CpDNA-based species identification and phylogeography: application to a complex of African tropical tree species

Despite their importance as a hotspot of biodiversity, the history of the African tropical lowland rainforests is poorly known. In particular the respective influence of past climatic factors, environmental heterogeneity and physical barriers on the demographic history of plant species still have to be studied. Molecular approaches that characterise the distribution of genetic diversity in plant species and try to interpret it in the light of past historical events are promising in this respect. We examine here the distribution of genetic diversity at maternally-inherited markers (chloroplast DNA) of two tropical timber tree species, Erythrophleum ivorense and Erythrophleum suaveolens (Leguminosae-Caesalpinioideae), in their Lower Guinea distribution (essentially Gabon and Cameroon). As for many tropical sister-taxa, species identification is almost impossible in the field when flowers or fruits are not available. Using a blind-sampling approach and confronting molecular and morphological markers it was possible to attribute sampled individuals to one or the other species. The two species appear to have different ecological requirements and are rarely found in sympatry. A phylogeographic signal was found for E. suaveolens and, for both species, higher levels of diversity were observed in the South than in the North of the Lower Guinea domain. A recent period of forest perturbation, potentially human-induced, has probably favoured the expansion of these two light-demanding species. An observed genetic signal of demographic decline and the poor recruitment of the species can be interpreted as consequences of the natural succession of the forest formations. (Texte intégral

Cartographic Representation of Averaged Pairwise Information (CRAPI): a new exploratory tool to investigate spatial structures illustrated with genetic data from the Watermelon mosaic virus. [O.15]

Dedicated analyses in landscape genetics require a priori knowledge on species dispersal abilities. When little is known about the species under study these methods are difficult to apply and, therefore, we rely on exploratory approaches allowing to visualize and confront genetic and environmental variation patterns. We developed a novel exploratory method, free from assumptions, to investigate spatial variations in pairwise genetic metrics computed between georeferenced samples. Graphical outputs can be mapped on landscape layers to further explore potential relationships between genetic and environmental structures. The method relies on both a spatial grid and a network for which the links are materialized by ellipsoidal polygons bearing the pairwise metric values computed between samples. The network is overlayed on the spatial grid and a given cell receives the weighted mean of all ellipses values intersecting a top this cell. CRAPI includes a randomization procedure to test the relevance of the spatial structure emerging from the analysis. To illustrate our method we analysed 396 sequences of native and invasive strains of the Watermelon mosaic virus obtained from cucurbits collected between 2004 and 2008 in South Eastern France. The CRAPI analyses allowed to visualize both the contact zone between native and invasive strains, arising during the early stage of the invasion, and potential effects of landscape features on virus dissemination. (Résumé d'auteur

In and out of Madagascar : dispersal to peripheral islands, insular speciation and diversification of Indian Ocean daisy trees (Psiadia, Asteraceae)

This study was supported by the European Union’s HOTSPOTS Training Network (MEST-2005-020561)Madagascar is surrounded by archipelagos varying widely in origin, age and structure. Although small and geologically young, these archipelagos have accumulated disproportionate numbers of unique lineages in comparison to Madagascar, highlighting the role of waif-dispersal and rapid in situ diversification processes in generating endemic biodiversity. We reconstruct the evolutionary and biogeographical history of the genus Psiadia (Asteraceae), a plant genus with near equal numbers of species in Madagascar and surrounding islands. Analyzing patterns and processes of diversification, we explain species accumulation on peripheral islands and aim to offer new insights on the origin and potential causes for diversification in the Madagascar and Indian Ocean Islands biodiversity hotspot. Our results provide support for an African origin of the group, with strong support for non-monophyly. Colonization of the Mascarenes took place by two evolutionary distinct lineages from Madagascar, via two independent dispersal events, each unique for their spatial and temporal properties. Significant shifts in diversification rate followed regional expansion, resulting in co-occurring and phenotypically convergent species on high-elevation volcanic slopes. Like other endemic island lineages, Psiadia have been highly successful in dispersing to and radiating on isolated oceanic islands, typified by high habitat diversity and dynamic ecosystems fuelled by continued geological activity. Results stress the important biogeographical role for Rodrigues in serving as an outlying stepping stone from which regional colonization took place. We discuss how isolated volcanic islands contribute to regional diversity by generating substantial numbers of endemic species on short temporal scales. Factors pertaining to the mode and tempo of archipelago formation and its geographical isolation strongly govern evolutionary pathways available for species diversification, and the potential for successful diversification of dispersed lineages, therefore, appears highly dependent on the timing of arrival, as habitat and resource properties change dramatically over the course of oceanic island evolution.Publisher PDFPeer reviewe

