Arnaud Brayard

Chargé de Recherches CNRS



UMR 5561 CNRS/uB Biogéosciences

Université de Bourgogne

6 boulevard Gabriel

21000 Dijon


Tel : +33 380-39-36-95

Fax : +33 380-39-63-87

Email : arnaud.brayard [AT]

MY WEBSITE (CV, research interests, publications, oral communications, posters...):

HERE !!!

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Last updated: 03/07/2012

Émilie Arnoux

Phd student (2nd year)

Office number 307, Building "Sciences Gabriel"

Equipe Ecologie Evolutive - Laboratory of Ecology

UMR CNRS 5561 - Biogéosciences

6 boulevard Gabriel

21000 DIJON


+33 (0)3 80 39 91 57

This email address is being protected from spambots. You need JavaScript enabled to view it.

Phd topic: Conservation of the Forest thrush (Turdus lherminieri), an endemic bird in Lesser Antillean (Guadeloupe, Dominica, Santa-Lucia and Montserrat)


Endemic species are described as having small size of population and small distribution area (Pimm, 1991) that’s why they are more concerned by the risk of locale extinction (Gaston 1994). Small population is more vulnerable to the risk of extinction because of stochastic factors (e.g. demographic, environmental, catastrophic and genetic) (Gaston 1994). This risk is combined with other factors of an anthropic origin. In this context of insularity, the impacts are enhanced by density of humans (Davies et al. 2006), loss or fragmentation of habitats (Beissinger 2000), climate modification (Forester & Machlis 1996), and introduction of species (Fritts & Rodda 1998). These endemic species became species of interest in problematic of conservation.

The Forest Thrush, Cichlherminia lherminieri is endemic to 4 islands of Lesser Antilles: Guadeloupe, Montserrat, Santa Lucia and Dominica. In this specie, four sub-species are describing on each island (Clement & Hathway 2000) following distinct morphological criterions. The population has severely declined since 15 years and the forest thrush is now classified as vulnerable on list of International Union for Conservation of Nature. Recently, the St Lucia subspecies is listed as “Endangered” in the US Federal Register (Agency of Fish and Wildlife service, 2010). Measures of protection were taken for these birds on three islands whereas they are always hunted in Guadeloupe. Then, stakes of conservation are really important for this bird. To conserve populations in danger, many factors must be studied. It seems necessarily to know the biology of species (vital area, alimentation, biometry…), the interaction with their environment (parasitology, competition between invasive species…) and genetic structure.

To manage species in natural population, the knowledge of the population genetic structure of threatened species can contribute substantially towards evaluating population viability (Haig 1998) and identifying appropriate conservation strategies. This information is unavailable for the Forest thrush. Indeed, many studies show that populations having low genetic variability, have a capacity of adaptation reduced facing to environmental modifications and a high risk of extinction (Frankham 2005). Working on variability genetic allows also to identify differentiated population and gene flow (for example migration of birds) (Johnson  et al. 2004). For the Forest thrush, we plan to study the genetic variability between the island (Guadeloupe, Montserrat, Dominica and Santa Lucia) and between areas on each island.

Second, four sub-species are described in literature (Clement & Hathway 2001) corresponding to each islands. This differentiation is based on morphological criteria. Different body sizes reflect trade-offs and selective pressures (e.g., environmental conditions, sexual selection) acting on different populations and between the sexes (Wikelski and Trillmich 1997) that’s why it should be interesting to compare genetic diversity with biometric measures between islands and between locality inside each islands.

Third, populations can be sensible to interactions with their environment as parasites. Parasites can be responsible of demographic decline in endemic species (Kilpatrick 2006) and can have a spatial distribution specific to each habitat (Wood et al. 2007). That’s why, we plan to do a study on different parasites present in blood, in feathers and in faeces.


