efficiency of the dna-barcode expertise and its relationships with the practice of alpha-taxonomy...
TRANSCRIPT
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
> 229 specimens > 17 species / 26 described> 9 holotypes et 24 paratypes (13 species)
> COI (« barcode fragment», 658pb)> 28S (C1’-D2, 867pb)
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
> 229 specimens > 17 species / 26 described> 9 holotypes et 24 paratypes (13 species)
> COI (« barcode fragment», 658pb)> 28S (C1’-D2, 867pb)
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. annulosa (holotype)
E. marginataE. minor
E. bispinata
E. keijiE. treguieri
E. squamiferaE. funambulus
> 229 specimens > 17 species / 26 described> 9 holotypes et 24 paratypes (13 species)
> COI (« barcode fragment», 658pb)> 28S (C1’-D2, 867pb)
E. parva + E. karubar + E. smithii
One cluster correspond to three names (including the types of two of
them)
E. annulosa (holotype)
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
E. annulosa (holotype)
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)
> 229 specimens > 17 species / 26 described> 9 holotypes et 24 paratypes (13 species)
> COI (« barcode fragment», 658pb)> 28S (C1’-D2, 867pb)
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.