Inférences sur l'histoire des populations à partir de leur diversité génétique (étude de séquences démographiques de type fondation-explosion)

PARIS-BIUSJ-Thèses (751052125) / SudocPARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

Barcoding type specimens helps to identify synonyms and an unnamed new species in Eumunida Smith, 1883 (Decapoda : Eumunididae)

13 páginas, 2 figuras, 3 tablas.The primary purpose of DNA-barcoding projects is to generate an efficient expertise and identification tool. This is an important challenge to the taxonomy of the 21st century, as the demand increases and the expert capacity does not. However, identifying specimens using DNA-barcodes requires a preliminary analysis to relate molecular clusters to available scientific names. Through a case study of the genus Eumunida (Decapoda : Eumunididae), we illustrate how naming molecule-based units, and thus providing an accurate DNA-based identification tool, is facilitated by sequencing type specimens. Using both morphological and unlinked molecular markers (COI and 28S genes), we analysed 230 specimens from 12 geographic areas, covering two-thirds of the known diversity of the genus, including type specimens of 13 species. Most hypotheses of species delimitation are validated, as they correspond to molecular units linked to only one taxonomic name (and vice versa). However, a putative cryptic species is also revealed and three entities previously named as distinct species may in fact belong to a single one, and thus need to be synonymised. Our analyses, which integrate the current naming rules, enhance the a-taxonomy of the genus and provide an effective identification tool based on DNA-barcodes. They illustrate the abilityThis work was supported by the ‘Consortium National de Recherche en Génomique’, and the ‘Service de Systematique Moléculaire’ of the Muséum National d’Histoire Naturelle (UMS 2700 CNRS-MNHN). It is part of the agreement n 2005/67 between the Genoscope and the Muséum National d’Histoire Naturelle on the project ‘Macrophylogeny of Life’ directed by Guillaume Lecointre. These data fed the MarBol project supported by the Sloan Foundation.Peer reviewe

An integrative approach to species delimitation in Benthomangelia (Mollusca: Conoidea)

DNA sequences are currently used to propose primary hypotheses of species delimitation, especially when morphological variability is difficult to assess. In an integrative taxonomy framework, these hypotheses are then compared with other characters, such as morphology or geography, to produce robust species delimitations. For this purpose, the cytochrome oxidase subunit I (COI) gene has been sequenced for almost 50 specimens of the genus Benthomangelia, a deep-sea marine gastropod genus, collected in the South-West Pacific. Five genetic groups, displaying low and high genetic distances respectively within and between groups, were defined. COI hypotheses were compared with both the results obtained with the independent nuclear 28S gene and with an elliptic Fourier analysis of the shape of the last whorl of the shell. 28S gene analysis confirmed the same well-supported groups as COI, and elliptic Fourier analysis identified several morphological characters that vary similarly to genetic variability

FIGURE 12 in First stage zoeal descriptions of five Galatheoidea species from Western Pacific (Crustacea: Decapoda: Anomura)

FIGURE 12. Eumunida annulosa de Saint Laurent and Macpherson, 1990, first zoea. A, lateral view; B, dorsal view. Scale bar = 0.5 mm

Data from: Use of RAD sequencing for delimiting species

RAD-tag sequencing is a promising method for conducting genome-wide evolutionary studies. However, to date, only a handful of studies empirically tested its applicability above the species level. In this communication, we use RAD tags to contribute to the delimitation of species within a diverse genus of deep-sea octocorals, Chrysogorgia, for which few classical genetic markers have proved informative. Previous studies have hypothesized that single mitochondrial haplotypes can be used to delimit Chrysogorgia species. On the basis of two lanes of Illumina sequencing, we inferred phylogenetic relationships among 12 putative species that were delimited using mitochondrial data, comparing two RAD analysis pipelines (Stacks and PyRAD). The number of homologous RAD loci decreased dramatically with increasing divergence, as >70% of loci are lost when comparing specimens separated by two mutations on the 700-nt long mitochondrial phylogeny. Species delimitation hypotheses based on the mitochondrial mtMutS gene are largely supported, as six out of nine putative species represented by more than one colony were recovered as discrete, well-supported clades. Significant genetic structure (correlating with geography) was detected within one putative species, suggesting that individuals characterized by the same mtMutS haplotype may belong to distinct species. Conversely, three mtMutS haplotypes formed one well-supported clade within which no population structure was detected, also suggesting that intraspecific variation exists at mtMutS in Chrysogorgia. Despite an impressive decrease in the number of homologous loci across clades, RAD data helped us to fine-tune our interpretations of classical mitochondrial markers used in octocoral species delimitation, and discover previously undetected diversity

Effects of landscape features and demographic history on the genetic structure of Testudo marginata populations in the southern Peloponnese and Sardinia

Testudo marginata, the largest European land tortoise, is suffering habitat degradation and destruction. Some populations, in markedly degraded habitats, are characterized by divergent morphotypes. However, the evolutionary significance of these morphotypes is of debate. Using 11 polymorphic microsatellites, we studied: (1) marginated tortoises from Sardinia that display a divergent morphotype this population was potentially introduced from Greece; and (2) an area in the southern Peloponnese that includes a small and degraded zone in which marginated tortoises are dwarf. Genetic analyses run without any a priori assignment clearly acknowledge the specimens sampled in the territory of the dwarf form as a single group whilst Sardinian specimens are clustered with other specimens from the northern part of the area sampled in Greece. Demographic analyses suggest that Sardinian tortoises originated recently from some of the populations sampled in the northern part of the area sampled in Greece. Over locations sampled in Greece, a landscape-genetic analysis allowed us to detect potential landscape features that may reduce gene flow between the dwarf form territory and surrounding areas. Our results suggest that the territory of the dwarf form is particularly propitious for marginated tortoises and that conservation regulations in Greece should be reinforced to protect this area from increasing impact of human activities changing from traditional agriculture to mechanization and extensive use of chemicals. (C) 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 591606

Sup mat 1 - genetic structure

Genetic structure calculated with the COI and 28S genes for respectively eight and five PSH. Fst values are calculated between each pair of stations for which at least six specimens were available. Into parentheses: number of specimens. An AMOVA was also performed for the PSH 67 between two groups (Philippines and Vanuatu) and four populations in the Vanuatu

Sup mat 2 - specimens list

List of the 1,000 specimens analysed in this study