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Salamin Group - Molecular Phylogenetics and Speciation.

Phyloinformatics and Molecular Phylogenetics

Please visit my group website for more details (http://www2.unil.ch/phylo).

My group is interested in developping and testing methods to build and use phylogenetic trees to study evolution. Three areas of research are investigated in my group:

1. Building the Tree of Life.
Building large phylogenetic trees is an NP-hard problem, and heuristic strategies have to be used to infer trees containing hundreds of terminal taxa. We are investigating the performances of current methods of reconstruction with computer simulations and empirical examples from the angiosperms. We are also developping new methods to build the Tree of Life.

2. Mode and tempo of evolution.
Phylogenetic trees can give insight into the mode and tempo of species evolution. We are developping methods to estimate the rate of speciation and extinction through time using a Maximum Likelihood approach.

3. Grass evolution.
Grasses are one of the most ecologically and economically important plant family, and we are interesting in understanding what are the patterns and processes driving grass evolution. At the molecular level, we are investigating the evolution of enzyme involved in the C4 photosynthetic pathways (collaboration with Guillaume Besnard). We are also investigating the macroevolution of this family by looking at the traits affecting grass diversification and testing coevolution between grass species and herbivores (collaboration with Trevor Hodkinson at the University of Dublin, Trinity College).

In press |  2016 |  2015 |  2014 |  2013 |  2012 |  2011 |  2010 |  2009 |  2008 |  2007 |  2006 |  2005 |  2004 |  2003 |  2002 |  Thèses (doctorat) | 

