Projet de thèse 2016 -2019 :
Une perspective génomique de l’évolution en petite taille de population: le cas des oiseaux endémiques de la Réunion

Résumé scientifique: Les îles océaniques, c’est à dire qui n’ont jamais était connecté à une masse continentale, constituent de véritables laboratoires à ciel ouvert pour étudier l’évolution. Les rares espèces qui ont eu l’opportunité de coloniser ces habitats ont évolué indépendamment de leurs ancêtres continentaux et souvent de manière extravagante. Dans ce projet, nous proposons d’étudier l’évolution des espèces insulaires du point de leurs génomes. Les îles océaniques constituent une opportunité unique d’étudier l’impact de la taille des populations sur l’évolution moléculaire et la structure des génomes. Dans le présent projet, le candidat analysera un jeu de données de génomique des populations pour quatres d’espèces insulaires et continentales appartenant au genre Zosterops.

Des détails (en anglais) sur le projet est disponible ci-dessous.

Profil candidat : Nous recherchons un(e) candidat(e) ayant des bases en biologie de l’évolution et génétique des populations et un intérêt marqué pour comprendre les processus évolutifs au niveau moléculaire. Elle/il devra s’investir dans l’analyse de jeux de données de taille génomique. Un intérêt pour la programmation informatique et l’analyse statistique est fortement recommandé.

Descriptif de l’encadrement de la thèse : La thèse sera co-encadrée par Benoit Nabholz (Maître de Conférences, ISEM, Montpellier) et Nicolas Galtier (DR CNRS, ISEM, Montpellier). Elle sera aussi suivie par les partenaires du projet collaboratif (ANR) dans lequel elle s’inscrit (Pierre-Alexandre Gagnaire & Céline Scornovacca, CNRS, ISEM, Montpellier)

Pour postuler: La thèse débutera en septembre 2016. Les dossiers de candidatures, comprenant un CV, une lettre de motivation, les bulletins de notes de Master 1 et 2 (provisoire), et un ou deux contacts susceptibles de donner un avis sur le candidat devront être adressés à Benoit Nabholz ([email protected]) et Nicolas Galtier ([email protected]) à partir d’aujourd’hui.

Scientific abstract : Oceanic islands provide great opportunities for studying biological evolution (Losos and Ricklefs 2009). From gene sequence to genome size, understanding the influence of population size variation on molecular evolution is currently a major topic of the field (Lynch 2007; Wright and Andolfatto 2008; Ellegren 2009; Woolfit 2009) that, itself, is grounded in the fifty years old neutralist-selectionist debate (Kimura 1983; Gillespie 1991). Since island species have evolved in isolated and small populations, they provide an unique opportunity to study the impact of non-adaptive forces on biological evolution.

In this project, we propose to investigate island evolution from a genomic point-of-view. The candidate will have to analyses a population genomic dataset for two island endemic bird species and their mainland relatives, using endemic birds (White-eyes of the genus Zosterops) of the Réunion Island and their mainland south-African relative as model organisms. Indeed, mainland/island comparison provide one of the best empirical set-up to study the impact of non-adaptive forces on genome evolution in natural population. This project aims at gathering a genome-wide dataset of island and mainland White-eyes, already partially available, to be able to tackle two fundamentals questions in molecular evolution :

1) What is the effect of population size variation on the efficacy of selection at the molecular level ?
Using a genome-wide dataset, the level of purifying and positive selection will be estimated by contrasting the pattern of polymorphism and divergence in putatively functional regions against the patterns observed in introns and intergenic sequences. Comparing these estimates between mainland and islands populations will allow us to (i) test how much the efficacy of selection is reduced in island populations and (ii) establish if different regions of the genome are differentially affected by the reduction in population size.

2) What is the effect of population size on genome architecture?
Using complete genome sequences, we propose to study the microevolution of the genome size between island and mainland species. The fraction of non-coding DNA (including repetitive DNA sequences) and the number of duplicated genes will be estimated and compared among island/mainland populations. This work represents a attempt to test, at a low evolutionary time-scale, if the evolution of genome architecture is influence by non-adaptive force such as genetic drift (Lynch 2007).

