Special Issue "Evolutionary Dynamics of Wild Populations"

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 (30 November 2020).

Special Issue Editors

Dr. Delphine Legrand
Website
Guest Editor
Station d’Ecologie Théorique et Expérimentale, UMR 5321, Centre National pour la Recherche Scientifique et Université Paul Sabatier, 09200 Moulis, France
Interests: evolutionary ecology; genomics; dispersal; freshwater microbiology; experimental evolution; metapopulation dynamics
Dr. Simon Blanchet
Website
Guest Editor
Station d’Ecologie Théorique et Expérimentale, UMR 5321, Centre National pour la Recherche Scientifique et Université Paul Sabatier, 09200 Moulis, France
Interests: freshwater biology; evolutionary ecology; host–parasite interactions; non-genetic inheritance; community and ecosystem ecology; eco-evolutionary dynamics

Special Issue Information

Dear Colleagues,

Wild populations are facing rapid and sometimes extreme environmental changes that are currently exacerbated by pressing human activities. A major scientific endeavor is to unravel the evolutionary processes allowing wild populations to adequately respond to these rapid and drastic environmental changes. In recent decades, the accumulation of empirical data as well as the development of new theories and molecular tools have largely improved our ability to tackle such a major question. In particular, there is now growing evidence that evolutionary processes (gene flow, drift, mutation, and natural selection) interact in sometimes complex ways to shape the rapid responses of organisms to changing environments, and this can lead to unexpected feedback between evolutionary and ecological dynamics. These rapid responses are sustained by genetic determinants in addition to alternative inheritance systems, including epigenetic and/or social avatars of information. Unravelling these underlying molecular mechanisms may change the design of management and conservation plans for wild populations.

In this Special Issue, we aim to present these novel research avenues on the evolutionary dynamics of wild populations so as to generate a general overview of the most up-to-date and fascinating studies. We specifically aim to integrate experimental, observational, and theoretical studies on wild populations that focus on (i) the role of dispersal as a process sustaining metapopulation dynamics in spatially structured landscapes, (ii) the genetic and non-genetic (including epigenetic) bases of adaptation, (iii) the reciprocal links between evolutionary and ecological dynamics over contemporary timescales, and (iv) the genomic and epigenomic conservation of wild populations. 

Dr. Delphine Legrand
Dr. Simon Blanchet
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 papers will be 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 2000 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
  • wild populations
  • heritability
  • quantitative genetics
  • dispersal
  • biodiversity
  • global change

Published Papers (6 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Open AccessArticle
Patterns of Epigenetic Diversity in Two Sympatric Fish Species: Genetic vs. Environmental Determinants
Genes 2021, 12(1), 107; https://doi.org/10.3390/genes12010107 - 16 Jan 2021
Abstract
Epigenetic components are hypothesized to be sensitive to the environment, which should permit species to adapt to environmental changes. In wild populations, epigenetic variation should therefore be mainly driven by environmental variation. Here, we tested whether epigenetic variation (DNA methylation) observed in wild [...] Read more.
Epigenetic components are hypothesized to be sensitive to the environment, which should permit species to adapt to environmental changes. In wild populations, epigenetic variation should therefore be mainly driven by environmental variation. Here, we tested whether epigenetic variation (DNA methylation) observed in wild populations is related to their genetic background, and/or to the local environment. Focusing on two sympatric freshwater fish species (Gobio occitaniae and Phoxinus phoxinus), we tested the relationships between epigenetic differentiation, genetic differentiation (using microsatellite and single nucleotide polymorphism (SNP) markers), and environmental distances between sites. We identify positive relationships between pairwise genetic and epigenetic distances in both species. Moreover, epigenetic marks better discriminated populations than genetic markers, especially in G. occitaniae. In G. occitaniae, both pairwise epigenetic and genetic distances were significantly associated to environmental distances between sites. Nonetheless, when controlling for genetic differentiation, the link between epigenetic differentiation and environmental distances was not significant anymore, indicating a noncausal relationship. Our results suggest that fish epigenetic variation is mainly genetically determined and that the environment weakly contributed to epigenetic variation. We advocate the need to control for the genetic background of populations when inferring causal links between epigenetic variation and environmental heterogeneity in wild populations. Full article
(This article belongs to the Special Issue Evolutionary Dynamics of Wild Populations)
Open AccessArticle
Targeted Sequencing of Mitochondrial Genes Reveals Signatures of Molecular Adaptation in a Nearly Panmictic Small Pelagic Fish Species
Genes 2021, 12(1), 91; https://doi.org/10.3390/genes12010091 - 13 Jan 2021
Abstract
Ongoing climatic changes, with predictable impacts on marine environmental conditions, are expected to trigger organismal responses. Recent evidence shows that, in some marine species, variation in mitochondrial genes involved in the aerobic conversion of oxygen into ATP at the cellular level correlate with [...] Read more.
Ongoing climatic changes, with predictable impacts on marine environmental conditions, are expected to trigger organismal responses. Recent evidence shows that, in some marine species, variation in mitochondrial genes involved in the aerobic conversion of oxygen into ATP at the cellular level correlate with gradients of sea surface temperature and gradients of dissolved oxygen. Here, we investigated the adaptive potential of the European sardine Sardina pilchardus populations offshore the Iberian Peninsula. We performed a seascape genetics approach that consisted of the high throughput sequencing of mitochondria’s ATP6, COI, CYTB and ND5 and five microsatellite loci on 96 individuals coupled with environmental information on sea surface temperature and dissolved oxygen across five sampling locations. Results show that, despite sardines forming a nearly panmictic population around Iberian Peninsula, haplotype frequency distribution can be explained by gradients of minimum sea surface temperature and dissolved oxygen. We further identified that the frequencies of the most common CYTB and ATP6 haplotypes negatively correlate with minimum sea surface temperature across the sampled area, suggestive of a signature of selection. With signatures of selection superimposed on highly connected populations, sardines may be able to follow environmental optima and shift their distribution northwards as a response to the increasing sea surface temperatures. Full article
(This article belongs to the Special Issue Evolutionary Dynamics of Wild Populations)
Show Figures

