Publications

The Small Subunit Ribosomal RNA gene (SSU rDNA) is a widely used tool to reconstruct phylogenetic relationships among foraminiferal species. Recently, the highly variable regions of this gene have been proposed as DNA barcodes to identify foraminiferal species. However, the resolution of these barcodes has not been well established, yet. In this study, we evaluate four SSU rDNA hypervariable regions (37/f, 41/f, 43/e, and 45/e) as DNA barcodes to distinguish among species of the genus Bolivina, with particular emphasis on Bolivina quadrata for which ten new sequences (KY468817-KY468826) were obtained during this study. Our analyses show that a single SSU rDNA hypervariable sequence is insufficient to resolve all Bolivina species and that some regions (37/f and 41/f) are more useful than others (43/e and 45/e) to distinguish among closely related species. In addition, polymorphism analyses reveal a high degree of variability. In the context of barcoding studies, these results emphasize the need to assess the range of intraspecific variability of DNA barcodes prior to their application to identify foraminiferal species in environmental samples; our results also highlight the possibility that a longer SSU rDNA region might be required to distinguish among species belonging to the same taxonomic group (i.e., genus). This article is protected by copyright. All rights reserved.

Collinear regulation of Hox genes in space and time has been an outstanding question ever since the initial work of Ed Lewis in 1978. Here we discuss recent advances in our understanding of this phenomenon in relation to novel concepts associated with large-scale regulation and chromatin structure during the development of both axial and limb patterns. We further discuss how this sequential transcriptional activation marks embryonic stem cell-like axial progenitors in mammals and, consequently, how a temporal genetic system is further translated into spatial coordinates via the fate of these progenitors. In this context, we argue the benefit and necessity of implementing this unique mechanism as well as the difficulty in evolving an alternative strategy to deliver this critical positional information.

We derive a fully covariant theory of the mechanics of active surfaces. This theory provides a framework for the study of active biological or chemical processes at surfaces, such as the cell cortex, the mechanics of epithelial tissues, or reconstituted active systems on surfaces. We introduce forces and torques acting on a surface, and derive the associated force balance conditions. We show that surfaces with in-plane rotational symmetry can have broken up-down, chiral, or planar-chiral symmetry. We discuss the rate of entropy production in the surface and write linear constitutive relations that satisfy the Onsager relations. We show that the bending modulus, the spontaneous curvature, and the surface tension of a passive surface are renormalized by active terms. Finally, we identify active terms which are not found in a passive theory and discuss examples of shape instabilities that are related to active processes in the surface.

Multiple technologies and software are now available facilitating the de novo sequencing and assembly of any vertebrate genome. Yet the quality of most available sequenced genomes is substantially poorer than that of the golden standard in the field: the human genome. Here, we present a step-by-step protocol for the successful sequencing and assembly of a high-quality snake genome that can be applied to any other reptilian or avian species. We combine the great sequencing depth and accuracy of short reads with the use of different insert size libraries for extended scaffolding followed by optical mapping. We show that this procedure improved the corn snake scaffold N50 from 3.7 kbp to 1.4 Mbp, currently making it one of the snake genomes with the longest scaffolds. Short guidelines are also given on the extraction of long DNA molecules from reptilian blood and the necessary modifications in DNA extraction protocols. This chapter is accompanied by a website ( www.reptilomics.org/stepbystep.html ), where we provide links to the suggested software, examples of input and output files, and running parameters.

The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD genes in developing digits is controlled by regulatory elements located in the centromeric TAD (C-DOM) through long-range contacts.

Remains of a coelacanth specimen are described from Rhaetian deposits of the Var Department, southeastern France. They comprise the lower part of a branchial apparatus associated with a left lower jaw and a basisphenoid. Osteological features of the angular and basisphenoid and the teeth ornamentation allow the inclusion of the specimen in the mawsoniid family, genus and species indeterminate. Mawsoniids are known in freshwater environments from the Triassic of North America and from the Cretaceous of Western Gondwana and Europe, as well as from Late Jurassic marine environments from Europe. The new discovery here reported represents the first coelacanth from the marine Triassic of France and improves the understanding of the palaeobiogeography of the Mawsoniidae.

The extinct group of the Pycnodontiformes is one of the most characteristic components of the Mesozoic and early Cenozoic fish faunas. These ray-finned fishes, which underwent an explosive morphological diversification during the Late Cretaceous, are generally regarded as typical shell-crushers. Here we report unusual cutting-type dentitions from the Paleogene of Morocco which are assigned to a new genus of highly specialized pycnodont fish. This peculiar taxon represents the last member of a new, previously undetected 40-million-year lineage (Serrasalmimidae fam. nov., including two other new genera and Polygyrodus White, 1927) ranging back to the early Late Cretaceous and leading to exclusively carnivorous predatory forms, unique and unexpected among pycnodonts. Our discovery indicates that latest Cretaceous-earliest Paleogene pycnodonts occupied more diverse trophic niches than previously thought, taking advantage of the apparition of new prey types in the changing marine ecosystems of this time interval. The evolutionary sequence of trophic specialization characterizing this new group of pycnodontiforms is strikingly similar to that observed within serrasalmid characiforms, from seed- and fruit-eating pacus to flesh-eating piranhas.

We analyse new genomic data (0.05–2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200–3500 BC) to the Middle Bronze Age (1740–1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature.

This study confirms the presence of two species of the non-native mosquitofish Gambusia in Argentina. The risks that they represent to native biota, their potential dispersal in the region, and their effectiveness in mosquito larvae control are discussed.

The monotypic genus Oschmarinolepis Spassky and Spasskaja, 1954 (Cestoda, Hymenolepididae) is reviewed. Its validity is confirmed with an updated diagnosis, and its type-species, Oschmarinolepis microcephala (Rudolphi, 1819), is redescribed. The new monotypic genus Paraoschmarinolepis gen n. is erected with Paraoschmarinolepis multiformis (Creplin, 1829) comb. n., as its type-species. The morphology of both type-species, O. microcephala and P. multiformis comb. n. is reviewed on the basis of published data and examination of collection material from Plegadis falcinellus from Ukraine and Ciconia ciconia from Slovakia. We show that some material previously assigned to O. microcephala, belong in fact P. multiformis comb. n.