Publications

The osteology of Thaiichthys buddhabutrensis, nov. gen., from the Late Jurassic – Early Cretaceous of Thailand is described on the basis of a collection of well-preserved specimens. The mode of preservation of the material allows describing the external anatomy, as well as some elements of the internal anatomy (braincase, elements of the vertebral column). Most of the cranial and postcranial skeleton shows a rather conservative anatomy for ‘semionotiformes’, but the jaw apparatus displays specializations. Variations observed in the ossification pattern of the skull roof and of the cheek, in the morphology of the median dorsal scales and in fin rays’ count indicate that caution should be applied when these characters are used in diagnoses and in phylogenetic analyses. A phylogenetic analysis including a set of gars, of ‘semionotiformes’, of Macrosemiiformes and of Halecomorphi shows the following features: (1) the monophyly of Holostei; (2) sister-pair relationships between Tlayuamichin/Semiolepis, Isanichthys/’Lepidotes’ latifrons and Araripelepidotes/Pliodetes; (3) the latter pair, together with Thaiichthys and possibly ‘Lepidotes’ mantelli, are resolved as stem Lepisosteiformes; and (4) the ‘semionotiformes’ (a group gathering species of Semionotus and Lepidotes) do not form a clade.

Rhizaria is one of the six supergroups of eukaryotes, which comprise the majority of amoeboid and skeleton-building protists living in freshwater and marine ecosystems. There is an overall lack of molecular data for the group and therefore the deep phylogeny of rhizarians is unresolved. Molecular data are particularly scarce for the clade of Retaria, which include two prominent groups of microfossils: foraminiferans and radiolarians. To fill this gap, we have produced and sequenced EST libraries for 14 rhizarian species including seven foraminiferans, Gromia and six taxa belonging to traditional Haeckel's Radiolaria: Acantharea, Polycystinea, and Phaeodarea. A matrix was constructed for phylogenetic analysis based on 109 genes and a total of 56 species, of which 22 are rhizarians. Our analyses provide the first multigene evidence for branching of Phaeodarea within Cercozoa, confirming the polyphyly of Haeckel's Radiolaria. It confirms the monophyly of Retaria, a clade grouping Foraminifera with other lineages of Radiolaria. However, contrary to what could be expected from morphological observations, Foraminifera do not form a sister group to radiolarians, but branch within them as sister to either Acantharea or Polycystinea depending on the multigene data set. While the monophyly of Foraminifera and Acantharea is well supported, that of Polycystinea, represented in our data by Spumellaria and Collodaria is questionable. In view of our study, Haeckel's Radiolaria appears as both, a polyphyletic and paraphyletic assemblage of independent groups that should be considered as separate lineages in protist classification.

We present here the results of the Analysis of HLA Population Data (AHPD) project of the 16th International HLA and Immunogenetics Workshop (16IHIW) held in Liverpool in May-June 2012. Thanks to the collaboration of 25 laboratories from 18 different countries, HLA genotypic data for 59 new population samples (either well-defined populations or donor registry samples) were gathered and 55 were analysed statistically following HLA-NET recommendations. The new data included, among others, large sets of well-defined populations from north-east Europe and West Asia, as well as many donor registry data from European countries. The Gene[rate] computer tools were combined to create a Gene[rate] computer pipeline to automatically (i) estimate allele frequencies by an expectation-maximization algorithm accommodating ambiguities, (ii) estimate heterozygosity, (iii) test for Hardy-Weinberg equilibrium (HWE), (iv) test for selective neutrality, (v) generate frequency graphs and summary statistics for each sample at each locus and (vi) plot multidimensional scaling (MDS) analyses comparing the new samples with previous IHIW data. Intrapopulation analyses show that HWE is rarely rejected, while neutrality tests often indicate a significant excess of heterozygotes compared with neutral expectations. The comparison of the 16IHIW AHPD data with data collected during previous workshops (12th-15th) shows that geography is an excellent predictor of HLA genetic differentiations for HLA-A, -B and -DRB1 loci but not for HLA-DQ, whose patterns are probably more influenced by natural selection. In Europe, HLA genetic variation clearly follows a north to south-east axis despite a low level of differentiation between European, North African and West Asian populations. Pacific populations are genetically close to Austronesian-speaking South-East Asian and Taiwanese populations, in agreement with current theories on the peopling of Oceania. Thanks to this project, HLA genetic variation is more clearly defined worldwide and better interpreted in relation to human peopling history and HLA molecular evolution.

