Balao F, Medrano M, Bazaga P, Paun O, Alonso C. 2024. Long-term methylome changes after experimental seed demethylation and their interaction with recurrent water stress in Erodium cicutarium (Geraniaceae). Plant Biology 26: 1199-1212. Pre-print: bioRxiv 2023.01.19.524693.

Cauz-Santos LA, Samuel RM, Metschina D, Christenhusz MJM, Dixon KW, Coran JG, Paun O, Chase MW. 2023. Recent speciation and adaptation to aridity in the ecologically diverse Pilbara region of Australia enabled the native tobaccos (Nicotiana; Solanaceae) to colonize all Australian deserts. Molecular Ecology 33: e17498. Pre-print: bioRxiv 2024.06.12.598428.

Emelianova K, Hawranek A-S, Eriksson M, Wolfe TM, Paun O. 2024. Ecological divergence is marked by specific plastic gene expression and distinct rhizosphere among sibling allopolyploid marsh orchids (Dactylorhiza). bioRxiv 2024.04.24.590886.

Groot Crego C, Hess J, Yardeni G, de la Harpe M, Beclin F, Cauz-Santos LA, Saadain S, Temsch EM, Weiss-Schneeweiss H, Barfuss MHJ, Till W, Heyduk K, Lexer C, Paun O*, Leroy T*. 2024. CAM evolution is associated with gene family expansion in an explosive bromeliad radiation. The Plant Cell 36: 4109-4131. Pre-print: bioRxiv 2023.02.01.526631.

Groot Crego C, Saadain S, de la Harpe M, Hess J, Barfuss MHJ, Till W, Lexer C, Paun O. 2024. Closely related facultative and constitutive CAM phenotypes show little transcriptomic overlap in the subgenus Tillandsia. bioRxiv 2024.05.09.593278 .

Larsson D, Šarhanová P, Paun O, Schneeweiss GM. 2024. Recent origin of a range-restricted species with subsequent introgression in its widespread congener in the Phyteuma spicatum group (Campanulaceae). Molecular Ecology in press.

Martin-Blazquez R, Medrano M, Bazaga P, Balao F, Paun O, Alonso C. 2024. Decoupled genetic and epigenetic variation at local scale in an endemic and a widespread Erodium (Geraniaceae) species. bioRxiv 2024.04.18.589719.

Rúrik I, Melichárková A, Gbúrová Štubová E, Kochjarová J, Kučera, J, Paun O, Vďačný P, Slovák M. 2024. Homoplastic versus xenoplastic evolution: exploring the emergence of key intrinsic and extrinsic traits in the montane genus Soldanella (Primulaceae). The Plant Journal 118: 753-765.

Groot Crego C. 2024. Molecular sources of variation and their role in the adaptive radiation of Tillandsia, Bromeliaceae. PhD Dissertation, University of Vienna.

Brück FL. 2024. Population genomics of a selected clade within the New Caledonian Diosypros radiation. MSc Thesis, University of Vienna.

Moser L. 2024. Transcriptomic drivers of plant adaptation to the desert in Nicotiana sect. Suaveolentes (Solanaceae). MSc Thesis, University of Vienna.

Oberauer F. 2024. Epigenetic responses to cadmium pollution in Lumbricus terrestris. MSc Thesis, University of Vienna.

Zechmeister J. 2024. Whole genome re-sequencing unravels complex speciation processes within the RRc clade of the radiated Diospyros in New Caledonia. MSc Thesis, University of Vienna.

Chase MW, Samuel RM, Leitch AR, Guignard MS, Conran JG, Nollet F, Fletcher P, Jakob A, Cauz-Santos LA, Vignolle G, Dodsworth S, Christenhusz MJM, Buril MT, Paun O. 2023. Down, then up: non-parallel genome size changes and a descending chromosome series in a recent radiation of Australian allotetraploid plant species in Nicotiana section Suaveolentes (Solanaceae). Annals of Botany 131: 123-142.

Kirschner P, Seifert B, Kröll J, Steppe Consortium, Schlick-Steiner BC, Steiner FM. 2023. Phylogenomic inference and demographic model selection suggest peripatric separation of the cryptic steppe ant species Plagiolepis pyrenaica stat. rev. Molecular Ecology 32: 1149-1168.

Slovak M, Melichárková A, Štubňová EG, Kučera J, Mandáková T, Smyčka J, Lavergne S, Passalacqua NP, Vďačný P, Paun O. 2023. Pervasive introgression during rapid diversification of the European mountain genus Soldanella (L.) (Primulaceae). Systematic Biology 72: 491-502.

