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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.

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slide1

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
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.

slide3

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 ?

slide4

Extinction

Speciation

A species

A species

Speciation

Speciation

Delimiting species =

 recovering the structure of the genealogical network

A species is a permanently diverging lineage

De Quieroz, 1998

Samadi & Barberousse, 2006

A species is a piece of genealogical network that is definitively divergent from others part of the network

slide5

(i) alpha-Taxonomy (morphology or molecules)

(phenetic criteria)

(i) Similarity in heritable characters

(ii) Populations genetics and biology

(biological criteria)

(ii) Interfecondity, gene flows

(iii) Phylogenetic reconstruction

(phylogenetic criteria)

(iii) Share a common history using heritable characters

Delimiting species =

 resolving the structure of the genealogical network

How in practice do we resolve the structure of the network ?

Samadi & Barberousse, 2006

 a species is a reproductive community

 Divergence with others such species is definitive

slide6

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 includeseveral 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

slide7

COI is DNA fragmentthat 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 …)

slide8

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

slide9

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

slide10

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 fragment is less variable than COI but the genetic clusters are the same

COI data are more easily obtained

For some old specimens we did not obtain the 28S sequence

COI was obtained for all except one specimens

slide11

E. sternomaculata

E. similor

E. spinosa

E. keiji

E. treguieri

E. multineata

E. annulosa (holotype)

E. laevimana

E. marginata

E. minor

E. capilata

E. 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)

When no type specimens is included in a genetic cluster the morphological determination key is used

The type specimens are used to give names to the genetic clusters

slide12

E. sternomaculata

E. similor

E. spinosa

E. keiji

E. treguieri

E. multineata

One cluster correspond to three names (including the types of two of them)

E. annulosa (holotype)

E. laevimana

E. marginata

E. minor

E. capilata

E. bispinata

E. parva + E. karubar + E. smithii

E. picta

E. squamifera

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 diagnostic for one cluster correspond to a name already attributed, using the position of the holotype, to another cluster

E. annulosa

Overall, the species recognized using the traditional approach are recovered … but

E. annulosa (holotype)

E. funambulus

slide13

Spines on the carpus of the chelipeds

The genus Eumunida

One cryptic species is detected

E. annulosa

E. annulosa (holotype)

This character is diagnostic only for

adult specimens

 Such characters are often used in determination keys

In such a case the DNA-barcode expertise is more efficient than the traditional morphological approach

Moreover it works for all the stages of the life cycle

slide14

The genus Eumunida

Type specimens and localities are mixed

for the three species

Three species correspond to a unique genetic cluster

S

P

K

S

K H

K P

K P

K P

K P

P

K P

P

P

K

P

Ph

P

P

K

E. smithii

E. karubar

E. parva

P

P

The hypothesis of synonymy is supported by the 28S data

slide15

The genus Eumunida

> 229 specimens

> 17 species / 26 described

> 9 holotypes et 24 paratypes (13 species)

This sampling and the associated molecular data set allow us to :

> COI (« barcode fragment», 658pb)

> 28S (C1’-D2, 867pb)

(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)

slide16

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

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