Yannick Le Parco

Institut d'Océanographie de Marseille

The extent of within-species genetic variation across the diversity of animal life is an underexplored problem in ecology and evolution. Although neutral genetic variation should scale positively with population size, mitochondrial diversity levels are believed to show little variation across animal species. Here, we report an unprecedented case of...

The extent of within-species genetic variation across the diversity of animal life is a fundamental but largely unexplored problem in ecology and evolution. The neutral theory of molecular evolution predicts that genetic variation scales positively with population size. However, the genetic diversity of mitochondrial DNA, a prominent marker used in...

Little is known about the relationships between genome polymorphism, mobile element dynamics, and population size among animal populations. The chaetognath species Spadella cephaloptera offers a unique perspective to examine this issue because they display a high level of genetic polymorphism at the population level. Here, we have investigated in d...

Multiple lines of evidence have been proposed to resolve the tree of metazoans. Views based on morphology and development were often questioned because they relied on characters whose evolutionary orientation is difficult. Molecules offer an independent perspective and the employment of some genes, such as ribosomal RNA subunits (SSU/LSU) or Hox ge...

A recent study by Barthélémy et al. described a set of ribosomal protein (RP) genes extracted from a collection of expressed sequence tags (ESTs) of the chaetognath (arrow worm) Spadella cephaloptera. Three main conclusions were drawn in this paper. First, the authors stated that RP genes present paralogous copies, which have arisen through allopol...

PCR Primers and annealing conditions used for PCR experiments.

Examples of unrelated trans-spliced genes retrieved in the S. cephaloptera EST library. The presence of the TAC and TTT classes of splice-leaders is indicated for both ribosomal protein genes and other genes.

Structure of the ribosomal protein S8 gene with alignment of used primers, transcript sequences from the EST library and genomic sequence deduced from sequencing of PCR products. The alignment especially stresses the absence of the splice-leader sequence from the 5'UTR and upstream promoter region.

Bayesian trees calculated using Phylobayes implementing the CAT model for the shorter contig (A), longer contig (B) and both of them (C) from S. cephaloptera, as described in Additional file 3. Significant posterior probability values (pp > 0.95) are retrieved for all nodes and only lower ones are displayed in plain text. Both topology and support...

Description of the composite taxa employed in phylogenomic analysis. The amount of missing data was determined for the final Gblocked alignment of 12,764 amino acid positions. p-values are from the chi-square test, which tests whether the amino acid composition of each sequence is identical to the average amino acid composition of the whole alignme...

Unit of the 5S cluster including the two splice-leader genes organized in tandem, the splice-leader sequences and the outrons. Primers employed for amplification are also specified.

List of ribosomal proteins available in the chaetognaths Flaccisagitta enflata (Fe) and Spadella cephaloptera (Sc) and their divergence rates. The molecular divergence of each alternative form is indicated as ML patristic distance to the root (assuming WAG+Γ4+I) as well as the content of best contig (least divergient of all species and variants), s...

The chaetognaths (arrow worms) have puzzled zoologists for years because of their astonishing morphological and developmental characteristics. Despite their deuterostome-like development, phylogenomic studies recently positioned the chaetognath phylum in protostomes, most likely in an early branching. This key phylogenetic position and the peculiar...

Alignment of amino acid sequences of RUX paralogs and variants from S. cephaloptera and some other eukaryotic taxa.

Alignment of cytochrome oxydase III transcripts retrieved from the EST library.

Sequences were amplified from the body (B) or head (H) of individuals as indicated in the sequence name.

All the alignments in Additional data files 15, 16, 17 clearly exhibit lack of a SL motif in the genomic sequence.

Figure S1: EST library statistics. Figure S2: Gene Ontology annotation. Figure S3: alignment of GAMT in selected taxa. Figure S4: trees illustrating the divergence between copies of nuclear and mitochondrial genes in the library. Figure S5: transition versus transversion ratios for the five targeted genes. Figure S6: mismatch analyses and testing f...

All the alignments in Additional data files 15, 16, 17 clearly exhibit lack of a SL motif in the genomic sequence.

Trans-spliced genes conserved between S. cephaloptera and C. elegans and homologous to a SwissProt entry (Figure S6 in Additional data file 1).

Transcript sequences of RP L36 exhibiting the alternative forms corresponding to paralogous copies and the position of primers designed to specifically amplify these forms.

Primers employed for the specific amplifications are included.

Alignment of cytochrome oxydase I transcripts retrieved from the EST library.

Sequences were amplified from the body (B) or head (H) of individuals as indicated in the sequence name.

All the alignments in Additional data files 15, 16, 17 clearly exhibit lack of a SL motif in the genomic sequence.

Table S1: composition of the composite taxa involved in phylogenomic analyses. Table S2: list of all clusters of transcripts corresponding to alternative forms or not with Ka/Ks ratios. Table S3: list of primers employed for PCR amplifications of alternative forms. Table S4: comparison of molecular evolution trends for four genes retrieved in nine...

This dataset was employed for phylogenomic reconstruction.

Transcript sequences of RP L40 exhibiting the alternative forms corresponding to paralogous copies and the position of primers designed to specifically amplify these forms.

