wp4- developping innovative monitoring tools · kick-off meeting, heraklion 17-19 april 2013 wp4 :...
TRANSCRIPT
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
WP4- Developping innovative monitoring tools
Kick-off meeting CIGESMED projectHeraklion april 2013
Didier AURELLE Aix-Marseille University / [email protected]
Resp. Anne CHENUIL-MAUREL CNRS / [email protected]
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
WP4 : use molecular tools to monitor the good ecological WP4 : use molecular tools to monitor the good ecological status of the coralligenous biotope. status of the coralligenous biotope.
Three identified actions :
1) Barcoding and species delimitation : rhodophytes (indigenous or aliens)
2) Phylogeography → connectivity and demography3) Characterization of the genetic diversity for various
population and species (not only rhodophytes ?)
0 or 4) link with a « good ecological » status ?
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Task 1: Barcoding Task 1: Barcoding coralligenous red algaecoralligenous red algae
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Task 1: Barcoding coralligenous red algaeTask 1: Barcoding coralligenous red algae
• Objectives ?
– Species delimitation● high diversity : corallinales ≈ 600 species● plasticity● cryptic diversity (Bittner et al., 2011)● hybridisation ?
– Identification tool– Phylogeny ?– Community diversity and evolution
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Task 1: Barcoding coralligenous red algaeTask 1: Barcoding coralligenous red algae
Strategy ?
– Sampling collection – several « individuals » / species– Species identification :
● Who ? → identify referent taxonomists– Photo / type– Molecular characterization– Phylogenetic and population genetics
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
DNA sequences
barcoding species delimitation
phylogeny
community evolution and conservation ?
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Phylogeny for conservation and species prioritisation ?(Mouquet et al., 2012)
threatened species
Phylogenetic diversity as indicator ? (WP3)
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Field collection :Disrupt « hard species »Dry sample rapidly at sun, then in silicagelCheck under a binocular if necessary and collect separately if distinct species ; Excise epiphytes
Molecular work: Extract DNA (e.g. DNeasy Plant Kit)PCR, Sequence, Alignment
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Which molecular marker ?
Depending on the question (phylogeny, barcoding, species delimitation) :
18S, 28S, EF2 nuclear
COI mitochondrial
psbA chloroplast
Primers and sequences available
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Remark 1: in corallinales, DNA is very easily amplified from dried museum specimens (LeGall, ongoing project)
Remark 2: Line LeGall (MNHN, France), open to collaborate and gave her protocols
Remark 3: Kostas Tsianis is a good taxonomist of rhodophytes according to Line Le Gall
→ who knows him ?
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Task 2: Phylogeography• Objectives :
• Connectivity / gene flow
→ recolonization abilities→ genetic diversity→ potential for local adaptation
• Intra-specific : frequency and sequences of haplotypes among populations
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Task 2: Phylogeography• Example : Eunicella cavolinii
(Masmoudi et al.In prep)
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Task 2: Phylogeography• Which species ?
– Common species– Easy to sample and recognize– Particular interest ? (see below)– Not studied elsewhere
e.g. Mesophyllum expansum in France
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Task 2: Phylogeography•Which species ?Invasive speciese.g.Womersleyella setacea
Origin and invasion dynamics...
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Task 2: Phylogeography• How ?
– Identify now or during the project the potential species
– Identify informative genetic markers● Sequences ?
– Use of NGS ?
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Task 2: Phylogeography• How ?
– Statistical analyzes– Connectivity :
● Isolation / migration● Migrate● Assignment methods ?
(if suitable markers)
long term
short term
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
• How ?
– Statistical analyzes– Historical demography :
● Selective neutrality tests● Beast● → bottleneck ?● → link with past fluctuations ?
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Task 3: multispecific genetic diversity as an indicator
- intraspecific genetic diversity
- substrate for natural selection
- basis for adaptive response toperturbations
- correlation with population size
potential indicator of ecological status ?(hot topic!!!)
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Population size, genetic diversity and genetic drift...
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Population size, genetic diversity and genetic drift...
time
diversity
Bottleneck → slow recovery...
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Genetic diversity estimated for a panel of reference species→ variation in space (and time?)
Which reference species and sites?(see task phylogeography)
Which genetic markers ?
Need of population sampling !
Comparative population genetics7 common localities x 7 species ( + more species ongoing)
France
NW Mediterranean sea
Catalonia Scandola
Marseille (3)
Porquerolle
Nice
Gulf of Lion
Spain
ItalyNew natural park les Calanques
2 GorgoniansParamuricea clavataCorallium rubrum
2 Ophiuroids (+)Ophioderma longicaudaAmphipholis squamata
3 Echinoids (+)Paracentrotus lividusEchinocardium mediterraneumE. Cordatum
Species complex
Species complex
Low dispersal species High dispersal species
Marine ProtectedArea
Relative genetic diversity / species /site
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
Genetic diversity as an indicator of ecological status :Genetic diversity as an indicator of ecological status :
• Various estimates of genetic diversity• Allelic richness, heterozygosity...• Standardized
• Comparison / analysis along with ecological data
• Comparison with ecological indicators(Sartoretto, Deter...)
• Integration in a multivariate indicator
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
What do we need now ?
1 - list of participants + list of human ressources
(students...)
2 - list of species for phylogeography → input from other Wps (2)
3 - samples from as many species as possible+ (putative) species names ! → barcoding
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
What do we need now ?
4 - samples for phylogeography and genetic diversity :
→ several individuals (30?) per site
5 - ecological informations / independent indicators for pilot sites
→ what informations from genetics ? → input from other WPs (2, 3) and from litterature
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
What outputs ?
- data for database
- molecular tools for species recognition
- evolutionary history of populations and communities
- genetically based indexes :• Populations (species)• Community
• collaborations on other projects
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
What do we need now ?
- list of participantslabs people
- collaborations : Line Le Gall, Florian Holon
- who does what ?
- laboratory workshop ? → common protocols ?
Kick-off meeting, Heraklion 17-19 April 2013Kick-off meeting, Heraklion 17-19 April 2013
risks ?
- suitable genetic markers (intra specific)– specific development for reference species ?
- geographical coverage of sampling– Informative ?
- species recognition : – population or species genetic differences ?