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Rapid Evolution
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Rapid Evolution

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (15 May 2020) | Viewed by 32326

Special Issue Editors

Prof. Michael Kopp

E-Mail Website
Guest Editor
Aix-Marseille University, Marseille, France
Interests: theoretical biology; evolution; population genetics; adaptation; speciation
Dr. Tom Van Dooren

E-Mail Website
Guest Editor
Institute of Ecology and Environmental Sciences iEES Paris, Paris, France
Interests: eco-evo-devo; climate change and adaptation; ecological and evolutionary feedbacks

Special Issue Information

Dear Colleagues,

Over the last two decades, evolutionary biologists have increasingly recognized that selection-driven evolutionary change in populations or species is not restricted to geological timescales but can happen so fast as to be observable in real time. Beyond the fascinating opportunities this offers for basic research, rapid or contemporary evolution has at least two major and interrelated consequences: First, rapid evolution defies the traditional distinction between ecological and evolutionary timescales. Evolutionary processes can have direct consequences on ecological dynamics and ecosystem functioning and are themselves influenced by ecological processes (eco-evolutionary feedback). Second, rapid evolution may allow certain populations to adapt to anthropogenic changes in their environment and, in some cases, prevent population extinction (evolutionary rescue). In this context, much research has been focused on the potential of populations for rapid adaptation (e.g., amount of standing genetic variation, phenotypic plasticity, genetic architecture). However, even when the adaptive potential is high, rapid evolution may produce desired (in the case of endangered species) or undesired outcomes (in the case of invasive species or pathogens) at the ecosystem level. In addition, the evolution of one species may affect both the population dynamics and the selection pressures experienced by interacting species. Taking all these effects into account and gaining a fuller understanding of the scope and limits of rapid evolution in changing environments thus requires an eco-evolutionary perspective, therefore closing the loop to point one above.
This Special Issue aims at bringing together reviews and original research on diverse aspects of rapid evolution in natural populations subject to environmental change, with a focus on population-level and ecosystem effects of phenotypic and genetic adaptation. We welcome contributions using a variety of observational, experimental, and theoretical approaches. The aim is to assemble a list of papers reflecting the state-of-the-art of current research on rapid evolution.

Prof. Michael Kopp
Dr. Tom Van Dooren
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • eco-evolutionary dynamics
  • evolutionary rescue
  • global change
  • adaptation
  • anthropogenic selection
  • community genetics

Published Papers (5 papers)

