Publications

While narratives of the spread of agriculture are central to interpretation of African history, hard evidence of past crops and cultivation practices are still few. This research aims at filling this gap and better understanding the evolution of agriculture and foodways in West Africa. It reports evidence from systematic flotation samples taken at the settlement mounds of Sadia (Mali), dating from 4 phases (phase 0=before first-third century AD; phase 1=mid eighth-tenth c. AD; phase 2=tenth-eleventh c. AD; phase 3=twelfth-late thirteenth c. AD). Flotation of 2200 l of soil provided plant macro-remains from 146 archaeological samples. As on most West African sites, the most dominant plant is pearl millet (). But from the tenth century AD, sorghum () and African rice () appear in small quantities, and fonio () and barnyard millet/hungry rice ( sp.), sometimes considered weeds rather than staple crops, are found in large quantities. Some samples also show remains of tree fruits from savannah parklands, such as baobab (), marula (), jujube ( sp.), shea butter () and African grapes (). Fonio and sp. cultivation appears here to be a later addition that helped to diversify agriculture and buffer against failures that might affect the monoculture of pearl millet. This diversification at the end of the 1st millennium AD matches with other evidence found in West Africa.

In this issue of Developmental Cell, Chuyen et al. (2021) suggest that the Scf/Kit pathway controls mutual repulsion of multiciliated cells and their affinity for epidermal cell junctions through soluble and membrane-associated Scf ligands, respectively. Effective self-organizational patterning emerges at the mesoscopic scale as a small set of effective behaviors.

The Ravin Blanc I archaeological occurrence, dated to MIS 5, provides unprecedented data on the Middle Stone Age (MSA) of West Africa since well-contextualized archaeological sites pre-dating MIS 4/3 are extremely rare for this region. The combined approach on geomorphology, phytolith analysis, and OSL date estimations offers a solid framework for the MSA industry comprised in the Ravin Blanc I sedimentary sequence. The paleoenvironmental reconstruction further emphasizes on the local effects of the global increase in moisture characterizing the beginning of the Upper Pleistocene as well as the later shift to more arid conditions. The lithic industry, comprised in the lower part of the sequence and dated to MIS 5e, shows core reduction sequences among which Levallois methods are minor, as well as an original tool-kit composition, among which pieces with single wide abrupt notches, side-scrapers made by inverse retouch, and a few large crudely shaped bifacial tools. The Ravin Blanc I assemblage has neither a chronologically equivalent site to serve comparisons nor a clear techno-typological correspondent in West Africa. However, the industry represents an early MSA technology that could either retain influences from the southern West African 'Sangoan' or show reminiscences of the preceding local Acheulean. A larger-scale assessment of behavioral dynamics at work at the transition period between the Middle to Upper Pleistocene is discussed in view of integrating this new site to the global perception of this important period in the MSA evolutionary trajectories.

Actinopterygians (ray‐finned fishes) are the most diversified group of vertebrates and are characterized by a variety of protective structures covering their integument, the evolution of which has intrigued biologists for decades. Paleontological records showed that the first mineralized vertebrate skeleton was composed of dermal bony plates covering the body, including odontogenic and skeletogenic components. Later in evolution, the exoskeleton of actinopterygian's trunk was composed of scale structures. Although scales are nowadays a widespread integument cover, some contemporary lineages do not have scales but bony plates covering their trunk, whereas other lineages are devoid of any such structures. To understand the evolution of the integument coverage and particularly the transition between different structures, we investigated the pattern of scale loss events along with actinopterygian evolution and addressed the functional relationship between the scaleless phenotype and the ecology of fishes. Furthermore, we examined whether the emergence of trunk bony plates was dependent over the presence or absence of scales. To this aim, we used two recently published actinopterygian phylogenies, one including >11,600 species, and by using stochastic mapping and Bayesian methods, we inferred scale loss events and trunk bony plate acquisitions. Our results reveal that a scaled integument is the most frequent state in actinopterygians, but multiple independent scale loss events occurred along their phylogeny with essentially no scale re‐acquisition. Based on linear mixed models, we found evidence supporting that after a scale loss event, fishes tend to change their ecology and adopt a benthic lifestyle. Furthermore, we show that trunk bony plates appeared independently multiple times along the phylogeny. By using fitted likelihood models for character evolution, we show that trunk bony plate acquisitions were dependent on a previous scale loss event. Overall, our findings support the hypothesis that integument cover is a key evolutionary trait underlying actinopterygian radiation.

The order Himatismenida (Amoebozoa, Discosea) comprises naked amoebae with an organic coat that is located on the dorsal surface of the cell. The phylogenetic relationships among deeply branching genera of the Himatismenida are unclear, as data on the species diversity of the himatismenid genera is largely restricted to the derived genus . Here, we describe two new amoeba species that branch at the base of the order Himatismenida, evidenced by SSU rRNA gene and multigene analyses. Among them, a freshwater species gen. nov., sp. nov. has a dorsal cell coat consisting of flat, oval scales. This species forms a clade at the base of the Himatismenida, and the previously described , its closest relative, is transferred into the new genus as comb. nov. Although the two species are barely distinguishable by their sequence data, they are clearly distinct in morphology. Using this data, we can report the first evidence of a dorsal cell coat consisting of scales outside of the genus . The other species has a marine origin and branches deeply, close to the root of the phylogenetic tree of Himatismenida. Based on the morphology of this amoeba, it should be described as sp. nov., a new species of the genus . Analyses of the phylogenetic relationships and the ultrastructure of the deeply branching himatismenids, together with several of the newly obtained gene sequences of and suggest that some elements of the dorsal cell coat of may be ancestral for Himatismenida and have been partly retained in various more derived species of this clade, in particular, . Although actin and gene data do not resolve the higher-level relationships in Himatismenida, they correspond to the grouping of species within most genera.

