Publications

The replacement of hunter-gatherer lifestyles by agriculture represents a pivotal change in human history. The initial stage of this Neolithic transition in Europe was instigated by the migration of farmers from Anatolia and the Aegean basin. In this study, we modeled the expansion of Neolithic farmers into central Europe along the continental route of dispersal. We used spatially explicit simulations of paleogenomic diversity and high-quality paleogenomic data from 67 prehistoric individuals to assess how population dynamics between Indigenous European hunter-gatherers and incoming farmers varied across space and time. Our results demonstrate that admixture between the two groups increased locally over time at each stage of the Neolithic expansion along the continental route. We estimate that the effective population size of farmers was about five times that of hunter-gatherers. In addition, we infer that sporadic long-distance migrations of early farmers contributed to their rapid dispersal, while competitive interactions with hunter-gatherers were limited.

Regeneration restores a damaged body part to its original size, shape and structure. Research over the last decades identified signaling pathways, cell types and cellular processes that are key for regeneration. Moreover, mechanical cues and electric potentials are increasingly implicated in modulating regenerative processes. An intriguing open question regards how these chemical, mechanical and electric signals are dynamically organized to coordinate cell behaviors across large regenerating tissues and long regenerative timescales for proper morphogenesis. In addition, it is less explored how regeneration is stopped once tissues reach their proper final form. These questions and related models cross-talk with physical notions like information, pattern formation, self-organization, and control. An interdisciplinary approach combining methods and concepts of developmental biology and physics is offering new quantitative insights on these questions. In this approach, researchers characterize the spatial organization and temporal dynamics of chemical, mechanical and electric signal inputs and relate them to cell and tissue behaviors. Initial observations inform theory; in turn, theory guides experiments and data analysis, while state-of-the-art perturbations allow testing these models. After illustrating this approach, we provide examples of its application to animal regeneration in vivo. These works are extending the notion of "morphogen", contributing to establishing the emerging field of quantitative regeneration and uncovering principles of multicellular organization.

Xenophyophores dominate the abyssal megafauna across many areas of the Pacific Ocean. These giant agglutinated foraminifera have been studied mainly in the tropics, including within the Clarion-Clipperton Zone (CCZ), from where the majority of recently described taxa have originated. Here, we describe three new species, one of them assigned to a new genus, from an area further north (30–32.5° N) near the Japanese Archipelago. Specimens were collected in pushcores during dives of the manned submersible Shinkai 6500 and preserved in the cores after removal of fragments for genetic analyses, allowing them to be examined in life position using X-ray micro-computed tomography (µCT). The three species have basically plate-like tests composed largely of mineral grains. Two, both from 32.5° N, are assigned to the genus Psammina. They are closely related to each other and to P. tenuis from the western CCZ. In Psammina yokosukae sp. nov., the test comprises curved plates, whereas in Psammina contorta sp. nov., it comprises a confusing array of contorted plates and other poorly defined structures. The third new species, Laminarena variabilis gen. et sp. nov., is genetically distinct from the others. In typical specimens from 30° N, the plates are large, curved or sinuous, relatively thin, and marked by a distinct surface pattern of concentric zones, traversed by closely spaced, radial ridges that correspond to internal partitions. A form from 32.5° N is shown to be conspecific with the 30° N specimens based on molecular evidence but is morphologically more complex, comprising elongate bar- and plate-like elements, some with fan-like terminations. A fourth taxon, resembling a bumpy pebble and occupied by bubble-like internal compartments, is described informally. These new taxa enhance our knowledge of Pacific xenophyophores, as well as our understanding of the morphological diversity of xenophyophores in general.

This study conducted a spatiotemporal review of the coelacanth fossil record and explored its distribution and diversity patterns. Coelacanth research can be divided into two distinct periods: the first period, which is based solely on the fossil record, and the second period following the discovery of extant taxa, significantly stimulating research interest. The distribution and research intensity of coelacanth fossils exhibit marked spatial heterogeneity, with Europe and North America being the most extensively studied regions. In contrast, Asia, South America, and Oceania offer substantial potential for future research. Temporally, the coelacanth fossil record also demonstrates significant variation across geological periods, revealing three diversity peaks in the Middle Devonian, Early Triassic, and Late Jurassic, with the Early Triassic peak exhibiting the highest diversity. With the exception of the Late Devonian, Carboniferous, and Late Cretaceous, most periods remain understudied, particularly the Permian, Early Jurassic, and Middle Jurassic, where the record is notably scarce. Integrating the fossil record with phylogenetic analyses enables more robust estimations of coelacanth diversity patterns through deep time. The diversity peak observed in the Middle Devonian is consistent with early burst models of diversification, whereas the Early and Middle Triassic peaks are considered robust, and the Late Jurassic peak may be influenced by taphonomic biases. The low population abundance and limited diversity of coelacanths reduce the number of specimens available for fossilization. The absence of a Cenozoic coelacanth fossil record may be linked to their moderately deep-sea habitat. Future research should prioritize addressing gaps in the fossil record, particularly in Africa, Asia, and Latin America; employing multiple metrics to mitigate sampling biases; and integrating a broader range of taxa into phylogenetic analyses. In contrast to the widespread distribution of the fossil record, extant coelacanths exhibit a restricted distribution, underscoring the urgent need to increase conservation efforts.