The genetic diversity of Europeans has been shaped by various evolutionary forces including their demographic history. Genetic data can thus be used to draw inferences on the population history of Europe using appropriate statistical methods such as computer simulation, which constitutes a powerful tool to study complex models.

Understanding the factors that determine waterfowl nesting site selection is an essential tool for wetland management, but, unfortunately, this information is lacking for most species in the Southern Hemisphere. During the 2007 breeding season, reproductive biology and nesting habitat selection of the Red Shoveler (Anas platalea) were investigated in a wetland of Central Chile. Red Shoveler nests were clumped, primarily in scrubby meadows, containing an average of 8.56 ± 1 eggs (n = 2 3). Nesting microhabitat was characterized by well-covered ground and an intermediate height of the rich herbaceous layer close to the water. Hatching success was 80 ± 20% and was negatively associated with the number of cattle dung piles and the proportion of dry vegetation, but positively explained by herbaceous height and the distance to watercourse. Results suggest that the risk of predation, the access to food, and cattle disturbance would affect the selection of breeding sites and nest success of Red Shoveler. Management should focus on increasing diversity the herbaceous layer, ensuring easy access to water sources, and decreasing livestock pressure during the nesting period.

The specific status of several pygmy chameleons endemic to mountain massifs in the Eastern Arc Mountains, Tanzania has long been controversial due to their lack of distinctive morphological characters. In this work we extend our previous sampling of Rieppeleon and Rhampholeon species, especially from the Rhampoleon moyeri/Rhampholeon uluguruensis complex, and add data from a new mitochondrial marker to address this problem. Our results show that there is geographical structure between populations of pygmy chameleons from different mountains. This structure is especially well defined for Rhampholeon (Rhinodigitum). Phylogenetic analyses confirm that both Rh. uluguruensis Tilbury and Emmrich, 1995 and Rh. moyeri Menegon, Salvidio and Tilbury, 2002 are distinct lineages, the former from the Uluguru Mountains and the latter from the Udzungwa Mountains. However, the paratype material used to erect Rh. moyeri belongs to a separate lineage from the holotype. Similarly, a number of additional lineages within the Rh. moyeri/Rh. uluguruensis complex recovered in the analysis may deserve specific status. At present, there is a lack of morphological characters that can be used to distinguish these lineages, suggesting that there are multiple cryptic taxa in this complex. 

In this article, we first present four significant cases where human leukocyte antigen (HLA) studies have been useful for the reconstruction of human peopling history on the worldwide scale; i.e., the spread of modern humans from East Africa, the colonization of East Asia along two geographic routes, the co-evolution of genes and languages in Africa, and the peopling of Europe through a main northward migration. These examples show that natural selection did not erase the genetic signatures of our past migrations in the HLA genetic diversity patterns observed today. In the second part, we summarize our studies on Easter Island. Using genomic HLA typing, we could trace an introduction of HLA alleles of native American (Amerindian) origin to Easter Island before the Peruvian slave trades; i.e., before the 1860s, and provide suggestive evidence that they may have already been introduced in prehistoric time. Our results give further support to an initial Polynesian population of the island, but also reveal an early contribution by Amerindians. Together, our data illustrate the usefulness of typing for HLA alleles to complement genetic analyses in anthropological investigations.

HLA genes are highly polymorphic in human populations as a result of diversifying selection related to their immune function. However, HLA geographic variation worldwide suggests that demographic factors also shaped their evolution. We here analyzed in detail HLA genetic variation in Europe in order to identify signatures of migration history and/or natural selection.