Thèse Étude des Mécanismes de la Diversification Cryptique des Microcèbes Genre Microcebus Cheirogaleidae Primates H/F - Doctorat.Gouv.Fr

Établissement : Université de Toulouse École doctorale : SEVAB - Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingenieries Laboratoire de recherche : CRBE - Centre de Recherche sur la Biodiversité et l'Environnement Direction de la thèse : Lounès CHIKHI ORCID 0000000211400718 Début de la thèse : 2026-10-01 Date limite de candidature : 2026-06-01T23:59:59 Madagascar est une région exceptionnellement riche en biodiversité et joue un rôle majeur dans l'étude des processus de diversification. Plusieurs scénarios ont été proposés pour expliquer la richesse de la biodiversité de Madagascar et sa répartition spatiale, comme le rôle des oscillations climatiques, des bassins versants, de l'altitude ou des rivières. Une étude récente portant sur le genre Microcebus, un genre de primate morphologiquement peu variable, mais diversifié avec environ 20 espèces, a montré que la diversification de ce groupe semblait avoir été facilitée par un effet de 'pompe à espèces' dans la forêt tropicale humide et les fluctuations climatiques lors de la fin du Pléistocène. Cependant, ce scénario reste encore à démontrer et d'autres études suggèrent que différents épisodes de flux génique entre espèces non sympatriques pourraient avoir laissé des traces dans les génomes de ces espèces. Le projet de doctorat vise à comprendre les mécanismes évolutifs à l'origine de la radiation cryptique en utilisant des données génomiques déjà obtenues sur l'ensemble des espèces du genre. Cette étude explorera les mécanismes géographiques, moléculaires et écologiques qui ont contribué à cette diversification.
Madagascar's rich biodiversity is a recognized model for the study of diversification1,2 and a major conservation priority3,4,5. Several diversification hypotheses have been proposed to explain Madagascar astonishing biodiversity and its spatial distribution1,2,5, such as the role of climatic oscillations, watersheds, elevation and rivers. With up to 120 described species, the radiation of Malagasy primates, the iconic lemurs, represents a unique setup to investigate diversification processes in a natural lab1,6. In particular, the diversity of microendemic6 and cryptic10 taxa is little investigated due to their restricted distributions and low phenotypic distinctiveness. A recent innovative integrative framework leveraged genomic, morphological, ecological, and behavioral data, to clarify the evolutionary relationships and the cryptic diversification processes of the highly speciose mouse lemur primate genus (Microcebus)11. Following a revised taxonomy, this study demonstrated that mouse lemur cryptic diversification was possibly facilitated by climatic fluctuations and a species-pump effect of humid rainforests during the late Pleistocene. This comprehensive genomic, morphological, ecological, and behavioral dataset offers the unique opportunity to answer several long-standing evolutionary questions, and more specifically to evaluate the roles of geographic12, molecular13 and behavioral14 mechanisms in driving the cryptic diversification in mouse lemurs.
