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Introduction
Additional affiliations
January 2011 - present
January 2007 - December 2010
Ecole normale supérieure de Lyon
January 2007 - December 2010
Institut de Génomique Fonctionnelle,
Publications
Publications (82)
Background
Sex chromosomes change more frequently in fish than in mammals or birds. However, certain chromosomes or genes are repeatedly used as sex determinants in different members of the teleostean lineage. East African cichlids are an enigmatic model system in evolutionary biology representing some of the most diverse extant vertebrate adaptiv...
Background
The factors determining sex are diverse in vertebrates and especially so in teleost fishes. Only a handful of master sex-determining genes have been identified, however great efforts have been undertaken to characterize the subsequent genetic network of sex differentiation in various organisms. East African cichlids offer an ideal model...
Males and females of the same species differ largely in gene expression, which accounts for most of the morphological and physiological differences and sex-specific phenotypes. Here, we analyzed sex-specific gene expression in the brain and the gonads of cichlid fishes from Lake Tanganyika belonging to four different lineages, so-called tribes (Ere...
Teleost fishes are the most species-rich clade of vertebrates and feature an overwhelming diversity of sex-determining mechanisms, classically grouped into environmental and genetic systems. Here, we review the recent findings in the field of sex determination in fish. In the past few years, several new master regulators of sex determination and ot...
Sex determination mechanisms are highly variable across teleost fishes and sexual development is often plastic. Nevertheless, downstream factors establishing the two sexes are presumably conserved. Here, we study sequence evolution and gene expression of core genes of sexual development in a prime model system in evolutionary biology, the East Afri...
In this study we present an in-depth analysis of the Eurasian Minnow (Phoxinus phoxinus) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated an annotated haplotype-phased, chromosome-level genome assembly (2n = 25) by integrating high-fidelity (HiFi) long reads and chromosome conformation ca...
We present a genome assembly from an individual male Muscardinus avellanarius (the hazel dormouse; Chordata; Mammalia; Rodentia; Gliridae). The genome sequence is 2,497.5 megabases in span. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled...
Teleost fish show an enormous diversity of sex determination systems, varying from environmental sex determination to full sex chromosomes. Traditionally sex chromosomes are considered within a framework of sexually antagonistic relationships and are viewed not only as sex determination systems but also as a means to resolve sexual conflict by conf...
Bees are major pollinators of flowering plants and thus are important ecosystem service providers for natural habitats and crops. Evolution led to a wide range of adaptations in behaviors, morphology and ecological traits. Many plants rely on specialized bee species for pollination events, and so this interdependence can make them increasingly vuln...
Transitions from no parental care to extensive care are costly and involve major changes in life history, behaviour and morphology. Nevertheless, in Sulawesi ricefishes, pelvic brooding evolved from transfer brooding in two distantly related lineages within the genera Adrianichthys and Oryzias, respectively. Females of pelvic brooding species carry...
The European Reference Genome Atlas (ERGA) consortium aims to generate a reference genome catalogue for all of Europe's eukaryotic biodiversity. The biological material underlying this mission, the specimens and their derived samples. are provided through ERGA's pan-European network. To demonstrate the community's capability and capacity to realise...
The recent increase in available molecular and genomic data for diverse taxa helps to shed new light on long-standing theories. Research into sex chromosome evolution has particularly benefited from a growing number of studies of fish, motivated by their highly diverse mechanisms of sex determination. Sexual antagonism is regularly cited as an infl...
Sex determination (SD) is not conserved among teleost fishes and can even differ between populations of the same species. Across the outstandingly species-rich fish family Cichlidae, more and more SD systems are being discovered. Still, the picture of SD evolution in this group is far from being complete. Lake Tanganyika and its affluent rivers are...
Transitions between reproductive strategies are costly and involve major changes in life history, behaviour and morphology. Nevertheless, in Sulawesi ricefishes, pelvic-brooding evolved from transfer-brooding in two distantly related lineages within in the genera Adrianichthys and in Oryzias , respectively. Females of pelvic-brooding species carry...
Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics,...
The unique male pregnancy in pipefishes and seahorses ranges from basic attachment (pouch-less species: Nerophinae) of maternal eggs to specialized internal gestation in pouched species (e.g. Syngnathus and Hippocampus) with many transitions in between. Due to this diversity, male pregnancy offers a unique platform for assessing physiological and m...
The evolution of pregnancy exposes parental tissues to new, potentially stressful conditions, which can
trigger inflammation.1 Inflammation is costly2,3 and can induce embryo rejection, which constrains the evolution
of pregnancy.1 In contrast, inflammation can also promote morphological innovation at the maternalembryonic
interface as exemplified...
Sex is a fundamental trait determined by environmental and/or genetic factors, including sex chromosomes. Sex chromosomes are studied in species scattered across the tree of life, yet little is known about tempo and mode of sex chromosome evolution among closely related species. Here, we examine sex chromosome evolution in the adaptive radiation of...
Cichlids are well known for their propensity to radiate generating arrays of morphologically and ecologically diverse species in short evolutionary time. Following this rapid evolutionary pace, cichlids show high rates of sex chromosome turnover. We here studied the evolution of sex-biased gene (SBG) expression in 14 recently diverged taxa of the L...
Changes in gene expression play a fundamental role in phenotypic evolution. Transcriptome evolutionary dynamics have so far mainly been compared among distantly related species and remain largely unexplored during rapid organismal diversification, in which gene regulatory changes have been suggested as particularly effective drivers of phenotypic d...
Adaptive radiation is the likely source of much of the ecological and morphological diversity of life1–4. How adaptive radiations proceed and what determines their extent remains unclear in most cases1,4. Here we report the in-depth examination of the spectacular adaptive radiation of cichlid fishes in Lake Tanganyika. On the basis of whole-genome...
Cichlid fishes are celebrated for their vast taxonomic, phenotypic, and ecological diversity; however, a central aspect of their evolution - the timeline of their diversification - remains contentious. Here, we generate draft genome assemblies of 14 species representing the global cichlid diversity and integrate these into a new phylogenomic hypoth...
Variation in gene expression contributes to ecological speciation by facilitating population persistence in novel environments. Likewise, immune responses can be of relevance in speciation driven by adaptation to different environments. Previous studies examining gene expression differences between recently diverged ecotypes have often relied on on...
Sex is a fundamental trait that is determined, depending on the species, by different environmental and/or genetic factors, including various types of sex chromosomes. However, while the functioning and evolution of sex chromosomes have been explored in species scattered across the eukaryotic tree of life, little is known about tempo and mode of se...
Background:
Differential gene expression can be translated into differing phenotypic traits. Especially during embryogenesis, specific gene expression networks regulate the development of different body structures. Cichlid fishes, with their impressive phenotypic diversity and propensity to radiate, are an emerging model system in the genomics era...
Why sex chromosomes turn over and remain undifferentiated in some taxa, whereas they degenerate in others, is still an area of ongoing research. The recurrent occurrence of homologous and homomorphic sex chromosomes in distantly related taxa suggests their independent evolution or continued recombination since their first emergence. Fishes display...
When trying to find a mate, one might think about using a dating app. Imagine that someone else has installed the same app and tries to access the same potential mates that you have chosen, and that this someone uses false facts about him/herself to increase the chance of dating someone before you or anyone else with honest status information does....
Disentangling the processes and mechanisms underlying divergent selection in diversification is facilitated by the comparative study of replicate population pairs that have diverged along a similar environmental gradient. Such a setting is realized in a cichlid fish from southern Lake Tanganyika, Astatotilapia burtoni, which occurs both within the...
Sex steroids are major drivers of sexual development and also responsible for the maintenance of the established gender. Especially fishes exhibit great plasticity and less conservation in sex determination and sexual development compared to other vertebrate groups. In addition, fishes have a constant sex steroid production throughout their entire...