In Press
Davydov I.I., Robinson-Rechavi M., Salamin N., In Press. State aggregation for fast likelihood computations in molecular evolution. Bioinformatics (oxford, England) . [DOI] [Pubmed]
Davydov Iakov I, Robinson-Rechavi Marc, Salamin Nicolas, In Press. State aggregation for fast likelihood computations in phylogenetics. Bioinformatics . [url editor site] [DOI]
Delhaye J., Salamin N., Roulin A., Criscuolo F., Bize P., Christe P., In Press. Interspecific correlation between red blood cell mitochondrial ROS production, cardiolipin content and longevity in birds. Age . [DOI] [Pubmed]
Ren G., Mateo R.G., Liu J., Suchan T., Alvarez N., Guisan A., Conti E., Salamin N., In Press. Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site-associated DNA sequencing. New Phytologist . [DOI] [Pubmed]
Cattin L., Schuerch J., Salamin N., Dubey S., 2016. Why are some species older than others? A large-scale study of vertebrates. BMC Evolutionary Biology 16(1) p. 90. [DOI] [Web of Science] [Pubmed]
Kostikova A., Silvestro D., Pearman P.B., Salamin N., 2016. Bridging inter- and intraspecific trait evolution with a hierarchical bayesian approach. Systematic Biology 65(3) pp. 417-431. [DOI] [Web of Science] [Pubmed]
Pellissier L., Litsios G., Fishbein M., Salamin N., Agrawal A.A., Rasmann S., 2016. Different rates of defense evolution and niche preferences in clonal and nonclonal milkweeds (Asclepias spp.). New Phytologist 209(3) pp. 1230-1239. [DOI] [Web of Science] [Pubmed]
Pellissier L., Moreira X., Danner H., Serrano M., Salamin N., van Dam N.M., Rasmann S., 2016. The simultaneous inducibility of phytochemicals related to plant direct and indirect defences against herbivores is stronger at low elevation. Journal of Ecology 104(4) pp. 1116-1125. [DOI] [Web of Science]
Ren G., Mateo R.G., Liu J., Suchan T., Alvarez N., Guisan A., Conti E., Salamin. N., 10-2016. Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on RAD sequencing. New Phytologist . [embargo unspecified] [DOI]
Silvestro D., Zizka A., Bacon C.D., Cascales-Miñana B., Salamin N., Antonelli A., 2016. Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 371(1691) p. 20150225. [Document] [DOI] [Web of Science] [Pubmed]
Dib L., Meyer X., Artimo P., Ioannidis V., Stockinger H., Salamin N., 2015. Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree. BMC Bioinformatics 16 p. 394. [DOI] [Web of Science] [Pubmed]
Laurent S., Robinson-Rechavi M., Salamin N., 2015. Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions. BMC Evolutionary Biology 15 p. 157. [Document] [DOI] [Web of Science] [Pubmed]
Pillonel T., Bertelli C., Salamin N., Greub G., 2015. Taxogenomics of the order Chlamydiales. International Journal of Systematic and Evolutionary Microbiology 65(Pt 4) pp. 1381-1393. [DOI] [Web of Science] [Pubmed]
Pirie M.D., Litsios G., Bellstedt D.U., Salamin N., Kissling J., 2015. Back to Gondwanaland: can ancient vicariance explain (some) Indian Ocean disjunct plant distributions? Biology Letters 11(6) p. 20150086. [DOI] [Web of Science] [Pubmed]
Serrano-Serrano M.L., Perret M., Guignard M., Chautems A., Silvestro D., Salamin N., 2015. Decoupled evolution of floral traits and climatic preferences in a clade of Neotropical Gesneriaceae. BMC Evolutionary Biology 15 p. 247. [DOI] [Web of Science] [Pubmed]
Silvestro D., Antonelli A., Salamin N., Quental T.B., 2015. The role of clade competition in the diversification of North American canids. Proceedings of the National Academy of Sciences of the United States of America 112(28) pp. 8684-8689. [DOI] [Web of Science] [Pubmed]
Silvestro D., Kostikova A., Litsios G., Pearman P.B., Salamin N., 2015. Measurement Errors Should Always Be Incorporated in Phylogenetic Comparative Analysis. Methods in Ecology and Evolution 6(3) pp. 340-346. [DOI] [Web of Science]
Witsenburg F., Clément L., López-Baucells A., Palmeirim J., Pavlinić I., Scaravelli D., ?evčík M., Dutoit L., Salamin N., Goudet J. et al., 2015. How a haemosporidian parasite of bats gets around: the genetic structure of a parasite, vector and host compared. Molecular Ecology 24(4) pp. 926-940. [Document] [DOI] [Web of Science] [Pubmed]
