Publications

SELECTOR is a software package for studying the evolution of multiallelic genes under balancing or positive selection while simulating complex evolutionary scenarios that integrate demographic growth and migration in a spatially explicit population framework. Parameters can be varied both in space and time to account for geographical, environmental, and cultural heterogeneity. SELECTOR can be used within an approximate Bayesian computation estimation framework. We first describe the principles of SELECTOR and validate the algorithms by comparing its outputs for simple models with theoretical expectations. Then, we show how it can be used to investigate genetic differentiation of loci under balancing selection in interconnected demes with spatially heterogeneous gene flow. We identify situations in which balancing selection reduces genetic differentiation between population groups compared with neutrality and explain conflicting outcomes observed for human leukocyte antigen loci. These results and three previously published applications demonstrate that SELECTOR is efficient and robust for building insight into human settlement history and evolution.

The available data concerning the environmental changes and faunal replacements that occurred during the Cenomanian marine transgression in the North of Iberia are integrated and discussed on the basis of new evidence from the invertebrate and vertebrate fossil record. New stratigraphical data and the reassessment of known stratigraphic sections support the correlation of the Cenomanian carbonate-ramp successions from the Iberian margin to the centre of the Basque-Cantabrian Basin during a major transgressive episode. This new stratigraphical framework is the key to understand the changing oceanographic conditions in the area that resulted from a progressive inundation of the Iberian continental platform. This transgression seems to have triggered major faunal replacements in this particular geographic area, starting out around the Albian-Cenomanian transition. Ammonite faunal replacement led to a new radiation of this group that spread out rapidly until their new decline around the Cenomanian-Turonian boundary. A new record of Calycoceras (Newboldiceras) asiaticum spinosum and the first record of a Pachyrhizodontidae indet. (Actinopterygii, Teleostei, Crossognathiformes) from the Iberian Peninsula are reported here from the Cenomanian basal units of the major Late Cretaceous transgressive episode. The two new specimens come from the same level in an outer marine ramp succession near Amurrio, Basque Country, northern Spain, and are representatives of the Cenomanian faunal turnover. The new record of a pachyrhizodontoid fish from the Cretaceous of Iberia is an indication of the ichthyofaunal replacement in this part of the world. The relict fish faunas from the Early Cretaceous of the former island of Iberia were mostly formed by basal neopterygian taxa closely related to those of the marine Jurassic of other parts of Europe. During the Early-Late Cretaceous transition they were replaced by the teleostean-based new stock that constitutes the basis of the Late Cretaceous, Cenozoic, and Recent faunas.

The onset and conservation of genetic polymorphism is a major question in evolutionary ecology. The influence of temporal fluctuations in the environment was invoked by early theorists such as J.B.S. Haldane and S. Jayakar in a controversial article published in, 1963, but their frequently cited model has almost never been used with empirical evidence. In this paper, we present a simulation model inspired by the biology of common gorse (Ulex europaeus), a species which shows polymorphism of flowering phenology: long flowering plants produce flowers from winter to spring and short flowering plants only flower in the spring. The early fruits of the former run the risk of frost, but largely escape seed predation, while those of the latter escape the risk of frost but are subject to a strong risk of seed predation. These two selection pressures vary unpredictably from year to year, making this flowering phenotype a good candidate to test Haldane and Jayakar’s model. Assuming that both flowering types are determined by a single major locus, we devise a simulation model firstly in a diploid form, and secondly by taking into account the hexaploid characteristic of gorse. Our results show that the combination of the two selective pressures acting on gorse flowering phenology can lead to fitness values meeting the Haldane and Jayakar’s conditions on geometric and arithmetic means, and to long term maintenance of polymorphism. In addition, the values of the parameters allowing polymorphism persistence and the relative proportions obtained are in agreement with values observed in natural populations. We also show that hexaploidy strongly increases the range of parameters in which polymorphism is self sustaining. These results are discussed in the context of climatic change, where increases of both mean temperature and its variance are predicted.

The mouse vomeronasal organ (VNO) is a chemosensory structure that detects both hetero- and conspecific social cues. Based on largely monogenic expression of either type 1 or 2 vomeronasal receptors (V1Rs/V2Rs) or members of the formyl peptide receptor (FPR) family, the vomeronasal sensory epithelium harbors at least three neuronal subpopulations. While various neurophysiological properties of both V1R- and V2R-expressing neurons have been described using genetically engineered mouse models, the basic biophysical characteristics of the more recently identified FPR-expressing vomeronasal neurons have not been studied. Here, we employ a transgenic mouse strain that coexpresses an enhanced variant of yellow fluorescent protein together with FPR-rs3 allowing to identify and analyze FPR-rs3-expressing neurons in acute VNO tissue slices. Single neuron electrophysiological recordings allow comparative characterization of the biophysical properties inherent to a prototypical member of the FPR-expressing subpopulation of VNO neurons. In this study, we provide an in-depth analysis of both passive and active membrane properties, including detailed characterization of several types of voltage-activated conductances and action potential discharge patterns, in fluorescently labeled vs. unmarked vomeronasal neurons. Our results reveal striking similarities in the basic (electro) physiological architecture of both transgene-expressing and non-expressing neurons, confirming the suitability of this genetically engineered mouse model for future studies addressing more specialized issues in vomeronasal FPR neurobiology.

