computational Biology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Life Sciences, Other Ecology and Evolutionary Biology, Population Biology

Predicting how populations respond to selection is a key goal of evolutionary biology. The field of quantitative genetics provides predictions for the response to directional selection through the breeder’s equation. However, differences between the observed responses to selection and those predicted by the breeder’s equation occur. The sources of these errors include omission of traits under [...]

Many defense systems in microbial genomes, but which is defending whom from what?

Eduardo P. C. Rocha, David Bikard

Published: 2021-09-18
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Life Sciences, Microbiology, Other Microbiology

Prokaryotes have numerous mobile genetic elements (MGE) that mediate horizontal gene transfer between cells. These elements can be costly, even deadly, and cells use numerous defense systems to filter, control or inactivate them. Surprisingly, many phages, conjugative plasmids, and their parasites, phage satellites or mobilizable plasmids, encode defense systems homologous to those of bacteria. [...]

Supergenes on Steroids

Donna Maney, Clemens Küpper

Published: 2021-09-09
Subjects: Behavior and Ethology, Ecology and Evolutionary Biology, Genetics and Genomics, Genomics, Life Sciences

At the birth of supergenes, the genomic landscape is dramatically re-organized leading to pronounced differences in phenotypes and increased intrasexual diversity. Two of the best- studied supergenes in vertebrates are arguably the inversion polymorphisms on chromosomes 2 and 11 in the white-throated sparrow (Zonotrichia albicollis) and the ruff (Calidris pugnax), respectively. In both species, [...]

Impact of Infectious Disease on Humans and Our Origins

Petar Gabrić

Published: 2021-06-19
Subjects: Anthropology, Archaeological Anthropology, Arts and Humanities, Bacteriology, Biochemistry, Biophysics, and Structural Biology, Biological and Physical Anthropology, Biological Phenomena, Cell Phenomena, and Immunity, Cell and Developmental Biology, Cell Biology, Ecology and Evolutionary Biology, Evolution, Genetic Phenomena, Genetics, Genetics and Genomics, History of Art, Architecture, and Archaeology, Life Sciences, Medical Biochemistry, Medical Cell Biology, Medical Genetics, Medical Immunology, Medical Microbiology, Medical Molecular Biology, Medical Pathology, Medical Sciences, Medicine and Health Sciences, Microbiology, Molecular Biology, Molecular Genetics, Pathogenic Microbiology, Pharmacology, Pharmacology, Toxicology and Environmental Health, Social and Behavioral Sciences, Virology

On May 16, 2020, the Center for Academic Research and Training in Anthropogeny organized the symposium “Impact of Infectious Disease on Humans and Our Origins”. The symposium aimed to gather experts on infectious diseases in one place and discuss the interrelationship between different pathogens and humans in an evolutionary context. The talks discussed topics including SARS-CoV-2, dengue and [...]

The macroevolutionary consequences of niche construction in microbial metabolism

Djordje Bajic, Maria Rebolleda-Gomez, Martha Munoz, et al.

Published: 2021-05-31
Subjects: Bioinformatics, Computational Biology, Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Evolution, Genetics and Genomics, Life Sciences, Microbiology, Population Biology, Systems Biology

Microorganisms display a stunning metabolic diversity. Understanding the origin of this diversity requires understanding how macroevolutionary processes such as innovation and diversification play out in the microbial world. Metabolic networks, which govern microbial resource use, can evolve through different mechanisms, e.g. horizontal gene transfer or de novo evolution of enzymes and pathways. [...]

Current applications and future promise of genetic/genomic data for conservation in an Aotearoa New Zealand context

Natalie Forsdick, Clare I. M. Adams, Alana Alexander, et al.

