scholarly journals Ecology drives the degree of convergence in the gene expression of extremophile fishes

2021 ◽  
Author(s):  
Michael Tobler ◽  
Ryan Greenway ◽  
Joanna L Kelley
Keyword(s):  
Gene Expression ◽  
Extreme Environments ◽  
Ecological Factors ◽  
Strong Relationship ◽  
Evolutionary Processes ◽  
Major Question ◽  
Evolutionary Contingency ◽  
Evolutionary Changes ◽  
Chance Events ◽  
Degree Of Convergence

Convergent evolution, where independent lineages evolve similar traits when adapting to similar habitats, is a common phenomenon and testament to the repeatability of evolutionary processes. Still, non-convergence is also common, and a major question is whether apparently idiosyncratic, lineage-specific evolutionary changes are reflective of chance events inherent to evolutionary processes, or whether they are also influenced by deterministic genetic or ecological factors. To address this question, we quantified the degree of convergence in genome-wide patterns of gene expression across lineages of livebearing fishes (family Poeciliidae) that span 40 million years of evolution and have colonized extreme environments in the form of toxic, hydrogen-sulfide-rich springs. We specifically asked whether the degree of convergence across lineage pairs was related to their phylogenetic relatedness or the ecological similarity of the habitats they inhabit. Using phylogenetic comparative analyses, we showed that the degree of convergence was highly variable across lineage pairs residing in sulfide springs. While closely related lineages did not exhibit higher degrees of convergence than distantly related ones, we uncovered a strong relationship between degree of convergence and ecological similarity. Our results indicate that variation in the degree of convergence is not merely noise associated with evolutionary contingency. Rather, cryptic environmental variation that is frequently ignored when we employ reductionist approaches can significantly contribute to adaptive evolution. This study highlights the importance of multivariate approaches that capture the complexities of both selective regimes and organismal design when assessing the roles of determinism and contingency in evolution.

Biology of pathogenic microorganisms

2020 ◽  
pp. 651-656
Author(s):  
Duncan J. Maskell ◽  
James L.N. Wood
Keyword(s):  
Gene Expression ◽  
Ecological Niche ◽  
Rich Source ◽  
Ecological Niches ◽  
Pathogenic Microorganisms ◽  
Evolutionary Processes ◽  
Host Animal ◽  
Host Environment ◽  
The Rich

Microorganisms are present at most imaginable sites on the planet, and have evolved to occupy these ecological niches successfully. A host animal is simply another ecological niche to be occupied. This chapter describes how the ability to cause disease may in some cases be an accidental bystander event, or it may be the result of evolutionary processes that have led to specific mechanisms allowing the pathogen to exploit the rich source of nutrients present in the host, and then be transmitted to another fresh host. Pathogenicity often relies on a series of steps, with specific and often distinct mechanisms operating at each of them. Some types of pathogen must adapt to the host environment by altering gene expression, and most must retain the ability to be transmitted readily between hosts.

scholarly journals Evolutionary Changes in Gene Expression, Coding Sequence and Copy-Number at the Cyp6g1 Locus Contribute to Resistance to Multiple Insecticides in Drosophila

PLoS ONE ◽  
2014 ◽  
Vol 9 (1) ◽  
pp. e84879 ◽  
Author(s):  
Thomas W. R. Harrop ◽  
Tamar Sztal ◽  
Christopher Lumb ◽  
Robert T. Good ◽  
Phillip J. Daborn ◽  
...  
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
Coding Sequence ◽  
Evolutionary Changes

scholarly journals Comparison of the transcriptomes of two tardigrades with different hatching coordination

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yuki Yoshida ◽  
Kenta Sugiura ◽  
Masaru Tomita ◽  
Midori Matsumoto ◽  
Kazuharu Arakawa
Keyword(s):  
Gene Expression ◽  
Embryonic Development ◽  
Juvenile Hormone ◽  
Extreme Environments ◽  
Regulation Mechanism ◽  
Egg Hatching ◽  
Terrestrial Species ◽  
Juvenile Hormone Analog ◽  
Hormone Analog ◽  
Multiple Species

Abstract Background Tardigrades are microscopic organisms, famous for their tolerance against extreme environments. The establishment of rearing systems of multiple species has allowed for comparison of tardigrade physiology, in particular in embryogenesis. Interestingly, in-lab cultures of limnic species showed smaller variation in hatching timing than terrestrial species, suggesting a hatching regulation mechanism acquired by adaptation to their habitat. Results To this end, we screened for coordinated gene expression during the development of two species of tardigrades, Hypsibius exemplaris and Ramazzottius varieornatus, and observed induction of the arthropod molting pathway. Exposure of ecdysteroids and juvenile hormone analog affected egg hatching but not embryonic development in only the limnic H. exemplaris. Conclusion These observations suggest a hatching regulation mechanism by the molting pathway in H. exemplaris.