Christin P.A., Spriggs E., Osborne C.P., Strömberg C.A., Salamin N., Edwards E.J., 2014. Molecular dating, evolutionary rates, and the age of the grasses. Systematic Biology 63(2) pp. 153-165. [Document] [DOI] [Web of Science] [Pubmed]
Dib L., Silvestro D., Salamin N., 2014. Evolutionary footprint of coevolving positions in genes. Bioinformatics 30(9) pp. 1241-1249. [DOI] [Web of Science] [Pubmed]
Kostikova A., Litsios G., Burgy S., Milani L., Pearman P.B., Salamin N., 2014. Scale-dependent adaptive evolution and morphological convergence to climatic niche in Californian eriogonoids (Polygonaceae). Journal of Biogeography 41(7) pp. 1326-1337. [DOI] [Web of Science]
Kostikova A., Salamin N., Pearman P.B., 2014. The role of climatic tolerances and seed traits in reduced extinction rates of temperate polygonaceae. Evolution 68(7) pp. 1856-1870. [DOI] [Web of Science] [Pubmed]
Lexer C., Wüest R.O., Mangili S., Heuertz M., Stölting K.N., Pearman P.B., Forest F., Salamin N., Zimmermann N.E., Bossolini E., 2014. Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae). Molecular Ecology 23(17) pp. 4373-4386. [DOI] [Web of Science] [Pubmed]
Litsios G, Pearman P.B., Lanterbecq D., Tolou N., Salamin N., 2014. The radiation of the clownfishes has two geographical replicates. Journal of Biogeography 41(11) pp. 2140-2149. [embargo unspecified] [DOI] [Web of Science]
Litsios G., Kostikova A., Salamin N., 2014. Host specialist clownfishes are environmental niche generalists. Proceedings of the Royal Society. B Biological Sciences 281(1795) pp. 20133220-20133220. [DOI] [Web of Science] [Pubmed]
Litsios G., Salamin N., 2014. Hybridisation and diversification in the adaptive radiation of clownfishes. BMC Evolutionary Biology 14(1) p. 245. [Document] [DOI] [Web of Science] [Pubmed]
Litsios G., Wüest R.O., Kostikova A., Forest F., Lexer C., Linder H.P., Pearman P.B., Zimmermann N.E., Salamin N., 2014. Effects of a fire response trait on diversification in replicated radiations. Evolution 68(2) pp. 453-465. [Document] [DOI] [Web of Science] [Pubmed]
Moretti S., Laurenczy B., Gharib W.H., Castella B., Kuzniar A., Schabauer H., Studer R.A., Valle M., Salamin N., Stockinger H. et al., 2014. Selectome update: quality control and computational improvements to a database of positive selection. Nucleic Acids Research 42(1) pp. D917-D921. [Document] [DOI] [Web of Science] [Pubmed]
Ndiribe C., Pellissier L., Dubuis A., Vittoz P., Salamin N., Guisan A., 2014. Plant functional and phylogenetic turnover correlate with climate and land use in the Western Swiss Alps. Journal of Plant Ecology 7(5) pp. 439-450. [Document] [DOI] [Web of Science]
Pellissier L., Niculita-Hirzel Hélène, Dubuis A., Pagni M., Guex N., Ndiribe C., Salamin N., Xenarios I., Goudet J., Sanders I.R. et al., 2014. Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps. Molecular Ecology 23(17) pp. 4274-4290. [DOI] [Web of Science] [Pubmed]
Pio D.V., Engler R., Linder H.P., Monadjem A., Cotterill F.P.D., Taylor P.J., Schoeman M.C., Price B.W., Villet M.H., Eick G. et al., 2014. Climate change effects on animal and plant phylogenetic diversity in southern Africa. Global Change Biology 20(5) pp. 1538-1549. [DOI] [Web of Science]
Silvestro D., Salamin N., Schnitzler J., 2014. PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data. Methods in Ecology and Evolution 5(10) pp. 1126-1131. [DOI] [Web of Science]
Silvestro D., Schnitzler J., Liow L.H., Antonelli A., Salamin N., 2014. Bayesian estimation of speciation and extinction from incomplete fossil occurrence data. Systematic Biology 63(3) pp. 349-367. [DOI] [Web of Science] [Pubmed]
Valle M., Schabauer H., Pacher C., Stockinger H., Stamatakis A., Robinson-Rechavi M., Salamin N., 2014. Optimization strategies for fast detection of positive selection on phylogenetic trees. Bioinformatics 30(8) pp. 1129-1137. [Document] [DOI] [Web of Science] [Pubmed]
Zaheri M., Dib L., Salamin N., 2014. A generalized mechanistic codon model. Molecular Biology and Evolution 31(9) pp. 2528-2541. [Document] [DOI] [Web of Science] [Pubmed]
