Blue tit project: Evergreen and deciduous forests in Southern France and Corsica

In the Mediterranean region, blue tits (Cyanistes caeruleus) breed in habitats dominated by broad-leaf deciduous downy oak (Quercus humilis) and in habitats dominated by evergreen holm oak (Q. ilexI). The two oak habitat types generally differ in timing and amount of food available for breeding tits, which, as we have shown in our long-term blue tit study, has major consequences for the expression of life-history traits and reproductive success. The core of our blue tit project is very much centered around evolutionary consequences of this habitat heterogeneity.

  

  Deciduous study site of Muro, in Corsica

 

  

 Evergreen study sites of Arinelle and Pirio, in Corsica

 

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Artemia: salterns in Southern France

Artemia are small crustacean found in hypersaline environments. Along the mediterreanean coest they can be found mainly in salterns. Our main field study is Aigues-Mortes saltern near Montpellier. The saltern is a unique ecosystem with a rich bird community and a specific aquatic community.

Aigues-Mortes saltern near Montpellier, Southern France

 

Aigues-Mortes fortified city seen from the saltern. The pink color is due to the bloom of Dunaliella salina, a unicellular algae which is major food source for artemias.

 

 

Flock of flamingos that are one of the main predators of artemias in the saltern.

     

From left to right: sampling cysts floating on the surface of water - sampling brine shrimp from the water column - dilling a core for cysts stored in the sediment.

 

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Metacommunities of freshwater snails Martinique and Guadeloupe (West Indies)

            For three decades, we have performed yearly surveys of freshwater habitats and associated mollusc communities in Guadeloupe and Martinique (French Antilles). These communities are extremely dynamic, subject to both long-term and short-term changes. Long-term variation relies on environmental change (anthropization, climate change) but also, to a great extent, on successive waves of invasions by introduced species, including competitors and predators. Short-term variation is driven by natural cycles of habitat perturbations (dessication, floods) which result in an extinction-recolonization dynamics of local snail populations. We refer to these systems as metacommunities to describe, by analogy with metapopulations, both spatial fragmentation and temporal instability in these species assemblages. More information on these surveys (in French at this point) at https://oreme.org/observation/ocoa/mollusques-eaux-douces/. The Guadeloupe database (MORNING) can be accessed at https://doi.org/10.15148/4f9fa6f8-b4db-4322-8cd6-8c9c5c366e05.

            Questions we ask

            - what are the rules of coexistence within a set of species, and in what way are they dependent on species traits ? What processes maintain biodiversity within sites and in the whole metacommunity ? Are genetic diversity within species and community diversity (species richness) governed by similar processes ?

            - What role does the evolution of life-history traits and mating systems play in the success or failure of an invasive species, and in the response of local species to invasions ?

     

Two sites among 250 surveyed yearly in Grande-Terre (Guadleoupe) and the neighbouring island of Marie-Galante : the Saint-Félix pond (left) and Grande-Ravine, a freshwater mangrove swamp.

 

      

All the habitats we survey in Martinique are rivers; yet they are very different from one another. From left to right, a stream within pristine forest habitat, an open and anthropised river, and an artificial urban channel. All these habitats have been reached by successive waves of invasion of snails of the Thiaridae family.

Below are some images of snail searching, sampling, counting ... and 10 minutes of rest at the beach. 

        

    

 

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Amphibian communities in Mediterranean ponds

Many amphibian communities throughout the globe have been deeply altered by a combination of direct human actions and indirect factors such as climate change, pathogens and invasive species. We have since a long time been maintaining a low-intensity monitoring of amphibian communities in a network of ponds around Montpellier, which shows a reassuring global stability in species abundance. We have also recently examined the evolutionary basis for polymorphism on breeding time in the parsley frog Pelodytes punctatus (PhD of Hélène Jourdan, supervised by Patrice David and Pierre-André Crochet; program currently interrupted). We currently focus on the ecological factors that allow or prevent the invasive marsh frog Pelophylax ridibundus invading the local green frog communities, currently the greatest threat to the conservation of the near-endemic Pelophylax kl.grafi.