Mots clés

biodiverity ; conservation ; endemism ;  parasite ; competition ; Turdus lherminieri


- Population genetic

- Spatial analysis: Estimation of vital area with ArcGIS

- Parasitology (Identification and quantification by molecular biology)

- Radio-tracking


Previous researches: Research technician during 3 years

  • Effect of early conditions on antioxidant system and consequences on life-history traits (Zebra finch)
  • Ageing and senescence (Zebra finch)
  •  Resource allocation trade-offs (carotenoids) between secondary sex characteristics and antioxidant system
  • Heritability of antioxidant defenses (Great tit, Blue tit)

diamant_mandarin                                pigeons_au_nid

Student period

Research intership

  • Ecotoxicology : Effects of pollutants on immune response in blackbirds, Turdus merula, Renaud Scheifler, University of Franche-Comté, Besançon, France
  • Conservation : Population fragmentation and impact on individual quality : study on antimicrobial peptides in skin, Jean-Paul Léna & Sandrine Plénet, Université Claude Bernard, Lyon, France
  • Senescence and longevity in albatross, Centre biologique de Chizé.


  • Leclaire S., White J., Arnoux E., Faivre B, Vetter N., Hatch S.A. & E. Danchin. Integument coloration signals reproductive success, heterozygosity and antioxidant levels in chick-rearing black-legged kittiwakes. Naturwissenschaften. (In press)
  • Cote J., Arnoux E., Sorci G. and Faivre B. 2010. Age-dependent allocation of carotenoids to coloration versus antioxidant defences. Journal of Experimental Biology. 213: 271-277
  • Lecomte V., Sorci G., Cornet S., Jaeger A., Faivre B., Arnoux E., Gaillard M., Trouvé C., Besson D., Chastel O., and H. Weimerskirsch. 2010 Patterns of aging in the long-lived wandering albatross. National Academy of Sciences of the USA (PNAS), 107(14):6370-6375
  • Belloni V., Faivre B., Guerreiro R., Arnoux E., Bellenger J. and Sorci G. 2010. Suppressing an Anti-Inflammatory Cytokine Reveals a Strong Age-Dependent Survival Cost in Mice. Plos Biology


  • Arnoux E., Thomas A., Eraud C., Garnier S., Levesque A. And B. Faivre. Morphological differentiation at a small scale in an endangered species: The Forest thrush in a Guadeloupe island. Poster EOU conference Riga 2011.
  • Scheifler R., Fritsch C., Arnoux E., Coeurdassier M., Raoul F., Giraudoux P., Chastel O., Douay F., de Vaufleury A. and Faivre B. Accumulation and effects of Cd, Pb and Zn in blackbirds (Turdus merula) along a heavy metal pollution gradient. Poster SETAC Europe Göteborg 2009.


  • Eraud C., Arnoux E., Gaillard M. and Faivre B. Eye colouration reflects current immune status in feral pigeons, ISBE, Tours, France 2006
  • Arnoux E., Eraud C. and Faivre B. Maternel investment in eggs : Mechanism of compensation of hatching asynchrony in collared doves Streptopelia decaocto, PPD, Lille, France, 2006

Laboratory skills

  • High Performance Liquid Chromatography (carotenoids, pteridins)
  • Spectrophotometry: quantification of total antioxidant capacity, superoxide dismutase, lipid peroxidation, carotenoid, haptoglobin, lysozyme and peptides
  • Microbiology : Quantification of bacterial inhibition by antimicrobial peptides on agarose gel
  • Genetic : Molecular sexing (blood and tissue)
  • Hormone quantification with Radio Immuno Assay

Technics in avian structure and fieldwork

  • Manager
  • Entretien, nourrissage, gestion des stocks, commande
  • Biometric measures on bird
  • Blood sampling
  • Mist-netting
  • Radio-tracking
  • Nests recording (Blue tits and Great tits)


  • Real-time PCR
  • HPLC et UPLC
  • Permission to manipulate animals in laboratory (level 1)
  • Knowledge about chemical risks
  • Permission to use gaz


  • 2004 - 2005 : Msc in Biology and Ecology
  • 2000- 2003 : Licence in cellular biology and physiology
  • 2000 : Bachelor in Sciences
Last update 15 july 2011

Emmanuel Fara

ImageEmmanuel FARA, Ph.D.

