Project

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Adaptive evolution and key innovation in Neotropical fishes

English title Adaptive evolution and key innovation in Neotropical fishes
Applicant Montoya-Burgos Juan-Ignacio
Number 141233
Funding scheme Project funding (Div. I-III)
Research institution Département de Génétique et Evolution Faculté des Sciences Université de Genève
Institution of higher education University of Geneva - GE
Main discipline Genetics
Start/End 01.11.2012 - 30.04.2016
Approved amount 358'000.00
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All Disciplines (2)

Discipline
Genetics
Embryology, Developmental Biology

Keywords (5)

skeletogenesis; Evolution; Development; Adaptation; Selection

Lay Summary (French)

Lead
Titre Evolution adaptative et innovation clé chez les poissons cuirassés néotropicauxLeadUne grande partie de la biodiversité rencontrée sur notre planète semble provenir d’explosions de spéciations adaptatives. Les processus impliqués dans l’évolution adaptative sont donc centraux pour comprendre l’émergence de biodiversité. Cependant, les mécanismes génétiques responsables de l’évolution de traits adaptatifs sont encore mal compris.
Lay summary

Contenu et objectifs

Les objectifs sont d’investiguer l’évolution de gènes impliqués dans des réponses adaptatives et de comprendre l’apparition d’innovations clés à l’origine de diversifications exceptionnelles. Les poissons chats de la famille Loricariidae ont été choisis comme modèle car ils montrent une extraordinaire diversité d’espèces.

Dans la première partie de ce travail, nous investiguerons les changements génétiques qui sont à l’origine de l’innovation clé responsable du succès évolutif de cette famille. Cette innovation est une cuirasse composée d’os dermiques recouverts de dents, une protection contre les prédateurs. Chez les vertébrés, ces structures dérivent des cellules de la crête neurale et sont normalement présentent dans la région de la tête.

Dans la deuxième partie, nous caractériserons les gènes impliqués dans l’évolution de traits adaptatifs et nous établirons des corrélations entre l’émergence de mutations adaptatives et des phénotypes. Nous déterminerons également les fonctions biologiques les plus soumises à des pressions adaptatives, jouant donc un rôle important dans l’évolution adaptative.

Signification

Ce travail générera des informations essentielles quant aux mécanismes impliqués dans l’évolution adaptative et sont rôle dans l’émergence de nouvelles biodiversités. Il générera aussi des informations sur les mécanismes qui spécifient la destinée des cellules de crête neurale pour former des structures particulières en des endroits précis du corps. Les Loricariidae deviendront un modèle pour l’étude de la formation et de la régénération des os dermiques et des dents.

 

Direct link to Lay Summary Last update: 06.03.2013

Lay Summary (English)

Lead
Adaptive evolution and key innovation in Neotropical fishesLeadA significant part of the functional diversity of life on earth is thought to have evolved through multiple bursts of adaptive speciation. The process of adaptive evolution is therefore central in the field of evolutionary biology and the understanding of the genetic mechanisms underlying the evolution of adaptive traits remains a challenging task.
Lay summary

Objectives and content

The aims of this project are to investigate the evolution of genes that are involved in adaptive responses and to understand the emergence of a key innovation that is thought to be responsible for the outstanding species diversification in a phenotypic-rich family of catfishes, the Loricariidae.


Loricariids display an exceptional external skeleton composed of dermal bony plates covered with teeth. In vertebrates, these skeletal structures derive from neural crest cells and are normally restricted to the head region. In the first part of this project we will investigate the genetic changes that originated the development of head structures all over the body of loricariids.
The second subproject will consist in the characterization of genes involved in the evolution of adaptive traits and to establish correlations between the emergences of positively selected mutations and particular phenotypes. We will determine whether particular biological functions are enriched in positively selected genes and, therefore, have important roles in adaptive evolution.

 

Significance of the results

The expected outcomes will not only contribute to the understanding of the process underlying adaptive evolution, but will certainly offer new insights into the mechanisms of neural crest cells fate specification. Loricariids may become an innovative and naturally occuring model system to study dermal bones and tooth development.

Direct link to Lay Summary Last update: 06.03.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Cryptic Biological Invasions: a General Model of Hybridization
Quilodrán Claudio S., Austerlitz Frédéric, Currat Mathias, Montoya-Burgos Juan I. (2018), Cryptic Biological Invasions: a General Model of Hybridization, in Scientific Reports, 8(1), 2414-2414.
Multifactorial genetic divergence processes drive the onset of speciation in an Amazonian fish
Jardim de Queiroz Luiz, Torrente-Vilara Gislene, Quilodran Claudio, Rodrigues da Costa Doria Carolina, Montoya-Burgos Juan I. (2017), Multifactorial genetic divergence processes drive the onset of speciation in an Amazonian fish, in PLOS ONE, 12(12), e0189349-e0189349.
Trunk dental tissue evolved independently from underlying dermal bony plates but is associated with surface bones in living odontode-bearing catfish
Rivera-Rivera Carlos J., Montoya-Burgos Juan I. (2017), Trunk dental tissue evolved independently from underlying dermal bony plates but is associated with surface bones in living odontode-bearing catfish, in Proceedings of the Royal Society B: Biological Sciences, 284(1865), 20171831-20171831.
LS³: A method for improving phylogenomic inferences when evolutionary rates are heterogeneous among Taxa
Rivera-Rivera C. J. Montoya-Burgos J. I (2016), LS³: A method for improving phylogenomic inferences when evolutionary rates are heterogeneous among Taxa, in Molecular Biology and Evolution, 33(6), 1625.
Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification
Covain R Fisch-Muller S Oliveira C Mol J H Montoya-Burgos J I Dray S (2016), Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification, in Molecular Phylogenetics and Evolution , (94), 492-517.
Modelling interspecific hybridization with genome exclusion to identify conservation actions: the case of native and invasive Pelophylax waterfrogs
Quilodran C. Montoya-Burgos J. I. Currat M (2015), Modelling interspecific hybridization with genome exclusion to identify conservation actions: the case of native and invasive Pelophylax waterfrogs, in Evolutionary Applications , 8(2), 199-210.
A General Model of Distant Hybridization Reveals the Conditions for Extinction in Atlantic Salmon and Brown Trout
Quilodran C. Currat M. Montoya-Burgos J. I (2014), A General Model of Distant Hybridization Reveals the Conditions for Extinction in Atlantic Salmon and Brown Trout, in PLoSONE, 9(7), e101736.
Positive selection drives sperm motility in the brittle star species complex Ophioderma longicauda
Weber A. A-T. Abi-Rached L. Galtier N. Bernard A. Montoya-Burgos J. I. and Chenuil A, Positive selection drives sperm motility in the brittle star species complex Ophioderma longicauda, in Molecular Ecology, 1111.