scholarly journals Eight Million Years of Satellite DNA Evolution in Grasshoppers of the Genus Schistocerca Illuminate the Ins and Outs of the Library Hypothesis

2020 ◽  
Vol 12 (3) ◽  
pp. 88-102 ◽  
Author(s):  
Octavio M Palacios-Gimenez ◽  
Diogo Milani ◽  
Hojun Song ◽  
Dardo A Marti ◽  
Maria D López-León ◽  
...  
Keyword(s):  
Satellite Dna ◽  
Schistocerca Gregaria ◽  
Rate Of Change ◽  
High Rate ◽  
Consensus Sequences ◽  
Evolutionary Changes ◽  
Chance Events ◽  
Quantitative Changes ◽  
Library Hypothesis ◽  
Chromosomal Loci

Abstract Satellite DNA (satDNA) is an abundant class of tandemly repeated noncoding sequences, showing high rate of change in sequence, abundance, and physical location. However, the mechanisms promoting these changes are still controversial. The library model was put forward to explain the conservation of some satDNAs for long periods, predicting that related species share a common collection of satDNAs, which mostly experience quantitative changes. Here, we tested the library model by analyzing three satDNAs in ten species of Schistocerca grasshoppers. This group represents a valuable material because it diversified during the last 7.9 Myr across the American continent from the African desert locust (Schistocerca gregaria), and this thus illuminates the direction of evolutionary changes. By combining bioinformatic and cytogenetic, we tested whether these three satDNA families found in S. gregaria are also present in nine American species, and whether differential gains and/or losses have occurred in the lineages. We found that the three satDNAs are present in all species but display remarkable interspecies differences in their abundance and sequences while being highly consistent with genus phylogeny. The number of chromosomal loci where satDNA is present was also consistent with phylogeny for two satDNA families but not for the other. Our results suggest eminently chance events for satDNA evolution. Several evolutionary trends clearly imply either massive amplifications or contractions, thus closely fitting the library model prediction that changes are mostly quantitative. Finally, we found that satDNA amplifications or contractions may influence the evolution of monomer consensus sequences and by chance playing a major role in driftlike dynamics.

scholarly journals Analysis of Synaptic Gene Expression in the Neocortex of Primates Reveals Evolutionary Changes in Glutamatergic Neurotransmission

2014 ◽  
Vol 25 (6) ◽  
pp. 1596-1607 ◽  
Author(s):  
Gerard Muntané ◽  
Julie E. Horvath ◽  
Patrick R. Hof ◽  
John J. Ely ◽  
William D. Hopkins ◽  
...  
Keyword(s):  
Gene Expression ◽  
Glutamatergic Neurotransmission ◽  
Evolutionary Changes

scholarly journals The interactive effects of competition and predation risk on dispersal in an insect

2014 ◽  
Vol 10 (6) ◽  
pp. 20140287 ◽  
Author(s):  
Celina B. Baines ◽  
Shannon J. McCauley ◽  
Locke Rowe
Keyword(s):  
Predation Risk ◽  
Intraspecific Competition ◽  
Aquatic Insects ◽  
Ecological Factors ◽  
Factorial Experiment ◽  
Interactive Effects ◽  
Factorial Experiments ◽  
Evolutionary Processes ◽  
Factors Affecting ◽  
Ecological Conditions

Dispersal dynamics have significant consequences for ecological and evolutionary processes. Previous work has demonstrated that dispersal can be context-dependent. However, factors affecting dispersal are typically considered in isolation, despite the probability that individuals make dispersal decisions in response to multiple, possibly interacting factors. We examined whether two ecological factors, predation risk and intraspecific competition, have interactive effects on dispersal dynamics. We performed a factorial experiment in mesocosms using backswimmers ( Notonecta undulata ), flight-capable, semi-aquatic insects. Emigration rates increased with density, and increased with predation risk at intermediate densities; however, predation had minimal effects on emigration at high and low densities. Our results indicate that factorial experiments may be required to understand dispersal dynamics under realistic ecological conditions.

scholarly journals Genome-wide repressive capacity of promoter DNA methylation is revealed through epigenomic manipulation

2018 ◽  
Author(s):  
Keegan Korthauer ◽  
Rafael A. Irizarry
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Statistical Inference ◽  
Transcriptional Repression ◽  
Strong Association ◽  
Large Body ◽  
Strong Relationship ◽  
Open Science ◽  
Promoter Dna Methylation ◽  
Promoter Dna