Man-made drinking place for cattle on Causse d’Aumelas (NW of Montpellier). Such very artificial habitats are of great importance for amphibian in Mediterranean landscapes (photo Yoann Mansier).

 

A more “natural” pond on Causse d’Aumelas. Although less artificial, such ponds have also been excavated to provide cattle with water. This pond (locally famous as “La Fertalière” pond) holds many of the Mediterranean species of amphibians. It has been colonised by Marsh Frog Pelophylax ridibundus in the past 10 years (photo Yoann Mansier).

 

A map of the ponds included in the detailed study of the breeding phenology of the Parsley Frog Pelodytes punctatus. Each green frog represents a pond. Brown areas are the “causses” (dry calcareous plateau) included in the study (from Hélène Jourdan’s PhD thesis). 

 

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Speciation patterns and biodiversity assessment in amphibians and reptiles around the Mediterranean

These programs involve a detailed mapping of contact areas between evolutionary lineages of the Iberian Wall Lizards (Podarcis hispanicus species complex) in the Iberian Peninsula, and broad-scale sampling of arid-habitats reptile communities in North Africa and the Middle East.

Map of all male samples of Podarcis hispanicus complex in the BEV-CEFE collection. The various grey levels correspond to position along the first two axis of a PCA on morphology that was used to asses geographic variation in morphology. Black dots correspond to Podarcis hispanicus sensu stricto.

 

Recent field trips (yellow) where herptile specimens or tissue samples have been collected. These samples are usually combined with those from other teams, covering missing areas, to provide more complete coverage of the region.

An example of combined coverage: dark green dots = distribution of the genus Stenodactylus based on museum specimens. Red dots = tissue samples available for genetic analyses through field work of CIBIO / Univ of Porto, CSIC – Univ of Barcelona, Crete Natural History Museum, R. Sindaco, S Baha El Din and BEV & GENEV teams at CEFE (from Metallinou et al. 2010, XI Congreso Luso-Español de Herpetologia / XV Congreso Español de Herpetologia, Sevilla, Octobre 2010).

 

A fishing rod with a slipknot remains the best non-destructive method to catch lizards (here an Acanthodactylus dumerili). Near Awserd, Morocco (Western Sahara), March 2010 (photo Eric Didner).

 

When no voucher specimen is collected, each tissue sample is linked to a series of photos of the live specimen to serve as a “digital” voucher. Kuwait, February 2009 (photo Eric Didner).

 

Tissue sampling of an adult Rhagerhis moilensis, Kuwait, February 2009 (photo Eric Didner)

 

Some species are trickier to handle than others... Cerastes cerastes, Awserd road, Morocco (Western Sahara), March 2010 (photo Eric Didner).

Nos modèles biologiques

Oiseaux (Céline Teplitsky)

Mésange bleue (Cyanistes caeruleus)

 

Cygne tuberculé (Cygnus olor): Nos analyses sur le cygne tuberculé se font en collaboration avec le site d’Abbostbury et les professeurs Chris Perrins et Ben Sheldon à l’Edward Grey Institute de l’Université d’Oxford.

Grand albatros (Diomedea exulans): L’exploitation des données sur le grand albatross est une collaboration avec Henri Weimerskirch à Chizé.

Sterne pierregarin (Sterna hirundo): Les analyses sur les sternes pierregarins se font dans le cadre d’une collaboration avec Peter Becker de l’Institute of Avian Research "Vogelwarte Helgoland" à Wilhelmshaven, Allemagne.

 

 

Artémies/Daphnies (Thomas Lenormand, Luis-Miguel Chevin, Christoph Haag)

Artémies (Artemia franciscana, A. parthenogenetica): modèle d'étude pour l'adaptation à la salinité et l'évolution de l'asexualité. 

    

 

Mollusques (Patrice David, Philippe Jarne)

Physa acuta : cette espère originaire d’Amérique du Nord et maintenant cosmopolite nous sert de modèle pour étudier l’évolution de l’autofécondation ou de la sénescence, mais aussi la sélection sexuelle.

 

Aplaxa marmorata : phylogénétiquement proche de Physa acuta, cette espèce de la zone néotropicale, est au centre de nos études sur le terrain en Guadeloupe (Antilles).