Most mouse lemurs are thought to have speciated in allopatry during the late Pleistocene climatic oscillations, therefore suggesting a prevalent role of geographic barriers (e.g. rivers, grasslands) in initiating divergence events6,12. However, recent and ancient gene flows have been inferred across the mouse lemur radiation15,16,17, but only between currently allopatric species and not among those co-occurring in sympatry18,19, questioning the timing and nature of reproductive isolation20 in mouse lemurs. Pre-zygotic reproductive isolation in mouse lemurs has been suggested to take the form of shifted reproductive schedules11, acoustic14 and olfactory signatures13,21. In contrast, at the post-zygotic level, little is known about possible molecular mechanisms facilitating or limiting the diversification of the genus. Similarly, nothing is known about possible coupling processes22,23 among the above-mentioned mechanisms. The timely understanding of the driving forces of the rapid cryptic diversification in this emerging primate model organism24,25, will be of fundamental evolutionary and applied interest for biomedical25,26 and conservation3,4,5 purposes. The objective of this study is to comprehensively identify and understand the evolutionary mechanisms driving the rapid radiation of mouse lemurs (genus Microcebus). To achieve this, the study aims to explore the (1) biogeographic and (2) molecular mechanisms driving mouse lemur diversification and (3) evaluate the contributions of shifts in reproductive and sensorial recognition mechanisms to this exceptional radiation. Ultimately, (4) it will integrate findings from these analyses to develop a comprehensive understanding of the mechanisms underlying the rapid diversification of mouse lemurs. The PhD work will predominantly rely on the analysis of genomic data generated over the past decade within the mouse lemur phylogenomic consortium. Thus, the data available represent the most comprehensive genomic, morphological, acoustic, behavioral and geographical occurrence datasets ever compiled for a non-human primate genus. It results from the efforts of more than 50 collaborators, through more than 30 years of field research, across the still largely unexplored and inaccessible forests of Madagascar. Most of the analyses detailed below will focus on dense genome-wide RADseq27 data available for > 1000 individuals, from all recognised species and across hundreds of populations. The project also benefits from a chromosome-level high-quality reference genome28, multiple sister species genome-wide data11,15,18,19,29,30,31 and genome re-sequencing data generated either within or outside the consortium15,17 and at the CRBE.
The innovative nature of this dataset resides in its composition of replicates spanning the 'speciation continuum,' encompassing multiple pairs of: (i) population-structured species, (ii) incipient species, (iii) sister species, and (iv) long-diverged sympatric species. This comprehensive dataset, characterized by its numerous replicates, will enable the PhD candidate to statistically test alternative diversification mechanisms across the evolutionary strata represented within the continuum.
1. Assessing the role of geography. The potential role of geographic barriers (e.g. rivers, grasslands) in generating diversity and initiating allopatric divergence events6,12, will be evaluated using landscape genomics32 and biogeographic reconstructions40-41. Autosomes, allosomes and plastid DNA will be explicitly considered to integrate the potential effects of sex-biased dispersal42. The above-mentioned replicates along the speciation continuum'11 will allow evaluating the timescale, strength and generality underlying the effect of each landscape feature. Dedicated efforts will focus on the role of rivers12 and forests33, under current and past configurations across late quaternary climatic fluctuations.
2. Making sense of genomic islands of differentiation. The presence of genomic regions of elevated differentiation compared to the levels expected under neutrality may indicate the presence of selective or adaptive processes. Some authors use the terminology of speciation genes or barrier loci. We will investigate the potential causal relationship between genes identified using a top-down approach relying on genome scans34. The experimental setup, composed of replicated sampling along the speciation continuum11,43, will be pivotal to distinguish genomic footprints of adaptation and reproductive isolation from signatures of confounding factors35 (e.g. recombination rate heterogeneity, drift, background and linked selection). Gene flow36 and recombination landscapes37 will be inferred from population based approaches. Identified outlier regions will be potentially narrowed using a posteriori search for candidate genes35.
3. Evaluating the role of reproductive phenology and sensorial recognition. Pre-zygotic reproductive isolation44 in mouse lemur has been suggested to take the form of shifted reproductive schedules11, acoustic14 and olfactory signatures13,21. We will investigate the signatures of differentiation35 and selection39 with a bottom-up focus on the genes previously identified as playing major roles in these processes, for instance WFDC1221, V1R-strep13. We will evaluate the presence of signatures at the gene scale, in its surrounding region, and at the scale of its network of interacting genes. Again, here, the above-mentioned experimental setup will be pivotal to compare signatures among replicates and along the speciation continuum35. Optional field work may be planned to increase sampling and acoustic signature recordings in regions of sympatry and along barriers to gene flow.

Bonne connaissance des méthodes de génomique et de génétique des populations. Maîtrise des bases de R, BASH, SLURM. Bases en SIG seraient un plus. Qualité organisationnelle et indépendance, capacité de travailler de manière collaborative et capacité d'initiative.