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St Pee

Aquapôle INRA

Inra Bordeaux-Aquitaine
Quartier Ibarron
64310 Saint-Pée-sur-Nivelle

tél : +33 (0) 5 59 51 59 51
fax : +33 (0) 5 59 54 51 52

Matthias Vignon

Assistant professor

Matthias Vignon
© inra, 2015
Analyses écologiques, évolutives et morphologiques des pièces sclérifiées


Contact | Research Activities | Software | Teaching | Publications


Université de Pau et des Pays de l' Adour
UFR Sciences et Techniques de la Côte Basque
Allée du parc de Montaury
64600 Anglet
Tel : 05 59 57 44 48
Fax : 05 59 54 51 52
e-mail : mvignon@st-pee.inra.fr

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Research Activities

Academic achievements and Employment history

  • 2010-present: Assistant professor, INRA, UMR 1224 ECOBIOP “Behavioural Ecology Group”, St-Pée/Nivelle (France). Statutory Lecturer, Department of Biology, UFR Sciences & Techniques, University of Pau & Pays Adour, Anglet (France)
  • 2008-2009: Teaching Fellow "Marine Parasitology". Ecole Pratique des Hautes Etudes (EPHE). UMR 5244 CNRS-EPHE-UPVD: Tropical and Mediterranean Biology and Ecology Laboratory, Perpignan University (France)
  • 2005-2008: PhD in Ecological and Evolutionary Parasitology (Pierre & Marie Curie University, Paris). French Ministry of Research and Education Grant. UMR 5244 CNRS-EPHE-UPVD (France) and Insular Research Center and Environment Observatory (French Polynesia). PhD dissertation: "Biological introductions and parasites in coral reefs ecosystems: risk and consequences – Fish introduction into the Hawaiian archipelago" (suppervised by Dr R. Galzin and P. Sasal).
  • 2002-2005: Magistère (Higher Education Establishment degree) Biology, Environment and Ecology. Three years in parallel to classic University Degree. École Normale Supérieure (Ulm Paris, France).
  • 2004-2005: Master in Biological Oceanography and Marine Environment. Paris VI University (France).
  • 2000-2004: Full university curriculum in Biology, Populations and Physiology. Paris VI University (France).

Current research topics


I am mostly involved in analyzing sclerochronological structures from fish in ecological and evolutionary contexts. Brown trout (Salmo trutta) remains my main model from both Kerguelen Island were the species was introduced and from its native range in the Pyrenean rivers (France). Most of my work relies on quantitative analysis of otoliths and scales, with specific interest in methodological developments. Other parts consist in experimental approaches dealing with the sensory role of otolith

  • Evolution of life history traits during the colonization of Kerguelen island. Long-term archives allow examining the invasion dynamics of the invasive brown trout over the past 50 years. Data shed light on the future of polar regions where, because of climate change, fish-free ecosystems become increasingly accessible to invasion by fish species.


    Colonization dynamics of the Brown trout between 1980 and 2000 (colonized river systems in black)

  • Quantitative analysis of microchemical profiles. I currently develop methods to facilitate analyzing microchemical profiles from fish otoliths. This allows extracting environmental histories from otolith based on typical elemental sequences generated using methods such as LA-ICPMS. Microchemical analysis is indeed widely used in fisheries management and fisheries biology to identify stocks and characterize fish movements.


    Typical Sr:Ca profile depicting salinity-based habitat used by fish (left) and recursive partitioning of time series data for computing piecewise constant model (right)

  • Ecological relevance of microchemical data. This part explores using both descriptive and experimental approaches in which way otolith microchemistry represent a permanent record of the growing habitats experienced by the fish throughout its entire life time. This include investigating, among others, the seasonality and time-lags in incorporating elements from the environment.


