CNRS · ISEM · Montpellier

Camille Roux

Ongoing research

ANR PRCI project, co-led by Camille Roux and Ovidiu Paun.

RadiaSpe: Exploring drivers of reproductive isolation in plant evolutionary radiations

RadiaSpe asks whether plant evolutionary radiations are accompanied by faster accumulation of reproductive barriers, and which ecological and genomic mechanisms contribute to this acceleration.

Evolutionary radiations generate striking bursts of species diversity, but it remains unclear whether they also correspond to faster accumulation of barriers to gene flow. RadiaSpe addresses this question in two plant genera, Diospyros and Tillandsia, where radiating and non-radiating clades can be compared within the same evolutionary framework.

Biological systems

Diospyros, a genus used in RadiaSpe to compare radiating and non-radiating lineages — Diospyros

Diospyros includes a rapid New Caledonian radiation alongside non-radiating relatives, providing a comparative framework to study the genomic and ecological drivers of diversification.

Tillandsia, a diverse bromeliad genus studied in RadiaSpe — Tillandsia

Tillandsia is a diverse bromeliad genus with strong variation in ecology, morphology, photosynthetic strategies, and pollination-related traits.

WP1: Gene flow and reproductive barriers

Compare radiating and non-radiating clades to test whether reproductive barriers accumulate faster during evolutionary radiations.

WP2: Ecological determinants

Assess whether pollinators, soil chemistry, climate, morphology, and other ecological factors help explain divergence among closely related species.

WP3: Genomic determinants

Characterize selection, structural variation, transposable elements, and other genomic features that may contribute to diversification.

Participants

Camille Roux CNRS, Institut des Sciences de l'Évolution de Montpellier (ISEM)
Ovidiu Paun University of Vienna, Department of Botany and Biodiversity Research
Bert Van Bocxlaer CNRS, Université de Lille
Thibault Leroy INRAE, GenPhySE, Toulouse
Christelle Fraïsse CNRS, Institut des Sciences de l'Évolution de Montpellier (ISEM)

Past research

Comparative curve showing genetic connectivity declining with net divergence in animals and plants

2025 Science

Rapid establishment of species barriers in plants compared with that in animals

Last author

We show that plants tend to lose genetic connectivity faster than animals at comparable levels of genomic divergence, suggesting faster establishment of species barriers in plants.

Diagram and photographs illustrating cross-species cloning in Messor ants

2025 Nature

One mother for two species via obligate cross-species cloning in ants

Co-author

Juvé et al. reveal an extraordinary reproductive system in Messor ants, where M. ibericus queens produce males of another species and require their sperm to generate workers.

Demographic models used to infer genetic isolation among Silene nutans lineages

2025 Plant and Cell Physiology

Genetic Isolation among Four Lineages of Silene nutans

Co-author

Postel et al. use DILS and transcriptomic data to show that four Silene nutans lineages diverged in strict isolation, with rapid reproductive isolation possibly linked to plastid–nuclear incompatibilities.

Likelihood profiles for pollen-acting genetic incompatibilities in Arabidopsis

2025 Evolution Letters

Diverging Arabidopsis populations quickly accumulate pollen-acting genetic incompatibilities

Co-author

Condon et al. show that pollen-acting segregation distortion can arise rapidly within and between Arabidopsis lineages, suggesting that haploid-stage incompatibilities may contribute early to reproductive isolation.

Phylogenetic tree of Blattodea with dN/dS estimates highlighting termites

2024 Peer Community Journal

The impact of social complexity on the efficacy of natural selection in termites

First author

We show that termites have elevated dN/dS compared with other Blattodea, suggesting that eusociality and social complexity reduce the genome-wide efficacy of natural selection.

Effective population size through time for several Ophrys aveyronensis populations

2024 Journal of Biogeography

Holocene climate change promoted allopatric divergence and disjunct geographic distribution in a bee orchid species

Co-author

Gibert et al. combine population genomics and ecological niche modelling to show that Holocene climate change promoted recent allopatric divergence between disjunct Ophrys aveyronensis populations.

