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Balao F, Trucchi E, Wolfe T, Hao B-H, Lorenzo MT, Baar J, Sedman L, Kosiol C, Amman F, Chase MW, Hedren M, Paun O. 2017. Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima. Molecular Ecology 26: 3649-3662.

Balao F, Paun O, Conchita A. 2017. Uncovering the contribution of epigenetics to plant phenotypic variation in Mediterranean ecosystems. Plant Biology in press.

Bateman R, Szramko G, Paun O. 2017. Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among species groups of bee orchids. Annals of Botany in press.

Brandrud M, Paun O, Lorenzo MT, Nordal I, Krag Brysting A. 2017. RADseq provides evidence for parallel ecotypic divergence in the autotetraploid Cochlearia officinalis in Northern Norway. Scientific Reports 7: 5573.

Gratton P, Marta S, Bocksberger G, Winter M, Trucchi E, Kühl H. 2017. A world of sequences: can we use georeferenced nucleotide databases for a robust automated phylogeography? Journal of Biogeography 44: 475–486.

Richards CL, Alonso C, Becker C, Bossdorf O, Bucher E, Colome-Tatche M, Durka W, Engelhardt J, Gaspar B, Gogol-Doring A, Grosse I, van Gurp TP, Heer K, Kronholm I, Lampei C, Latzel V, Mirouze M, Opgenoorth L, Paun O, Prohaska S, Rensing SA, Stadler P, Trucchi E, Ullrich K, Verhoeven KJF. 2017. Ecological plant epigenetics: Evidence from model and non-model species, and the way forward. Ecology Letters in press.

Trucchi E, Frajman B, Haverkamp T, Schönswetter P, Paun O. 2017. Genomic analyses suggest parallel ecological divergence in Heliosperma pusillum (Caryophyllaceae). New Phytologist 216: 267-278.


Balao F, Tannhäuser M, Lorenzo MT, Hedren M, Paun O. 2016. Genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex. Heredity 116: 351–361.

Cristofari R, Bertorelle G, Ancel A, Benazzo A, Le Maho Y,  Ponganis P J, Stenseth N C, Trathan P N, Whittington J D, Zanetti E, Zitterbart D P, Le Bohec C, Trucchi E. 2016. Full circumpolar migration ensures evolutionary unity in the Emperor penguin. Nature Communications 7: 11842.

Gratton P, Marta S, Bocksberger G, Winter M, Trucchi E, Kühl H. 2016. A world of sequences: can we use georeferenced nucleotide databases for a robust automated phylogeography? Journal of Biogeography 10.111/jbi.12786.

Gratton P, Trucchi E, Trasatti A, Riccarducci G, Marta S, Allegrucci G, Cesaroni D, Sbordoni V. 2016. Testing classical species properties with contemporary data: How “bad species” in the brassy ringlets (Erebia tyndarus complex, Lepidoptera) turned good. Systematic Biology 65: 292-303.

Malinsky M, Trucchi E, Lawson D, Falush D. 2016. RADpainter and fineStructure: population inference from RADseq data. bioRxiv 057711.

Mazzarella AB, Boessenkool S, Ostbye K, Vollestad LA, Trucchi E. 2016. Genomic signatures of the plateless phenotype in the threespine stickleback. Ecology and Evolution 6: 3161-3173.

Paun O, Turner B, Trucchi E, Munzinger J, Chase MW, Samuel R. 2016. Processes driving the adaptive radiation of a tropical tree (Diospyros, Ebenaceae) in New Caledonia, a biodiversity hotspot. Systematic Biology 65: 212-217.

Trucchi E, Facon B, Gratton P, Mori E, Stenseth N C, Jentoft S. 2016. Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) longlasting and successful invasion? Molecular Ecology 25: 3527–3539.

Trucchi E, Mazzarella AB, Gilfillan GD, Lorenzo Romero M, Schönswetter P, Paun O. 2016. BsRADseq: screening DNA methylation in natural populations of non-model species. Molecular Ecology 25: 1697-1713.