The emergence of the steroid system is coupled to the evolution of multicellular animals. In vertebrates in particular, the steroid receptor repertoire has been shaped by genome duplications characteristic to this lineage. Here, we investigate for the first time the composition of the androgen receptor signaling pathway in ray-finned fish genomes f...
The origin of novel phenotypic characters is a key component in organismal diversification; yet, the mechanisms underlying the emergence of such evolutionary novelties are largely unknown. Here we examine the origin of egg-spots, an evolutionary innovation of the most species-rich group of cichlids, the haplochromines, where these conspicuous male...
In two swordtail species of the genus Xiphophorus, the onset of puberty has been shown to be modulated at the P locus by sequence polymorphism and gene copy number variation affecting the type 4 melanocortin hormone receptor Mc4r. The system works through the interaction of two allelic types, one encoding wild-type, and the other dominant-negative...
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Background / Purpose:
The East African Great Lakes Tanganyika, Malawi and Victoria are home to one of the most fascinating examples of adaptive radiations: more than 2000 endemic cichlid species evolved in a few million years only, making these cichlid species-flocks prime model systems in evolutionary biology. Yet, the abiotic and biotic factors...
Teleost fish genomes display remarkable features, possibly linked to the impressive biodiversity observed in these animals. An event of genome duplication has taken place in the ray-finned fish lineage before teleost radiation. From this event, thousands of genes have been kept as duplicates, with frequent divergent evolution in different teleost s...
Transposable elements are widespread mobile DNA sequences able to integrate into new locations within genomes. Through transposition and recombination, they significantly contribute to genome plasticity and evolution. They can also regulate gene expression and provide regulatory and coding sequences (CDSs) for the evolution of novel gene functions....
Genes used for synteny analysis.
Real-time qPCR primers used.
Makorin sequence accession numbers.
Members of the makorin (mkrn) gene family encode RING/C3H zinc finger proteins with U3 ubiquitin ligase activity. Although these proteins have been described in a variety of eukaryotes such as plants, fungi, invertebrates and vertebrates including human, almost nothing is known about their structural and functional evolution.
Via partial sequencing...
A consensus sequence, encoding a putative DNA polymerase type B derived from a Polinton transposon, was assembled from the sex determination region of Xiphophorus maculatus. This predicted protein, which is 1,158 aa in length, contains a DNA_pol_B_2 domain and a DTDS motif. The DNA polymerase type B gene has about 10 copies in the haploid X. macula...
In contrast to mammals and birds, fish display an amazing diversity of genetic sex determination systems, with frequent changes during evolution possibly associated with the emergence of new sex chromosomes and sex-determining genes. To better understand the molecular and evolutionary mechanisms driving this diversity, several fish models are studi...
In an attempt to study the sex-determining region in the platyfish Xiphophorus maculatus bacterial artifical chromosome (BAC)-Contigs have been assembled covering the sex-determining region on the X and the Y chromosome. Rearrangements, characterized by duplication or inversions, have been noticed in the genomic structure of this region. Sequencing...
Poeciliids, a family of live-bearing freshwater fish, including among others platyfish, swordtails and guppies, fully illustrate the diversity of genetic sex determination mechanisms observed in teleosts. Besides unisexuality, a variety of sex-determining systems has been described in this group of fish, including male and female heterogamety with...
The development of high-throughput DNA sequencing methods has opened the era of genomics, which has revolutionized biology, medicine, and biotechnology over the last decade. The rise of genomics has generated an impressive wave of novel information concerning genome structure, function, and evolution. Massive analysis of functional gene variability...
In order to better understand the molecular and evolutionary mechanisms driving sex determination in fish,
bacterial artificial chromosome (BAC) contigs covering the sex determination region of the X and Y sex chromosomes of the platyfish Xiphophorus maculatus have been constructed. Initial analysis of these contigs led to the identification of ele...
Comparative genomics has revealed that major vertebrate lineages contain quantitatively and qualitatively different populations of retrotransposable elements and DNA transposons, with important differences also frequently observed between species of the same lineage. This is essentially due to (i) the differential evolution of ancestral families of...