Published: 2021-05-20
Subjects: Genetics and Genomics, Life Sciences

The field of conservation biology has a long history of incorporating diverse disciplines into its ‘toolbox’ for improved outcomes. One such discipline is conservation genomics, which has experienced fast-paced growth and development over the last decade, and offers exciting opportunities to help achieve the vision outlined in Aotearoa New Zealand’s national strategy for biodiversity, Te Mana o [...]

met v1: Expanding on old estimations of biodiversityfrom eDNA with a new software framework

David Molik

Published: 2021-04-27
Subjects: Bioinformatics, Computational Biology, Genetics and Genomics, Life Sciences

A long-standing problem in environmental DNA has been the inability to compute across large number of datasets. Here we introduce an open-source software framework that can store a large number of environmental DNA datasets, as well as provide a platform for analysis, in an easily customizable way. We show the utility of such an approach by analyzing over 1400 arthropod metabarcode datasets. This [...]

Reefscape genomics: leveraging advances in 3D imaging to assess fine-scale patterns of genomic variation on coral reefs

Pim Bongaerts, Caroline E. Dubé, Katharine Prata, et al.

Published: 2021-04-16
Subjects: Biology, Genetics and Genomics, Life Sciences, Marine Biology

Coral reefs across the world are undergoing rapid deterioration, and understanding the ecological and evolutionary processes that govern these ecosystems is critical to our ability to protect them. Molecular ecological studies have been instrumental in advancing such understanding, and while initially focused primarily on broad-scale patterns, they have gradually uncovered the prevalence of local [...]

Qualitative and quantitative methods show stability in patterns of Cepaea nemoralis shell polymorphism in the Pyrenees over five decades

Angus Davison, Daniel Ramos Gonzalez

Published: 2020-12-01
Subjects: Biodiversity, Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences

One of the emerging strengths of working with the land snail genus Cepaea is that historical collections can be compared against modern day samples, for instance to understand the impact of changing climate and habitat upon shell morph frequencies. However, one potential limitation is that prior studies scored shell ground colour by eye, usually in the field, into three discrete colours yellow, [...]

Mobilising molluscan models and genomes in biology

Angus Davison, Maurine Neiman

Published: 2020-11-24
Subjects: Biodiversity, Bioinformatics, Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Laboratory and Basic Science Research Life Sciences, Life Sciences

Molluscs are amongst the most ancient, diverse, and important of all animal taxa. Even so, no individual mollusc species has emerged as a broadly applied model system in biology. We here make the case that both perceptual and methodological barriers have played a role in the relative neglect of molluscs as research organisms. We then summarize the current application and potential of molluscs and [...]

Maturation in Atlantic salmon (Salmo salar, Salmonidae): a synthesis of ecological, genetic, and molecular processes

Kenyon Mobley, Tutku Aykanat, Yann Czorlich, et al.

Published: 2020-11-10
Subjects: Behavior and Ethology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Genomics, Life Sciences, Physiology, Population Biology

Over the past decades, Atlantic salmon (Salmo salar, Salmonidae) has emerged as a model system for sexual maturation research, owing to the high diversity of life history strategies, knowledge of trait genetic architecture, and their high economic value. The aim of this synthesis is to summarize the current state of knowledge concerning maturation in Atlantic salmon, outline knowledge gaps, and [...]

Removing the bad apples: a simple bioinformatic method to improve loci-recovery in de novo RADseq data for non-model organisms

José Cerca, Marius F. Maurstad, Nicolas Rochette, et al.

Published: 2020-08-31
Subjects: Bioinformatics, Computational Biology, Genetics and Genomics, Genomics, Life Sciences

The restriction site-associated DNA (RADseq) family of protocols involves digesting DNA and sequencing the region flanking the cut site, thus providing a cost and time efficient way for obtaining thousands of genomic markers. However, when working with non-model taxa with few genomic resources, optimization of RADseq wet-lab and bioinformatic tools may be challenging, often resulting in allele [...]

Climate change prompts monitoring and systematic utilization of honey bee diversity in Turkey

Mert Kükrer, C.Can Bilgin

Published: 2020-07-28
Subjects: Agriculture, Apiculture, Biodiversity, Ecology and Evolutionary Biology, Entomology, Genetics and Genomics, Life Sciences

Quantitative studies concerning the impact of climate change on pollinators are generally lacking. Relationship between honey bee diversity, present local adaptations and adaptive capacity of subspecies and ecotypes in the face of climate change is an urgent but rather poorly studied topic worldwide. Actually, such an effort lies at the crossroads of various fields of inquiry. Those include [...]

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