Turner B, Paun O, Munzinger J, Chase MW, Samuel R. 2016. Sequencing of whole plastid genomes and nuclear ribosomal DNA of Diospyros species (Ebenaceae) endemic to New Caledonia: many species, little divergence. Annals of Botany 117: 1175-1185.


Balao F, Casimiro-Soriguer R, Garcia-Castano JL, Terrab A, Talavery S. 2015. Big thistle eats the little thistle: does unidirectional introgressive hybridization endanger the conservation of Onopordum hinojense? New Phytologist 206: 448-458.

Rueness EK, Trosvik P, Atickem A, Sillero-Zubiri C, Trucchi E. 2015. The African wolf is a missing link in the wolf-like canid phylogeny. bioRxiv 017996.


Hojsgaard D, Greilhuber J, Pellino M, Paun O, Sharbel TF, Hörandl E. 2014. Emergence of apospory and bypass of meiosis via apomixis after sexual hybridisation and polyploidisation. New Phytologist 204: 1000-1012.

Trucchi E, Gratton P, Whittington JD, Cristofari R, Le Maho Y, Stenseth NC and Le Bohec C. 2014 King penguin demography since the last glaciation inferred from genome-wide data.  Proceedings of the Royal Society B  281: 20140528.

Wang S, Hao B, Li J, Gu H, Peng J, Xie F, Zhao X, Frech C, Chen N, Ma B, Li Y. 2014. Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics.  BMC Genomics 15: 440.

Hodač L, Scheben AP, Hojsgaard D, Paun O, Hörandl E. 2014. ITS polymorphisms shed light on hybrid evolution in apomictic plants: a case study on the Ranunculus auricomus complex. PLoS One 9(7): e103003.

Alao JP, Sjölander JJ, Baar J, Özbaki-Yagan N, Kakoschky B, Sunnerhagen P. 2014. Caffeine stabilizes Cdc25 independently of Rad3 in Schizosaccharomyces pombe contributing to checkpoint override. Molecular Microbiology 92: 777-796.

Peng J, Hao B, Liu L, Wang S, Ma B, Yang Y, Xie F, Li Y. 2014. RNA-Seq and microarrays analyses reveal global differential transcriptomes of Mesorhizobium huakuii 7653R between bacteroids and free-living cells. PLoS One 9(4): e93626.


Turner B, Paun O, Munzinger J, Duangjai S, Chase MW, Samuel R. 2013. Analyses of amplified fragment length polymorphisms (AFLP) indicate rapid radiation of Diospyros species (Ebenaceae) endemic to New Caledonia. BMC Evolutionary Biology 13: 269.

Kuzmanović N, Comanescu P, Paun O, Frajman B, Schönswetter P, Lazarević M, Lakušić D. 2013. Genetic and morphological differentiation within the Balkan-Carpathian Sesleria rigida sensu Fl. Eur. (Poaceae), a taxonomically intricate tetraploid-octoploid complex. Taxon 62: 458-472.

Fay MF, Kelly LJ, Micheneau C, Paun O, Whitten WM. 2013. Developing conservation genetics tools for non-model species in the era of next-generation sequencing. Pp. 173-177 in: Elliott J, Kurzweil HF, O’Byrne P, Tan KW, van der Schans AS, Wong SM, Yam TW (eds.), Where New and Old World Orchids Meet [Proceedings of the 20th World Orchid Conference]. Singapore: National Parks Board & Orchid Society of Southeast Asia.