Davies T.J., Wolkovich E.M., Kraft N.J.B., Salamin N., Allen J.M., Ault T.R., Betancourt J.L., Bolmgren K., Cleland E.E., Cook B.I. et al., 2013. Phylogenetic conservatism in plant phenology. Journal of Ecology 101(6) pp. 1520-1530. [Document] [DOI] [Web of Science]
Kostikova A., Litsios G., Salamin N., Pearman P.B., 2013. Linking life-history traits, ecology, and niche breadth evolution in north american eriogonoids (polygonaceae). American Naturalist 182(6) pp. 760-774. [DOI] [Web of Science] [Pubmed]
Lexer C., Mangili S., Bossolini E., Forest F., Stölting K.N., Pearman P.B., Rimmermann N.E., Salamin N., 2013. 'Next generation' biogeography: towards understanding the drivers of species diversification and persistence. Journal of Biogeography 40(6) pp. 1013-1022. [DOI] [Web of Science]
Mazer S.J., Travers S.E., Cook B.I., Davies T.J., Bolmgren K., Kraft N.J., Salamin N., Inouye D.W., 2013. Flowering date of taxonomic families predicts phenological sensitivity to temperature: Implications for forecasting the effects of climate change on unstudied taxa. American Journal of Botany 100(7) pp. 1381-1397. [Document] [DOI] [Web of Science] [Pubmed]
Ndiribe C., Pellissier L., Antonelli S., Dubuis A., Pottier J., Vittoz P., Guisan A., Salamin N., 2013. Phylogenetic plant community structure along elevation is lineage specific. Ecology and Evolution 3(15) pp. 4925-4939. [Document] [DOI] [Web of Science]
Ndiribe C., Salamin N., Guisan A., 2013. Understanding the concepts of community phylogenetics. Evolutionary Ecology Reserach 15(8) pp. 853-868. [Web of Science]
Papadopulos A.S., Powell M.P., Pupulin F., Warner J., Hawkins J.A., Salamin N., Chittka L., Williams N.H., Whitten W.M., Loader D. et al., 2013. Convergent evolution of floral signals underlies the success of Neotropical orchids. Proceedings of the Royal Society B Biological Sciences 280(1765) p. 20130960. [Document] [DOI] [Web of Science] [Pubmed]
Pellissier L., Ndiribe C., Dubuis A., Pradervand J.N., Salamin N., Guisan A., Rasmann S., 2013. Turnover of plant lineages shapes herbivore phylogenetic beta diversity along ecological gradients. Ecology Letters 16(5) pp. 600-608. [DOI] [Web of Science] [Pubmed]
Pellissier L., Rohr R.P., Ndiribe C., Pradervand J.-N., Salamin N., Guisan A., Wisz M., 2013. Combining food web and species distribution models for improved community projections. Ecology and Evolution 3(13) pp. 4572-4583. [Document] [DOI] [Web of Science]
Perret M., Chautems A., De Araujo A.O., Salamin N., 2013. Temporal and spatial origin of Gesneriaceae in the New World inferred from plastid DNA sequences. Botanical Journal of the Linnean Society 171(1) pp. 61-79. [Document] [DOI] [Web of Science]
Christin P.A., Besnard G., Edwards E.J., Salamin N., 2012. Effect of genetic convergence on phylogenetic inference. Molecular Phylogenetics and Evolution 62(3) pp. 921-927. [DOI] [Web of Science] [Pubmed]
Cook B.I., Wolkovich E.M., Davies T.J., Ault T.R., Betancourt J.L., Allen J.M., Bolmgren K., Cleland E.E., Crimmins T.M., Kraft N.J.B. et al., 2012. Sensitivity of Spring Phenology to Warming Across Temporal and Spatial Climate Gradients in Two Independent Databases. Ecosystems 15(8) pp. 1283-1294. [DOI] [Web of Science]
Davies T.J., Kraft N.J., Salamin N., Wolkovich E.M., 2012. Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism. Ecology 93(2) pp. 242-247. [DOI] [Web of Science] [Pubmed]
Grass Phylogeny Working Group II, 2012. New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins. New Phytologist 193(2) pp. 304-312. [DOI] [Web of Science] [Pubmed]
Litsios G., Pellissier L., Forest F., Lexer C., Pearman P.B., Zimmermann N.E., Salamin N., 2012. Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae). Proceedings of the Royal Society of London B Biological Sciences 279(1743) pp. 3662-3669. [DOI] [Web of Science] [Pubmed]
Litsios G., Salamin N., 2012. Effects of phylogenetic signal on ancestral state reconstruction. Systematic Biology 61(3) pp. 533-538. [DOI] [Web of Science] [Pubmed]