Assistant Professor in Palaeontology (with Habilitation)

Laboratoire Biogéosciences (UMR CNRS / uB 6282)

UFR Sciences de la Vie, de la Terre et de l'Environnement (SVTE)

Université de Bourgogne

6 boulevard Gabriel

21000 Dijon


Tél : +33 380-39-39-70

Fax : +33 380-39-63-87

Email : This email address is being protected from spambots. You need JavaScript enabled to view it.


What are the processes structuring biodiversity at the local, regional, and global scale? How do biological communities respond to environmental changes and what are the associated kinetics?

My research activities revolve around these questions and they concern two major axes:

  • The first one focuses on the evolution and structure of local and regional communities in relation to palaeoenvironment. Both the temporal and spatial components of the patterns are investigated using fossil assemblages of invertebrates and vertebrates.
  • The second axis is a long term project with an ambitious aim: to define macroevolutionary patterns and processes for Phanerozoïc diversifications. It consists in the development of new datasets and algorithms for testing current models of diversification and recovery dynamics.

The general objective is to identify the mechanisms driving biodiversity and extinction through time and to define the spatio-temporal scales at which these processes occur. As such, my research is well-anchored into macroevolution and macroecology, two disciplines for which the fossil record is an ideal working area.

Studied models


Tethyan ammonites from the Pliensbachian (Early Jurassic). Collaboration with Jean-Louis Dommergues, Christian Meister and Pascal Neige.

Marine benthic macrofaunas from the Lutetian (Eocene) of the Paris Basin. Collaboration with Didier Merle (MNHN) et Pascal Neige (uB).

Ichthyofauna of the Early Cretaceous Santana Formation, northeastern Brazil.

Mammal assemblages from the Mio-Pliocene of Africa. Collaboration with MPFT research group (Mission Paléoanthropologique Franco-Tchadienne).

Datasets on fossil tetrapods and participation to the Paleobiology Database

Main results

Quality of the fossil record

  • Re-evaluation of the « Lazarus effect », an important marcoevolutionary notion at the interface between biological processes and the quality of the fossil record (Fara 2001)
  • Demonstration of the good quality of the fossil record for Cretaceous continental tetrapods (Fara & Benton 2000, Fara 2002, Fara 2004).

Global diversification dynamics

  • Documentation of mega-biases in the current global diversification paradigms for tetrapods (Alroy et al. 2003, and MS submitted), and participation to the Paleobiology Database.
  • Evidence for a strong extinction selectivity among tetrapod families during the K/T biotic crisis (Fara 2000).
  • Proposal of a new method for assessing the minimal species diversity of taxonomic groups with poor fossil records (Fara 2004).
  • First quantitative estimates of the diversity dynamics for lissamphibians and lepidosaurs in the Jurassic-Eocene interval (Ph.D. thesis and Fara, 2004)
  • First quantitative estimate of the fossil record and diversity of gonorynchiform fishes (Fara et al 2007, Fara et al. 2009)

Community evolution

  • Evidence for a local environemental control upon the structure of Pliocene mammal communities in Chad (Fara et al., 2005a).
  • Evidence for the structural evolution of Cretaceous bony fish communities (Santana Formation, Araripe Basin, northeastern Brazil) during the opening of the South Atlantic Ocean (Fara et al., 2005b)


  • Revision of a phytosaurs species (Archosauria) and challenge of its use as a biochronological indicator for the Triassic (Fara & Hungerbühler 2000)
  • Description of the first occurrence of thalattosuchian crocodiles in the Jurassic of Tunisia (Fara et al. 2002)
  • Discovery of the oldest fossil snake from Brazil, an anilioïd from the Late Cretaceous (Zaher et al., 2003).