Sumoylation, the covalent attachment of SUMO, a 90 amino acid peptide related to ubiquitin, is a major modulator of protein functions. Fluorescent SUMO protein fusions have been used in cell cultures to visualize SUMO in vivo but not in multicellular organisms. We generated a transgenic line of Drosophila expressing an mCherry-SUMO fusion. We analyzed its pattern in vivo in salivary gland nuclei expressing Venus-HP1 to recognize the different chromatin components (Chromocenter, chromosome IV). We compared it to SUMO immunostaining on squashed polytene chromosomes and observed similar patterns. In addition to the previously reported SUMO localizations (chromosome arms and chromocenter), we identify 2 intense binding sites: the fourth chromosome telomere and the DAPI-bright band in the region 81F.

Hox genes are required during the morphogenesis of both vertebrate digits and external genitals. We investigated whether transcription in such distinct contexts involves a shared enhancer-containing landscape. We show that the same regulatory topology is used, yet with some tissue-specific enhancer-promoter interactions, suggesting the hijacking of a regulatory backbone from one context to the other. In addition, comparable organizations are observed at both HoxA and HoxD clusters, which separated through genome duplication in an ancestral invertebrate animal. We propose that this convergent regulatory evolution was triggered by the preexistence of some chromatin architecture, thus facilitating the subsequent recruitment of the appropriate transcription factors. Such regulatory topologies may have both favored and constrained the evolution of pleiotropic developmental loci in vertebrates.

Foraminifera are commonly defined as marine testate protists, and their diversity is mainly assessed on the basis of the morphology of their agglutinated or mineralized tests. Diversity surveys based on environmental DNA (eDNA) have dramatically changed this view by revealing an unexpected diversity of naked and organic-walled lineages as well as detecting foraminiferal lineages in soil and freshwater environments. Moreover, single-cell analyses have allowed discrimination among genetically distinctive types within almost every described morphospecies. In view of these studies, the foraminiferal diversity appeared to be largely underestimated, but its accurate estimation was impeded by the low speed and coverage of a cloning-based eDNA approach. With the advent of high-throughput sequencing (HTS) technologies, these limitations disappeared in favor of exhaustive descriptions of foraminiferal diversity in numerous samples. Yet, the biases and errors identified in early HTS studies raised some questions about the accuracy of HTS data and their biological interpretation. Among the most controversial issues affecting the reliability of HTS diversity estimates are (1) the impact of technical and biological biases, (2) the sensitivity and specificity of taxonomic sequence assignment, (3) the ability to distinguish rare species, and (4) the quantitative interpretation of HTS data. Here, we document the lessons learned from previous HTS surveys and present the current advances and applications focusing on foraminiferal eDNA. We discuss the problems associated with HTS approaches and predict the future trends and avenues that hold promises for surveying foraminiferal diversity accurately and efficiently.

Several demographic events have been postulated to explain the contemporaneous structure of European genetic diversity. First, an initial settlement of the continent by anatomically modern humans; second, the re-settlement of northern latitudes after the Last Glacial Maximum; third, the demic diffusion of Neolithic farmers from the Near East; and, fourth, several historical events such as the Slavic migration.

Monothalamous (single-chambered) foraminifera have long been considered as the "poor cousins" of multichambered species, which calcareous and agglutinated tests dominate in the fossil record. This view is currently changing with environmental DNA surveys showing that the monothalamids may be as diverse as hard-shelled foraminifera. Yet, the majority of numerous molecular lineages revealed by eDNA studies remain anonymous. Here, we describe a new monothalamous species and genus isolated from the sample of sea grass collected in Gulf of Eilat (Red Sea). This new species, named Leannia veloxifera, is characterized by a tiny ovoid theca (about 50-100 μm) composed of thin organic wall, with two opposite apertures. The examined individuals are multinucleated and show very active reticulopodial movement. Phylogenetic analyses of SSU rDNA, actin, and beta-tubulin (ß-tubulin) show that the species represents a novel lineage branching separately from other monothalamous foraminifera. Interestingly, the SSU rDNA sequence of the new species is very similar to an environmental foraminiferal sequence from Bahamas, suggesting that the novel lineage may represent a group of shallow-water tropical allogromiids, poorly studied until now.