Publications

Evo-Devo studies rely on a collection of animal model systems belonging to different phylogenetic branches to try and understand how organisms carrying a similar set of genes and pathways can develop into such a variety of shapes and sizes. The squamate clade, however, has only recently started to receive the attention it deserves in particular due to extreme morphological and metabolic aspects and, consequently, the important insights that it could bring in different fields. The recent sequencing of several squamate genomes as well as the generation of high quality trancriptomes for different snake tissues now provide the necessary tools to complement biological studies. Here, we briefly report on recent work involving developing snake embryos to illustrate their interest to assess vertebrate developmental mechanisms. We also discuss the relevance to use snake species as Evo-Devo model systems and potential ways to cross the important limitations intrinsically associated with developmental and genetic studies of these fascinating animals.

We describe a technique for interactive rendering of diffraction effects produced by biological nanostructures, such as snake skin surface gratings. Our approach uses imagery from atomic force microscopy that accurately captures the geometry of the nanostructures responsible for structural colouration, that is, colouration due to wave interference, in a variety of animals. We develop a rendering technique that constructs bidirectional reflection distribution functions (BRDFs) directly from the measured data and leverages pre-computation to achieve interactive performance. We demonstrate results of our approach using various shapes of the surface grating nanostructures. Finally, we evaluate the accuracy of our pre-computation-based technique and compare to a reference BRDF construction technique

Squamates (snakes and lizards) exhibit a striking variety of phenotypes, with little known on their generative mechanisms. Studies aiming to understand the genetic basis of this wide diversity in morphology, physiology and ecology will greatly benefit from whole genome sequencing initiatives, as they provide the foundation for comparative analyses and improve our understanding of the evolution, development and diversification of traits. Here, we present the first draft genome of the corn snake Pantherophis guttatus, an oviparous snake that we promote as a particularly appropriate model species for evolutionary developmental studies in squamates. We sequenced 100-base paired-end reads from multiple individuals of a single family (parents and offspring) that produced a genome assembly of 1.53 gigabases (Gb), roughly covering 75% of the expected total genome size, and 297,768 scaffolds >1 Kb. We were able to fully retrieve 86, and partially another 106, of the 248 CEGMA core genes, indicating that a high genome completeness was achieved, even though the assembly is fragmented. Using MAKER2, we annotated 10,917 genes with high confidence (Annotation Edit Distance (AED)

Fecal microbiota transplantation (FMT) has been shown to be a superior therapeutic modality for the treatment of recurrent Clostridium difficile infection (RCDI). Recently the US Food and Drug Administration (FDA) determined that human stool should be classified as a biological agent and its use should be regulated to ensure patient safety. Consequently, the FDA determined that prescribers of FMT must possess an approved investigational new drug (IND) permit to administer FMT for the purpose of conducting research or treating any gastrointestinal condition other than RCDI. Although an IND is not required for use of FMT to treat RCDI, an IND is strongly encouraged and may ultimately be required. This article provides step-by-step guidance to infectious disease specialists on how to navigate the regulatory requirements and successfully obtain an IND before they can begin to use FMT as part of their clinical practice.

Rhizaria are a major branch of eukaryote evolution with an extensive microfossil record, but only scarce molecular data are available. The rhizarian species Reticulomyxa filosa, belonging to the Foraminifera, is free-living in freshwater environments. In culture, it thrives only as a plasmodium with thousands of haploid nuclei in one cell. The R. filosa genome is the first foraminiferal genome to be deciphered.

Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates. In contrast to the platypus, the only other venomous vertebrate with a sequenced genome, we find that snake toxin genes evolve through several distinct co-option mechanisms and exhibit surprisingly variable levels of gene duplication and directional selection that correlate with their functional importance in prey capture. The enigmatic accessory venom gland shows a very different pattern of toxin gene expression from the main venom gland and seems to have recruited toxin-like lectin genes repeatedly for new nontoxic functions. In addition, tissue-specific microRNA analyses suggested the co-option of core genetic regulatory components of the venom secretory system from a pancreatic origin. Although the king cobra is limbless, we recovered coding sequences for all Hox genes involved in amniote limb development, with the exception of Hoxd12. Our results provide a unique view of the origin and evolution of snake venom and reveal multiple genome-level adaptive responses to natural selection in this complex biological weapon system. More generally, they provide insight into mechanisms of protein evolution under strong selection.

Professor Jean-Pierre Berger joined the Fribourg University (Switzerland) in 1989 as a lecturer (chargé de cours), quickly rising to the rank of head assistant with a postdoctoral lecture qualification in 1992, and becoming Associate Professor for palaeontology in 1997. Fribourg, Lausanne, Tübingen and Munich were important places in his professional career.

New coelacanth material from the Middle Triassic Prosanto Formation of the Ducan and Landwasser area near Davos in eastern Switzerland, Canton Graubünden, is described. A sub-complete individual is visible in ventral view, and shows details of its branchial apparatus. In particular, it possesses relatively large teeth on the ceratobranchials, and possible ossified hypobranchials. Few diagnostic characters are observable, and most of them are visible on the mandibles preserved in lateral view. This specimen shares characters with Ticinepomis peyeri, a smaller form from the Middle Triassic of Monte San Giorgio, whose holotype is re-described in part here. A second specimen, a fragmentary caudal skeleton shows the typical supplementary lobe of coelacanths, and meristic characters indicating probable close affinities with T. peyeri. We refer this material to Ticinepomis cf. T. peyeri. Because the new specimen is larger than the holotype, we refute the possible juvenile status of the small specimen from Monte San Giorgio. The new material of Ticinepomis from Canton Graubünden shows anatomical features not preserved on the holotype and allows the addition of new characters to a previously published data matrix of actinistians. A phylogenetic analysis is performed, which supports that Ticinepomis is nested among the Latimeriidae. The diversity of post-Palaeozoic coelacanths is assessed. The taxic diversity of observed occurrences shows a peak in the Early Triassic and a peak in the Late Jurassic, as detected in previous studies. When ghost lineages are included in the computation, the Late Jurassic peak is smoothened. By comparing the taxic diversity curves with the curve of average ghost lineage duration, we conclude that the Early Triassic peak of diversity was probably caused by a biological radiation, whereas the Late Jurassic peak of observed diversity is probably the result of a Lagerstätten effect.

A recently discovered fish assemblage from the “Schistes à Meletta” facies (Lower Oligocene) of the Glières Plateau, Bornes Massif, Haute–Savoie, eastern France is described. The assemblage, comprising specimens ranging from fully-articulated skeletons to isolated scattered ossifications, is composed of Anenchelum cf. glarisianum, Pristigenys sp., Fistularia sp., Caranx cf. glarisianus alongside indeterminate teleosts. This new assemblage greatly increases the fish diversity previously known from the “Schistes à Meletta” of this area. The fauna shows biogeographic affinities with assemblages from the Peritethys domain, in particular from the Helvetic molassic basin and from the Paratethys. The genera identified at the Glières locality are represented today by species living in tropical nearshore environments together with species from the open sea. A possible explanation is that the environment of deposition was rather deep, and that shallow-water fishes were brought in by turbidity currents.