    Decomposition of microchemical profiles into seasonal ("Perc") and ontogenetic ("age") components for three elements from a landlocked salmon populations


    Time-lags in response to environmental changes may lead to discrepancy between real and inferred habitat use. This can results in important bias in estimating residency time in a particular river system

  • Determinants of otolith shape variation. This work quantitatively investigates the main determinants of otolith shape variation using a geometric morphometric framework. Multi-scale analysis are conducted with emphasis on ontogenetic trajectories, effect of stress on shape asymmetry, modularity and environmentally-induced plasticity.

    Ontogenetic trajectory during shift in habitat use (left) and modeling shape change using internal homology (right)

  • image018petit
    Morpho-functional ecology
    . This work is essentially experimental and investigates the effect of otolith shape on the individual behaviour of fish, as well as the reciprocal effect of individual behaviour on otolith ontogenetic trajectory. Otolith shape indeed strongly affect the swimming, hearing and balancing performance of fishes, so that their ability to escape predator is changed

C-start escape response of one fish after sound production


Development of open-source software tools in R


Tampo (Tools for the Analysis of Microchemical Profiles from Otoliths): a R package to facilitate analyzing microchemical profiles (both mono- and multielemental composition) from fish otoliths (stones from the inner ear) using a recursive partitioning approach that can accommodate some form of user-specified constraints. This package provides a number of functions to extract environmental histories from otolith based on typical elemental sequences generated using methods such as LA-ICPMS. Microchemical analysis is widely used in fisheries management and fisheries biology to identify stocks and characterize fish movements but the provided functions may be considered from the more general perspective of the chronological clustering of multivariate time series using piecewise constant regressions.


  • I give lectures on the Anglet campus of Pau University.
  • Undergraduate: Population and Ecosystem Ecology, Evolution, Environment, Biological conservation.
  • Graduate: Biostatistics, morphology.