Vertebrate reproduction is controlled by 2 pituitary gonadotropin hormones (GtHs), FSH and LH, binding to gonadotropin hormone receptors (GtHRs) in gonadal tissues. All gnathostome vertebrates have been confirmed to possess at least 1 receptor for each GtH [LH receptor (LHR) and FSH receptor (FSHR)], except for species of the reptilian (nonavian sauropsidan) orders, such as lepidosauria, testudines, and crocodylia, which showed inexplicable reactions to heterologous amphibian, avian, and mammalian GtHs in early endocrinological studies. This study investigated the number and function of reptilian GtHRs. Genomic and transcriptomic analyses of selected tetrapod species now strongly suggest the inactivation of the LHR in all nonavian sauropsidans. This gene inactivation likely occurred independently in 3 branches of the sauropdisan clade, sparing only the avian class. Bioassays served to investigate the binding specificity of squamate, chelonian, crocodilian, avian, and mammalian GtHRs with their homologous and heterologous GtHs. The FSHR of a squamate lizard proved completely promiscuous to both its homologous GtHs, while the chelonian FSHR responded slightly stronger to the homologous LH than FSH, and the crocodylian FSHR was only stimulated by the homologous LH but not FSH. We therefore propose a modified paradigm with a neuroendocrine control of nonavian reptilian reproduction by a single GtHR and either 1 GtH in crocodylians or 2 GtHs in chelonians and squamate reptiles. Finally, we discuss hypotheses of tightly regulated temporal and spatial expression of the remaining FSHR in different gonadal somatic cells and temperature-dependent functions of the single nonavian reptilian GtHR.

Vertebrate skin appendages are diverse micro-organs such as scales, feathers, and hair. These units typically develop from placodes, whose spatial patterning involves conserved chemical reaction-diffusion dynamics. Crocodile head scales are a spectacular exception to this paradigm, as they instead arise from a mechanically dominated process of compressive folding driven by constrained skin growth. Here, we reveal that chemical versus mechanical processes pattern tortoise scales in different regions of their head. Indeed, we show that placode-derived scales emerge across the peripheral head surfaces while remaining absent from the central dorsal region where scales subsequently form through a mechanical folding process. Using light sheet microscopy, we build a three-dimensional mechanical model that qualitatively recapitulates the diversity of scale patterns observed in this central head region in different tortoise species. Overall, our analyses indicate that mechanical head-scale patterning likely arose before the divergence between Testudinata and Archosauria, and was subsequently lost in birds.

Blood vessels expand and contract actively as they continuously experience dynamic external stresses from blood flow. The mechanical response of the vessel wall is that of a composite material: its mechanical properties depend on its cellular components, which change dynamically as the cells respond to external stress. Mapping the relationship between these underlying cellular processes and emergent tissue mechanics is an ongoing challenge, particularly in endothelial cells. Here we assess the mechanics and cellular dynamics of an endothelial tube using a microstretcher that mimics the native environment of blood vessels. The characterization of the instantaneous monolayer elasticity reveals a strain-stiffening, actin-dependent and substrate-responsive behaviour. After a physiological pressure increase, the tissue displays a fluid-like expansion, with the reorientation of cell shape and actin fibres. We introduce a mechanical model that considers the actin fibres as a network in the nematic phase and couples their dynamics with active and elastic fibre tension. The model accurately describes the response to the pressure of endothelial tubes.

Monothalamous (single-chambered) foraminifera are widespread in marine benthic environments and are also a common part of freshwater and soil microbial communities. Based on molecular and morphological characteristics, seven non-marine families are currently recognized, branching either as sisters to marine clades or independently within the paraphyletic class Monothalamida. In this study, we describe a new monothalamous freshwater foraminifera sampled from a Pyrenean pond near the French town of Cauterets. We erect the novel genus Poseidonella, with its type species Poseidonella transaquatica sp. nov. The new species branches within the marine clade E, which includes the genera Psammophaga, Vellaria, Niveus, and Nellya. This represents the first evidence of a mixed clade comprising both marine and freshwater monothalamids, highlighting an ongoing transition from coastal marine environments to freshwater habitats.

The discovery in 1938 of a living coelacanth, Latimeria chalumnae, triggered much research and discussion on the evolutionary history and phylogeny of these peculiar sarcopterygian fishes. Indeed, coelacanths were thought to represent the 'missing link' between fishes and tetrapods, a phylogenetic position which is now dismissed. Since the first analyses using a phylogenetic approach were carried out three decades ago, a relatively similar data matrix has been consistently used by researchers for running analyses, with no significant changes aside from the addition of new taxa and characters, and minor corrections to the states' definition and scorings. Here, we investigate the phylogeny of Actinistia with an updated data matrix based on a list of partially new or modified characters. From the initial list of characters available in the most recent studies, we removed 16 characters, modified 16 other characters' definition and added 18 new characters, resulting in a list of 112 characters. We also revised the data matrix by correcting 171 miscoding found for 37 taxa. Based on the new phylogeny, we propose a new classification of coelacanths including 46 coelacanth genera, part of them allocated within nine families and four sub-families. Most of these groups were already named but were not recognised as clades, or poorly or not diagnosed in previous phylogenetic analyses. We provide several new or emended diagnoses for each clade. For the first time, a set of Palaeozoic coelacanth genera are found gathered within a clade, namely the Diplocercidae. All Mesozoic coelacanths, including extant Latimeria, are resolved as members of the order Coelacanthiformes, a clade that arose in the Permian, with Coelacanthus diverging first. We also found that most Mesozoic coelacanths are gathered into a clade, the Latimerioidei, itself divided into the Latimeriidae and the Mawsoniidae, each of which is divided into two subfamilies. Although these important changes, the new phylogeny of the Actinistia shows no significant alteration, and it remains relatively similar compared to previous studies. This demonstrates that the coelacanth phylogeny is now rather stable despite the weak support for most nodes in the phylogeny, and despite the difficulty of defining relevant morphological characters to score in this relatively slowly evolving lineage.

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