CJB - Unit of Phylogeny and Molecular Genetics

Conservatoire et Jardin botaniques de la Ville de Gen�ve

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Unit of Phylogeny and Molecular Genetics

Unit of Phylogeny and Molecular Genetics

Research types (in French)
Research programmes
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

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
- Ezgi Ogutçen, Post-doctorante FNS (2018-2020)
- Carlos Galan Boluda, Post-doctorant FNS et Fondation Franklinia (2017-2022)
- Aina Randriarisoa, PhD, Boursière d'excellence de la Confédération Helvétique (2018-2021)
- Antoine Jousson, Master en Systématique et Biodiversité (2018-2020)
- Karine Durand, Master en Systématique et Biodiversité (2018-2020)
- Daniel Rodrigues Nunes, Master en Systématique et Biodiversité (2018-2020)
Apprentices
- Dani Cardoso (2016-2020)
- Antonio Castro Barriero (Apprenti laborantin en biologie, 2018-2020)
- Samuel Jordan (Stagiaire, 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
- Marcele Farias do Valle (Master en Systématique et Biodiversité obtenu en 2019)
- Luisa Carvalho (CFC de laborantine obtenu en 2019)
- Alice Gerlach (PhD obtenu en 2018, Swiss Government Excellence Scholarships, Université de Porto Allegre, Brésil)
- Zeynep Toprak (Postdoc en collaboration avec Prof. Bengt Oxelman, University of Göteborg, Suède)
- Gabriel E. Ferreira (PhD obtenu en 2019, INPA, Manaus, Brésil)
- Angela Cano (PhD obtenu 2018, en collaboration avec Prof. Antonelli, Univ. Göteborg, Suède)
- Pierre-Emmanuel Du Pasquier (PhD obtenu en 2017)
- Martha Serrano-Serrano (PhD obtenu en 2016, codirection avec Prof. Salamin, Univ. Lausanne)
- Rhéa Garratt (Master en Systématique et Biodiversité obtenu en 2016)

Recent publications

NACIRI Y., C. CHRISTE, S. BÉTRISEY, Y.-G. SONG, M. DENG, G. GARFÍ & G. KOZLOWSKI. 2019. Species delimitation in the East Asian species of the relict tree genus Zelkova (Ulmaceae): a complex history of diversification and admixture among species. Molecular Phylogenetics and Evolution 134:172-185.

GERLACH A. DA C.L., Z. TOPRAK, Y. NACIRI, E. ARAUJO CAVIRÓD, R.M. BORGES DA SILVEIRA, & P. CLERC. 2019. New insights into the Usnea cornuta aggregate (Parmeliaceae, lichenized Ascomycota): Molecular analysis reveals high genetic diversity correlated with chemistry. Molecular Phylogenetics and Evolution 131:125-137.

CANO A., C. D. BACON, F. W. STAUFFER, A. ANTONELLI, M. L. SERRANO-SERRANO, & M. PERRET. 2018. The roles of dispersal and mass extinction in shaping palm diversity across the Caribbean. Journal of Biogeography 45:1432-1443. (DOI: 10.1111/jbi.13225)

DU PASQUIER P.-E., D. JEANMONOD & Y. NACIRI. 2017. Morphological convergence within recently diversified Silene gigantea complex (Caryophyllaceae) in the Balkan Peninsula and SW Turkey, with the description of a new subspecies. Botanical Journal of the Linnean Society 183: 474–493.

CHAUTEMS A. & M. PERRET. 2017. Description and phylogenetic position of a new species of Nematanthus (Gesneriaceae) from Bahia, Brazil. Candollea 72 (2): 353-361.

SERRANO-SERRANO M. L., A. MARCIONETTI, M. PERRET, & N. SALAMIN. 2017. Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae). Applications in Plant Sciences 5(4): 1600135; http://www.bioone.org/loi/apps

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.