Articles in journals and book chapters

  • Hardy C., Fara E., Laffont R., Dommergues J.-L., Meister C. & Neige P. (2012) - Deep-time phylogenetic clustering of extinctions in an evolutionarily dynamic clade (Early Jurassic ammonites) -   PLoS ONE 7(5): e37977. doi:10.1371/journal.pone.0037977  [PDF]
  • Moreau J.-D., Gand G., Fara E. & Michelin A. (2012) - Biometric and morphometric approaches on Lower Hettangian dinosaur footprints from the Rodez Strait (Aveyron, France) - C. R. Palevol 11 (4): 231-239. [PDF]
  • Le Fur S., Fara E. & Vignaud P. (2011) - Effect of simulated faunal impoverishment and mixture on the ecological structure of modern mammal faunas: implications for the reconstruction of Mio-Pliocene African palaeoenvironments - Palaeogeography Palaeoclimatology Palaeoecology 305:295-309. [PDF]
  • Escarguel, G., Fara E., Brayard, A. & Legendre, S. (2011) – Biodiversity is not (and never has been) a bed of roses ! – Comptes Rendus Biologies 334: 351-359. [PDF]
  • Dera G., Neige P., Dommergues J.-L., Fara E., Laffont R. & Pellenard P. (2010) High-resolution dynamics of Early Jurassic marine extinctions: the case of Pliensbachian-Toarcian ammonites (Cephalopoda) - Journal of the Geological Society of London 167: 21-33. [PDF]
  • Tabuce R, Marivaux L, Lebrun R., Adaci M., Bensalah M., Fabre P-H., Fara E., Gomes Rodrigues H., Hautier L., Jaeger J-J., Lazzari V., Mebrouk F., Peigné S., Sudre J, Tafforeau P., Valentin X. & Mahboubi M. (2009) - Anthropoid versus strepsirhine status of the African Eocene primates Algeripithecus and Azibius: craniodental evidence - Proceedings of the Royal Society B (2009) 276: 4087-4094. Published online at doi:10.1098/rspb.2009.1339. [PDF]
  • Fara E., Gayet M. & Taverne L. (2009) Chapter 6: "The Fossil Record of Gonorynchiforms". In: Poyato-Ariza, F.J., Grande, T., & Diogo, R. (Eds.) - Teleostean Fish Biology; A Comprehensive Examination of Major Taxa.  Vol. 1: Gonorhynchiformes and Ostariophysan Relationships: a Comprehensive Review. Science Publishers Inc., Enfield, New Hampshire, USA, pp. 173-226. [PDF]
  • Dommergues J-L., Fara E. & Meister C. (2009). Ammonite diversity and its palaeobiogeographical structure during the early Pliensbachian (Jurassic) in the western Tethys and adjacent areas - Palaeogeography Palaeoclimatology Palaeoecology 280: 64-77. [PDF]
  • Le Fur S., Fara E., Mackaye H.T., Vignaud P. & Brunet M. (2009). The mammal assemblage of the hominid site TM266 (Late Miocene, Chad Basin): ecological structure and paleoenvironmental implications - Naturwissenschaften 96: 565-574. [PDF]
  • Viriot L., Vignaud P., Boisserie J.-R., Fara E., Guy F., Lihoreau F., Lehman T., Schuster M., Blondel C., Duringer Likius A., Mackaye H.T., Otero O.& Brunet M. (2008) Late Miocene to Early Pliocene Chadian vertebrate faunas: palaeoenvironmental and palaeobiogeographical implications - The Geology of East Libya 3, 303-308. [PDF]
  • Saraiva A.Á.F., Hessel M.H., Guerra N.C. & Fara E. (2007) Concreções calcárias da Formação Santana, Bacia do Araripe: uma proposta de classificação Estudos Geológicos 17 (1): 40-57. [PDF]
  • Fara E., Gayet M. & Taverne L. (2007) Les Gonorynchiformes fossiles: distribution et diversité – Cybium 31  (2): 115-122. [PDF]
  • Pinton A., Fara E. & Otero O. (2006) - Spine anatomy reveals the diversity of catfish through time: a case study of Synodontis (Siluriformes) -  Naturwissenschaften 93: 22-26. [PDF]
  • Fara E., Likius A., Mackaye H.T., Vignaud, P. & Brunet, M. (2005) - Pliocene large-mammal assemblages from northern Chad: sampling and ecological structure - Naturwissenschaften 92: 537-541. [PDF]
  • Fara E., Saraiva A., Campos D.A., Moreira J.K.R., Siebra D.C. & Kellner A.W.A. (2005) - Controlled excavations in the Romualdo Member of the Santana Formation (Araripe Basin, Lower Cretaceous, northeastern Brazil): stratigraphic, palaeoenvironmental and palaeoecological implications - Palaeogeography Palaeoclimatology Palaeoecology 218 (1-2): 145-160. [PDF]
  • Fara E. & Langer M.C. (2004) - Estimates of phylogeny and biochronology - Revista Brasileira de Paleontologia 7(3) : 301-309. [PDF]
  • Fara E. (2004) - Estimating minimum global species diversity for groups with a poor fossil record: a case study of Late Jurassic-Eocene lissamphibians - Palaeogeography Palaeoclimatology Palaeoecology, 207 (1-2): 59-82. [PDF]
  • Fara E. (2002) - Sea-level variations and the quality of the continental fossil record -  Journal of the Geological Society of London, 159: 489-491. [PDF]
  • Fara E., Ouja M., Buffetaut E. & Srarfi D. (2002) - First occurrences of thalattosuchian crocodiles in the Middle and Upper Jurassic of Tunisia - Neues Jahrbuch für Geologie und Paläontologie, Monatshefte, 2002 (8): 465-476. [PDF]
  • Fara E. (2001) - What are Lazarus taxa? - Geological Journal, 36: 291-303. [PDF]
  • Fara E. & Hungerbühler A. (2000) - "Paleorhinus magnoculus" from the Upper Triassic of Morocco: a juvenile primitive phytosaur (Archosauria) - Comptes-Rendus de l'Académie des Sciences, Paris IIa, 331 (12): 831-836. [PDF]
  • Fara E. & Benton M.J. (2000) - The fossil record of Cretaceous tetrapods - Palaios, 15 (2): 161-165. [PDF]
  • Fara E. (2000) - Diversity of Callovian-Ypresian (Middle Jurassic-Eocene) tetrapod families and selectivity of extinctions at the K/T boundary - Geobios, 33(3): 387-396. [PDF]