AbstractThe scientific community is increasingly embracing open science. This growing commitment to open science should be applauded and encouraged, especially when it occurs voluntarily and prior to peer review. Thanks to other researchers’ dedication to open science, we have had the privilege of conducting a reanalysis of a landmark experiment published as a preprint with data made available in a public repository. The study in question found that promoter DNA methylation is frequently insufficient to induce transcriptional repression, which appears to contradict a large body of observational studies showing a strong association between DNA methylation and gene expression. This study was the first to evaluate whether forcibly methylating thousands of DNA promoter regions is sufficient to suppress gene expression. The authors’ data analysis did not find a strong relationship between promoter methylation and transcriptional repression. However, their analyses did not make full use of statistical inference and applied a normalization technique that removes global differences that are representative of the actual biological system. Here we reanalyze the data with an approach that includes statistical inference of differentially methylated regions, as well as a normalization technique that accounts for global expression differences. We find that forced DNA methylation of thousands of promoters overwhelmingly represses gene expression. In addition, we show that complementary epigenetic marks of active transcription are reduced as a result of DNA methylation. Finally, by studying whether these associations are sensitive to the CG density of promoters, we find no substantial differences in the association between promoters with and without a CG island. The code needed to reproduce are analysis is included in the public GitHub repository github.com/kdkorthauer/repressivecapacity.

scholarly journals Genomic variation, population history and within-archipelago adaptation between island bird populations

2021 ◽  
Vol 8 (2) ◽  
pp. 201146
Author(s):  
Claudia A. Martin ◽  
Claire Armstrong ◽  
Juan Carlos Illera ◽  
Brent C. Emerson ◽  
David S. Richardson ◽  
...  
Keyword(s):  
Gene Flow ◽  
Spatial Scales ◽  
Abiotic Factors ◽  
Ecological Factors ◽  
Genomic Variation ◽  
Population History ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Processes ◽  
Bird Populations ◽  
A Genome

Oceanic island archipelagos provide excellent models to understand evolutionary processes. Colonization events and gene flow can interact with selection to shape genetic variation at different spatial scales. Landscape-scale variation in biotic and abiotic factors may drive fine-scale selection within islands, while long-term evolutionary processes may drive divergence between distantly related populations. Here, we examine patterns of population history and selection between recently diverged populations of the Berthelot's pipit ( Anthus berthelotii ), a passerine endemic to three North Atlantic archipelagos. First, we use demographic trees and f 3 statistics to show that genome-wide divergence across the species range is largely shaped by colonization and bottlenecks, with evidence of very weak gene flow between populations. Then, using a genome scan approach, we identify signatures of divergent selection within archipelagos at single nucleotide polymorphisms (SNPs) in genes potentially associated with craniofacial development and DNA repair. We did not detect within-archipelago selection at the same SNPs as were detected previously at broader spatial scales between archipelagos, but did identify signatures of selection at loci associated with similar biological functions. These findings suggest that similar ecological factors may repeatedly drive selection between recently separated populations, as well as at broad spatial scales across varied landscapes.

Urban Evolutionary Biology

2020 ◽  
Keyword(s):  
Urban Space ◽  
Evolutionary Biology ◽  
Current Knowledge ◽  
Social Characteristics ◽  
Urban Habitat ◽  
Evolutionary Processes ◽  
Urban Neighbourhoods ◽  
Evolutionary Changes ◽  
Research Themes ◽  
New Research

Cities occupy about 3 per cent of the Earth’s habitable land area and are home to one out of two humans worldwide; both estimates are predicted to grow. Urban space is thus becoming an important, novel ecological niche for humans and wildlife alike. Building on knowledge gathered by urban ecologists during the last half century, evidence of evolutionary responses to urbanization has rapidly emerged. Urban evolutionary biology is a nascent yet fast-growing field of research—and a fascinating testing ground for evolutionary biologists worldwide. Urbanization offers a great range of opportunities to examine evolutionary processes because of the radically altered and easily quantifiable urban habitat, and the large number of cities worldwide, enabling rigorous, replicated tests of evolutionary hypotheses. Urban populations are increasingly exhibiting both neutral and adaptive evolutionary changes at levels ranging from genotypes to phenotypes. The novelty of urban evolutionary biology is that these changes are driven by the cities we have built, including effects of infrastructure, pollution, and social characteristics of our urban neighbourhoods. It will thereby enrich the field of evolutionary biology with emergent yet incredibly potent new research themes where the urban habitat is key. In a series of sixteen chapters written by leading evolutionary biologists working on urban drivers of evolution, Urban Evolutionary Biology is the first academic book in the field. It synthesizes current knowledge on evolutionary processes occurring literally on our doorstep, across the globe, and in each city independently.

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