Litsios G., Sims C.A., Wüest R.O., Pearman P.B., Zimmermann N.E., Salamin N., 2012. Mutualism with sea anemones triggered the adaptive radiation of clownfishes. BMC Evolutionary Biology 12(1) p. 212. [Document] [DOI] [Web of Science] [Pubmed]
Moretti S., Murri R., Maffioletti S., Kuzniar A., Castella B, Salamin N., Robinson-Rechavi M., Stockinger H., 2012. gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution. pp. 59-68 in Glatard T, Silverstein J (eds.) HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences. Studies in Health Technology and Informatics 175. IOS Press Books online. [Document] [url editor site] [DOI]
Naciri Y., Caetano S., Salamin N., 2012. Plant DNA barcodes and the influence of gene flow. Molecular Ecology Resources 12(4) pp. 575-580. [DOI] [Web of Science] [Pubmed]
Pellissier L., Litsios G., Fiedler K., Pottier J., Dubuis A., Pradervand J.N., Salamin N., Guisan A., 2012. Loss of interactions with ants under cold climate in a regional myrmecophilous butterfly fauna. Journal of Biogeography 39(10) pp. 1782-1790. [DOI] [Web of Science]
Schabauer H., Valle M., Pacher C., Stockinger H., Stamatakis A., Robinson-Rechavi M., Yang Z., Salamin N., 2012. SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model. pp. 700-708 in Aluru S., Bader D.A. (eds.) HiCOMB (11th IEEE International Workshop on High Performance Computational Biology). IEEE. [Document] [DOI]
Wolkovich E.M., Cook B.I., Allen J.M., Crimmins T.M., Betancourt J.L., Travers S.E., Pau S., Regetz J., Davies T.J., Kraft N.J. et al., 2012. Warming experiments underpredict plant phenological responses to climate change. Nature 485(7399) pp. 494-497. [DOI] [Web of Science] [Pubmed]
Yang S.Y., Grønlund M., Jakobsen I., Grotemeyer M.S., Rentsch D., Miyao A., Hirochika H., Kumar C.S., Sundaresan V., Salamin N. et al., 2012. Nonredundant Regulation of Rice Arbuscular Mycorrhizal Symbiosis by Two Members of the PHOSPHATE TRANSPORTER1 Gene Family. Plant Cell 24(10) pp. 4236-4251. [DOI] [Web of Science] [Pubmed]
Buerki S., Forest F., Salamin N., Alvarez N., 2011. Comparative performance of supertree algorithms in large data sets using the soapberry family (Sapindaceae) as a case study. Systematic Biology 60(1) pp. 32-44. [DOI] [Web of Science] [Pubmed]
Osborne C.P., Visser V., Freckleton R.P., Simpson D., Clayton D., Barker A., Chapman S., Salamin N., Uren V., GrassPortal Dev Team, 2011. GrassPortal: an online ecological and evolutionary data facility for the grasses. pp. 566-566 in Van Staden J. (eds.) South African Journal of Botany. South African Journal of Botany 77(2). Elsevier. [DOI] [Web of Science]
Pio D.V., Broennimann O., Barraclough T.G., Reeves G., Rebelo A.G., Thuiller W., Guisan A., Salamin N., 2011. Spatial predictions of phylogenetic diversity in conservation decision making. Conservation Biology 25(6) pp. 1229-1239. [DOI] [Web of Science] [Pubmed]
Burri R., Salamin N., Studer R.A., Roulin A., Fumagalli L., 2010. Adaptive divergence of ancient gene duplicates in the avian MHC class II beta. Molecular Biology and Evolution 27(10) pp. 2360-2374. [DOI] [Web of Science] [Pubmed]
Edwards E.J., Osborne C.P., Strömberg C.A., Smith S.A., C4 Grasses Consortium, Bond W.J., Bond W.J., Christin P.A., Cousins A.B., Duvall M.R. et al., 2010. The origins of C4 grasslands: integrating evolutionary and ecosystem science. Science 328(5978) pp. 587-591. [DOI] [Web of Science] [Pubmed]
Hodkinson T. R., Chonghaile G. N., Sungkaew S., Chase M. W., Salamin N., Stapleton C. M. A., 2010. Phylogenetic analysis of plastid and nuclear DNA sequences reveals a rapid late Miocene radiation of the temperate bamboo tribe Arundinarieae (Poaceae, Bambusoideae). Plant Ecology and Diversity 3(2) pp. 109-120. [DOI] [Web of Science]
Salamin N., Wüest R.O., Lavergne S., Thuiller W., Pearman P.B., 2010. Assessing rapid evolution in a changing environment. Trends in Ecology and Evolution 25(12) pp. 692-698. [DOI] [Web of Science] [Pubmed]
Besnard G., Muasya A.M., Russier F., Roalson E.H., Salamin N., Christin P.A., 2009. Phylogenomics of C(4) photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence. Molecular biology and evolution 26(8) pp. 1909-1919. [DOI] [Web of Science] [Pubmed]