Shang H, Field DL, Paun O, Rendon-Anaya M, Hess J, Vogl C, Liu J, Ingvarsson PK, Lexer C, Leroy T. 2023. Drivers of genomic landscapes of differentiation across Populus divergence continuum. Molecular Ecology 32: 4348-4361. Pre-print: bioRxiv 2021.08.26.457771.

Szukala A, Bertel C, Frajman B, Schönswetter P, Paun O. 2023. Parallel adaptation to lower altitudes is associated with enhanced plasticity in Heliosperma pusillum (Caryophyllaceae). The Plant Journal 115: 1619-1632. Pre-print: bioRxiv 2022.05.28.493825.

Szukala A, Lovegrove-Walsh J, Luqman H, Fior S, Wolfe TM, Frajman B, Schoenswetter P, Paun O. 2023. Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae). Molecular Ecology 32: 1832-1847. Pre-print: bioRxiv 2021.07.05.451094. *Research Highlight: Battlay 2023 MolEcol 32: 1811-1813.

Tonin R, Klees S, Gültas M, Gerdol R, Paun O, Schmitt A, Trucchi E, Wellstein C. 2023. Ice holes microrefugia harbor genetically and functionally distinct populations of Vaccinium vitis-idaea (Ericaceae). Scientific Reports 13: 13055.

Wolfe T, Balao F, Trucchi E, Bachmann G, Gu W, Baar J, Hedren M, Weckwerth W, Leitch AR, Paun O. 2023. Recurrent allopolyploidization events diversify eco-physiological traits in marsh orchids. Molecular Ecology 32: 4777-4790. Pre-print: bioRxiv 2021.08.28.458039.

Xue Z, Chiapella JO, Paun O, Volkova P, Peintinger M, Wasowicz P, Tikhomirov N, Grigoryan M, Barfuss MHJ, Greimler J. 2023. Phylogeographic patterns of Deschampsia cespitosa (Poaceae) in Europe inferred from genomic data. Botanical Journal of the Linnean Society 201: 341-360.

Yardeni G, Barfuss MHJ, Till W, Thornton MR, Groot Crego C, Lexer C, Leroy T*, Paun O*. 2023. The explosive radiation of the Neotropical Tillandsia subgenus Tillandsia (Bromeliaceae) has been facilitated by pervasive hybridization. bioRxiv 2023.11.16.567341.

Ahmad M. 2023. Population genetics of selected Boraginaceae and their transcriptomic changes upon phytohormonal and microbial interaction. PhD Dissertation, University of Vienna.

Bilke A. 2023. The role of smRNA regulation during recurrent ecotype formation in Heliosperma pusillum (Caryophyllaceae). MSc Thesis, University of Vienna.

Briceno Huayta EM. 2023. Transposable element dynamics during the adaptive radiation of Diospyros from New Caledonia. MSc Thesis, University of Vienna.

Gruber KR. 2023. Comparative analysis of transposable elements in beet (Beta vulgaris). MSc Thesis, University of Vienna.

Ahmad M, Alonso AV, Koletti AE, Rodić N, Rödel P, Assimopoulou AN, Paun O, Declerck S, Schneider C, Molin EM. 2022. Dynamics of alkannin/shikonin biosynthesis in response to jasmonate and salicylic acid in Lithospermum officinale. Scientific Reports 12(1): 17093.

Ahmad M, Alonso AV, Koletti AE, Assimopoulou AN, Declerck S, Schneider C, Molin EM. 2022. Transcriptional dynamics of Chitinophaga sp. strain R-73072-mediated alkanin/shikonin biosynthesis in Lithospermum officinale. Frontiers in Microbiology fmicb.2022.978021.

Cauz-Santos LA, Dodsworth S, Samuel R, Christenhusz MJM, Patel D, Shittu T, Jakob A, Paun O, Chase MW. 2022. Genomic insights into recent species divergence in Nicotiana benthamiana and natural variation in Rdr1 gene controlling viral susceptibility. The Plant Journal 111: 7-18. Pre-print: bioRxiv 2022.02.01.478068 . *Research Highlight: Pierroz 2022 PlantJ 111: 5-6.

Dellinger A, Paun O, Baar J, Temsch E, Fernández-Fernández D, Schönenberger J. 2022. Population structure in Neotropical plants: integrating pollination biology, topography and climatic niches. Molecular Ecology 31: 2264-2280.

