Publications

The mechanisms by which novel differentiation pathways evolve to produce new cell types are still not fully understood. Chromatophores, the pigmented cells in the skin, offer an ideal paradigm because each type independently develops from neural crest cells to produce a distinct colour using well-characterised biosynthetic pathways. Here we show, using single-cell gene expression analyses, that canonical chromatophores develop in the embryonic skin of corn snakes and bearded dragon lizards. Yet, we identify previously undescribed chromatophore subtypes in the bearded dragon. These populations co-express progenitor and mature markers and possibly contribute to embryonic skin patterning, as revealed by whole-mount in situ hybridisation. Comparative analyses uncover that while mature chromatophores show cross-species similarity reflecting shared pigmentary function, progenitor states differ in transcription factor usage, including species-specific deployment of MITF, PAX7, and TFEC. Integration with teleost and amphibian datasets confirms that diversification of pigmentation arises through distinct progenitor trajectories converging on similar mature states.

The spatial patterning of mammalian hair follicle precursors in embryonic skin is most commonly studied in the laboratory mouse (), where new follicles form equidistantly from preexisting ones in successive waves. This simple geometric rule has been effectively described as emerging from an expansion-induction process. However, such a description is incompatible with more recent developmental data indicating instead that scale, feather, and hair placodes self-organize through reaction-diffusion-chemotaxis cell interactions involving epidermal and dermal signaling. Here, we suggest that the chemotactic component of this framework suffices to describe the dynamics of placode insertion in two mammalian species that exhibit drastically different patterns. More specifically, we investigate a continuum dynamical model capturing interactions between motile dermal mesenchymal cells and an epidermal chemoattractant, embedded in a two-dimensional, isotropically expanding domain representing the growing embryonic skin. Through numerical simulations, mathematical analysis, and comparison to experimental developmental data, we first show that the chemotaxis model gives rise to the effective geometric rule that initially justified the development of the expansion-induction model in the laboratory mouse. Second, we show that the strikingly regular hair placode pattern in the spiny mouse ()-with long-range order, specific orientation and anisotropies-is not generated by an expansion-induction mechanism, but is recapitulated by an anisotropic chemotaxis model combined with experimentally observed anisotropic growth. Overall, our findings reveal that variation in the chemotactic component of the corresponding self-organizational system might be a key determinant of interspecific differences in hair placode patterning dynamics and resulting spatial organizations.

Sex Peptide (SP) induces many of the most studied female post-mating responses (PMRs) in Drosophila melanogaster but has been lost multiple times in the Drosophila genus. We decided to explore the PMRs of Drosophila hydei, a species without SP. Our work shows that the PMRs in D. hydei are somewhat different than those found in D. melanogaster and may be the consequence of a selection for producing a reduced number of extremely long sperm. D. hydei females lack the substantial post-mating increase in egg production found in D. melanogaster, mostly displaying only a brief induction in the laying of stored eggs. Mated females do not show a reduction in lifespan that has been linked to changes in metabolism and egg production. To further explore the reproductive biology of this species, we performed sperm competition experiments that suggest that D. hydei females may select sperm based on characteristics linked to changes in seminal fluid proteins. This was further investigated by examining the structure of the seminal fluid-producing accessory glands and the egg laying PMRs in different Drosophila species. Finally, video-based monitoring of D. hydei females was used to uncover novel changes in circadian rhythm and light preference in mated females.

The elephant trunk is a highly dexterous muscular hydrostat whose continuous, distributed deformations pose significant challenges for mathematical modeling. We introduce linear "stereotypical" laws that map desired trunk configurations, parameterized by curvature and length, directly to the internal muscle-analogue forces required in our rod-based dynamic model. The trunk is represented as a simplified multi-segment structure of point masses linked through longitudinal and radial muscle analogues and connective tissue, all modeled using rods. Using these laws, the model predicts biological reaching trajectories with tip-position errors below 8% while maintaining hydrostatic volume across trials. The resulting force-shape mappings reveal consistent, repeatable internal force patterns underlying trunk postures, providing a compact representation of actuation strategies that generate specific planar shapes. By reducing high-dimensional continuum dynamics to simple linear relationships, this framework preliminarily enables the inference of muscle-force distributions from shape configurations, laying the groundwork for deeper exploration of the elephant trunk motion strategies and their translation into advanced robotic systems control.

Non-marine foraminifera remain among the least explored groups within the Rhizaria, despite their ecological and evolutionary significance. We report the rediscovery of the agglutinated monothalamid Limnogromia saxicola (Penard, 1905) and provide the first integrative morphological and molecular characterization of this species since its original description. In addition, we describe four new organic-walled monothalamids based on morphological and molecular data: Claparedellus arenivagus sp. nov., C. dunicola sp. nov., Perseforaminifer crypticus gen. et sp. nov., and Edaphoallogromia bettighoferi sp. nov. Morphological differentiation is challenging due to limited diagnostic characters and intraspecific variability, although nuclear architecture and birefringent cytoplasmic crystals provide useful markers. Limnogromia saxicola and P. crypticus include environmental sequences that are nearly identical to those obtained from individually extracted specimens. This is the first time that environmental sequences can be confidently linked to defined species. Additionally, brief descriptions and illustrations are provided for seven undetermined monothalamous morphotypes for which no sequences could be obtained. Our findings expand the known diversity, ecological range, and cryptic complexity of freshwater monothalamids. This study underscores the importance of integrating morphological, molecular, and ecological data to resolve taxonomy, detect cryptic diversity, and better understand the evolutionary history of non-marine monothalamids.