Sequences were amplified from the body (B) or head (H) of individuals as indicated in the sequence name.

Sequences were amplified from the body (B) or head (H) of individuals as indicated in the sequence name.

cDNA library construction, EST sequencing and data processing The species Spadella cephaloptera, Busch 1851 was chosen because of its availability related to benthic way of life. Specimens were collected in several stations in the South of France (Brusc lagoon and bay of la Ciotat, near Marseille). To build cDNA library, total RNA was isolated from...

While the phylogenetic position of Chaetognatha has became central to the question of early bilaterian evolution, the internal systematics of the phylum are still not clear. The phylogenetic relationships of the chaetognaths were investigated using newly obtained small subunit ribosomal RNA nuclear 18S (SSU rRNA) sequences from 16 species together...

Hox genes encode a set of evolutionarily conserved transcription factors that regulate anterior-posterior patterning. Here we report the first developmental expression of a Hox gene from Chaetognatha. These metazoans have been shown recently to be part of the protostome group of bilaterians. We describe the analysis of the SceMed4 gene (a Spadella...

Determining the phylogenetic position of enigmatic phyla such as Chaetognatha is a longstanding challenge for biologists. Chaetognaths (or arrow worms) are small, bilaterally symmetrical metazoans. In the past decades, their relationships within the metazoans have been strongly debated because of embryological and morphological features shared with...

The Brachyury family of T-domain containing transcription factor has been recently the subject of a number of Evo-Devo studies, with expression data obtained from a wide sampling of eumetazans, pointing to a possible conserved role in the formation of the blastopore and the extremities of the digestive tract. Here we present a comparative analysis...

On the basis of morphological and genetic studies (rDNA ITS1, 5.8S, ITS2, and a 18S rDNA intron), we confirm here that Caulerpa racemosa var. cylindracea (Sonder) Verlaque, Huisman et Boudouresque, a southwestern Australian taxon recently introduced into the Mediterranean Sea also occurs in the Canary Islands. This is the first report of C. racemos...

Urodele amphibians are the only adult vertebrates possessing the capacity to regenerate their limbs and tail after amputation. Epimorphic regeneration is characterized by the accumulation of undifferentiated and dividing mesenchymal cells originating from the tissues of the stump, which form a blastema. It has been proposed that the ability to rege...

Recent morphological and genetic studies on the Caulerpa racemosa (Forsskål) J. Agardh complex have demonstrated that three taxa occur in the Mediterranean Sea. One of them, the ‘invasive variety’, provisionally regarded as close to C. racemosa var. occidentalis J. Agardh, is currently spreading spectacularly throughout the Mediterranean. On the ba...

Because calcareous sponges are triggering renewed interest with respect to basal metazoan evolution, a phylogenetic framework of their internal relationships is needed to clarify the evolutionary history of key morphological characters. Morphological variation was scored at the suprageneric level within Calcispongia, but little phylogenetic informa...

We present the isolation of six Hox genes in the chaetognath Spadella cephaloptera. We identified one member of the paralogy group 3, four median genes and a mosaic gene that shares features of both median and posterior classes ( SceMedPost). Several hypotheses may account for the presence of a mosaic Hox gene in this animal. Here we propose that S...

Morphological data has provided a basis for the hypothesis that three taxa belonging to the Caulerpa racemosa complex occur in the Mediterranean Sea: var. turbinata–uvifera, var. lamourouxi, and the `invasive variety'. In order to test this hypothesis and to determine the origin of the `invasive variety', the transcribed spacer ITS1–ITS2 and an 18S...

In order to allow critical evaluation of the interrelationships between the three sponge classes, and to resolve the question of mono- or paraphyly of sponges (Porifera), we used the polymerase chain reaction (PCR) to amplify almost the entire nucleic acid sequence of the 18S rDNA from several hexactinellid, demosponge and calcareous sponge species...

The definition of an Ecdysozoa clade among the protostomians, including all phyla with a regularly molted alpha-chitin-rich cuticle, has been one of the most provocative hypotheses to arise from recent investigations on animal phylogeny. Here we present evidence in favor of an arthropod-nematode clade, from the comparison of beta-thymosin homologue...

Knowledge of the developmental mechanisms in living basal metazoan phyla is crucial for understanding the genetic bases of morphological evolution in early animal history. We looked for homeobox genes in the calcareous sponge, Sycon raphanus, using the polymerase chain reaction. Partial sequences of eight homeoboxes were recovered, five of which ar...

We report the isolation and characterization of two NK-3-related genes (PwNkx-3.2 and PwNkx-3.3) and their expression patterns during embryonic development, in the adult CNS, and during tail regeneration in the urodele Pleurodeles waltl. PwNkx-3.2 is the ortholog of the mouse and Xenopus genes, Bapx 1 and Xbap, but PwNkx-3.3 has no known homologue...

To understand the early evolution of the Metazoa, it is necessary to determine the correct phylogenetic status of diploblastic animals. Despite cladistic studies of morphological characters and recent molecular phylogenetic studies, it remains uncertain whether diploblasts are monophyletic or paraphyletic, and how the phyla of diploblasts are phylo...

