Unit of Phylogeny and Molecular Genetics

Types of Research (in french)
Programs of Research
Researchers
Laboratories

Laboratory of Phylogeny and Molecular Genetics
(resp. Dr M. Perret)

The aim of the laboratory is to explore the evolution of biodiversity based on the analysis of molecular data. Research activities are carried out at two different levels: one is interspecific using phylogenetic approaches and the other is intraspecific using the tools of population genetics and phylogeography.

By providing new insights into the evolutionary history of plants and fungi, our results contribute to improve their classification and to better understand the origin of their outstanding diversity.

Principal techniques used in the laboratory

• Extraction of DNA from herbarium or fresh material
• PCR amplification and DNA sequencing
• Microsatellite markers and genotyping
• DNA fragment cloning
• Library construction, sequence capture and next generation sequencing (NGS)

The laboratory has the capacity to receive 6-8 people fulltime. The laboratory is fully equipped with an automatic sequencer (GenomeLab GeXP™ Genetic Analysis System), which is also able to analyze DNA fragments (microsatellites, AFLP, SNP) and several PCR machines, including a real-time PCR instrument (Corbett RotorGene).

Research projects at the CJB conducted in the laboratory

• Systematics of the Lichen Genus Usnea Adans.
• Speciation, Diversification and Intraspecific Structuring
• Palms (Arecaceae) Systematics
• Systematics and Evolution of Neotropical Gesneriaceae
• Systematics and Taxonomy of Aquifoliaceae
• Systématique et taxonomie des Sapotaceae de Madagascar

Academic and Professional training

The laboratory hosts students from the University of Geneva, within the framework of Doctoral and Masters thesis (option “Biodiversity and Systematics” and “Molecular Plant Science”).

The laboratory also welcome visiting students from other Swiss and foreign academic institutions (doc and posdoc) and trains laboratory technicians in biology (CFC) linked with the AGEMEL.

Current members

• Staff
  • Mathieu Perret (Curator)
  • Yamama Naciri (Curator)
  • Camille Christe (Scientific assistant)
  • Régine Niba (Lab technicien)
• Students
  • Angela Cano (PhD, en collaboration avec Prof. Antonelli, Univ. Göteborg, Suède; site web)
  • Alice Gerlach (PhD, Swiss Government Excellence Scholarships)
  • Zeynep Topprak (Postdoc en collaboration avec Prof. Bengt Oxelman, University of Göteborg, Suède; site web)
• Apprentices
  • Louisa Carvalho (2015-2018)
  • Dani Cardoso (2016-2019)
• Associate researcher and students
  • Gabriel E. Ferreira (PhD, INPA, Manaus, Brésil)
  • Andréa O. Araujo (Prof. Univ Universidade Federal do ABC, Brésil; site web)
• Former students
  • Pierre-Emanuel Dupasquier (PhD obtenu en 2017)
  • Martha Serrano-Serrano (PhD obtenu en 2016, codirection avec Prof. Salamin, Univ. Lausanne)
  • Rhéa Garratt (Master obtenu en 2016)

Recent publications

NACIRI Y., P.-E. DU PASQUIER, M. LUNDBERG, D. JEANMONOD & B. OXELMAN. 2017. A phylogenetic circumscription of Silene sect. Siphonomorpha (Caryophyllaceae) in the Mediterranean Basin. Taxon 66 (1): 91-108.

SERRANO-SERRANO M. L., J. ROLLAND, J. L. CLARK, N. SALAMIN AND M. PERRET. 2017. Hummingbird pollination and the diversification of angiosperms: an old and successful association in Gesneriaceae. Proceedings of the Royal Society B 284: 2016.2816.

ARAUJO A. O., A. CHAUTEMS, P. CARDOSO-GUSTAVSON, V. C. SOUZA, AND M. PERRET. 2016. Taxonomic Revision and Phylogenetic Position of the Brazilian Endemic Genus Sphaerorrhiza (Sphaerorrhizineae, Gesneriaceae) Including Two New Species. Systematic botany 41: 651-664.

FERREIRA G. F., A. CHAUTEMS, M. J. G. HOPKINS, AND M. PERRET. 2016. Independent evolution of pouched flowers in the Amazon is supported by the discovery of a new species of Lesia (Gesneriaceae) from Serra do Aracá tepui in Brazil. Plant Systematics and Evolution, 302 (8) : 1109–1119

NACIRI Y., LINDER P. (2015). Species identification and delimitation: the dance of the seven veils. Taxon, 64: 3–16.

LEUZINGER M., NACIRI Y., DU PASQUIER P.-E. & JEANMONOD D. (2015). Molecular diversity, phylogeography and genetic relationships of the Silene paradoxa group of section Siphonomorpha (Caryophyllaceae). Plant Systematics and Evolution, 301(1): 265-278.

SERRANO-SERRANO M. L., M. PERRET, M. GUIGNARD, A. CHAUTEMS, D. SILVESTRO AND N. SALAMIN. 2015. Decoupled evolution of floral traits and climatic preferences in a clade of Neotropical Gesneriaceae. BMC Evolutionary Biology 15: 247.

CHRISTE, C., G. KOZLOWSKI, D. FREY, L. FAZAN, S. BETRISEY, S. PIRINTSOS, J. GRATZFELD & NACIRI Y. (2014). Do living ex situ collections capture the genetic variation of wild populations?: a molecular analysis of two relict tree species: Zelkova abelica and Zelkova carpinifolia. Biodiversity & Conservation, 23: 2945-2959.

CHRISTE C., KOZLOWSKI G., FREY D., BÉTRISEY S., MAHARRAMOVA E., GARFÌ G., PIRINTSOS S. & NACIRI Y. (2014). Footprints of past intensive diversification and structuring for the genus Zelkova (Ulmaceae) in south-western Eurasia. Journal of Biogeography, 41: 1081-1093.

CHRISTE C., CAETANO S., AESCHIMANN D., KROPF M., DIADEMA K., NACIRI Y. (2014). The intraspecific genetic variability of siliceous and calcareous Gentiana species is shaped by contrasting demographic and re-colonization processes. Molecular Phylogenetics and Evolution 70: 323-336.

GAUTIER L., NACIRI Y., ANDERBERG A.A., SMEDMARK J.E.E., RANDRIANAIVO R. & SWENSON U. (2013). A new species, a new genus and a new tribe of Sapotaceae, endemic to Madagascar. Taxon 62: 972-983.

PERRET M., A. CHAUTEMS, ARAUJO A. O., AND N. SALAMIN. 2013. Temporal and spatial origin of Gesneriaceae in the New World inferred from plastid DNA sequences. Botanical Journal of the Linnean Society 171: 61-79.

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