Taberlet P, Zimmermann NE, Englisch T, Tribsch A, Holderegger R, Alvarez N, Niklfeld H, Coldea G, Mirek Z, Moilanen A, Ahlmer W, Marsan PA, Bona E, Bovio M, Choler P, Cieślak E, Colli L, Cristea V, Dalmas J-P, Frajman B, Garraud L, Gaudeul M, Gielly L, Gutermann W, Jogan N, Kagalo AA, Korbecka G, Küpfer P, Lequette B, Letz DR, Manel S, Mansion G, Marhold K, Martini F, Negrini R, Niño F, Paun O, Pellecchia M, Perico G, Piękoś-Mirkowa H, Prosser F, Puşcaş M, Ronikier M, Scheuerer M, Schneeweiss GM, Schönswetter P, Schratt-Ehrendorfer L, Schüpfer F, Selvaggi A, Steinmann K, Thiel-Egenter C, van Loo M, Winkler M, Wohlgemuth T, Wraber T, Gugerli F, IntraBioDiv C. 2012. Genetic diversity in widespread species is not congruent with species richness in alpine plant communities. Ecology Letters 15: 1439-1448.

Flatscher R, Frajman B, Schönswetter P, Paun O (2012) Environmental heterogeneity and phenotypic divergence: can heritable epigenetic variation aid speciation? Genetics Research International 10.1155/2012/698421.

Paun O, Schönswetter P (2012) Amplified Fragment Length Polymorphism: an invaluable fingerprinting technique for genomic, transcriptomic, and epigenetic studies. Pg. 75-87, in: Sucher NJ, Hennell J, Carles M (eds.), Plant DNA Fingerprinting and Barcoding: Methods and Protocols. USA: Humana Press. [Methods in Molecular Biology, vol. 862] DOI:10.1007/978-1-61779-609-8_7


Paun O, Bateman R, Fay MF, Luna JA, Moat J, Hedrén M, Chase MW (2011) Altered gene expression and ecological divergence in sibling allopolyploids of Dactylorhiza (Orchidaceae). BMC Evolutionary Biology 11: 113. *BMC Highly accessed

Paun O, Forest F, Fay MF, Chase MW (2011) Parental divergence and hybrid speciation in angiosperms revisited. Taxon 60: 1241-1244.

Paun O, Chase MW. 2011. Epigenetic information – unexplored source of natural variation. Lankesteriana 11: 319-324.

Hedrén M, Paun O, Sayers B. 2011. The polymorphic early marsh orchids, Dactylorhiza incarnata s.l. (Orchidaceae), at Lough Gealain, Ireland. New Journal of Botany 1: 16-23.


Paun O, Bateman RM, Fay MF, Hedrén M, Civeyrel L, Chase MW (2010) Stable epigenetic effects and adaptation in allopolyploid orchids (Dactylorhiza: Orchidaceae). Molecular Biology and Evolution 27: 2465-2473. *Reviewed as “of special interest” by Richards 2011, Curr Opin Plant Biol 14: 204

Górniak M, Paun O, Chase MW. 2010. Phylogenetic relationships within Orchidaceae based on nuclear low copy protein coding gene, Xdh: Congruence with organellar and nuclear ribosomal DNA results. Molecular Phylogenetics and Evolution 56: 784-795.

Chase MW, Paun O, Fay MF. 2010. Hybridization and speciation in angiosperms: a role for pollinator shifts? BMC Biology 8: 45.

Winkler M, Tribsch A, Paun O, Englisch T, IntrabioDiv Consortium, Schönswetter P. 2010. Pleistocene distribution range shifts were accompanied by breeding system divergence within Hornungia alpina (Brassicaceae) in the Alps. Molecular Phylogenetics and Evolution 54: 571-582.

Paun O, Luna JA, Fay MF, Bateman RM, Chase MW (2010) Genomic responses drive adaptation in allotetraploid species of Dactylorhiza (Orchidaceae; Orchidinae). Pg. 169-192, in: Seberg O, Petersen G, Barfod AS, Davis JI (eds.), Diversity, Phylogeny, and Evolution in the Monocotyledons. Århus, Denmark: Aarhus Univ. Press. DOI: 10.13140/2.1.1272.9123