Urodele amphibians are nearly the only adult vertebrates able to regenerate their missing or amputated tail. An interesting aspect of this biological model lies in the ability of regenerates to differentiate the spinal cord (SC), the vertebral cartilage, and muscles. The main questions addressed in this study concern the possible roles of Wnt genes...

Adult urodele amphibians such as Pleurodeles waltl are able to regenerate their amputated limbs or tail. The mechanisms implicated in growth control and formation of the blastema are unknown but it has been proposed that regeneration in newts may proceed through reactivation of genes involved in embryonic development. Knowing the role of Wnt genes...

Type IV collagen forms a network that provides the major structural support for basement membranes. Basement membranes are specialized forms of extracellular matrix with important functions in development. One collagen gene (Dcg1) was characterized in Drosophila melanogaster and shown to encode a collagen chain related to vertebrate basement membra...

We report the cloning of a Distal-less-like gene (PwDlx-3) and its pattern of expression during embryonic development and adult tail regeneration in the urodele Pleurodeles waltl. Using RT-PCR and in situ hybridization experiments we determined that, during regeneration, PwDlx-3 is expressed in the epidermis, the cells associated with muscle masses...

A collagen gene (Dcg1) was characterized in Drosophila melanogaster and shown to encode a peptide related to vertebrate basement membrane type IV collagen chains. To study the function of type IV collagen during Drosophila development, we transformed flies with a partially truncated Dcg1 gene under the control of a heat-shock promotor. This constru...

The urodele amphibians are nearly the only adult vertebrates able to regenerate their missing or amputated tail. The most striking feature of this model lies in the ability of the spinal cord (SC) to differentiate, within the regenerating tail, a new ependymal tube from which the SC and the peripheral nervous system originate. A fundamental questio...

Variegation in Drosophila is a manifest illustration of the important role played by chromatin structure in gene expression. We have isolated mutants of modulo (mod) and shown that this gene is a dominant suppressor of variegation. Null mutants are recessive lethal with a melanotic tumour phenotype. The mod protein directly binds DNA, which indicat...

By means of immunocytochemistry with a battery of specific antibodies, we describe the expression of the collagen IV chain produced by the gene DCg1 during the two phases of Drosophila neurogenesis. DgC1 was not expressed in neuronal tissues as shown by in situ hybridization, but the onset of its expression in cells of mesodermal origin was concomi...

During post-traumatic regeneration of the polychaete annelid Owenia fusiformis, the extracellular matrix (ECM) formation was studied by light and electron microscopy and by histoautoradiography after incorporation of tritiated proline as marker for collagenic proteins. Three days after amputation, a new basement membrane was reformed in the blastem...

We have developed and characterized a battery of specific polyclonal antibodies directed against specific portions of the alpha-chain of collagen type IV synthesized in Drosophila by the gene DCg1. Here, we describe the use of these antibodies together with in situ hybridization experiments in an attempt to study the expression and localization of...

We report the purification and characterization of three sequence-specific polyclonal antibodies raised against specific portions of the Drosophila αIV collagen chain produced from the gene DCg1. These antibodies were used for immunolocalization experiments on tissue sections from embryonic organogenesis stages (13–17) and first larval stages. This...

We have examined directly the expression of one collagen gene (DCg1) during Drosophila melanogaster embryogenesis by means of in situ hybridization. Transcripts of this gene, which were demonstrated to encode a basement membrane type IV collagen chain, began to accumulate specifically in mesodermal derivatives at stages 12-13 of embryogenesis, and...

Type IV collagen, a major structural component of basement membrane, has been characterized only in vertebrates. It is unique among the collagenous proteins in that it forms specific lattice networks by end-to-end interactions. In particular, in mammals the C-terminal noncollagenous domain (NCl) of collagen IV was shown to be one of the major cross...

We report a direct examination of the expression of one collagen gene (DCg1) during Drosophila melanogaster metamorphosis, based on data from in situ hybridization. The transcripts of this gene, thought to encode a basement membrane type IV collagen, are mainly accumulated during ecdysis in wandering haemocytes. Our results demonstrate that haemocy...

Based on data from developmental RNA profiles and in situ hybridization, we report a direct examination of the expression of one collagen gene (Dcg1) during drosophila melanogaster life cycle. These studies show, for the first time, that the expression of a collagen gene is both differential and tissue-specific during the course of development. Mor...

We have used a cloned chicken collagen cDNA sequence to help identify hypothetic members of the collagen gene family from Drosophila melanogaster. Several experimental evidences have been obtained which indicate that the Drosophila genome contains numerous collagen-like sequences. We have characterized in more detail ten distinct DNA sequences that...

Studies on the dynamics and genetics of the popualtions of the newt Triturus alpestris, in the national park of Ecrins

One of the earliest events observed in the 'dedifferentiation phase' of traumatic regeneration is an in vivo increase in transcription. In order to see whether that increase corresponds to a variation at the level of genetic material, we prepared chromatin from normal and regenerating animals (12 h after amputation) for transcription in vitro by E....