Figure 1

Open AccessArticle
The Role of Microbiome and Genotype in Daphnia magna upon Parasite Re-Exposure
Genes 2021, 12(1), 70; https://doi.org/10.3390/genes12010070 - 07 Jan 2021
Abstract
Recently, it has been shown that the community of gut microorganisms plays a crucial role in host performance with respect to parasite tolerance. Knowledge, however, is lacking on the role of the gut microbiome in mediating host tolerance after parasite re-exposure, especially considering [...] Read more.
Recently, it has been shown that the community of gut microorganisms plays a crucial role in host performance with respect to parasite tolerance. Knowledge, however, is lacking on the role of the gut microbiome in mediating host tolerance after parasite re-exposure, especially considering multiple parasite infections. We here aimed to fill this knowledge gap by studying the role of the gut microbiome on tolerance in Daphnia magna upon multiple parasite species re-exposure. Additionally, we investigated the role of the host genotype in the interaction between the gut microbiome and the host phenotypic performance. A microbiome transplant experiment was performed in which three germ-free D. magna genotypes were exposed to a gut microbial inoculum and a parasite community treatment. The gut microbiome inocula were pre-exposed to the same parasite communities or a control treatment. Daphnia performance was monitored, and amplicon sequencing was performed to characterize the gut microbial community. Our experimental results showed that the gut microbiome plays no role in Daphnia tolerance upon parasite re-exposure. We did, however, find a main effect of the gut microbiome on Daphnia body size reflecting parasite specific responses. Our results also showed that it is rather the Daphnia genotype, and not the gut microbiome, that affected parasite-induced host mortality. Additionally, we found a role of the genotype in structuring the gut microbial community, both in alpha diversity as in the microbial composition. Full article
(This article belongs to the Special Issue Evolutionary Dynamics of Wild Populations)
Show Figures

Figure 1

Open AccessArticle
Soft Selective Sweep on Chemosensory Genes Correlates with Ancestral Preference for Toxic Noni in a Specialist Drosophila Population
Genes 2021, 12(1), 32; https://doi.org/10.3390/genes12010032 - 29 Dec 2020
Abstract
Understanding how organisms adapt to environmental changes is a major question in evolution and ecology. In particular, the role of ancestral variation in rapid adaptation remains unclear because its trace on genetic variation, known as soft selective sweep, is often hardly recognizable from [...] Read more.
Understanding how organisms adapt to environmental changes is a major question in evolution and ecology. In particular, the role of ancestral variation in rapid adaptation remains unclear because its trace on genetic variation, known as soft selective sweep, is often hardly recognizable from genome-wide selection scans. Here, we investigate the evolution of chemosensory genes in Drosophila yakuba mayottensis, a specialist subspecies on toxic noni (Morinda citrifolia) fruits on the island of Mayotte. We combine population genomics analyses and behavioral assays to evaluate the level of divergence in chemosensory genes and perception of noni chemicals between specialist and generalist subspecies of D. yakuba. We identify a signal of soft selective sweep on a handful of genes, with the most diverging ones involving a cluster of gustatory receptors expressed in bitter-sensing neurons. Our results highlight the potential role of ancestral genetic variation in promoting host plant specialization in herbivorous insects and identify a number of candidate genes underlying behavioral adaptation. Full article
(This article belongs to the Special Issue Evolutionary Dynamics of Wild Populations)
Show Figures

