In recent years there has been a desire to definitively catalogue the life on our planet. In light of the increasing extinction rates that are driven by human activities, it is unlikely that this will be achieved using traditional methods. Whilst most organisms which have a body size of more than 1cm have been described, the vast majority of animal life is smaller than this, collectively known as meiofauna, and is yet to be catalogued. Meiofaunal organisms present a range of problems for traditional taxonomy. Firstly they are microscopic, meaning that morphological features are often difficult to resolve. Secondly these creatures often exhibit cryptic diversity meaning that different species often look the same. Thirdly, it is often the case that the organisms are poorly described in the literature making it very difficult to confirm identification, assuming that someone has already described it. It is possible, however, to obtain DNA sequences from these organisms. DNA barcoding, the use of short sequences of DNA to identify individuals, is now commonly used in a wide range of applications. It has been proposed that a single target gene should be sufficient to describe all organisms this way. Barcodes can be acquired from individuals or from bulk extractions from environmental samples. In the latter case, many of the sequences obtained are novel and unlikely to ever have a type specimen associated with them. When this is the case, assessing the diversity of a sample becomes a computational exercise. However, as yet, there is no agreed standard method adopted for analyzing the barcodes produced. Indeed most methods currently employed lack objectivity. This thesis investigates the efficiency of a range of gene targets and analysis methods for DNA barcoding, with an emphasis on meiofaunal organisms (nematodes, tardigrades and thrips). DNA barcodes were generated for up to three genes for each specimen. Sequences for each gene were analysed using two programs, MOTU_define.pl and DOTUR. These programs use different methods to assign sequences to operational taxonomic units (OTU), which were then compared. An objective method for analysing sequences such as MOTU_define.pl, which relies on only the information contained in the sequences, was found to be most suitable for designating taxa. It does not attempt to apply evolutionary models to the data, and then infer taxa from the derived data. In addition to barcoding, some samples were pre-processed using video capture and editing (VCE). This creates a virtual slide of a specimen so that a sequence can be linked to a morphological identification. VCE proved to be an efficient method to preserve morphological data from specimens.

No description available.

Les morpho-espèces de foraminifères planctoniques sont composées d'éco-génotypes parfois différentiables sur la base de la morphologie de leur coquille. Cette découverte récente d'une diversité ainsi qualifiée de « pseudo-cryptique » ouvre des perspectives d'amélioration de la précision des reconstructions paléocéanographiques. Malheureusement, ces génotypes ont été définis de façon subjective et ne sont pas homogènes quant à leur rang taxonomique, ce qui est pourtant un pré-requis pour leur intégration dans les modèles de reconstruction. Grâce à l'application de méthodes quantitatives de délimitation d'unités taxinomiques sur les séquences partielles de la petite sous-unité ribosomale (SSU) disponibles chez l'ensemble des morpho-espèces de foraminifères planctoniques, nous montrons que 49 de ces génotypes sont suffisamment divergents pour constituer d'authentiques espèces. Deux morpho-espèces clefs de la paléocéanographie sont étudiées plus en détail. Chez Neogloboquadrina pachyderma, l'obtention des premières séquences complètes de la SSU et la comparaison morphogénétique de spécimens (sub)polaires permettent de proposer un nouveau scénario évolutif et de montrer que les variations morphologiques sont ici d'origine éco-phénotypique, et donc indépendantes de la diversité génétique. Chez Globigerinoides sacculifer, caractérisé par une forte diversité morphologique, il existe au contraire une seule et unique espèce cosmopolite dans les eaux (sub)tropicales de l'Océan mondial. Ces deux cas particuliers montrent que, contrairement à ce que suggéraient les études précédentes, la spéciation pseudo-cryptique n'a pas valeur de règle chez les foraminifères planctoniques / Morphospecies of planktonic foraminifera are clusters of eco-genotypes that show small but significant shell morphological differences (pseudo-cryptic species).This discovery opens a new perspective for improving the accuracy and resolving power of paleoceanographic reconstructions. Unfortunately, current genetic type delimitations suffer subjectivity, inducing non-homogenous taxonomic status while homogenous taxonomic status is a prerequisite for including genetic types in reconstruction models. By applying quantitative and complementary methods for taxonomic units delimitation to the available dataset of partial sequences of SSU (ribosomal small sub-unit), we delimited 49 genuine (pseudo)cryptic species of planktonic foraminifera. We studied two paleoceanographic key-species. Complete sequencing of the SSU and morpho-genetic comparison within austral (sub)polar genetic types of Neogloboquadrina pachyderma lead to a new phylogeographic hypothesis and showed that morphological variations are the result of ecophenotypic effects and are not related with genetic types. The morphologically diverse Globigerinoides sacculifer is the first case of a planktonic foraminifera morphospecies corresponding to a single genetic type distributed world-wide in (sub) tropical waters. These two cases show that, contrary to previous studies conclusions, pseudo-cryptic speciation is not a rule within planktonicForaminifera