Finally, depending on the candidate’s interest, the datasets could also be used to tackle other interesting evolutionary questions related to sex chromosomes evolution and the genomic of speciation.

References
Ellegren H. 2009. A selection model of molecular evolution incorporating the effective population size. Evolution 63:301–305.
Gagnaire P-A, Normandeau E, Bernatchez L. 2012. Comparative genomics reveals adaptive protein evolution and a possible cytonuclear incompatibility between European and American Eels. Mol. Biol. Evol. 29:2909–2919.
Gagnaire P-A, Pavey SA, Normandeau E, Bernatchez L. 2013. The genetic architecture of reproductive isolation during speciation-with-gene-flow in lake whitefish species pairs assessed by RAD sequencing. Evol. Int. J. Org. Evol. 67:2483–2497.
Gillespie JH. 1991. The causes of molecular evolution. Oxford University Press, USA
Gossmann TI, Keightley PD, Eyre-Walker A. 2012. The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes. Genome Biol. Evol. 4:658–667.
Gregory TR. 2002. A bird’s-eye view of the C-value enigma: genome size, cell size, and metabolic rate in the class aves. Evol. Int. J. Org. Evol. 56:121–130.
Künstner A, Nabholz B, Ellegren H. 2011a. Significant selective constraint at 4-fold degenerate sites in the avian genome and its consequence for detection of positive selection. Genome Biol. Evol. 3:1381–1389.
Künstner A, Nabholz B, Ellegren H. 2011b. Evolutionary constraint in flanking regions of avian genes. Mol. Biol. Evol. 28:2481–2489.
Lanfear R, Kokko H, Eyre-Walker A. 2014. Population size and the rate of evolution. Trends Ecol. Evol. 29:33–41.
Loire E, Chiari Y, Bernard A, Cahais V, Romiguier J, Nabholz B, Lourenço JM, Galtier N. 2013. Population genomics of the endangered giant Galapagos tortoise. Genome Biol. 14:R136.
Lynch M. 2007. The Origins of Genome Architecture. Sinauer Associates.
Losos J & Ricklefs RE. 2009.Adaptation and diversification on islands. Nature 457, 830-836
Milá B, Warren BH, Heeb P, Thébaud C. 2010. The geographic scale of diversification on islands: genetic and morphological divergence at a very small spatial scale in the Mascarene grey white-eye (Aves: Zosterops borbonicus). BMC Evol. Biol. 10:158.
Nabholz B, Ellegren H, Wolf JBW. 2013. High Levels of Gene Expression Explain the Strong Evolutionary Constraint of Mitochondrial Protein-Coding Genes. Mol. Biol. Evol. 30:272–284.
Nabholz B, Künstner A, Wang R, Jarvis ED, Ellegren H. 2011. Dynamic evolution of base composition: causes and consequences in avian phylogenomics. Mol. Biol. Evol. 28:2197–2210.
Nabholz B, Uwimana N, Lartillot N. 2013. Reconstructing the Phylogenetic History of Long-Term Effective Population Size and Life-History Traits Using Patterns of Amino Acid Replacement in Mitochondrial Genomes of Mammals and Birds. Genome Biol. Evol. 5:1273–1290.
Nguyen L-P, Galtier N, Nabholz B (2015) Gene expression, chromosome heterogeneity and the fast-X effect in mammals. Biology Letters, 11, 20150010.
Ohta T. 1992. The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Syst. 23:263–286.
Woolfit M. 2009. Effective population size and the rate and pattern of nucleotide substitutions. Biol. Lett. 5:417–420.
Woolfit M, Bromham L. 2005. Population size and molecular evolution on islands. Proc. Biol. Sci. 272:2277–2282.
Wright SI, Andolfatto P. 2008. The impact of natural selection on the genome: emerging patterns in drosophila and arabidopsis. Annu. Rev. Ecol. Evol. Syst. 39:193–213.

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