Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Efficiency of the DNA-barcode expertise and its relationships with the practice of alpha-taxonomy illustrated by the study of the genus Eumunida (Decapoda). Sarah Samadi (IRD) UMR 7138, Dept Syst & Evol, MNHN, Paris. Nicolas Puillandre, Enrique Macpherson, Josie Lambourdière, Marie-Catherine Boisselier The context Given the estimated amount of biological species that needs to be described Offering an efficient expertise tool is an important challenge for the taxonomy of the 21st century. Our positions > The taxonomic expertise directly lies on the taxonomic knowledge which continually evolves with the new data provided by the taxonomic research. > New expertise tools must be directly linked to taxonomic research. > The constitution of DNA barcode dataset on a given set of organisms must follow the requirements of specimens sampling of the taxonomic research. TAXONOMIC EXPERTISE = to link a specimen to a species name TAXONOMIC RESEARCH = To propose hypotheses of species delimitations > What is a species ? > How in practice do we delimit species ? > How names are linked to these hypotheses ? A species Delimiting species = is a permanently diverging lineage recovering the structure of the genealogical network De Quieroz, 1998 Samadi & Barberousse, 2006 Extinction Speciation A species A species Speciation Speciation A species is a piece of genealogical network that is definitively divergent from others part of the network Delimiting species = resolving the structure of the genealogical network Samadi & Barberousse, 2006 a species is a reproductive community How in practice do we resolve the structure of the network ? Divergence with others such species is definitive (i) Similarity in heritable characters (i) alpha-Taxonomy (morphology or molecules) (ii) Interfecondity, gene flows (ii) Populations genetics and biology (biological criteria) (iii) Share a common history using heritable characters (iii) Phylogenetic reconstruction (phylogenetic criteria) (phenetic criteria) DNA offers many polymorphic and heritable characters on which the different criteria can be applied … But with some sampling requirements > to measure similarity or to estimate gene flows sampling must include several specimens > Sampling must cover the known geographic distribution > Phylogenetically close species must be included (the evolutionary context) > In addition : The analysis of type-specimens permits to link the DNA-barcode to the names COI is DNA fragment that offers many polymorphic and heritable characters But … other data should be integrated to test the primary hypotheses > unlinked molecular characters (nuclear versus mitochondrial) > Morphological characters > Life histroy traits > Ecological data (biotic and abiotic environnement …) The genus Eumunida Well studied by « classical » taxonomy Collections preserved in ethanol Many specimens available for each species (MUSORSTOM cruises) http://www.mnhn.fr/musorstom/ Many type specimens available in the collections of the MNHN (Paris) Among the 26 described species we were able to extract and sequence DNA from specimens of the 17 species available in the collections of the MNHN, that cover the known distribution area Type specimens were available for 13 species 9 holotypes & 24 paratypes The genus Eumunida > 229 specimens > 17 species / 26 described > 9 holotypes et 24 paratypes (13 species) > COI (« barcode fragment», 658pb) > 28S (C1’-D2, 867pb) Distribution of pairwise genetic distances for COI In black, the distribution of the distances between pairs of type specimens The genus Eumunida > 229 specimens > 17 species / 26 described > 9 holotypes et 24 paratypes (13 species) > COI (« barcode fragment», 658pb) > 28S (C1’-D2, 867pb) 28S Forfragment some oldis less variable specimens wethan did COIobtain but the not the genetic clusters 28S sequence are the same COI was obtained COI data areone for all except more easily specimens obtained The genus Eumunida > 229 specimens > 17 species / 26 described > 9 holotypes et 24 paratypes (13 species) > COI (« barcode fragment», 658pb) > 28S (C1’-D2, 867pb) E. sternomaculata E. similor E. spinosa E. keiji E. treguieri When no type specimens The type is included inare a specimens genetic used tocluster give the morphological names to the determination genetic clusters key is used E. multineata E. annulosa (holotype) E. E. E. E. E. laevimana marginata minor capilata bispinata E. picta E. squamifera E. funambulus The genus Eumunida > 229 specimens > 17 species / 26 described > 9 holotypes et 24 paratypes (13 species) > COI (« barcode fragment», 658pb) > 28S (C1’-D2, 867pb) The morphological Overall, the One cluster diagnostic for species correspond one clusterto recognized using three names correspond to a the traditional (including the name already approach are types of two of attributed, using recovered them)… but the position of the holotype, to another cluster E. sternomaculata E. similor E. spinosa E. keiji E. treguieri E. annulosa E. multineata E. E. annulosa annulosa(holotype) (holotype) E. E. E. E. E. laevimana marginata minor capilata bispinata E. parva + E. karubar + E. smithii E. picta E. squamifera E. funambulus The genus Eumunida One cryptic species is detected Spines on the carpus of the chelipeds E. annulosa E. annulosa (holotype) This character In such a caseisthe DNAdiagnostic only for is more barcode expertise adult specimens efficient than the traditional morphological approach Such characters are often used in Moreover it works determination keysfor all the stages of the life cycle The genus Eumunida Type specimens Three species and localities are correspond to a mixed unique for thegenetic three cluster species E. parva E. karubar E. smithii S P K S KH KP KP KP KP P KP P P K P Ph P P K P P The hypothesis of synonymy is supported by the 28S data The genus Eumunida > 229 specimens > 17 species / 26 described > 9 holotypes et 24 paratypes (13 species) > COI (« barcode fragment», 658pb) > 28S (C1’-D2, 867pb) This sampling and the associated molecular data set allow us to : (i) Support most of the primary species hypotheses based on morphology using the phenetic criterion on molecular data … but also to bring up new hypotheses (ii) For some of the species to show that gene flows occurs among populations over the geographic range of the species (Biological criterion) (… more details for two of them in Samadi et al, Mar Biol 2006) (iii) Using a close out-group outside the genus, to reveal that each of the proposed species has it own evolutionary history (Phylogenetical criterion) When the taxonomy is well established The DNA-barcode can be used as a determination key But sampling must cover the intra and inter specific variability, the geographic distribution and when possible type specimens When sampling is adequate such data should enhance taxonomy and bring up new hypotheses But only if we go back to specimens and morphology Thus, DNA-barcode is an efficient expertise tool only if sampling is adequate and directly linked to taxonomical research. acknowledgments The crew of the R/V Alis The staff of the ‘Service de systématique moléculaire’ at the ‘MNHN, Paris’ Régis Cleva (curator of crustacean collections) The ‘Consortium national de recherche en génomique’, Genoscope