Axis 1 : Historical biogeography

This axis aims at understanding and reconstructing the history of populations, species and communities. It is organized around three key challenges.
Past species’ demography and range changes

We intend to decipher the history of species distributions and the past demography of their populations in relation to past environmental changes. This challenge focuses on introduced and/or invasive organisms (plants, insects) in order to infer their recent colonization history, but also on domestic live-stocks to infer their history of selection and their links to human migrations. We also focus on alpine plants and arthropods to infer their past refugia during quaternary glaciations, and their recent range shifts in relation to glacial retreat and climate warming. Some approaches using natural archives (e.g. lake sediments, chronosequences of glacial retreat) analyzed with historical genetics (eDNA) are also employed, allowing to infer past scenarios of biodiversity dynamics with unprecedented levels of details.

Keywords : historical demography, coalescence, statistical phylogeography, approximate bayesian computation, species distribution models, DNA metabarcoding

 

Keywords : phylogenetic comparative methods, stochastic models of trait evolution, speciation rates, genomic islands of differentiation, reproductive barriersreproductives
Tempo, mode and drivers of clades diversification

We aim at reconstructing the evolutionary origins of biodiversity in order to decipher the tempo and mode of species diversification and niche evolution in particular for species-rich regions (e.g. tropical paramos, european mountain systems) or clades that have experienced rapid diversification in certain environments (e.g. Espeletinae and Primulaceae for plants, arctic birds). We are particularly trying to understand how these macroevolutionary patterns relate to past global physical and climatic changes such as mountain uplifts and Pleistocene cycles. We also aim at testing how speciation events were influenced by environmental factors (biotic and abiotic) and key phenotypic innovations driving adaptations to novel niches, or rather by spatial isolation, by examining patterns of genomic divergence across species’ genomes.

 

Community evolution and phylogeography

We aim at inferring the temporal changes of past assemblages of species across trophic levels and along environmental gradients such as in alpine regions, by the means of phylogeography applied to multiple co-occurring species — which we term community phylogeography. This challenge requires testing whether species assemblages experienced synchronous (or asynchronous) and coherent (or divergent) demographic and dispersal dynamics, in relation to the strength of their ecological interactions. It also requires testing whether certain species traits drive similar population and range dynamics (e.g. using clades consisting of many invasive species) and how past changes in the physical environment (climate, geology) drove these spatial dynamics.

Keywords : comparative phylogeography, approximate bayesian computation, phylogeny-based historical, biogeography, DNA barcoding

 

Key papers :
  • Yannic G, Helfer V, Sermier R, Schmidt BR, Fumagalli L (2021) Fine scale genetic structure in fire salamanders (Salamandra salamandra) along a rural-to-urban gradient. Conservation Genetics 22 (2), 275-292
  • Pouchon C, Lavergne S, Fernández A, Alberti A, Aubert S, Mavárez J (2021) Phylogenetic signatures of ecological divergence and leapfrog adaptive radiation in Espeletia. American Journal of Botany, 108(1):113–128
  • Verboom GA, Boucher FC, Ackerly DD, Wootton LM, Freyman WA (2020) Species selection regime and phylogenetic tree shape. Systematic Biology 69 (4), 774-794
  • Sherpa S, Renaud J, Guéguen M, Besnard G, Mouyon L, Rey D, Desprès L (2020) Landscape does matter : Disentangling founder effects from natural and human‐aided post‐introduction dispersal during an ongoing biological invasion. Journal of Animal Ecology 89 (9), 2027-2042
  • Dufour P, Descamps S, Chantepie S, Renaud J, Guéguen M, Schiffers K, Thuiller W, Lavergne S (2020) Reconstructing the geographic and climatic origins of long-distance bird migrations. Journal of Biogeography 47:155–166
  • Alsos I, Lavergne S, Merkel MKF, Boleda M, Lammers Y, Alberti A, Pouchon C, Denoeud F, Pitelkova I, Puscas M, Roquet C, Hurdu B, Thuiller W, Zimmermann N, Hollingsworth P, Coissac E (2020) The treasure vault can be opened : large scale genome skimming works equally well for herbarium as silica gel dried material. Plants 9:432
  • Barrabé L, Lavergne S, Karnadi-Abdelkader G, Drew B, Birnbaum P, Gâteblé G (2019) Changing ecological opportunities facilitated the explosive diversification of New Caledonian Oxera (Lamiaceae). Systematic Biology 68(3):460–481
  • Zinger L, Bonin A, (...), Boyer F, (...), Coissac E, (…) De Barba M, (...) Taberlet P (2019) DNA metabarcoding — Need for robust experimental designs to draw sound ecological conclusions. Molecular ecology 28 (8), 1857-1862
  • I Belabdi, (…) Pompanon F, (…), Da Silva A (2019) Genetic homogenization of indigenous sheep breeds in Northwest Africa. Scientific reports 9 (1), 7920