Eriksson MC, Mandakova T, McCann J, Temsch EM, Chase MW, Hedren M, Weiss-Schneeweiss H, Paun O. 2022. Repeat dynamics across timescales: a perspective from sibling allotetraploid marsh orchids (Dactylorhiza majalis s.l). Molecular Biology and Evolution 39: msac167.

Kirschner P, Perez MP, Zaveska E, Sanmartin I, Marquer L, Schlick-Steiner BC, Nadir Alvarez, Steppe Consortium, Steiner FM, Schönswetter P. 2022. Congruent evolutionary responses of European steppe biota to late Quaternary climate change. Nature Communication 13: 1921.

Yardeni G, Viruel J, Paris M, Hess J, Groot Crego C, de La Harpe M, Rivera N, Barfuss MHJ, Till W, Guzman-Jacob V, Kroemer T, Lexer C*, Paun O*, Leroy T*. 2022. Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations. Molecular Ecology Resources 22: 927-945. Pre-print: bioRxiv 2021.2005.2020.444989.

Eriksson M. 2022. Rinse and repeat: genome dynamics following repeated allopolyploidzation in marsh orchids (Dactylorhiza). PhD Dissertation, University of Vienna.

Szukala A. 2022. Parallel and adaptive processes during ecotype formation in Heliosperma pusillum. PhD Dissertation, University of Vienna.

Yardeni G. 2022. Phylogenetic relationships and the evolutionary history of Tillandsia, a species-rich genus of Bromeliaceae. PhD Dissertation, University of Vienna.

Thornton MR. 2022. Ecological and evolutionary consequences of smRNA activity after allopolyploidization in marsh orchids (Dactylorhiza majalis s.l.). MSc Thesis, University of Vienna.

Ahmad M, Leroy T, Krigas N, Temsch EM, Weiss-Schneeweiss H, Lexer C, Sehr EM*, Paun O*. 2021. Spatial and ecological drivers of genetic structure in Greek populations of Alkanna tinctoria (Boraginaceae), a polyploid medicinal herb. Frontiers in Plant Sciences 12: 706574. Pre-print: bioRxiv 2021.05.06.442843.

Chase MW, Christenhusz MJM, Palsson RL, Fay MF, Dodsworth S, Conran JG, Cauz-Santos LA, Nollet F, Samuel MR, Paun O. 2021. Species delimitation in Nicotiana sect. Suaveolentes (Solanaceae): reciprocal illumination leads to recognition of many new species. Curti's Botanical Magazine 38: 266-286.

Xue Z, Greimler J, Paun O, Ford K, Barfuss MHJ, Chiapella JO. 2021. The evolutionary history of New Zealand Deschampsia is marked by long-distance dispersal, endemism, and hybridization. Biology 10: 1001.

Shang H. 2021. Genomics of the speciation continuum in Eurasian Populus species. PhD dissertation, University of Vienna.

Hawranek AS. 2021. The impact of recurrent origins and gene flow on the genetic structure of allopolyploid marsh orchids (Dactylorhiza, Orchidaceae). MSc Thesis, University of Vienna.

Jakob A. 2021. Phylogenomics of Nicotiana section Suaveolentes (Solanaceae), with a focus on N. benthamiana. MSc Thesis, University of Vienna.

Janda M. 2021. Evolution of the Primula auricula complex (Primulaceae) in the Eastern Alps. MSc Thesis, University of Vienna.

Balao F, Lorenzo MT, Sanchez-Robles JM, Paun O, Garcia Castano JL, Terrab A. 2020. Early diversification and permeable species boundaries in the Mediterranean firs. Annals of Botany 125: 495–507.

Brandrud MK, Baar J, Lorenzo MT, Athanasiadis A, Bateman RM, Chase MW, Hedrén M*, Paun O*. 2020. Phylogenomic relationships of diploids and the origins of allotetraploids in Dactylorhiza. Systematic Biology 69: 91-109.

Eriksson M, Szukala A, Tian B, Paun O. 2020. Current research frontiers in Plant Epigenetics: an introduction to a Virtual Issue. New Phytologist 226: 285-288.

Kirschner P, Záveská E, Gamisch A, Hilpold A, Trucchi E, Paun O , Sanmartin I, Schlick-Steiner B, Frajman B, Arthofer W, Steppe Consortium, Steinere F, Schönswetter P. 2020. Long-term isolation of European steppe outposts boosts the biome's conservation value. Nature Communications 11: 1968.

Brandrud MK, Paun O, Lorenz R, Baar J, Hedrén M. 2019. Restriction-site associated DNA sequencing supports a sister group relationship of Nigritella and Gymnadenia (Orchidaceae). Molecular Phylogenetics and Evolution 136: 21-28.