Figure 1

Open AccessArticle
Using Reciprocal Transplants to Assess Local Adaptation, Genetic Rescue, and Sexual Selection in Newly Established Populations
Genes 2021, 12(1), 5; https://doi.org/10.3390/genes12010005 - 23 Dec 2020
Abstract
Small populations establishing on colonization fronts have to adapt to novel environments with limited genetic variation. The pace at which they can adapt, and the influence of genetic variation on their success, are key questions for understanding intraspecific diversity. To investigate these topics, [...] Read more.
Small populations establishing on colonization fronts have to adapt to novel environments with limited genetic variation. The pace at which they can adapt, and the influence of genetic variation on their success, are key questions for understanding intraspecific diversity. To investigate these topics, we performed a reciprocal transplant experiment between two recently founded populations of brown trout in the sub-Antarctic Kerguelen Islands. Using individual tagging and genetic assignment methods, we tracked the fitness of local and foreign individuals, as well as the fitness of their offspring over two generations. In both populations, although not to the same extent, gene flow occurred between local and foreign gene pools. In both cases, however, we failed to detect obvious footprints of local adaptation (which should limit gene flow) and only weak support for genetic rescue (which should enhance gene flow). In the population where gene flow from foreign individuals was low, no clear differences were observed between the fitness of local, foreign, and F1 hybrid individuals. In the population where gene flow was high, foreign individuals were successful due to high mating success rather than high survival, and F1 hybrids had the same fitness as pure local offspring. These results suggest the importance of considering sexual selection, rather than just local adaptation and genetic rescue, when evaluating the determinants of success in small and recently founded populations. Full article
(This article belongs to the Special Issue Evolutionary Dynamics of Wild Populations)
Show Figures

Graphical abstract

Open AccessArticle
A Disjunctive Marginal Edge of Evergreen Broad-Leaved Oak (Quercus gilva) in East Asia: The High Genetic Distinctiveness and Unusual Diversity of Jeju Island Populations and Insight into a Massive, Independent Postglacial Colonization
Genes 2020, 11(10), 1114; https://doi.org/10.3390/genes11101114 - 23 Sep 2020
Abstract
Jeju Island is located at a marginal edge of the distributional range of East Asian evergreen broad-leaved forests. The low genetic diversity of such edge populations is predicted to have resulted from genetic drift and reduced gene flow when compared to core populations. [...] Read more.
Jeju Island is located at a marginal edge of the distributional range of East Asian evergreen broad-leaved forests. The low genetic diversity of such edge populations is predicted to have resulted from genetic drift and reduced gene flow when compared to core populations. To test this hypothesis, we examined the levels of genetic diversity of marginal-edge populations of Quercus gilva, restricted to a few habitats on Jeju Island, and compared them with the southern Kyushu populations. We also evaluated their evolutionary potential and conservation value. The genetic diversity and structure were analyzed using 40 polymorphic microsatellite markers developed in this study. Ecological Niche Modeling (ENM) has been employed to develop our insights, which can be inferred from historical distribution changes. Contrary to our expectations, we detected a similar level of genetic diversity in the Jeju populations, comparable to that of the southern Kyushu populations, which have been regarded as long-term glacial refugia with a high genetic variability of East Asian evergreen trees. We found no signatures of recent bottlenecks in the Jeju populations. The results of STRUCTURE, neighbor-joining phylogeny, and Principal Coordinate Analysis (PCoA) with a significant barrier clearly demonstrated that the Jeju and Kyushu regions are genetically distinct. However, ENM showed that the probability value for the distribution of the trees on Jeju Island during the Last Glacial Maximum (LGM) converge was zero. In consideration of these results, we hypothesize that independent massive postglacial colonization from a separate large genetic source, other than Kyushu, could have led to the current genetic diversity of Jeju Island. Therefore, we suggest that the Jeju populations deserve to be separately managed and designated as a level of management unit (MU). These findings improve our understanding of the paleovegetation of East Asian evergreen forests, and the microevolution of oaks. Full article
(This article belongs to the Special Issue Evolutionary Dynamics of Wild Populations)
Show Figures

Figure 1

Back to TopTop