Preprints
Filtering by Subject: Genetics and Genomics
Detecting Signatures Of Selection In Regulatory Variation
Published: 2021-12-29
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics, Life Sciences
A substantial amount of phenotypic diversity results from changes in gene regulation. Understanding how regulatory diversity evolves is therefore a key priority in identifying mechanisms of adaptive change. However, in contrast to powerful models of sequence evolution, we lack a consensus model of regulatory evolution. Furthermore, recent work has shown that many of the comparative approaches [...]
The evolutionary impacts of synonymous mutations
Published: 2021-12-20
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Life Sciences, Molecular Genetics
During the 50 years since the genetic code was cracked, our understanding of the evolutionary consequences of synonymous mutations has undergone a dramatic shift. Synonymous codon changes were initially considered selectively neutral, and as such, exemplars of evolution via genetic drift. However, the pervasive and non-negligible fitness impacts of synonymous mutations are now clear across [...]
Ecology and the Evolution of Sex Chromosomes
Published: 2021-12-18
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Life Sciences
This article reviews and discusses ecological factors that affect sex chromosome evolution. Sex chromosomes are common features of animal genomes, and are often the location where master sex determination genes are found. Many important aspects of sex chromosome evolution are thought to be driven by sex-specific selection pressures, such as sexual antagonism and sexual selection. Sex-specific [...]
Genome sequence for the blue-flowered Andean shrub Iochroma cyaneum reveals extensive discordance across the berry clade of Solanaceae
Published: 2021-12-15
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics, Life Sciences
The tomato family, Solanaceae, is a model clade for a wide range of applied and basic research questions. Currently, reference-quality genomes are available for over 30 species from seven genera, and these include numerous crops as well as wild species (e.g., Jaltomata sinuosa and Nicotiana attenuata). Here we present the genome of the showy-flowered Andean shrub Iochroma cyaneum, a woody lineage [...]
Identifying cryptic fern gametophytes using DNA barcoding: A review
Published: 2021-12-14
Subjects: Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences, Plant Sciences
Ferns and lycophytes are unique among land plants for having sporophyte (diploid) and gametophyte (haploid) generations that can grow independently of each other. While most studies of fern ecology focus on the more obvious sporophytic stage, the gametophyte is critically important, as it is the sexual phase of the life cycle. Yet, fern gametophytes have long been neglected in field studies due [...]
Selfish, promiscuous, and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations
Published: 2021-12-05
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics, Life Sciences, Microbiology, Other Microbiology
Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned with those of their hosts. In general, transfer is costly to the donor cell while potentially beneficial to the recipients. The diversity and plasticity of cell-MGEs interactions, and those among MGEs, results in complex [...]
Ecology and conservation of a living fossil: Australias Wollemi Pine (Wollemia nobilis)
Published: 2021-10-22
Subjects: Biodiversity, Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Horticulture, Life Sciences, Plant Biology, Plant Pathology, Plant Sciences, Terrestrial and Aquatic Ecology
The iconic Wollemi Pine (Wollemia nobilis) is a critically endangered Australian conifer and one of the world’s rarest trees with only 46 mature individuals remaining in the wild. The species is regarded as a ‘living fossil’ and was discovered on the brink of extinction following a natural historical decline. While its discovery has enabled crucial intervention for its long-term conservation, it [...]
The contributions of Dr. Nettie Stevens to the field of sex chromosome biology
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)
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
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?
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
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
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
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
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 [...]