Christin P.A., Petitpierre B., Salamin N., Büchi L., Besnard G., 2009. Evolution of C(4) phosphoenolpyruvate carboxykinase in grasses, from genotype to phenotype. Molecular Biology and Evolution 26(2) pp. 357-365. [DOI] [Web of Science] [Pubmed]
Christin P.A., Salamin N., Kellogg E.A., Vicentini A., Besnard G., 2009. Integrating phylogeny into studies of C4 variation in the grasses. Plant Physiology 149(1) pp. 82-87. [Document] [DOI] [Web of Science] [Pubmed]
Christin P.A., Samaritani E., Petitpierre B., Salamin N., Besnard G., 2009. Evolutionary insights on C4 photosynthetic subtypes in grasses from genomics and phylogenetics. Genome Biology and Evolution 2009 pp. 221-230. [Document] [url editor site] [DOI] [Web of Science]
Roulin A., Wink M., Salamin N., 2009. Selection on a eumelanic ornament is stronger in the tropics than in temperate zones in the worldwide-distributed barn owl. Journal of Evolutionary Biology 22(2) pp. 345-354. [DOI] [Web of Science] [Pubmed]
Sungkaew S., Stapleton C.M., Salamin N., Hodkinson T.R., 2009. Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s. Journal of Plant Research 122(1) pp. 95-108. [DOI] [Web of Science] [Pubmed]
Bouchenak-Khelladi Y., Salamin N., Savolainen V., Forest F., Bank M., Chase M.W., Hodkinson T.R., 2008. Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling. Molecular Phylogenetics and Evolution 47(2) pp. 488-505. [DOI] [Web of Science] [Pubmed]
Burri R., Hirzel Hélène N., Salamin N., Roulin A., Fumagalli L., 2008. Evolutionary patterns of MHC class II B in owls and their implications for the understanding of avian MHC evolution. Molecular Biology and Evolution 25(6) pp. 1180-1191. [DOI] [Web of Science] [Pubmed]
Christin P.A., Besnard G., Samaritani E., Duvall M.R., Hodkinson T.R., Savolainen V., Salamin N., 2008. Oligocene CO2 decline promoted C4 photosynthesis in grasses. Current Biology 18(1) pp. 37-43. [DOI] [Web of Science] [Pubmed]
Christin P.A., Salamin N., Muasya A.M., Roalson E.H., Russier F., Besnard G., 2008. Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis. Molecular Biology and Evolution 25(11) pp. 2361-2368. [DOI] [Web of Science] [Pubmed]
Dubey S., Salamin N., Ruedi M., Barrière P., Colyn M., Vogel P., 2008. Biogeographic origin and radiation of the Old World crocidurine shrews (Mammalia: Soricidae) inferred from mitochondrial and nuclear genes. Molecular Phylogenetics and Evolution 48(3) pp. 953-963. [Document] [DOI] [Web of Science] [Pubmed]
Christin P.A., Salamin N., Savolainen V., Duvall M.R., Besnard G., 2007. C4 Photosynthesis evolved in grasses via parallel adaptive genetic changes. Current Biology 17(14) pp. 1241-1247. [DOI] [Web of Science] [Pubmed]
Dubey S., Salamin N., Ohdachi S.D., Barrière P., Vogel P., 2007. Molecular phylogenetics of shrews (Mammalia: Soricidae) reveal timing of transcontinental colonizations. Molecular Phylogenetics and Evolution 44(1) pp. 126-137. [Document] [DOI] [Web of Science] [Pubmed]
Hodkinson T.R., Savolainen V., Jacobs S.W.L., Bouchenak-Khelladi Y., Kinney M.S., Salamin N., 2007. Supersizing: progress in documenting and understanding grass species richness. pp. 275-298 in Hodkinson T.R., Parnell J.A.N. (eds.) Reconstructing the tree of life: taxonomy and systematics of species rich taxa. The Systematics Association special volume series 72. CRC Press, Boca Raton. [DOI]
Hodkinson T.R., Waldren S., Parnell J.A., Kelleher C.T., Salamin K., Salamin N., 2007. DNA banking for plant breeding, biotechnology and biodiversity evaluation. Journal of Plant Research 120(1) pp. 17-29. [DOI] [Web of Science] [Pubmed]
Basic N., Salamin N., Keller C., Galland N., Besnard G., 2006. Cadmium hyperaccumulation and genetic differentiation of Thlaspi caerulescens populations. Biochemical Systematics and Ecology 34(9) pp. 667-677. [DOI] [Web of Science]
Donnelly A., Salamin N., Jones M. B., 2006. Changes in tree phenology: an indicator of spring warming in Ireland? Biology and Environment: Proceedings of the Irish Royal Academy 106(1) pp. 49-56. [DOI]
