Biology subjects

RETAUX, S.

Publications and source records attributed to RETAUX, S..

6 recordsLinked to original sources

bioRxiv2026

A cellular atlas of Astyanax mexicanus embryogenesis reveals principles of developmental microevolution

The evolution of development is the primary mechanism by which morphological and functional diversity is generated. Comparing the developmental trajectories of single cells in entire embryos across species can reveal how gene expression is conserved and varies, as well as the molecular mechanisms underlying how cell- and tissue-specific changes in developmental regulation generate phenotypic differences. However, this perspective has not addressed the mechanisms of small-scale developmental microevolution, i.e, in closely-related species or even within a single species. The fish Astyanax mexicanus, which comes in two forms adapted to distinct environments - the eyed, river-dwelling morph and the eyeless, cave-adapted morph - is a remarkable model with which to investigate the evolution of gene regulation in a single species. Here, we generated and analyzed a single-nucleus RNA-seq atlas of the development of the two Astyanax morphs, from gastrula to swimming larva. Despite extensive changes in gene expression observed in the eight examined stages, for both ubiquitously-expressed and tissue-specific genes, and in both embryonic and extra-embryonic tissues, the temporal progression of cavefish and surface fish cells was similar in ordinal regression-based pseudotime models using 20-100 core genes. However, transcriptome-wide comparisons of gene expression waves revealed massive heterochronic shifts. In cavefish, some tissues had a majority of genes lagging behind in their transcriptional dynamics (e.g. the optic region), while in others, a majority of genes had accelerated dynamics (e.g. the mesoderm), or else, an equivalent number of genes were found in either category (e.g. the endoderm). Furthermore, cell fate acquisition and differentiation were variably affected in different cavefish lineages, with delays of ~6 hours in the retina, ~2 hours in the axial mesoderm and ~none in the extra-embryonic enveloping layer. Thus, cavefish embryos progress as a mosaic of different tissues, or modules, each following its own transcriptional tempo. Because gene expression differential regulation and time shifts were more prevalent in the early stages and gradually diminished throughout development, we propose that cavefish embryos initially undergo strong decanalisation before becoming re-canalized in line with the shared Astyanax developmental program.

developmental biology↗

bioRxiv2025

Water parameters and hydrodynamics in rivers and caves hosting Astyanax mexicanus populations reveal macro-, meso- and micro-habitat characteristics

The Mexican tetra (Astyanax mexicanus) has emerged as a leading model for evolutionary biology and the study of adaptation to extreme subterranean environments. The river-dwelling morph of the species is distributed in Mexico and Texas, while the blind and cave-adapted morph inhabits the karstic caves of the Sierra Madre Oriental in northeastern Mexico. The molecular, cellular and genetic underpinnings of Astyanax cavefish evolution are increasingly studied, but our understanding of its habitat and environment is incomplete, limiting the interpretations of its morphological, physiological, and behavioral adaptations. In particular, the physico-chemical parameters of the water and the hydrological regimes to which cavefish are subjected are largely unexplored. From 2009 to 2025, we have recorded the physico-chemical parameters of the water at localities hosting Astyanax mexicanus cavefish and surface fish in the Sierra de El Abra and Sierra La Colmena regions of the states of San Luis Potosi and Tamaulipas, Mexico. We sampled 13 caves out of the 33 known Astyanax caves and 30 surface stations (rivers, springs, ponds). Data were collected using a variety of devices and probes, including both point measurements (at the end of winter) and longitudinal measurements (throughout the year). The comparison of epigean and hypogean waters showed strong signatures of the two macro-habitats. As compared to surface, on average cave water was cooler, much less conductive and highly anoxic. Moreover, a comparison between different caves (i.e., meso-habitat level) revealed significant differences in both specific water parameters and hydrological regimes. One- or two-year longitudinal recordings demonstrated that some caves exhibit relatively stable hydrological regimes, while others experience multiple, sudden and significant fluctuations. Finally, distinct pools within a single cave showed notable differences, displaying a reproducible increasing gradient in water temperature as a function of distance from the cave entrance, and revealing specificities at the micro-habitat level. We interpret our comprehensive dataset on cave water quality and hydrodynamics in the context of an integrated view of cave biology and the evolution of cave organisms.