Published abstracts

  • Fara, E. & Saraiva, A. (2009) - Stratigraphy and vertebrate diversity of the Santana Formation (Lower Cretaceous, Brazil): two centuries of misappreciation - Journal of Vertebrate Paleontology, 29 (3): 94A.
  • Alroy J., Carrano M., Clyde W., Fara E., Head J., Hunter J., Uhen M. & Whateley R. (2005) - Ecological spectra through the Cretaceous and Cenozoic tetrapod fossil record - Journal of Vertebrate Paleontology, 25 (3): 31A.
  • Zaher H.D., Langer M.C., Fara E., Carvalho I.S., Arruda J.T. (2003) - A mais antiga serpente (anilioidea) brasileira: Cretaceo Superior do Grupo Bauru, General Salgado, SP - Paleontologia em Destaque 44: 50-51.
  • Alroy J., Behrensmeyer K., Carrano M., Clyde W., Fara E., Fortelius M., Head J., Hunter J., Uhen M. & Wang X. (2003) - The 5% Project: just how good is the fossil record of tetrapods? - Journal of Vertebrate Paleontology, 23 (3): 29A
  • Fara E. & Langer M.C. (2000) - Using cladograms for biostratigraphic inferences - Journal of Vertebrate Paleontology, 20 (3): 40A.