How morphological diversity arises from variations in biomechanical processes remains an open question. Although forces shape tissues, how force-generating systems differ across species to create diverse forms is unclear. Here, we combine comparative morphogenesis and active matter theory across six cnidarian species spanning 500 million years of divergence to identify the mechanical basis of larval shape diversity. We define species-specific configurations of mechanical modules-termed mechanotypes-that quantitatively predict larval shapes across taxa. We find that shape elongation is a simple trait at the mesoscale level, as its variation depends on one mechanical module, whereas shape polarity is a complex trait dependent on several modules. Perturbations mimicking interspecies regulatory differences reshape these modules, reprogramming larval morphology into forms resembling sister species. By establishing a mesoscale mechanical framework for cross-species comparison, this work reveals how variations in a limited set of tissue-scale parameters generate morphological diversity.

Since the discovery of Latimeria chalumnae, coelacanths have provided a critical comparative framework for reconstructing ancestral sarcopterygian anatomy. However, the function of several anatomical features in both extant and fossil coelacanths remains unresolved. Among these, the presence of large ossified chambers in the body cavity of fossil coelacanths has remained enigmatic, with different studies proposing respiratory or auditory functions. Here, we examine lung and inner ear anatomy based on new observations from synchrotron phase-contrast microCT scans of two 240-million-year-old latimerioid coelacanths, alongside multiple developmental stages of the extant L. chalumnae. These data, combined with archival histological sections of L. chalumnae and 3D reconstructions of a Devonian coelacanth, suggest that extinct coelacanths possessed an ossified lung capable of transmitting sound pressure to auditory sensory epithelia in the inner ear via a perilymphatic system. We propose that the lung of extinct coelacanths supported both respiratory and auditory functions.

Henderson (2023) gave informal descriptions of several soft-walled, monothalamid foraminifera from intertidal zones in the Lorne area of northwest Scotland based on morphology. In the present study, we use a combination of morphological and molecular data to formally establish one new genus and five new monothalamid species from the same area. Lorneia sphaerica gen. & sp. nov. (monothalamid Clade D) has a spherical, coarsely agglutinated test containing magnetic particles and minute aperture-like openings distributed around the test. Lorneia ovalis gen. & sp. nov. (Clade D) has similar characteristics, but the test is oval, and there is a terminal aperture situated at each end. Psammophaga owensi sp. nov. (Clade E) has an oval, finely agglutinated test with a simple terminal aperture and intracellular magnetic particles. In Hilla brevis sp. nov. (Clade Y), the test is broadly oval and finely agglutinated with a reflective sheen and a large terminal aperture with a pronounced collar. Flaviatella zaninettiae sp. nov. (Clade Y) has an elongate, finely agglutinated test with a reflective sheen, a tubular terminal apertural structure, and distinctive yellow cytoplasm. Two species, Flexammina islandica Voltski and Pawlowski, 2015 and Ovammina opaca Dahlgren, 1962, are reported for the first time in Scottish coastal waters. This study underlines the importance and diversity of monothalamid foraminifera in coastal settings.

Skin coloration is crucial for the survival of animals and ranges from spectacular colorful displays used to attract a mate to cryptic camouflage used to avoid predators. Among the 3 main types of chromatophores, melanophores are the most widespread in vertebrates and can set the skin tone by the amount of melanin they produce and store in dedicated vesicles, the melanosomes. Mutations associated with melanophore differentiation and maturation result in hypomelanistic and amelanistic phenotypes, both extensively studied in mammals but less so in snakes and lizards. Here, we characterize at the genomic, transcriptomic, and histological level, the Hypomelanistic corn snake morph and 3 hypomelanistic leopard gecko morphs. To minimize bias in studying leopard gecko color morphs, we first assembled a chromosome-level genome from a wild-type individual in terms of coloration. We propose that candidate mutations in 3 melanogenesis factors generate these phenotypes: (i) tyrosinase (TYR), an essential enzyme for melanin synthesis, (ii) NCKX5 (SLC24A5), an ion exchanger involved in melanosome maturation, and (iii) the P protein (OCA2), a transmembrane transporter for tyrosine. Our extended bulk RNA sequencing analyses show that additional pigmentation-related genes, affecting melanin production, melanosome motility, and melanophore migration, are dysregulated in the embryonic skin of the mutated animals. This observation highlights the likely associations among the corresponding pathways and is in line with our electron microscopy imaging results. Indeed, the subcellular structure of melanophores is uniquely altered at each of the 4 morphs and likely reflects a multigenic effect. These findings demonstrate that conserved pigmentation genes can produce species-specific effects, underscoring the modular nature of skin coloration in vertebrates. Our work establishes reptiles as comparative models for studying pigment cell biology and reveals evolutionary flexibility in the genetic regulation of melanogenesis.

The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human N-acetyltransferase 2 (NAT2) gene. NAT2 metabolizes several clinically used drugs including isoniazid, hydralazine, amifampridine, procainamide, and sulfonamides such as dapsone, and also some highly carcinogenic arylamines. Systematic nomenclature describing NAT2 variation is essential for pharmacogenetic testing, genotype interpretation, and translation to phenotype in research and clinical settings. This GeneFocus provides an overview of NAT2 variation and describes important changes to its star allele-based nomenclature that were made as it was transitioned to PharmVar in March 2024. We also highlight and discuss challenges regarding the characterization of allelic variation and determination of allele frequencies across world populations. The "new" NAT2 PharmVar nomenclature is utilized by ClinPGx (formerly PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).