 

Melanoides tuberculata : une espèce parthénogénétique, formée de nombreux clones morphologiquement distincts, que nous étudions en situation d’invasion aux Antilles françaises.

 

Papillons (Mathieu Joron)

Heliconius: un genre de papillon mimétique, dont nous étudions notamment le déterminisme génétique des motifs colorés. 

 

Phasmes (Patrik Nosil)

Camouflage à la plante hôte dans le genre Timema.

 

Micro-algues Dunaliella salina (Luis-Miguel Chevin)

Nous étudions l'évolution des mécanismes de tolérance exceptionnelle à salinité chez cette espèce à l'aide d'expériences au laboratoire et de suivis in natura.

Silènes (Aline Muyle, Thomas Lenormand)

Modèle d'étude pour l'évolution des sexes séparés et des chromosomes sexuels.

 

Bactéries (Thomas Lenormand, Stéphanie Bedhomme)

Nous utilisons Escherichia coli pour étudier l'évolution de la résistance aux antibiotiques, et le rôle des biais d'usage de codon dans les transferts horizontaux.

  

Amphibiens (Pierre-André Crochet)

 

Reptiles

 

If you use CFit, you can refer to the following publication :
Gay, L., P. Crochet, D. Bell, and T. Lenormand. 2008.
Comparing genetic and phenotypic clines in hybrid zones: a window on tension zone models.
Evolution 62: 2789-2806

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CFIT-6

If you have only genetic data, CFit-6 is the easiest user-friendly version.

You can download it here
Simply dezip in a folder and click on the cfit.exe to run.
An example for the input file is included in the zipped file.
You can find more information by using the 'help' button in CFit.

Another version of CFit6 can be used for 2-Dimensions data.
  ________________________________________________
CFIT-7 (Dec 09 version)

If you have genetic and/or phenotypic data, CFit-7 is the version to use.

You can download it here
Simply dezip the package in a folder and click on the cfit.exe to run.
An example for the input file is included in the zipped package.
An example of mathematica file using CFit7 output is also included in the zipped package.
This mathematica file shows how to produce figures such as the one displayed below.
You can find more information by using the 'help' button in CFit.

 

 

 

 

 

 

 

 

 

 

 

 

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CFIT-7 2D scaled (Dec 13 version)

Here is a version of CFit that incorporates 2D spatial data as well as scaled logit shapes
(i.e. semi diagnostic markers). It also contains a subversion allowing to fit dispersal from the
rate of decay of neutral clines through time. This method is implemented in Rieux et al (2013). 
The PDF of that paper is included in the zipped distribution package along with help files.
Refering to this publication would be apreciated if you use the method.

You can download it here

Simply dezip the package in a folder and click on the .exe to run.
An example for the input file is included in the zipped package.
An example of R file using CFit7 output is also included in the zipped package.
 

 

 

PhD

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I am interested in a broad range of topics from evolutionary biology to population ecology. I am especially interested in combining demographical, genetic and life-history trait studies to better understand metacommunity and metapopulation dynamics. During my PhD, at the Center for Evolutionary and Functional Ecology (CEFE-CNRS) in Montpellier, France, I focused on the freshwater snail metacommunity that inhabits a network of highly unstable freshwater habitats in Guadeloupe (a Island of the Lesser Antilles of about 570 km²) that frequently dry out to investigate how fragmentation affects both species diversity within local community and genetic diversity within local populations of a set of species (see my PhD thesis summary below).

Keywords: metapopulation, metacommunity, population genetics, extinction-colonization, fragmentation, selfing, mating systems, mollusk.

