wp4- developping innovative monitoring tools · kick-off meeting, heraklion 17-19 april 2013 wp4 :...

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 / IMBEdidier.aurelle@imbe.fr

Resp. Anne CHENUIL-MAUREL CNRS / IMBEanne.chenuil-maurel@imbe.fr

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 ?

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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

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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 ?

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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!!!)

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Population size, genetic diversity and genetic drift...

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Population size, genetic diversity and genetic drift...

time

diversity

Bottleneck → slow recovery...

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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

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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

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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

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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 ?