Colomban de Vargas

Evolution of homeobox genes: Q50 Paired-like genes founded the Paired class

Abstract The genes belonging to the Paired class exert primary developmental functions. They are characterized by six invariant amino acid residues in the homeodomain, while the residue at position 50 can be a serine, glutamine or lysine as in the Pax-type, Q50 Paired-like or the K50 Paired-like homeodomains respectively. Genes in this class emerged early in animal evolution: three distinct Pax genes and two Q50 Paired-like genes have recently been characterised from cnidarians. Phylogenetic molecular reconstructions taking into account homeodomain and paired-domain sequences provide some new perspectives on the evolution of the Paired-class genes. Analysis of 146 Paired-class homeodomains from a wide range of metazoan taxa allowed us to identify 18 families among the three sub-classes from which the aristaless family displays the least diverged position. Both Pax-type and K50 families branch within the Q50 Paired-like sequences implying that these are the most ancestral. Consequently, most Pax genes arose from a Paired-like ancestor, via fusion of a Paired-like homebox gene with a gene encoding only a paired domain; the Cnidaria appear to contain genes representing the ’before’ and ’after’ fusion events.

PHYLOGENY AND RATES OF MOLECULAR EVOLUTION OF PLANKTONIC FORAMINIFERA : SSU RDNA SEQUENCES COMPARED TO THE FOSSIL RECORD

Abstract. Planktonic foraminifera are marine protists, whose calcareous shells form oceanic sediments and are widely used for stratigraphic and paleoenvironmental analyses. The fossil record of planktonic foraminifera is compared here to their molecular phylogeny inferred from ribosomal DNA sequences. Eighteen partial SSU rDNA sequences from species representing all modern planktonic families (Globigerinidae, Hastigerinidae, Globorotaliidae, Candeinidae) were obtained and compared to seven sequences representing the major groups of benthic foraminifera. The phylogenetic analyses indicate a polyphyletic origin for the planktonic foraminifera. The Candeinidae, the Globorotaliidae, and the clade Globigerinidae + Hastigerinidae seem to have originated independently, at different epochs in the evolution of foraminifera. Inference of their relationships, however, is limited by substitution rates of heterogeneity. Rates of SSU rDNA evolution vary from 4.0 × 10−9 substitutions/site/year in the Globigerinidae to less than 1.0 × 10−9 substitutions/site/year in the Globorotaliidae. These variations may be related to different levels of adaptation to the planktonic mode of life. A clock-like evolution is observed among the Globigerinidae, for which molecular and paleontological data are congruent. Phylogeny of the Globorotaliidae is clearly biased by rapid rates of substitution in two species (G. truncatulinoides and G. menardii). Our study reveals differences in absolute rates of evolution at all taxonomic levels in planktonic foraminifera and demonstrates their effect on phylogenetic reconstructions.

Molecular evidence that Reticulomyxa filosa is a freshwater naked foraminifer.

ABSTRACT Reticulomyxa filosa is a freshwater protist possessing fine granular, branching and anastomosing pseudopodia and therefore traditionally placed in the class Granuloreticulosea, order Athalamida, as a sister group to the order Foraminiferida. Recent studies have revealed remarkable similarities in pseudopodial motility and ultrastructure between R. filosa and foraminifera (e.g. Allogromia laticollaris), prompting us to conduct a molecular phylogenetic analysis of these seemingly disparate organisms. We sequenced the complete small‐subunit of the ribosomal DNA of the cultured strain of R. filosa and compared it to the corresponding sequences of other protists including 12 species of foraminifera. We also sequenced and analyzed the actin coding genes from R. filosa and two species of foraminifera, Allogromia sp. and Ammonia sp. the analysis of both data sets clearly shows that R. filosa branches within the clade of foraminifera, suggesting that R. filosa is in fact a freshwater naked foraminiferan.

Species level variation in coccolithophores

Coccolithophores are an ideal test group for investigating fine-scale differentiation within the phytoplankton since their taxonomy is rather well-documented and their biomineralised periplasts – the coccoliths – provide a rich suite of qualitative and quantitative morphological characters and a uniquely extensive fossil record. In addition, extant coccolithophore species can be grown in culture and hence are available for studies of morphological variability under controlled conditions, molecular genetic studies and cytological research.

Anaerobic degradation of fluorinated aromatic compounds.

Abstract Anaerobic enrichment cultures with sediment from an intertidal strait as inoculum were established under denitrifying, sulfate-reducing, iron-reducing and methanogenic conditions to examine the biodegradation of mono-fluorophenol and mono-fluorobenzoate isomers. Both phenol and benzoate were utilized within 2–6 weeks under all electron-accepting conditions. However, no degradation of the fluorophenols was observed within 1 year under any of the anaerobic conditions tested. Under denitrifying conditions, 2-fluorobenzoate and 4-fluorobenzoate were depleted within 84 days and 28 days, respectively. No loss of 3-fluorobenzoate was observed. All three fluorobenzoate isomers were recalcitrant under sulfate-reducing, iron-reducing, and methanogenic conditions. The degradation of the fluorobenzoate isomers under denitrifying conditions was examined in more detail using soils and sediments from different geographic regions around the world. Stable enrichment cultures were obtained on 2-fluorobenzoate or 4-fluorobenzoate with inoculum from most sites. Fluoride was released stoichiometrically, and nitrate reduction corresponded to the values predicted for oxidation of fluorobenzoate to CO2 coupled to denitrification. The 2-fluorobenzoate-utilizing and 4-fluorobenzoate-utilizing cultures were specific for fluorobenzoates and did not utilize other halogenated (chloro-, bromo-, iodo-) benzoic acids. Two denitrifying strains were isolated that utilized 2-fluorobenzoate and 4-fluorobenzoate as growth substrates. Preliminary characterization indicated that the strains were closely related to Pseudomonas stutzeri.