Collaboration

Group / person Country
Types of collaboration
Natural History Museum of Geneva Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Laboratory of Prof. Denis Duboule Switzerland (Europe)
- Research Infrastructure

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Biology18 Talk given at a conference Origin of genetic diversity in an Amazonian fishand how to belong to a same population despite being separated by a strong environmental barrier 15.02.2018 Neuchâtel, Switzerland Montoya-Burgos Juan-Ignacio;
Biology16 Talk given at a conference Factors influencing species richness in the most speciose group of vertebrates: Teleostei 11.02.2016 Lausanne, Switzerland Cauwet Lucie; Montoya-Burgos Juan-Ignacio;
Biology16 Poster LS³: an algorithm to identify problematic sequence data and to aid in the rescue of phylogenetic signal 11.02.2016 Lausanne, Switzerland Montoya-Burgos Juan-Ignacio; Rivera-Rivera Carlos Javier;
SMBE 2015 Talk given at a conference LS³: A Criterion-Based Method to Reduce Long Branch Attraction Artifact in Multi-Gene Phylogenies 11.07.2015 Vienne, Austria Rivera-Rivera Carlos Javier;
Biology14, Swiss Conference on Organisaml Biology Talk given at a conference Comparative transcriptomics reveals genes underlying adaptive evolution in catfishes 13.02.2014 Genève, Switzerland Hot Chloé;


Self-organised

Title Date Place
Biology14, Swiss Conference on Organismal Biology 13.02.2014 Genève, Switzerland

Communication with the public

Communication Title Media Place Year
Media relations: radio, television Des dents sur les corps des poissons-chats rts Western Switzerland 2017
Media relations: radio, television La sardine amazonienne, un bon indicateur de l'impact humain sur l'environnement rts Western Switzerland 2017
Media relations: radio, television LA SIXIÈME EXTINCTION, DES ESPÈCES MENACÉES rts Western Switzerland 2016

Associated projects

Number Title Start Funding scheme
122303 Genomic screen for adaptive genes in fishes 01.12.2008 Project funding (Div. I-III)
150817 High-throughput sequencing for research on evolution and ecology of microeukaryotes 01.12.2013 R'EQUIP
185327 Adaptive evolution and key innovation in Neotropical fishes 01.10.2019 Project funding (Div. I-III)
122303 Genomic screen for adaptive genes in fishes 01.12.2008 Project funding (Div. I-III)

Abstract

SUMMARY A significant part of the functional diversity of life on earth is thought to have evolved through multiple bursts of adaptive speciation. The process of adaptive evolution is therefore central in the field of evolutionary biology and the understanding of the genetic mechanisms underlying the evolution of adaptive traits remains a challenging task. This proposal is organized into two sub-projects that are aimed at investigating the evolution of genes that are involved in adaptive responses and to understand the emergence of a key innovation that is thought to be responsible for the outstanding species diversification in a phenotypic-rich group of freshwater fishes, the Loricariidae catfishes.Loricariids display an exceptional external skeleton composed of dermal bony plates covered with teeth. In vertebrates, these skeletal structures derive from neural crest cells and are normally restricted to the head region. In the first sub-project of this proposal we will investigate the genetic changes that originated the ectopic development of head structures all over the body of loricariids. We will use in situ hybridization techniques to reveal changes in gene expression patterns that may explain the development of the exoskeleton of loricariids. Other non-loricariid catfishes and the zebrafish will be used as controls. Grafting experiments will also be assayed to decipher the role played by the microenvironment in neural crest cells specification. We hypothesize that this genetic change opened new niches for ancestral loricariids and permitted an extensive diversification, a situation that parallels acquisition of jaws during vertebrate's evolution. This hypothesis will be tested by analyzing pairs of sister clades, with and without exoskeleton. Also, multivariate analyses will permit to identify the variables that explain the best the changes in diversification rates.The second-subproject will consist in the characterization of genes involved in the evolution of adaptive traits and to establish correlations between the emergences of positively selected mutations and particular phenotypes. We will determine whether particular biological functions are enriched in positively selected genes and, therefore, have important roles in adaptive evolution. The role played by lineage-specific positively selected genes will also be assessed. To these aims, we propose a new combination of state-of-the-art techniques to obtain homologous DNA sequences of interest in a large panel of closely related species.The expected outcomes of this proposal will not only contribute significantly to the understanding of the processes underlying adaptive evolution, but will certainly offer new insights into the mechanisms of neural crest cells fate specification. We speculate that lorcariid catfishes will become an innovative and naturally occurring model system to study dermal bones and tooth development.
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