Heckenhauer J, Paun O, Chase MW, Ashton PS, Abu Salim K, Samuel R. 2019. Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes. Annals of Botany 123: 857-865.

Paun O, Verhoeven K, Richards C. 2019. Opportunities and limitations of reduced representation bisulfite sequencing in plant ecological epigenomics. New Phytologist 221: 738-742.

Samuel R, Dunagii S, Turner B, Munzinger J, Paun O, Barfuss MHJ, Chase MW. 2019. Systematics and evolution of the Old World Ebenaceae, a review with emphasis on the large genus Diospyros and its radiation in New Caledonia. Botanical Journal of the Linnenan Society 189: 99-114.

Sramko G, Paun O, Brandrud MK, Laczko L, Molnar VA, BatemanRM. 2019. Iterative allogamy-autogamy transitions drive actual and incipient speciation during the ongoing evolutionary radiation within the orchid genus Epipactis (Orchidaceae). Annals of Botany 124: 481-497.

Szukala A, Korotkova N, Gruenstaeudl M, Sennikov AN, Lazkov GA, Litvinskaya SA, Gabrielian E, Borsch T, von Raab-Straube E. 2019. Phylogeny of the Eurasian genus Jurinea (Asteraceae: Cardueae): Support for a monophyletic genus concept and a first hypothesis on overall species relationships. Taxon 68: 112-131.

Zaveska E, Maylandt C, Paun O, Bertel C, Frajman B, The STEPPE Consortium, Schönswetter P. 2019. Multiple auto- and allopolyploidisations marked the Pleistocene history of the widespread Eurasian steppe plant Astragalus onobrychiy (Fabaceae). Molecular Phylogenetics and Evolution 139: 106572.

Brandrud MK. 2019. The use of phylogenomic tools to investigate diploid and polyploid evolution in Dactylorhiza and other orchids. PhD dissertation, University of Vienna.

Wolfe TM. 2019. Genomic interactions and their eco-physiological implications for the evolution of allopolyploid marsh ochids. PhD dissertation, University of Vienna.

Fani A. 2019. Gene regulation by small RNAs at different altitudes in Heliosperma pusillum (Caryophyllaceae). MSc Thesis, University of Vienna.

van Loo M. 2019. North American Douglas-fir (Pseudotsuga menziesii) in Europe. Diploma Thesis, University of Vienna.

Balao F, Paun O, Conchita A. 2018. Uncovering the contribution of epigenetics to plant phenotypic variation in Mediterranean ecosystems. Plant Biology 20: 38–49.

Bateman R, Szramko G, Paun O. 2018. Integrating RAD-seq with morphological cladistic analysis clarifies evolutionary relationships among species groups of bee orchids. Annals of Botany 121: 85–105.

Cristofari R, Liu X, Bonadonna F, Cherel Y, Pistorius P, Le Maho Y, Raybaud V, Stenseth NC, Le Bohec C, Trucchi E. 2018. Climate-driven range shifts of the king penguin in a fragmented ecosystem. Nature Climate Change 8: 245-251.

Heckenhauer J, Samuel R, Aston PS, Salim KA, Paun O. 2018. Phylogenomics resolves evolutionary relationships and provides insights into floral evolution in the tribe Shoreeae. Molecular Phylogenetics and Evolution 127: 1-13.

Hedrén M, Nordström Olofsson S, Paun O. 2018. Orchid colonization: multiple parallel dispersal events and mosaic genetic structure in Dactylorhiza majalis ssp. lapponica on the Baltic island of Gotland. Annals of Botany 122: 1019-1032.

Staedler YM, Kreisberger T, Manafzadeh S, Chartier M, Handschuh S, Pamperl S, Sontag S, Paun O, Schönenberger J. 2018. Novel computed tomography-based tools reliably quantify plant reproductive investment. Journal of Experimental Botany 69: 525–535.

Viruel J, Forest F, Paun O, Chase MW, Devey D, Sousa Couto R, Segarra-Moragues JG, Catalan P, Wilkin P. 2018. A nuclear Xdh analysis of yams (Dioscorea, Dioscoreaceae) congruent with plastid trees reveals a new Neotropical lineage. Botanical Journal of the Linnean Society 187: 232-246.

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.

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 20: 1576–1590.

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 NC, Trathan PN, Whittington JD, Zanetti E, Zitterbart DP, Le Bohec C, Trucchi E. 2016. Full circumpolar migration ensures evolutionary unity in the Emperor penguin. Nature Communications 7: 11842.

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) long-lasting 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.

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.

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].

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.

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.

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