Preprints
Filtering by Subject: Genetics and Genomics
Achieving global biodiversity goals by 2050 requires urgent and integrated actions
Published: 2022-02-25
Subjects: Agriculture, Animal Sciences, Biodiversity, Ecology and Evolutionary Biology, Forest Sciences, Genetics and Genomics, Life Sciences, Marine Biology, Plant Sciences
Human impacts on the Earth’s biosphere are driving the global biodiversity crisis. Governments are preparing to agree on a set of actions intended to halt the loss of biodiversity and put it on a path to recovery by 2050. We provide evidence that the proposed actions can bend the curve for biodiversity, but only if these actions are implemented urgently and in an integrated manner.
Improving species conservation plans under IUCN’s One Plan Approach using quantitative genetic methods
Published: 2022-02-19
Subjects: Ecology and Evolutionary Biology, Genetics, Genetics and Genomics, Life Sciences
Human activities are resulting in altered environmental conditions that are impacting the demography and evolution of species globally. If we wish to prevent anthropogenic extinction and extirpation, we need to improve our ability to restore wild populations. Ex situ populations can be an important tool for species conservation. However, it is difficult to prevent deviations from an optimal [...]
A set of principles and practical suggestions for equitable fieldwork in biology
Published: 2022-02-05
Subjects: Biodiversity, Ecology and Evolutionary Biology, Entomology, Forest Sciences, Genetics and Genomics, Life Sciences, Marine Biology, Plant Sciences
Field biology is an area of research that involves working directly with living organisms in situ through a practice known as “fieldwork.” Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of the core team members. However, existing power [...]
Genomic evidence of a functional RH2 opsin in New Zealand parrots and implications for pest control
Published: 2022-01-25
Subjects: Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
Recent genomic evidence suggest that kea (Nestor notabilis) have a non-functional RH2 opsin gene potentially leading to impaired vision in the green region of the electromagnetic spectrum. In New Zealand, it is standard procedure to add green dye to aerial poison baits used in mammalian predator control operations to deter native birds from eating toxic bait. A visual deficiency could impact how [...]
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: 2021-12-21
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: 2021-12-19
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: 2021-12-16
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: 2021-12-15
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: 2021-10-06
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: 2021-09-28
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. [...]