Molecular Phylogenetics of Thecata (Hydrozoa, Cnidaria) Reveals Long-Term Maintenance of Life History Traits despite High Frequency of Recent Character Changes

Two fundamental life cycle types are recognized among hydrozoan cnidarians, the benthic (generally colonial) polyp stage either producing pelagic sexual medusae or directly releasing gametes elaborated from an attached gonophore. The existence of intermediate forms, with polyps producing simple medusoids, has been classically considered compelling evidence in favor of phyletic gradualism. In order to gain insights about the evolution of hydrozoan life history traits, we inferred phylogenetic relationships of 142 species of Thecata (= Leptothecata, Leptomedusae), the most species-rich hydrozoan group, using 3 different ribosomal RNA markers (16S, 18S, and 28S). In conflict with morphology-derived classifications, most thecate species fell in 2 well-supported clades named here Statocysta and Macrocolonia. We inferred many independent medusa losses among Statocysta. Several instances of secondary regain of medusoids (but not of full medusa) from medusa-less ancestors were supported among Macrocolonia. Furthermore, life cycle character changes were significantly correlated with changes affecting colony shape. For both traits, changes did not reflect graded and progressive loss or gain of complexity. They were concentrated in recent branches, with intermediate character states being relatively short lived at a large evolutionary scale. This punctuational pattern supports the existence of 2 alternative stable evolutionary strategies: simple stolonal colonies with medusae (the ancestral strategy, seen in most Statocysta species) versus large complex colonies with fixed gonophores (the derived strategy, seen in most Macrocolonia species). Hypotheses of species selection are proposed to explain the apparent long-term stability of these life history traits despite a high frequency of character change. Notably, maintenance of the medusa across geological time in Statocysta might be due to higher extinction rates for species that have lost this dispersive stag

Characterization of novel PAH dioxygenases from the bacterial metagenomic DNA of a contaminated soil.

International audienceRing hydroxylating dioxygenases (RHDs) play a crucial role in the biodegradation of a range of aromatic hydrocarbons found on polluted sites, including polycyclic aromatic hydrocarbons (PAHs). Current knowledge on RHDs comes essentially from studies on culturable bacterial strains while compelling evidence indicates that pollutant removal is mostly achieved by uncultured species. In this study, a combination of DNA-SIP labeling and metagenomic sequence analysis was implemented to investigate the metabolic potential of main PAH degraders on a polluted site. Following in situ labeling using (13)C-phenanthrene, the labeled metagenomic DNA was isolated from soil and subjected to shotgun sequencing. Most annotated sequences were predicted to belong to Betaproteobacteria, especially Rhodocyclaceae and Burkholderiales, consistent with previous findings showing that main PAH degraders on this site were affiliated to these taxa. Based on metagenomic data, four RHD gene sets were amplified and cloned from soil DNA. For each set, PCR yielded multiple amplicons with sequences differing by up to 321 nucleotides (17%), reflecting the great genetic diversity prevailing in soil. RHDs were successfully overexpressed in E. coli, but full activity required the co-expression of two electron carrier genes, also cloned from soil DNA. Remarkably, two RHDs exhibited much higher activity when associated with electron carriers from a Sphingomonad. The four RHDs showed markedly different preferences for 2- and 3-ring PAHs, but were poorly active on 4-ring PAHs. Three RHDs preferentially hydroxylated phenanthrene on the C-1 and C-2 positions rather than on the C-3, C-4 positions, suggesting that degradation occurred through an alternate pathway

The contrasted evolutionary fates of deep-sea chemosynthetic mussels (Bivalvia, Bathymodiolinae)

