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Biology
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Evolution and Ecology of Phenotypes in Nature
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Evolution and Ecology of Phenotypes in Nature

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Evolutionary Biology".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 12552

Special Issue Editor

Dr. Ugo Cenci

E-Mail Website
Guest Editor
University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F59000 Lille, France
Interests: phylogeny; genome; metabolism; evolution; ecology

Special Issue Information

Dear Colleagues,

Genes can be inherited by vertical inheritance or lateral gene transfer, and new functions can be acquired by mutation and subfunctionalization. It is the network of genes that ultimately results in phenotypes and diversity in living organisms. These phenotypes lead to organism specificity, allowing them to live in and adapt to various environments. While the same phenotype can be derived from evolutionarily related genes, a surprisingly high level of phenotype convergence has been described using evolutionarily unrelated genes. This indicates that through different evolutionary paths, a common phenotype can appear in nature. These observations strongly suggest flexibility in phenotype acquisition and show the importance and complexity of phenotype analyses in understanding both the ecology and evolution of organisms.

In this Special Issue, we want to highlight the diversity of phenotypes in nature, but also bring together microevolution, especially of metabolic pathways, and macroevolution analysis. Indeed, evolution can be seen either with a wide scope or a restricted lens. While the former can overlook specific phylogenetic signals and usually discard function, the second favors function, sometimes over phylogenetic signals, and is prone to overthink specific metabolism, forgetting the whole picture.

Thus, this Special Issue aims to create a place for discussion to better understand the evolution and ecology of organisms based on phenotypes by coupling both micro and macroevolution. We invite the submission of all types of articles covering all aspects of evolution and ecology relating to phenotypes, from bioinformatic analysis to functional biology, and attempting to couple micro and macroevolution.

Dr. Ugo Cenci
Guest Editor

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. Biology 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 2700 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

  • phylogeny
  • genome
  • metabolism
  • evolution
  • ecology

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Published Papers (5 papers)