Super-Species in the calcareous plankton

The most successful groups of pelagic protists in the modern Ocean have evolved convergent phenotypic traits, including the presence of hard skeletons enclosing the cell. These micro-skeletons – tests, coccoliths, frustules, theca – have accumulated kilometers of deep-sea sediments since the Jurassic, the most complete and continuous fossil record widely used for reconstructing Earth systems dynamics and microbial evolution. The use of the traditional morphological species concepts in those groups indicates that the relatively few species living at a given time have huge, often circum-global biogeographic distributions, and commonly last for many million years in the sediment record, which contrasts with the hectic biological pace of life occurring in the oceanic water masses, leading to one of the highest organismic turnover that any ecosystem sustains. Here we review all recent genetic data on coccolithophore and foraminifer biodiversity. In both groups, the sequencing of various genes shows that the morphological ‘species’ are in fact monophyletic assemblages of sibling species which diverged several million years ago according to molecular clock calculations. Furthermore the sibling species within a morphological entity may systematically occupy restricted geographic or temporal allopatric subdivisions of the total ecological range attributed to the traditional morphospecies. They display also stable and subtle – despite million years of genetic isolation – morphological differences that have been previously overlooked or interpreted as ecophenotypic variations. Obviously, various selective forces related to life in the marine planktic realm impose a strong stabilizing selection on pelagic organisms that maintains “optimal” phenotypes through the origination and possibly extinction of sibling species. We propose that this mode of evolution is characteristic of most marine planktic taxa, including metazoans, and we introduce a concept of ‘planktic super-species’ to describe these constrained morphological monophyletic entities that include several sibling species adapted to different ecological niches. Two different evolutionary models displaying different degrees of complexity in the spatio-temporal disconnection between morphological and genetic/ecologic differentiations are discussed in the frame of the existing morphometric and DNA data sets. The design of experimental protocols at the boundary between molecular phylogenetics and micropa-leontology will be a necessary condition to test which of our models reflect the real world. This will be also a crucial step to reveal the full potential of microfossil applications in paleoecology and stratigraphy, and to understand, at the level at which adaptation and selection operate, how pelagic biodiversity reacted to climatic changes in the past oceans and how it may react to the severe warming events projected in the near future.

Naked foraminiferans revealed

It is generally assumed that the first fossil appearance of a group of organisms corresponds to its evolutionary origin. But we have molecular evidence that extant members of the most abundant microfossil-forming group, the Foraminifera, include ‘naked’ amoeboid species, indicating that ancestral foraminiferans could be unfossilized. This means that the origin of the group might be much earlier than has been deduced from the fossil record. This might help to explain the conflicting molecular and fossil data on the origin of the Foraminifera.

Evolution all at sea

Evidence of gene flow between plankton in the Arctic and Antarctic is one surprise. Another is the discovery of hitherto hidden genetic diversity in these organisms.Some species of planktonic foraminifera - microscopic organisms that occur throughout the world’s oceans - are found in the chilly waters of both the Antarctic and Arctic. Given that the tropics lie between them, molecular evidence that there has been gene flow between these populations comes as a surprise.

CaCO3 OPTICAL DETECTION WITH FLUORESCENT IN SITU HYBRIDIZATION: A NEW METHOD TO IDENTIFY AND QUANTIFY CALCIFYING MICROORGANISMS FROM THE OCEANS 1

Open oceanic calcification is mainly driven by unicellular organisms and in particular by eukaryotes such as coccolithophores and foraminifers. Open ocean microcalcifiers, like most planktonic protists, are characterized by extremely fast generation times and occasional sexual reproduction. Populations can alternate between diploid and haploid stages, which often build different kinds of cell covers. In the most important pelagic calcifiers, the coccolithophores, the diploid and haploid stages, which can self‐replicate and grow independently, display radically different morphologies with different modes of calcification or even with the absence of calcification in at least one life cycle stage. Although life cycle strategies seem likely to fundamentally influence the where and when of open ocean calcification, this issue has yet to be seriously addressed in the natural environment. Here, we introduce a new morphogenetic method, “combined CaCO3 optical detection with fluorescent in situ hybridization,” or COD‐FISH, which is based on a combination of TSA‐FISH and polarized optical microscopy. This technique allows simultaneous assessment of the taxonomic and life cycle status of single coccolithophore cells collected from the ocean. We demonstrate the application of COD‐FISH using both laboratory culture and field samples and discuss its potential value for assessing the ecology, biodiversity, population structure, and life cycles of coccolithophores and other open ocean unicellular calcifiers.