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UMR CNRS 5558 - LBBE "Biométrie et Biologie Évolutive" UCB Lyon 1 - Bât. Grégor Mendel 43 bd du 11 novembre 1918 69622 VILLEURBANNE cedex
- Activities
- +PhD work -PhD work
My PhD work is to examin the role multidimensional methods can play in genetic data analysis. Ordination methods offer great opportunities to explore molecular marker data.
Presently, I have devoted attention to two particular points. First, a problem arises when trying to find typology of individuals or populations using molecular markers : each marker can perform its own typology.
Thus, it seems important to be able to find and compare the informations provided by each marker, and if possible, to find a compromise between these informations. On a statistical point of view, this question can be tackled in the K-tables ordination methods framework. A first appilcation using the Multiple Co-inertia Analysis (MCOA) allowed to propose a possible measure of the typological value of molecular markers (Jombart et al 2006, Laloë et al, accepted).Another point concerns the research of spatial structures in the genetic variability. When available, spatial information can be used along with genetic distances to infer underlying biological processes. This can be achieved using spatially constrained (or also ’spatially explicit’) ordination methods. In this context, I propose the spatial Principal Component Analysis (sPCA, Jombart et al, in prep).
This method, although new in genetics, relies on a well-known ordination method (Principal Component Analysis on allelic frequency data) and of spatial autocorrelation.These two questions are tackled through the analysis of genetic datasets, involving several collaborations. This interdisciplinary dialogue required software development, now regrouped in the adegenet package (http://pbil.univ-lyon1.fr/software/adegenet/) du lfor the free software R.
This package is devoted to genetic data handling, starting from data import from foreign softwares (e.g. GENETICS, Fstat) to their analysis using reduced space ordinations available in the ade4 package. Other common functionalities are also proposed (HW tests, hierarchical structuration tests, …) as well as data export to other R packages (hierfstat, genetics, …).
I also contribute to the ade4 package.
+Publications -Publications
article :
Dray S, Pélissier R, Couteron P, Fortin M-J, Legendre P, Peres-Neto P-R, Bellier E, Bivand R, Blanchet F-G, De Caceres M, Dufour A-B, Heegaard E, Jombart T, Munoz F, Oksanen J, Thioulouse J, Wagner H-H (2012)
Community ecology in the age of multivariate multiscale spatial analysis, Ecological Monographs, vol. 82 pp.257-275.
Munkemuller T, Lavergne S, Bzeznik B, Dray S, Jombart T, Schiffers K, Thuiller W (2012)
How to measure and test phylogenetic signal, Methods in Ecology and Evolution, vol. 3 pp.743-756.
Dray S, Jombart T (2011)
Revisiting Guerry`s data: introducing spatial constraints in multivariate analysis., The Annals of Applied Statistics, vol. 5 pp.2278-2299.
Jombart T, Balloux F, Dray S (2010)
adephylo: new tools for investigating the phylogenetic signal in biological traits, Bioinformatics, vol. 26(15) pp.1907-1909, DOI.
Jombart T, Devillard S, Balloux F (2010)
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations, BMC Genetics, vol. 11(94) pp.1-15, DOI.
Jombart T, Pavoine S, Devillard S, Pontier D (2010)
Putting phylogeny into the analysis of biological traits:A methodological approach, Journal of Theoretical Biology, vol. 264 pp.693-701, DOI.
Devillard S, Jombart T, Pontier D (2009)
Revealing cryptic genetic structuring in an urban population of stray cats (textit Felis silvestris catus, Mammalian Biology, vol. 74 pp.59-71, DOI.
Jombart T, Dray S, Dufour A-B (2009)
Finding essential scales of spatial variation in ecological data: a multivariate approach, Ecography, vol. 32(1) pp.161-168, DOI.
Jombart T, Pontier D, Dufour A-B (2009)
Genetic markers in the playground of multivariate analysis, Heredity, vol. 102 pp.330-341, DOI.
Jombart T (2008)
adegenet: a R package for the multivariate analysis of genetic markers, Bioinformatics, vol. 24 pp.1403-1405.
Jombart T, Devillard S, Dufour A-B, Pontier D (2008)
Revealing cryptic spatial patterns in genetic variability by a new multivariate method, Heredity, vol. 101 pp.92-103.
Laloe D, Jombart T, Dufour A-B, Moazami-Goudarzi K (2007)
Consensus genetic structuring and typological value of markers using multiple co-inertia analysis, Genetics Selection Evolution, vol. 39 pp.545-567.
Jombart T, Moazami-Goudarzi K, Dufour A-B, Laloë D (2006)
Fréquences alléliques et cohérence entre marqueurs moléculaires : des outils descriptifs, Les actes du Bureau des Ressources Génétiques, vol. 6 pp.25-39.
phdthesis :
Jombart T (2008)
Analyses multivariées de marqueurs génétiques : développements méthodologiques applications et extensions. .