Popularization articles

  • Fara E. (2006) - A Chapada do Araripe: riqueza e perspectiva paleontológica - Publicaçao Especial da Fundaçao Araripe, Crato, Brazil.


  • Fara E. 2011. “ From Macroevolution to macroecology: multi-scale analysis of fossil biodiversity"  – Habilitation Thesis (HDR), University of Burgundy [in French and English; 266 pages]

  • Fara E. 2001. “ Macroevolutionary patterns and the quality of the fossil record: from data to processes” – Ph. D. Thesis, University of Bristol [in English; 318 pages; 87 figures; 1 CD-Rom]

  • Fara E. 1998. “Les familles de tétrapodes au cours du Crétacé: diversité, paléoécologie, et registre fossile” – Master Thesis, Université de Montpellier II , France  [in French, 75 pages]

Current Fieldwork

* Santana Formation (Lower Cretaceous), Ceará State, Brazil.

* Baurú Group  (Upper Cretaceous), São Paulo State, Brazil

* Lutetian outcrops from the Paris Basin.

* Mio-Pliocene sites from the Djourab erg, Chad (org : MPFT).



As an Assitant Professor, Université de Bourgogne

Date: since January 2006

Site: Université de Bourgogne, Dijon, France

Level: From the first year to the fifth year (BSc and MSc levels)

Contents: Palaeontology, Geology, Ecology, Macroecology, Evolution, Embryology.

As a Demonstrator and Lecturer

Date: 1999-2006

Site: University of Bristol (UK), University of Mahasarakham (Thaïland), Universidade Federal do Pernambuco, Recife (Brazil), Université de Clermont-Ferrand (France), Université Montpellier II (France), Université de Poitiers (France).

Levels: the first year to the fifth year (BSc and MSc levels).

Contents: Palaeontology, Geology, Palaeoceanography, Systematics, Evolution, Database, Population genetics.


Selected conferences

  • Conference on the history of biodiversity [in French], International Conference Centre of Cluny (ENSAM), France (october 2008).
  • Conference on the evolution of biodiversity and mass extinctions [in French], La Cité des Sciences, Paris (June 2007). You can download it here.
  • Series of conferences entitled « Recent Advances and Methods in Palaeobiology », University of Mahasarakham, Thaïland (June 2004)

Documentaries and exhibits

  • Annual participations to the science popularization days.
  • Participation to the documentary « Toumaï, le nouvel ancêtre », by Pierre Stine (Gédéon Programmes). Co-production France Télévision-BBC-NHK-TSR-RTB.
  • Co-organizer of the exhibit "Ciências da Terra, Ciências da Vida - Chapada do Araripe", São Paulo, Brazil [August 30 - October 31, 2004] and scientific supervision of the catalogue ("Ciências da Terra, Ciências da Vida - Chapada do Araripe", São Paulo, Brazil, edited by the Fundação A.A. Penteado/MAB/FAAP, 2004).
  • Guided visits of various palaeontological excavation sites and exhibits.


2011: Habilitation to conduct and supervise research 

Since 2006 : Full-time Assistant Professor, Université de Bourgogne, Dijon, France

2003 – 2005: CNRS Post-doc on mammal communities, Université de Poitiers, France

2003 (July–Sept.): Visiting Fellow, Universidade Regional do Cariri –URCA (Brazil)

2002 - 2003: Lecturer, Université de Clermont-Ferrand (France) and Mahasarakham University (Thaïland).

2001 - 2002: self-funded Post-doc, Université Montpellier I, France.


1998-2001: Ph.D. in Palaeobiology, University of Bristol (U.K.)

Title: “Macroevolutionary patterns and the quality of the fossil record: from data to processes”, Supervisor: Pr. Michael. J. Benton

1998: M.Sc. in Palaeontology, Université Montpellier II (France)

1997: [National Service]

1995-1996: BSc and Graduation in Natural Sciences, Université Lyon I (France)