Conceptual models of polyploid origin and inheritance mode

2023 Methods in Molecular Biology Book chapter

Inferring the Demographic History and Inheritance Mode of Tetraploid Species Using ABC

First author

We present an ABC framework to infer the demographic history, origin, and inheritance mode of tetraploid species from population genomic data.

Evolutionary scenario for the spread of the fire ant social supergene

2022 PNAS

Radiation and hybridization underpin the spread of the fire ant social supergene

Co-author

Helleu et al. reconstruct the evolutionary history of the fire ant social supergene, showing that it assembled through sequential inversions before spreading across species boundaries by introgression.

Genomic scan showing a localized introgression hotspot in Ciona

2022 Peer Community Journal

Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?

Co-author

Fraïsse et al. show that introgression between highly divergent Ciona genomes is rare overall but concentrated in a chromosome 5 hotspot, with signatures consistent with recent positive selection.

Population graph showing migration and admixture among Sonchus oleraceus populations

2022 Diversity and Distributions

Population genomics reveal multiple introductions and admixture of Sonchus oleraceus in Australia

Co-author

Encinas-Viso et al. reconstruct the invasion history of Sonchus oleraceus in Australia, revealing multiple introductions, admixture, and a more complex demographic history than a single recent colonization.

Map of Arctic sampling sites for an ivory gull demographic study

2022 Heredity

Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations

Co-author

Charbonnel et al. test for genetic signatures of demographic decline in the ivory gull and show that overlapping generations can delay or weaken bottleneck signals in long-lived species.

Map and divergence plot illustrating demographic inference with DILS

2021 Molecular Ecology Resources

DILS: Demographic inferences with linked selection by using ABC

Last author

We present DILS, a statistical platform for demographic inference from population genomic data, designed to compare models of divergence, gene flow, linked selection, and genomic heterogeneity.

Population structure and shell diversity in viviparid gastropods of the Lake Victoria ecoregion

2021 Molecular Ecology

Population collapse in viviparid gastropods of the Lake Victoria ecoregion started before the Last Glacial Maximum

Co-author

Van Bocxlaer et al. use microsatellites and ABC to show that viviparid gastropods in the Lake Victoria ecoregion experienced a severe population decline that began well before the Last Glacial Maximum.

Three-dimensional flight tracks of Morpho butterflies around male and female dummies

2021 Nature Communications

Convergent morphology and divergent phenology promote the coexistence of Morpho butterfly species

Co-author

Le Roy et al. show that closely related Morpho butterflies can remain genetically isolated despite convergent wing patterns, partly through temporal segregation in male flight activity.

Diagram of the three floral morphs in a tristylous plant system

2019 New Phytologist

The opposing effects of genetic drift and Haldane’s sieve on floral-morph frequencies in tristylous metapopulations

First author

We use simulations of tristylous metapopulations to show how genetic drift and Haldane’s sieve can have opposing effects on floral morph frequencies.

Relationship between propagule size and the number of preferred codons in animals

2018 Molecular Biology and Evolution

Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion

Co-author

Galtier et al. disentangle translational selection from GC-biased gene conversion across 30 animal species, showing that codon usage is shaped by selection mainly in large-Ne species.

Demographic model and parameter estimates for divergence in Linaria cavanillesii

2018 Journal of Evolutionary Biology

The divergence history of the perennial plant Linaria cavanillesii confirms a recent loss of self-incompatibility

Co-author

Voillemot et al. use ABC to show that the self-compatible population of Linaria cavanillesii diverged recently from self-incompatible populations, suggesting an intermediate stage in the transition toward selfing.

Workflow for candidate Y-linked marker identification and confirmation in Mercurialis annua

2018 Genes

Size and Content of the Sex-Determining Region of the Y Chromosome in Dioecious Mercurialis annua, a Plant with Homomorphic Sex Chromosomes

Co-author

Veltsos et al. characterize the sex-determining region of the Y chromosome in Mercurialis annua, showing that a plant with homomorphic sex chromosomes can nevertheless carry a large non-recombining region.