  • Marengo, M., Baudouin, M., Viret,. A. Laporte, M., Berrebi, P., Vignon M., Marchand, B., Durieux, E.D.H. (2017) Combining microsatellite, otolith shape and parasites community analyses as a holistic approach to assess population structure of Dentex dentex. Journal of Sea Research. In Press.
  • Geffroy, B., Guilbaud F., Amilhat E., Beaulaton L., Vignon M., Huchet E., Rives J., Bobe J., Fostier A., Guiguen Y., Bardonnet A. (2016) Sexually dimorphic gene expressions in eels: useful markers for early sex assessment in a conservation context. Scientific Reports 6: 34041.
  • Vignon M. (2016) Investigating Morphospace occupation in multi-scale ecological and evolutionary data using regression tree: Case studies and perspectives. Evolutionary Biology 44: 120-134.
  • Aymes J.C., Vignon M., Beall E., Gueraud F., Gaudin P. (2016) Age validation of the Kerguelen Islands brown trout, Salmo trutta L.,and selection of the otolith optimal zone for investigating chronological data series. Fisheries Research 176: 22-29.
  • Vignon, M. (2015) Disentangling and quantifying sources of otolith shape variation across multiple scales using a new hierarchical partitioning approach. Marine Ecology Progress Series 534: 163-177.
  • Vignon, M. (2015) Extracting environmental histories from sclerochronological structures - Recursive partitioning as a mean to explore multielemental composition of fish otolith.  Ecological Informatics 30: 159-169.
  • Labonne, J., Vignon, M., Prévost, E., Lecomte, F., Dodson, J.J., Kaeuffer, R., Aymes, J.C., Jarry, M., Gaudin, P., Davaine, P., Beall, E. (2013). Invasion dynamics of a fish-free landscape by brown trout (Salmo trutta). PLoS ONE 8(8): e71052.
  • Gaither, M.R., Aeby, G., Vignon, M., Meguro, Y.-I., Rigby, M., Runyon, C., Toonen, R.J., Wood, C.L., Bowen, B.W. (2013) An invasive fish and the time-lagged spread of its parasite across the Hawaiian Archipelago. PLoS ONE 8(2): e56940.
  • Vignon M. (2012) Ontogenetic trajectories of otolith shape during shift in habitat use: Interaction between otolith growth and environment. Journal of Experimental Marine Biology and Ecology 420-421C: 26-32.
  • Vignon M. (2011) Putting in shape – Towards a unified approach for the taxonomic description of monogenean haptoral hard parts. Systematic Parasitology 79: 161-174.
  • Vignon M. (2011) Inference in morphological taxonomy using collinear data and small sample sizes: Monogenean sclerites (Platyhelminthes) as a case study. Zoologica Scripta 40(3): 306-316.
  • Vignon M., Pariselle A., Vanhove M.P.M. (2011) Modularity in attachment organs of African Cichlidogyrus (Platyhelminthes, Monogenea, Ancyrocephalidae) reflects phylogeny rather than host specificity or geographic distribution. Biological Journal of the Linnean Society 102: 694-706.
  • Vignon M., Dierking J. (2011) Prey regurgitation and stomach vacuity among groupers and snappers. Environmental Biology of Fishes 90(4): 361-366.
  • Vignon M., Morat F. (2010) Environmental and genetic determinant of otolith shape revealed by a non-indigenous tropical fish. Marine Ecology Progress Series 411: 231-241.
  • Work T.M., Vignon M., Aeby G.S. (2010) Microparasite ecology and health status of common bluestriped snapper Lutjanus kasmira from the Pacific Islands. Aquatic Biology 9: 185-192.
  • Vignon M., Sasal P. (2010) Multiscale determinant of parasite abundance: A quantitative hierarchical approach for coral reef fishes. International Journal for Parasitology 40: 443-451.
  • Vignon M., Sasal P. (2010). The use of geometric morphometrics in understanding shape variability of sclerotized haptoral structures of monogeneans (Platyhelminthes) with insights into biogeographic variability. Parasitology International 59: 183-191.
  • Vignon M., Sasal P. (2010). Fish introduction and parasite in marine ecosystems: A need for information. Environmental Biology of Fishes 87: 1-8.
  • Vignon M., Sasal P., Johnson R.L., Galzin R. (2010). Impact of shark-feeding tourism on surrounding fish populations: parasitological and physiological implication off Moorea Island (French Polynesia). Marine and Freshwater Research 61: 163-169.
  • Vignon M., Sasal P., Rigby M.C., Galzin R. (2009). Multiple parasite introduction and host management plan: Case study from Lutjanids fish in the Hawaiian archipelago. Diseases of Aquatic Organisms 85: 133-145.
  • Vignon M., Sasal P., Galzin R. (2009). Host introduction and parasites: a case study on the parasite community of the peacock grouper Cephalopholis argus (Serranidae) in the Hawaiian Islands. Parasitology Research. 104: 775-782.
  • Vignon M. (2009) Biological introductions and parasites in coral reefs ecosystems: Risk and consequences – Fish introduction into the Hawaiian archipelago. Cybium 33: 192.
  • Vignon M., Morat F., Galzin R., Sasal P. (2008). Evidence for spatial limitation of the bluestripe snapper in French Polynesia from parasite and otolith shape analysis. Journal of Fish Biology 73: 2305-2320.
  • Morat F., Banaru D., Mérigot B., Batjakas I E., Betoulle S.,Vignon M., Lecomte-Finiger R., Letourneur Y. (2008). Relationships between fish length and otolith length for nine fish species from the Mediterranean basin, Kerguelen Islands, and Pacific Ocean. Cybium 32: 265-269.
  • Justine J-L. & Vignon M. (2008). Monogeneans of the grouper Epinephelus tauvina (Perciformes, Serranidae) off Moorea, French Polynesia, with a description of Pseudorhabdosynochus pai n. sp. (Monogenea: Diplectanidae). Systematic Parasitology 72: 113-125.
  • Fels D., Vignon M., Kaltz O. (2008). Ecological and genetic determinants of multiple infection and aggregation in a microbial host-parasite system. Parasitology 135: 1373-1383