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Research

26 pages, 8913 KiB  
Article
Eco-Evolutionary Feedbacks and the Maintenance of Metacommunity Diversity in a Changing Environment
by Aidan P. Fielding and Jelena H. Pantel
Genes 2020, 11(12), 1433; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11121433 - 28 Nov 2020
Cited by 5 | Viewed by 2830
Abstract
The presence and strength of resource competition can influence how organisms adaptively respond to environmental change. Selection may thus reflect a balance between two forces, adaptation to an environmental optimum and evolution to avoid strong competition. While this phenomenon has previously been explored [...] Read more.
The presence and strength of resource competition can influence how organisms adaptively respond to environmental change. Selection may thus reflect a balance between two forces, adaptation to an environmental optimum and evolution to avoid strong competition. While this phenomenon has previously been explored in the context of single communities, its implications for eco-evolutionary dynamics at the metacommunity scale are largely unknown. We developed a simulation model for the evolution of a quantitative trait that influences both an organism’s carrying capacity and its intra- and interspecific competitive ability. In the model, multiple species inhabit a three-patch landscape, and we investigated the effect of varying the connectivity level among patches, the presence and pace of directional environmental change, and the strength of competition between the species. Our model produced some patterns previously observed in evolving metacommunity models, such as species sorting and community monopolization. However, we found that species sorting was diminished even at low rates of dispersal and was influenced by competition strength, and that monopolization was observed only when environmental change was very rapid. We also detected an eco-evolutionary feedback loop between local phenotypic evolution at one site and competition at another site, which maintains species diversity in some conditions. The existence of a feedback loop maintained by dispersal indicates that eco-evolutionary dynamics in communities operate at a landscape scale. Full article
(This article belongs to the Special Issue Rapid Evolution)
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13 pages, 2439 KiB  
Article
Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts
by Roman Matyášek and Aleš Kovařík
Genes 2020, 11(7), 761; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11070761 - 07 Jul 2020
Cited by 70 | Viewed by 10180
Abstract
The pandemic caused by the spread of SARS-CoV-2 has led to considerable interest in its evolutionary origin and genome structure. Here, we analyzed mutation patterns in 34 human SARS-CoV-2 isolates and a closely related RaTG13 isolated from Rhinolophus affinis (a horseshoe bat). We [...] Read more.
The pandemic caused by the spread of SARS-CoV-2 has led to considerable interest in its evolutionary origin and genome structure. Here, we analyzed mutation patterns in 34 human SARS-CoV-2 isolates and a closely related RaTG13 isolated from Rhinolophus affinis (a horseshoe bat). We also evaluated the CpG dinucleotide contents in SARS-CoV-2 and other human and animal coronavirus genomes. Out of 1136 single nucleotide variations (~4% divergence) between human SARS-CoV-2 and bat RaTG13, 682 (60%) can be attributed to C>U and U>C substitutions, far exceeding other types of substitutions. An accumulation of C>U mutations was also observed in SARS-CoV2 variants that arose within the human population. Globally, the C>U substitutions increased the frequency of codons for hydrophobic amino acids in SARS-CoV-2 peptides, while U>C substitutions decreased it. In contrast to most other coronaviruses, both SARS-CoV-2 and RaTG13 exhibited CpG depletion in their genomes. The data suggest that C-to-U conversion mediated by C deamination played a significant role in the evolution of the SARS-CoV-2 coronavirus. We hypothesize that the high frequency C>U transitions reflect virus adaptation processes in their hosts, and that SARS-CoV-2 could have been evolving for a relatively long period in humans following the transfer from animals before spreading worldwide. Full article
(This article belongs to the Special Issue Rapid Evolution)
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28 pages, 10296 KiB  
Article
Climate Change and Green Sea Turtle Sex Ratio—Preventing Possible Extinction
by Jana Blechschmidt, Meike J. Wittmann and Chantal Blüml
Genes 2020, 11(5), 588; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11050588 - 25 May 2020
Cited by 31 | Viewed by 12680
Abstract
Climate change poses a threat to species with temperature-dependent sex determination (TSD). A recent study on green sea turtles (Chelonia mydas) at the northern Great Barrier Reef (GBR) showed a highly female-skewed sex ratio with almost all juvenile turtles being female. This [...] Read more.
Climate change poses a threat to species with temperature-dependent sex determination (TSD). A recent study on green sea turtles (Chelonia mydas) at the northern Great Barrier Reef (GBR) showed a highly female-skewed sex ratio with almost all juvenile turtles being female. This shortage of males might eventually cause population extinction, unless rapid evolutionary rescue, migration, range shifts, or conservation efforts ensure a sufficient number of males. We built a stochastic individual-based model inspired by C. mydas but potentially transferrable to other species with TSD. Pivotal temperature, nest depth, and shading were evolvable traits. Additionally, we considered the effect of crossbreeding between northern and southern GBR, nest site philopatry, and conservation efforts. Among the evolvable traits, nest depth was the most likely to rescue the population, but even here the warmer climate change scenarios led to extinction. We expected turtles to choose colder beaches under rising temperatures, but surprisingly, nest site philopatry did not improve persistence. Conservation efforts promoted population survival and did not preclude trait evolution. Although extra information is needed to make reliable predictions for the fate of green sea turtles, our results illustrate how evolution can shape the fate of long lived, vulnerable species in the face of climate change. Full article
(This article belongs to the Special Issue Rapid Evolution)
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13 pages, 1823 KiB  
Article
Identification of Genic SSRs Provide a Perspective for Studying Environmental Adaptation in the Endemic Shrub Tetraena mongolica
by Zhenhua Dang, Lei Huang, Yuanyuan Jia, Peter J. Lockhart, Yang Fong and Yunyun Tian
Genes 2020, 11(3), 322; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11030322 - 18 Mar 2020
Cited by 7 | Viewed by 2595
Abstract
Tetraena mongolica is a xerophytic shrub endemic to desert regions in Inner Mongolia. This species has evolved distinct survival strategies that allow it to adapt to hyper-drought and heterogeneous habitats. Simple sequence repeats (SSRs) may provide a molecular basis in plants for fast [...] Read more.
Tetraena mongolica is a xerophytic shrub endemic to desert regions in Inner Mongolia. This species has evolved distinct survival strategies that allow it to adapt to hyper-drought and heterogeneous habitats. Simple sequence repeats (SSRs) may provide a molecular basis in plants for fast adaptation to environmental change. Thus, identifying SSRs and their possible effects on gene behavior has the potential to provide valuable information for studies of adaptation. In this study, we sequenced six individual transcriptomes of T. mongolica from heterogeneous habitats, focused on SSRs located in genes, and identified 811 polymorphic SSRs. Of the identified SSRs, 172, 470, and 76 were located in 5′ UTRs, CDSs, and 3′ UTRs in 591 transcripts; and AG/CT, AAC/GTT, and AT/AT were the most abundant repeats in each gene region. Functional annotation showed that many of the identified polymorphic SSRs were in genes that were enriched in several GO terms and KEGG pathways, suggesting the functional significance of these genes in the environmental adaptation process. The identification of polymorphic genic SSRs in our study lays a foundation for future studies investigating the contribution of SSRs to regulation of genes in natural populations of T. mongolica and their importance for adaptive evolution of this species. Full article
(This article belongs to the Special Issue Rapid Evolution)
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15 pages, 1323 KiB  
Article
Asymmetric Isolation and the Evolution of Behaviors Influencing Dispersal: Rheotaxis of Guppies above Waterfalls
by Léa Blondel, Sandra Klemet-N’Guessan, Marilyn E. Scott and Andrew P. Hendry
Genes 2020, 11(2), 180; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11020180 - 09 Feb 2020
Cited by 5 | Viewed by 3265
Abstract
Populations that are asymmetrically isolated, such as above waterfalls, can sometimes export emigrants in a direction from which they do not receive immigrants, and thus provide an excellent opportunity to study the evolution of dispersal traits. We investigated the rheotaxis of guppies above [...] Read more.
Populations that are asymmetrically isolated, such as above waterfalls, can sometimes export emigrants in a direction from which they do not receive immigrants, and thus provide an excellent opportunity to study the evolution of dispersal traits. We investigated the rheotaxis of guppies above barrier waterfalls in the Aripo and Turure rivers in Trinidad—the later having been introduced in 1957 from a below-waterfall population in another drainage. We predicted that, as a result of strong selection against downstream emigration, both of these above-waterfall populations should show strong positive rheotaxis. Matching these expectations, both populations expressed high levels of positive rheotaxis, possibly reflecting contemporary (rapid) evolution in the introduced Turure population. However, the two populations used different behaviors to achieve the same performance of strong positive rheotaxis, as has been predicted in the case of multiple potential evolutionary solutions to the same functional challenge (i.e., “many-to-one mapping”). By contrast, we did not find any difference in rheotactic behavior above versus below waterfalls on a small scale within either river, suggesting constraints on adaptive divergence on such scales. Full article
(This article belongs to the Special Issue Rapid Evolution)
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