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Research

18 pages, 5162 KiB  
Article
Multiple Instances of Adaptive Evolution in Aquaporins of Amphibious Fishes
by Héctor Lorente-Martínez, Ainhoa Agorreta, Iker Irisarri, Rafael Zardoya, Scott V. Edwards and Diego San Mauro
Biology 2023, 12(6), 846; https://doi.org/10.3390/biology12060846 - 12 Jun 2023
Cited by 3 | Viewed by 2000
Abstract
Aquaporins (AQPs) are a highly diverse family of transmembrane proteins involved in osmotic regulation that played an important role in the conquest of land by tetrapods. However, little is known about their possible implication in the acquisition of an amphibious lifestyle in actinopterygian [...] Read more.
Aquaporins (AQPs) are a highly diverse family of transmembrane proteins involved in osmotic regulation that played an important role in the conquest of land by tetrapods. However, little is known about their possible implication in the acquisition of an amphibious lifestyle in actinopterygian fishes. Herein, we investigated the molecular evolution of AQPs in 22 amphibious actinopterygian fishes by assembling a comprehensive dataset that was used to (1) catalogue AQP paralog members and classes; (2) determine the gene family birth and death process; (3) test for positive selection in a phylogenetic framework; and (4) reconstruct structural protein models. We found evidence of adaptive evolution in 21 AQPs belonging to 5 different classes. Almost half of the tree branches and protein sites that were under positive selection were found in the AQP11 class. The detected sequence changes indicate modifications in molecular function and/or structure, which could be related to adaptation to an amphibious lifestyle. AQP11 orthologues appear to be the most promising candidates to have facilitated the processes of the water-to-land transition in amphibious fishes. Additionally, the signature of positive selection found in the AQP11b stem branch of the Gobiidae clade suggests a possible case of exaptation in this clade. Full article
(This article belongs to the Special Issue Evolution and Ecology of Phenotypes in Nature)
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12 pages, 3252 KiB  
Article
Bergmann’s Rule under Rocks: Testing the Influence of Latitude and Temperature on a Chiton from Mexican Marine Ecoregions
by Raquel Hernández-P, Hugo A. Benítez, Claudia Patricia Ornelas-García, Margarita Correa, Manuel J. Suazo and Daniel Piñero
Biology 2023, 12(6), 766; https://doi.org/10.3390/biology12060766 - 24 May 2023
Cited by 1 | Viewed by 2247
Abstract
Bergmann’s rule relates the trend of increasing body size with higher latitudes, where colder climates are found. In the Mexican Pacific, three marine ecoregions are distinguishable across a latitudinal gradient. Stenoplax limaciformis is an abundant chiton species that is distributed on rocky shores [...] Read more.
Bergmann’s rule relates the trend of increasing body size with higher latitudes, where colder climates are found. In the Mexican Pacific, three marine ecoregions are distinguishable across a latitudinal gradient. Stenoplax limaciformis is an abundant chiton species that is distributed on rocky shores in these ecoregions. Geometric morphometric analyses were performed to describe the shape and size variation of S. limaciformis between marine ecoregions that vary in sea surface temperature with latitude, thus testing Bergmann’s rule. Individuals’ body shape ranged from elongated to wide bodies. Although there was variation in chitons’ body shape and size, the was no evidence of allometry among localities. The Gulf of California is the northernmost ecoregion evaluated in this work, where larger chitons were observed and lower sea surface temperature values were registered. The results suggest that S. limaciformis follows a trend to Bergmann’s rule, such as endotherms. These mollusks do not need heat dissipation, but they do need to retain moisture. In addition, larger chitons were observed in zones with high primary productivity, suggesting that chitons do not delay their maturation due to food shortage. Full article
(This article belongs to the Special Issue Evolution and Ecology of Phenotypes in Nature)
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19 pages, 2512 KiB  
Article
The Application of Quantitative Metabolomics for the Taxonomic Differentiation of Birds
by Ekaterina A. Zelentsova, Lyudmila V. Yanshole, Yuri P. Tsentalovich, Kirill A. Sharshov and Vadim V. Yanshole
Biology 2022, 11(7), 1089; https://doi.org/10.3390/biology11071089 - 21 Jul 2022
Cited by 7 | Viewed by 2662
Abstract
In the current pilot study, we propose the use of quantitative metabolomics to reconstruct the phylogeny of vertebrates, namely birds. We determined the concentrations of the 67 most abundant metabolites in the eye lenses of the following 14 species from 6 orders of [...] Read more.
In the current pilot study, we propose the use of quantitative metabolomics to reconstruct the phylogeny of vertebrates, namely birds. We determined the concentrations of the 67 most abundant metabolites in the eye lenses of the following 14 species from 6 orders of the class Aves (Birds): the Black kite (Milvus migrans), Eurasian magpie (Pica pica), Northern raven (Corvus corax), Eurasian coot (Fulica atra), Godlewski’s bunting (Emberiza godlewskii), Great crested grebe (Podiceps cristatus), Great tit (Parus major), Hawfinch (Coccothraustes coccothraustes), Hooded crow (Corvus cornix), House sparrow (Passer domesticus), Rock dove (Columba livia), Rook (Corvus frugilegus), Short-eared owl (Asio flammeus) and Ural owl (Strix uralensis). Further analysis shows that the statistical approaches generally used in metabolomics can be applied for differentiation between species, and the most fruitful results were obtained with hierarchical clustering analysis (HCA). We observed the grouping of conspecific samples independently of the sampling place and date. The HCA tree structure supports the key role of genomics in the formation of the lens metabolome, but it also indicates the influence of the species lifestyle. A combination of genomics-based and metabolomics-based phylogeny could potentially resolve arising issues and yield a more reliable tree of life. Full article
(This article belongs to the Special Issue Evolution and Ecology of Phenotypes in Nature)
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13 pages, 2227 KiB  
Article
Evolvability in the Cephalothoracic Structural Complexity of Aegla araucaniensis (Crustacea: Decapoda) Determined by a Developmental System with Low Covariational Constraint
by Erwin M. Barría, Hugo A. Benítez and Cristián E. Hernández
Biology 2022, 11(7), 958; https://doi.org/10.3390/biology11070958 - 24 Jun 2022
Cited by 1 | Viewed by 1669
Abstract
The integration of complex structures is proportional to the intensity of the structural fusion; its consequences are better known than the covariational effects under less restrictive mechanisms. The synthesis of a palimpsest model based on two early parallel pathways and a later direct [...] Read more.
The integration of complex structures is proportional to the intensity of the structural fusion; its consequences are better known than the covariational effects under less restrictive mechanisms. The synthesis of a palimpsest model based on two early parallel pathways and a later direct pathway explains the cephalothoracic complexity of decapod crustaceans. Using this model, we tested the evolvability of the developmental modularity in Aegla araucaniensis, an anomuran crab with an evident adaptive sexual dimorphism. The asymmetric patterns found on the landmark configurations suggest independent perturbations of the parallel pathways in each module and a stable asymmetry variance near the fusion by canalization of the direct pathway, which was more intense in males. The greater covariational flexibility imposed by the parallel pathways promotes the expression of gonadic modularity that favors the reproductive output in females and agonistic modularity that contributes to mating success in males. Under these divergent expressions of evolvability, the smaller difference between developmental modularity and agonistic modularity in males suggests higher levels of canalization due to a relatively more intense structural fusion. We conclude that: (1) the cephalothorax of A. araucaniensis is an evolvable structure, where parallel pathways promote sexual disruptions in the expressions of functional modularity, which are more restricted in males, and (2) the cephalothoracic palimpsest of decapods has empirical advantages in studying the developmental causes of evolution of complex structures. Full article
(This article belongs to the Special Issue Evolution and Ecology of Phenotypes in Nature)
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16 pages, 2440 KiB  
Article
Drosophila Wing Integration and Modularity: A Multi-Level Approach to Understand the History of Morphological Structures
by Hugo A. Benítez, Thomas A. Püschel and Manuel J. Suazo
Biology 2022, 11(4), 567; https://doi.org/10.3390/biology11040567 - 8 Apr 2022
Cited by 9 | Viewed by 2947
Abstract
Static, developmental, and evolutionary variation are different sources of morphological variation which can be quantified using morphometrics tools. In the present study we have carried out a comparative multiple level study of integration (i.e., static, developmental, and evolutionary) to acquire insight about the [...] Read more.
Static, developmental, and evolutionary variation are different sources of morphological variation which can be quantified using morphometrics tools. In the present study we have carried out a comparative multiple level study of integration (i.e., static, developmental, and evolutionary) to acquire insight about the relationships that exist between different integration levels, as well as to better understand their involvement in the evolutionary processes related to the diversification of Drosophila’s wing shape. This approach was applied to analyse wing evolution in 59 species across the whole genus in a large dataset (~10,000 wings were studied). Static integration was analysed using principal component analysis, thus providing an integration measurement for overall wing shape. Developmental integration was studied between wing parts by using a partial least squares method between the anterior and posterior compartments of the wing. Evolutionary integration was analysed using independent contrasts. The present results show that all Drosophila species exhibit strong morphological integration at different levels. The strong integration and overall similarities observed at multiple integration levels suggest a shared mechanism underlying this variation, which could result as consequence of genetic drift acting on the wing shape of Drosophila. Full article
(This article belongs to the Special Issue Evolution and Ecology of Phenotypes in Nature)
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