Joint site frequency spectrum summaries used for ABC inference in blue mussels

2018 PeerJ

The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: the effects of sequencing techniques and sampling strategies

Co-author

Fraïsse et al. evaluate ABC demographic inference in European blue mussels, showing that conclusions depend strongly on how genomic data are summarized and modelled.

Circular phylogenetic tree showing relationships among European white oak species

2017 New Phytologist

Extensive recent secondary contacts between four European white oak species

Co-author

Leroy et al. show that four European white oak species evolved largely in isolation before recent secondary contacts, leaving genomes shaped by both introgression and barriers to gene flow.

Diagram summarizing analytical biases associated with GC-content and GC-biased gene conversion

2017 Frontiers in Genetics

Analytical Biases Associated with GC-Content in Molecular Evolution

Last author

We review how GC-content heterogeneity and GC-biased gene conversion can bias phylogenetic reconstruction, tests of positive selection, and estimates of codon usage.

Plot showing the grey zone of speciation along a continuum of genomic divergence

2016 PLOS Biology

Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence

First author

We show that the grey zone of speciation in animals spans roughly 0.5–2% net synonymous divergence, where many lineages are semi-isolated and exchange genes at some loci but not others.

Map of European river and brook lamprey sampling sites

2016 PeerJ

Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations

Co-author

Rougemont et al. use ABC and random forests to compare divergence-with-gene-flow and secondary-contact scenarios in European river and brook lampreys.

Genome-wide scan of SNP weights used to detect candidate regions for reinforcement in house mice

2015 Molecular Ecology

Seeking signatures of reinforcement at the genetic level: a hitchhiking mapping and candidate gene approach in the house mouse

Co-author

Smadja et al. search for genetic signatures of reinforcement in the house mouse hybrid zone, using candidate regions linked to assortative mating and olfactory preference.

Models of polyploid speciation and inheritance modes

2015 Molecular Ecology

Inferring the mode of origin of polyploid species from next-generation sequence data

First author

We show that ABC can infer the origin and inheritance mode of polyploid species from sequence data, and support an allopolyploid origin of Capsella bursa-pastoris.

Relationship between fecundity, propagule size, and genetic diversity across animals

2014 Nature

Comparative population genomics in animals uncovers the determinants of genetic diversity

Co-author

Romiguier et al. show across 76 non-model animal species that genetic diversity is strongly associated with life-history traits, especially the trade-off between offspring quantity and quality.

Posterior distributions of migration rates across loci in a Mytilus hybrid zone

2014 Journal of Evolutionary Biology

Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a Mytilus hybrid zone

First author

We show that accounting for heterogeneity in introgression rates across loci changes the inferred history of the Mytilus hybrid zone, supporting secondary contact after a long period of allopatric divergence.

Chromosome map showing genomic hotspots of introgression in Ciona

2013 Molecular Biology and Evolution

Crossing the Species Barrier: Genomic Hotspots of Introgression between Two Highly Divergent Ciona intestinalis Species

First author

We detect recent secondary introgression between two highly divergent Ciona intestinalis species and identify genomic hotspots of gene flow across an otherwise strong species barrier.

Nucleotide diversity and divergence patterns around the S-locus in Arabidopsis

2012 Molecular Biology and Evolution

Recent and Ancient Signature of Balancing Selection around the S-Locus in Arabidopsis halleri and A. lyrata

First author

We show that balancing selection at the self-incompatibility S-locus leaves both recent and ancient signatures in nearby genes, but that recombination rapidly confines this effect to a narrow genomic region.

Estimated timing of Arabidopsis halleri HMA4 duplication relative to species divergence

2011 PLOS ONE

Does Speciation between Arabidopsis halleri and Arabidopsis lyrata Coincide with Major Changes in a Molecular Target of Adaptation?

First author

We show that major changes at the metal-homeostasis gene HMA4 in Arabidopsis halleri likely coincided with the split from A. lyrata, suggesting that adaptation to heavy metals was linked to speciation history.