International audienceBathymodiolinae are giant mussels that were discovered at hydrothermal vents and harboring chemosynthetic symbionts. Due to their close phylogenetic relationship with seep species and tiny mussels from organic substrates, it was hypothesized that they gradually evolved from shallow to deeper environments, and specialized in decaying organic remains, then in seeps, and finally colonized deep-sea vents. Here, we present a multigene phylogeny that reveals that most of the genera are polyphyletic and/or paraphyletic. The robustness of the phylogeny allows us to revise the genus-level classification. Organic remains are robustly supported as the ancestral habitat for Bathymodiolinae. However, rather than a single step toward colonization of vents and seeps, recurrent habitat shifts from organic substrates to vents and seeps occurred during evolution, and never the reverse. This new phylogenetic framework challenges the gradualist scenarios from shallow to deep. Mussels from organic remains tolerate a large range of ecological conditions and display a spectacular species diversity contrary to vent mussels, although such habitats are yet underexplored compared to vents and seeps. Overall, our data suggest that for deep-sea mussels, the high specialization to vent habitats provides ecological success in this harsh habitat but also brings the lineage to a kind of evolutionary dead end

Are all species of Pseudorhabdosynochus strictly host specific? - a molecular study

International audienceSpecies of the diplectanid monogenean genus Pseudorhabdosynochus are strictly host-specific (specialist), with the exception of P. cyanopodus, which was reported in New Caledonia, South Pacific, from two host species, Epinephelus cyanopodus and E. chlorostigma. We sequenced the COI gene of both host fish species and of their monogeneans. Morphological identification and pairwise distances showed that the two fish species were distinct (difference 6.1-6.6%), but that their monogeneans were not (difference 0-1.5%). A morphological study of sclerotised parts showed that specimens of P. cyanopodus are similar in both fish. Most species of groupers and their associated Pseudorhabdosynochus species are from warm surface waters, but the two groupers E. cyanopodus and E. chlorostigma are usually caught in deep-sea on the outer slope of the coral reef. This suggests that acquisition of a less strict host specificity is an adaptation of P. cyanopodus to deep-sea hosts

Patterns of genetic structure among Hawaiian corals of the genus Pocillopora yield clusters of individuals that are compatible with morphology.

International audienceSix variable sequence markers are developed and analyzed to find out species boundaries in Hawaiian corals of the genus Pocillopora: the putative mitochondrial control region; a recently discovered, hypervariable mitochondrial open reading frame; the internal transcribed spacer 2 (ITS2), located in the nuclear ribosomal DNA; three nuclear introns of calmodulin, elongation factor-1alpha and the ATP synthase beta subunit. Using the first two markers, we identify five distinct mitochondrial lineages and these lineages are compatible with morphology. The situation is more complex with nuclear markers since more than two haplotypes are observed in some individuals. To detect clusters of individuals, haplotype networks are constructed with additional connections drawn between co-occurring haplotypes to delineate potential fields for recombination: few clusters of nuclear haplotypes are found to correspond to clusters of individuals, but those that are detected (mostly in the ITS2 dataset) are also compatible with morphology

Evolution of diadromy in fish: insights from a tropical genus (Kuhlia species)

Diadromous species undergo regular migration between fresh and marine waters. This behavior is found in many species, including fish, mollusks, and crustaceans, some of which are commercially valuable species. Several attempts to trace the evolution of this behavior have been made in Salmonidae and Galaxiidae, but ambiguous phylogenies and multiple character state changes prevented unequivocal conclusions. The Kuhliidae family consists of 12 fish species that inhabit tropical islands in the Indo-Pacific region. The species have marine, partially catadromous, or fully catadromous life histories (i.e., they migrate from rivers to the sea to reproduce). The evolution of migratory behavior was traced on a well-resolved phylogeny. Catadromous Kuhlia species were basal, and partially catadromous and marine species formed derived monophyletic groups. This is, to our knowledge, the first time that a clear origin and polarity for the diadromous character has been demonstrated. We propose that the relative lack of resources in tropical, inshore, marine habitats and the ephemeral and isolated nature of freshwater environments of tropical islands, combined with phenotypic plasticity of migratory traits, play key roles in driving the evolution of diadromy in the Kuhliidae and probably in other groups. This work is an important starting point to understand the role of diadromy in speciation and adaptation in unstable habitats