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PhD thesis - from population genetics to community ecology: the case of the freshwater snail metacommunity in the French West Indies

            Striking similarities underlies the processes involved in the dynamics of genetic diversity and species diversity. However these diversities have been considered separately as part of population genetics and community ecology respectively. My work aims at quantifying processes that govern genetic diversity within species and species diversity within communities. To address this question I focus on the freshwater snail metacommunity from Grande-Terre Island (800 km²) in Guadeloupe. Twenty-nine snail species inhabit a network of highly unstable freshwater habitats that frequently dry out. This instability probably triggers extinction-colonization cycles of local populations. However, drying-out periods do not necessarily lead to extinction as some species are able to aestivate. First, I focused on the pulmonate gastropod Drepanotrema depressissimum. I used three complementary approaches: (1) an analysis of the spatial and temporal distribution of genetic diversity, (2) a patch occupancy model that take into account the presence of resistance forms such as aestivating snails and (3) a laboratory experiment in order to infer whether this species can rely on selfing to recolonize empty sites. These analyses reveal that extinction is not as frequent as previously thought and is not positively related to instability. Indeed, unstable sites are less prone to extinction. D. depressissimum overcome efficiently drying-out events aestivating in the ground and do not rely on selfing. Besides, extinction is more frequent in stable environments that encompass more speciose communities. Finally, at the scale of investigation, genetic diversity depends much more on patch size and connectivity than on apparent population age, suggesting that extinction-colonization cycles play a minor role in the species dynamics. In the last chapter, I quantify the impact of neutral processes on community assemblage. To this aim, I analyze the correlation between genetic diversity (microsatellites) of the two most-commonly encountered species – this diversity reflects neutral sampling process, with species diversity of local communities. This correlation is highly positive and relies on the parallel effect of a single site characteristic (connection to the local hydrographic network during the rainy season) on migration and colonization of both alleles and species. This suggests that neutral processes play an important role on the regulation of both genetic diversity and local species occurrence.

 

 

 

 

 

 

 

 

 

 

 

 

(A) Localization of Guadeloupe within the Lesser Antilles. (B) The Guadeloupe archipelago is divided in different islands. (C) Localization of the different freshwater environments in Guadeloupe. Black dots are the different sites surveyed since 2001 in the Islands of Grande-Terre and Marie-Galante while gray dots represent the different freshwater habitats that are not sampled.

 

 

 

 

Publications published

see the list at the bottom of the page

 

Publications in preparation

   4 - Lamy T, Pointier J-P, Jarne P, David P. Parallel processes drive species and genetic diversity in a freshwater snail metacommunity. In preparation.

  3 - Lamy T, Gimenez O, Pointier J-P, Jarne P, David P. A multistate occupancy model to infer metapopulation dynamics with hidden life stages. Submitted to Ecology.

 

Oral presentations and posters

• January 2011 “Community Genetics: what can a freshwater snail metacommunity from Lesser Antilles tell us?” Thomas Lamy, Jean Pierre Pointier, Philippe Jarne and Patrice David. CEFE Student seminary, 11 January 2011, Montpellier, France (Oral presentation)

• September 2010 “Link between genetic and species diversity in a metacommunity” Thomas Lamy, Géraldine Huth, Jean Pierre Pointier, Philippe Jarne and Patrice David. 1st French Ecology meeting, 2 - 4 September 2010, Montpellier, France (Oral presentation)

• July 2010 “Determinants of species diversity and genetic diversity in a community of tropical freshwater molluscs” Thomas Lamy, Géraldine Huth, Jean Pierre Pointier, Philippe Jarne and Patrice David.17th World Congress of Malacology, 18 - 24 July 2010, Phuket, Thailand (Oral presentation)

• November 2008 “Retracing history and the effect of human impact in European kelp forests”Myriam Valero, Christophe Destombe, Claire Daguin-Thiebaut, Thomas Lamy, Valeria Oppliger, Cécile Ribout, Anne Marie Jacob. World conference on Marine Biodiversity, 11-15 November 2008, Valencia, Spain (Oral presentation)

• August 2008 “History of the distribution area of the kelp Saccorhiza polyschides: relative importance of historical factors and genetic flow” Thomas Lamy and Myriam Valero. 30th meeting of the population genetics group, Petit Pois Déridé, Rennes, France (Poster)

 

Teaching (University Montpellier II)

• 2009 - 2011 Practical course and training sessions in Ecology, License (2nd and 3rd year students)
• 2008 - 2011 Courses and training sessions for students preparing the Agrégation and the Capes (teacher grade) in life sciences
• 2008 - 2009 Practical course in cellular Biology, License (1st and 2nd year students)