Distribution history of the widespread Neotropical genus Hypostomus was studied to shed light on the processes that shaped species diversity. We inferred a calibrated phylogeny, ancestral habitat preference, ancestral areas distribution, and the history of dispersal and vicariance events of this genus. The phylogenetic and distribution analyses indicate that Hypostomus species inhabiting La Plata Basin do not form a monophyletic clade, suggesting that several unrelated ancestral species colonized this basin in the Miocene. Dispersal to other rivers of La Plata Basin started about 8 Mya, followed by habitat shifts and an increased rate of cladogenesis. Amazonian Hypostomus species colonized La Plata Basin several times in the Middle Miocene, probably via the Upper Paraná and the Paraguay rivers that acted as dispersal corridors. During the Miocene, La Plata Basin experienced marine incursions, and geomorphological and climatic changes that reconfigured its drainage pattern, driving dispersal and diversification of Hypostomus. The Miocene marine incursion was a strong barrier and its retraction triggered Hypostomus dispersal, increased speciation rate and ecological diversification. The timing of hydrogeological changes in La Plata Basin coincides well with Hypostomus cladogenetic events, indicating that the history of this basin has acted on the diversification of its biota.

DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.

Albinism and leucism are phenotypes resulting from impaired melanin pigmentation in the skin and skin appendages. However, melanin pigmentation of eyes remains unaffected in leucism. Here, using transmission electron microscopy, we show that the leucistic morph of the Texas rat snake (Pantherophis obsoletus lindheimeri) lacks both melanophores and xanthophores in its skin and exhibits a uniform ivory white color generated by iridophores and collagen fibers. In addition, we sequenced the full genome of a leucistic individual and obtained a highly-contiguous near-chromosome quality assembly of 1.69 Gb with an N50 of 14.5 Mb and an L50 of 29 sequences. Using a candidate-gene approach, we then identify in the leucistic genome a single-nucleotide deletion that generates a frameshift and a premature termination codon in the melanocyte inducing transcription factor (MITF) gene. This mutation shortens the translated protein from 574 to 286 amino acids, removing the helix-loop-helix DNA-binding domain that is highly conserved among vertebrates. Genotyping leucistic animals of independent lineages showed that not all leucistic individuals carry this single-nucleotide deletion. Subsequent gene expression analyses reveal that all leucistic individuals that we analyzed exhibit a significantly decreased expression of MITF. We thus suggest that mutations affecting the regulation and, in some cases, the coding sequence of MITF, the former probably predating the latter, could be associated with the leucistic phenotype in Texas rat snakes. MITF is involved in the development and survival of melanophores in vertebrates. In zebrafish, a classical model species for pigmentation that undergoes metamorphosis, larvae and adults of homozygous mitfa mutants lack melanophores, show an excess of iridophores and exhibit reduced yellow pigmentation. On the contrary, in the leucistic Texas rat snake, a non-metamorphic species, only iridophores persist. Our results suggest that fate determination of neural-crest derived melanophores and xanthophores, but not of iridophores, could require the expression of MITF during snake embryonic development.

Foraminifera are single-cell eukaryotes common in all marine environments and generally characterized by shells, more specifically termed “tests”, which can either be organic, agglutinated, calcareous, and rarely siliceous. The diversity of foraminifera is commonly assessed microscopically based on morphological features of their tests. However, recent genetic and metagenetic studies show that this morphology-based diversity is largely underestimated. Many cryptic species and numerous lineages uncharacterized morphologically have been revealed, especially among the class of monothalamous (single-chambered) foraminifera. Here, we use an environmental DNA metabarcoding approach to explore the foraminiferal community in the Ubatuba region, northern São Paulo State coast, South-eastern Brazil, where no genetic foraminiferal studies have ever been conducted before. Our analyses revealed 42 phylotypes, among which 9 were identified as globothalamids and 31 have been assigned to monothalamids. All reported phylotypes are new to science and none of them could be assigned to species or genotypes present in foraminiferal barcoding database. These results demonstrate a huge gap that exist in our knowledge of the Southwest Atlantic shallow-waters foraminiferal genetic diversity. Filling this gap would be necessary for more accurate assessment of foraminiferal diversity in general and more specifically if DNA-based methods are to be used to identify potential foraminiferal indicators for ecological and biomonitoring studies in the future.

In the course of evolution, pecorans (i.e. higher ruminants) developed a remarkable diversity of osseous cranial appendages, collectively referred to as 'headgear', which likely share the same origin and genetic basis. However, the nature and function of the genetic determinants underlying their number and position remain elusive. Jacob and other rare populations of sheep and goats are characterized by polyceraty, the presence of more than two horns. Here, we characterize distinct POLYCERATE alleles in each species, both associated with defective HOXD1 function. We show that haploinsufficiency at this locus results in the splitting of horn bud primordia, likely following the abnormal extension of an initial morphogenetic field. These results highlight the key role played by this gene in headgear patterning and illustrate the evolutionary co-option of a gene involved in the early development of bilateria to properly fix the position and number of these distinctive organs of Bovidae.