Efficiency of the DNA-barcode expertise and its relationships with the practice of alpha-taxonomy illustrated by the study of the genus Eumunida (Decapoda)

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 constitution of DNA barcode dataset on a given set of organisms must follow the requirements of specimens sampling of the taxonomic research.

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.

> 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.

Our positions

> What is a species ?

> How in practice do we delimit species ?

> How names are linked to these hypotheses ?

TAXONOMIC EXPERTISE =

TAXONOMIC RESEARCH = To propose hypotheses of species delimitations

to link a specimen to a species name

A species is a permanently diverging lineage

Samadi & Barberousse, 2006

De Quieroz, 1998

Speciation

Speciation

Speciation

Extinction

A speciesA species

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

network

Delimiting species = recovering the structure of the genealogical network

(i) Similarity in heritable characters

(ii) Interfecondity, gene flows

(iii) Share a common history using heritable characters

(i) alpha-Taxonomy (morphology or molecules)

(phenetic criteria)(ii) Populations genetics and biology

(biological criteria)

(iii) Phylogenetic reconstruction(phylogenetic criteria)

Samadi & Barberousse, 2006

a species is a reproductive community

Divergence with others such

species is definitive

How in practice do we resolve

the structure of the network ?

Delimiting species = resolving the structure of the genealogical network

DNA offers many polymorphic and heritable characters

on which the different criteria can be applied …

> In addition : The analysis of type-specimens permits to link the DNA-barcode to the names

> Phylogenetically close species must be included

(the evolutionary context)

> Sampling must cover the known geographic distribution

> to measure similarity or to estimate gene flows sampling must include several specimens

But with some sampling requirements

COI is DNA fragment that offers many polymorphic and heritable characters

> unlinked molecular characters (nuclear versus mitochondrial)

> Morphological characters

> Life histroy traits

> Ecological data (biotic and abiotic

environnement …)

But … other data should be integrated to test the primary

hypotheses

Many type specimens available in the collections of the MNHN (Paris)

Well studied by « classical » taxonomy

Collections preserved in ethanol

The genus Eumunida

Many specimens available for each species (MUSORSTOM cruises)

http://www.mnhn.fr/musorstom/

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

> 229 specimens > 17 species / 26 described> 9 holotypes et 24 paratypes (13 species)

Distribution of pairwise genetic distances for COI

In black, the distribution of the distances between pairs of type specimens

> COI (« barcode fragment», 658pb)> 28S (C1’-D2, 867pb)

The genus Eumunida



The genus Eumunida

For some old specimens we did not obtain

the 28S sequence

COI was obtained for all

except one specimens

28S fragment is less variable

than COI but the genetic clusters

are the same

COI data are more easily

obtained

The type specimens are used to give names to the

genetic clusters

When no type specimens is included in a

genetic cluster the

morphological determination

key is used

E. sternomaculata

E. similorE. spinosa

E. annulosa (holotype)

E. marginataE. minor

E. bispinata

E. keijiE. treguieri

E. squamifera

E. multineata

E. laevimana

E. capilata

E. picta

E. funambulus



The genus Eumunida

Overall, the species

recognized using the traditional

approach are recovered …

but

E. annulosaE. multineata

E. laevimana

E. capilata

E. picta

E. sternomaculata

E. similorE. spinosa


E. marginataE. minor

E. bispinata

E. keijiE. treguieri

E. squamiferaE. funambulus



E. parva + E. karubar + E. smithii

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

them)


The genus Eumunida

The morphological diagnostic for one cluster

correspond to a name already

attributed, using the

position of the holotype, to

another cluster

E. annulosa


Spines on the carpus of the chelipeds

One cryptic species

is detected

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

The genus Eumunida

E. parva E. karubar

E. smithii

S

S

PP

P

PP

PP

Ph

KP

K P

K PK PK PK P

K H

P

K

K

Three species correspond to a unique genetic

cluster

Type specimens and localities

are mixedfor the three

species

The hypothesis of synonymy is supported by the 28S data

The genus Eumunida

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)



The genus Eumunida

When the taxonomy is well

established

The DNA-barcode can be used as a determination key

When sampling is adequate such data should enhance taxonomy and bring up new hypotheses

But sampling must cover the intra and inter specific variability, the geographic distribution and when possible type specimens

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

Documents

Efficiency of the DNA-barcode expertise and its relationships with the practice of alpha-taxonomy illustrated by the study of the genus Eumunida (Decapoda)