Biomedical subjects
C de Vargas
Publications and source records attributed to C de Vargas.
Molecular evidence of cryptic speciation in planktonic foraminifers and their relation to oceanic provinces.
The fossil record of planktonic foraminifers is a key source of data on the biodiversity and evolution of marine plankton. One of the most distinctive foraminiferal taxa, Orbulina universa, widely used as a stratigraphic and paleoclimatic index, has always been regarded as a single species. Here we present a phylogenetic analysis of Orbulina small subunit rDNA sequences from 25 pelagic stations covering 100 degrees latitude in the Atlantic Ocean. The genetic data reveal the presence of three cryptic species, whose distribution is clearly correlated to hydrographic provinces, and particularly to sea-surface total chlorophyll a concentration. Our results, together with previous studies, suggest that a considerable part of the diversity among planktonic foraminifers has been overlooked in morphological taxonomies. Our data also support the idea that planktonic foraminifers, even if adapted to particular hydrographic conditions, are high-dispersal organisms whose speciation may be similar to that of other high-dispersal taxa in which reproductive mechanisms and behavior, rather than just geographic barriers to dispersal, play key roles in species formation and maintenance.
Evolution of homeobox genes: Q50 Paired-like genes founded the Paired class.
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.
Molecular versus taxonomic rates of evolution in planktonic foraminifera.
Neogene planktonic foraminifera are among the most widely used microfossils in the study of tempo and mode of evolution. Comparisons of taxonomic rates between the two major clades in this group have shown that the nonspinose globorotaliids have undergone a significantly more rapid evolutionary turnover than the spinose globigerinids (S. M. Stanley et al., 1988, Paleobiology 14, 235-249). In order to test if similar fluctuations are observed in molecular data, we have used different methods to calculate absolute and relative rates of substitutions based on 16 partial SSU rDNA sequences from representatives of both groups. According to our data, rates of substitution are relatively constant within the globigerinids with a mean value of 4.3 subst./site/10(9) years, but vary in the globorotaliid clade with three species having a rate of about 1 subst./site/10(9) years and two species evolving much faster with rates of more than 7 subst./site/10(9) years. Assuming that the fast rates result from recent accelerations, the globorotaliids have basically much slower molecular evolutionary rates than the globigerinids, in opposition to the fossil data.
Phylogeny and rates of molecular evolution of planktonic foraminifera: SSU rDNA sequences compared to the fossil record.
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 x 10(-9) substitutions/site/year in the Globigerinidae to less than 1.0 x 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.
Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record.
Foraminifera have one of the best known fossil records among the unicellular eukaryotes. However, the origin and phylogenetic relationships of the extant foraminiferal lineages are poorly understood. To test the current paleontological hypotheses on evolution of foraminifera, we sequenced about 1,000 base pairs from the 3' end of the small subunit rRNA gene (SSU rDNA) in 22 species representing all major taxonomic groups. Phylogenies were derived using neighbor-joining, maximum-parsimony, and maximum-likelihood methods. All analyses confirm the monophyletic origin of foraminifera. Evolutionary relationships within foraminifera inferred from rDNA sequences, however, depend on the method of tree building and on the choice of analyzed sites. In particular, the position of planktonic foraminifera shows important variations. We have shown that these changes result from the extremely high rate of rDNA evolution in this group. By comparing the number of substitutions with the divergence times inferred from the fossil record, we have estimated that the rate of rDNA evolution in planktonic foraminifera is 50 to 100 times faster than in some benthic foraminifera. The use of the maximum-likelihood method and limitation of analyzed sites to the most conserved parts of the SSU rRNA molecule render molecular and paleontological data generally congruent.