Flannery M.L., Mitchell F.J., Coyne S., Kavanagh T.A., Burke J.I., Salamin N., Dowding P., Hodkinson T.R., 2006. Plastid genome characterisation in Brassica and Brassicaceae using a new set of nine SSRs. Theoretical and Applied Genetics 113(7) pp. 1221-1231. [DOI] [Web of Science] [Pubmed]
Savolainen V., Anstett M.C., Lexer C., Hutton I., Clarkson J.J., Norup M.V., Powell M.P., Springate D., Salamin N., Baker W.J., 2006. Sympatric speciation in palms on an oceanic island. Nature 441(7090) pp. 210-213. [DOI] [Web of Science] [Pubmed]
Savolainen V., Lexer C., Anstett M. C., Hutton I., Clarkson J. J., Norup M. V., Powell M. P., Springate D., Salamin N., Baker W. J., 10-2006. Evolutionary biology - Sympatric plant speciation in islands? Reply. Nature 443(7114) pp. E12-13. [DOI] [Web of Science]
Strauss S.Y., Webb C.O., Salamin N., 2006. Exotic taxa less related to native species are more invasive. Proceedings of the National Academy of Sciences of the United States of America 103(15) pp. 5841-5845. [DOI] [Web of Science] [Pubmed]
Chase M.W., Salamin N., Wilkinson M., Dunwell J.M., Kesanakurthi R.P., Haidar N., Savolainen V., 2005. Land plants and DNA barcodes: short-term and long-term goals. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 360(1462) pp. 1889-1895. [DOI] [Web of Science] [Pubmed]
Rønsted N., Weiblen G.D., Cook J.M., Salamin N., Machado C.A., Savolainen V., 2005. 60 million years of co-divergence in the fig-wasp symbiosis. Proceedings of the Royal Society of London B Biological Sciences 272(1581) pp. 2593-2599. [DOI] [Web of Science] [Pubmed]
Salamin N., Hodkinson T.R., Savolainen Coates V., 2005. Towards building the tree of life: a simulation study for all angiosperm genera. Systematic Biology 54(2) pp. 183-196. [DOI] [Web of Science] [Pubmed]
Salamin N., Davies T. J., 2004. Using supertrees to investigate species richness in grasses and flowering plants. pp. 461-486 in Bininda-Emonds O.R.P. (eds.) Phylogenetic supertrees. Computational Biology 4. Kluwer Academic Publishers, Dordrecht. [Document]
Salamin N., Chase M.W., Hodkinson T.R., Savolainen V., 2003. Assessing internal support with large phylogenetic DNA matrices. Molecular Phylogenetics and Evolution 27(3) pp. 528-539. [DOI] [Web of Science] [Pubmed]
Salamin N., Hodkinson T.R., Savolainen V., 2002. Building supertrees: an empirical assessment using the grass family (Poaceae). Systematic Biology 51(1) pp. 136-150. [DOI] [Web of Science] [Pubmed]
Savolainen V., Chase M.W., Salamin N., Soltis D.E., Soltis P.S., López A.J., Fédrigo O., Naylor G.J., 2002. Phylogeny reconstruction and functional constraints in organellar genomes: plastid atpB and rbcL sequences versus animal mitochondrion. Systematic Biology 51(4) pp. 638-647. [DOI] [Web of Science] [Pubmed]
Phd thesis
Laurent S., 08-2016. Long term evolutionary responses to whole genome duplication. 134 p., Université de Lausanne, Faculté de biologie et médecine, Robinson-Rechavi M. (dir.). [Document]
SERRANO SERRANO Martha Liliana, 09-2016. CORRELATES AND GENETIC BASIS OF PLANT DIVERSIFICATION IN THE NEOTROPICS: THE GESNERIACEAE AS A CASE STUDY. 116 p., Université de Lausanne, Faculté de biologie et médecine, Nicolas Salamin (dir.).
Kostikova A., 2014. Evolution of intraspecific variation : a comparative phylogenetic approach. 219 p., Université de Lausanne, Faculté de biologie et médecine, Salamin N. (dir.).
Litsios G., 2014. La spéciation écologique racontée au travers de l'étude de l'évolution des poissons-clowns et de quelques autres. 197 p., Université de Lausanne, Faculté de biologie et médecine, Salamin N. (dir.).
Zaheri M., 2014. KCM, a general framework for codon-based model of evolution. 118 p., Université de Lausanne, Faculté de biologie et médecine, Salamin N., Goudet J. (dir.).

Group Leader

Graduate students

Embedded Bioinformatician

Previous group members



Nicolas Salamin
Office room: 3212
Phone: +41 21 692 4154
Fax: +41 21 692 4165

Administrative assistant
Office room: 3106
Phone: +4121 692 4200
Fax: +4121 692 4265

Biophore - CH-1015 Lausanne  - Switzerland  -  Tel. +41 21 692 41 60  -  Fax +41 21 692 41 65
Swiss University