ecology↗

bioRxiv2022

Acoustic signatures in cavefish populations inhabiting different caves

Complex patterns of acoustic communication exist throughout the animal kingdom, including underwater. The river-dwelling and the Pachon cave-adapted morphs of the fish Astyanax mexicanus share a repertoire of sounds, but their trigger, use and meaning has changed in cavefish after their recent colonization of the subterranean environment. Here, we explored whether and how sounds produced by blind cavefishes inhabiting different Mexican caves may have evolved, too. We compared acoustic parameters of sounds produced by wild cavefish, recorded in their natural settings, in six different caves located in three mountains ranges in North-East Mexico. Multi-parametric analyses show that the six cavefish populations sampled present cave-specific acoustic signatures, as well as possible individual signatures. The variations in acoustic parameters do not seem related to fish phenotypes, phylogeography or ecological conditions. We propose that the evolution of such acoustic signatures would be neutral and occur by drift, progressively leading to the differentiation of local accents that may prevent interbreeding and thus contribute to speciation.

animal behavior and cognition↗

bioRxiv2021

A 3D molecular map of the cavefish neural plate illuminates eyefield organization and its borders in vertebrates

The vertebrate retinas originate from a specific anlage in the anterior neural plate called the eyefield. The eyefield shares its anterior border with the prospective telencephalon and is in contact ventrally and posteriorly with hypothalamic and diencephalic precursors. Eyefield identity is conferred by a set of "eye transcription factors", whose combinatorial expression has not been precisely characterized. Here, we use the dimorphic teleost species Astyanax mexicanus, which develops proper eyes in the wild type and smaller colobomatous eyes in the blind cavefish embryo, to unravel the molecular anatomy of the eyefield and its micro-evolutionary variations in the two Astyanax morphs. Using a series of markers (Rx3, Pax6, CxCr4b, Zic1, Lhx2, Emx3, Nkx2.1), we draw a comparative 3D expression map at the end of gastrulation/onset of neurulation, which highlights hyper-regionalization of the eyefield into sub-territories of distinct sizes, shapes, cell identities and putative fates along the three body axes. We also discover sub-domains within the prospective telencephalon, and we characterize cell identities at the frontiers of the eyefield. Analyses at the tissue scale and single cell level show variations in volumes and shapes of eyefield subdivisions as well as cellular gene expression levels and identity changes in cavefish. The ventro-medial border and the anterior border of the eyefield contain cells co-expressing hypothalamic and telencephalic marker, respectively, in cavefish embryos. Altogether, we provide a new model of eyefield patterning in 3D and suggest a developmental origin for the emergence of the coloboma phenotype in the natural mutant cavefish embryo.

developmental biology↗

bioRxiv2020

Embryological manipulation to probe early evo-devo in the fish Astyanax mexicanus

The fish species Astyanax mexicanus with its sighted and blind eco-morphotypes has become an original model to challenge vertebrate developmental evolution. Recently, we demonstrated that phenotypic evolution can be impacted by early developmental events starting from the production of oocytes in the fish ovaries. A. mexicanus offers an amenable model to test the influence of maternal effect on cell fate decisions during early development, yet the mechanisms by which the information contained in the eggs is translated into specific developmental programs remain obscure due to the lack of specific tools in this emergent model. Here we describe methods for the generation of gastruloids from yolkless-blastoderm explants to test the influence of embryonic and extraembryonic properties on cell fate decisions, as well as the production of chimeric embryos obtained by intermorph cell transplantations to probe cell autonomous or non-autonomous processes. We show that Astyanax gastruloids have the potential to recapitulate the main ontogenetic events observed in intact embryos, including the internalization of mesodermal progenitors and eye development, as followed with Zic:GFP reporter lines. In addition, intermorph cell grafts resulted in proper integration of exogenous cells into the embryonic tissues, with lineages becoming more restricted from mid-blastula to gastrula. The implementation of these approaches in A. mexicanus will bring new light on the cascades of events, from the maternal pre-patterning of the early embryo to the evolution of brain regionalization.

developmental biology↗

bioRxiv2019

Morphogenetic and patterning defects explain the coloboma phenotype of the eye in the Mexican cavefish

The morphogenesis of the vertebrate eye consists of a complex choreography of cell movements, tightly coupled to axial regionalization and cell type specification processes. Disturbances in these events can lead to developmental defects and blindness. Here, we have deciphered the sequence of defective events leading to coloboma in the embryonic eye of the blind cavefish of the species Astyanax mexicanus. Using comparative live imaging on targeted enhancer-trap Zic1:hsp70:GFP reporter lines of both the normal, river-dwelling morph and the cave morph of the species, we identified defects in migratory cell behaviors during evagination which participate in the reduced optic vesicle size in cavefish, without proliferation defect. Further, impaired optic cup invagination shifts the relative position of the lens and contributes to coloboma in cavefish. Based on these results, we propose a developmental scenario to explain the cavefish phenotype and discuss developmental constraints to morphological evolution. The cavefish eye appears as an outstanding natural mutant model to study molecular and cellular processes involved in optic region morphogenesis.

developmental biology↗