Transcript Efficiency of the DNA-barcode expertise and its

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. 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)
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. annulosa
annulosa(holotype)
(holotype)
E. laevimana
E. marginata
E. minor
E. capilata
E. 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