Publications by Type
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Peer-Reviewed Publication Types
, Urs Eggli, Reto Nyffeler, Isabel Larridon, Catherine McGinnie, Niroshini Epitawalage, Olivier Maurin, Félix Forest, & William J. Baker. (2025). Phylogenomics and classification of Cactaceae based on hundreds of nuclear genes. Plant Systematics and Evolution, 311(5). https://doi.org/10.1007/s00606-025-01948-z
Baan, Jochem, Holloway‐Phillips, Meisha, Nelson, Daniel B., , & Kahmen, Ansgar. (2025). Phylogenetic and biochemical drivers of plant species variation in organic compound hydrogen stable isotopes: novel mechanistic constraints [Journal-article]. New Phytologist, 246(1), 113–130. https://doi.org/10.1111/nph.20430
Carruthers, Tom, Moerland, Michelangelo S., Ebersbach, Jana, Favre, Adrien, Folk, Ryan A., Hawkins, Julie A., Muellner-Riehl, Alexandra N., Röser, Martin, Soltis, Douglas E., Tkach, Natalia, Baker, William J., , & Eiserhardt, Wolf L. (2024). Repeated upslope biome shifts in Saxifraga during late-Cenozoic climate cooling. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-45289-w
Bätscher, L., & de Vos, J. M. (2024). Avoiding impacts of phylogenetic tip-state-errors on dispersal and extirpation rates in alpine plant biogeography. Journal of Biogeography, 51(6), 1104–1116. https://doi.org/10.1111/jbi.14811
Zuntini, Alexandre R., Carruthers, Tom, Maurin, Olivier, Bailey, Paul C., Leempoel, Kevin, Brewer, Grace E., Epitawalage, Niroshini, Françoso, Elaine, Gallego-Paramo, Berta, McGinnie, Catherine, Negrão, Raquel, Roy, Shyamali R., Simpson, Lalita, Toledo Romero, Eduardo, Barber, Vanessa M. A., Botigué, Laura, Clarkson, James J., Cowan, Robyn S., Dodsworth, Steven, et al. (2024). Phylogenomics and the rise of the angiosperms. Nature, 629(8013), 843–850. https://doi.org/10.1038/s41586-024-07324-0
Mora-Carrera, E., Stubbs, R.L., Potente, G., Yousefi, N., Keller, B., , Szövényi, P., & Conti, E. (2024). Genomic analyses elucidate S-locus evolution in response to intra-specific losses of distyly in Primula vulgaris. Ecology and Evolution, 14(3). https://doi.org/10.1002/ece3.10940
Augustijnen, Hannah, Bätscher, Livio, Cesanek, Martin, Chkhartishvili, Tinatin, Dincă, Vlad, Iankoshvili, Giorgi, Ogawa, Kota, Vila, Roger, Klopfstein, Seraina, , & Lucek, Kay. (2024). A macroevolutionary role for chromosomal fusion and fission in Erebia butterflies. Science Advances, 10(16). https://doi.org/10.1126/sciadv.adl0989
Dos Santos,Patrícia, Oliveira, M. Alexandra, Karger,Dirk N, Lucek,Kay, Branquinho,Cristina, & . (2024). Niche evolution during allopatric and sympatric diversification of Aeonium (Crassulaceae) on the Canary Islands [Journal-article]. Evolutionary Journal of the Linnean Society, 3(1). https://doi.org/10.1093/evolinnean/kzae012
Pillon,Yohan, Crayn,D., Streiff, Serafin J.R., & (2024). A suprageneric classification of Oxalidales. Swainsona, 38, 8. https://know.ourplants.org/wp-content/uploads/2024/09/JABG38P153_Pillon.pdf
Liu, Jin-Mei, , Körner, Christian, & Yang, Yang. (2023). Phylogeny and phenotypic adjustments drive functional traits in Rhododendron across elevations in its diversity hot-spot in W-China [Journal-article]. Alpine Botany, 133(2), 69–84. https://doi.org/10.1007/s00035-023-00294-5
Messerschmid, T. F. E., Abrahamczyk, S., Bañares-Baudet, Á., Brilhante, M. A., Eggli, U., Hühn, P., Kadereit, J. W., dos Santos, P., de Vos, J. M., & Kadereit, G. (2023). Inter- and intra-island speciation and their morphological and ecological correlates in Aeonium (Crassulaceae), a species-rich Macaronesian radiation. Annals of Botany, 131(4), 697–721. https://doi.org/10.1093/aob/mcad033
Joyce, E. M., Appelhans, M. S., Buerki, S., Cheek, M., de Vos, J. M., Pirani, J. R., Zuntini, A. R., Bachelier, J. B., Bayly, M. J., Callmander, M. W., Devecchi, M. F., Pell, S. K., Groppo, M., Lowry, P. P., Mitchell, J., Siniscalchi, C. M., Munzinger, J., Orel, H. K., Pannell, C. M., et al. (2023). Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication. Frontiers in Plant Science, 14. https://doi.org/10.3389/fpls.2023.1063174
Carruthers, Tom, Sun, Miao, Baker, William J., Smith, Stephen A., , & Eiserhardt, Wolf L. (2022). The Implications of Incongruence between Gene Tree and Species Tree Topologies for Divergence Time Estimation. Systematic Biology, 71(5), 1124–1146. https://doi.org/10.1093/sysbio/syac012
dos Santos, Patricia, Brilhante, Miguel Angelo, Messerschmid, Thibaud F. E., Serrano, Helena Cristina, Kadereit, Gudrun, Branquinho, Cristina, & (2022). Plant growth forms dictate adaptations to the local climate. Frontiers in Plant Science, 13, 1023595. https://doi.org/10.3389/fpls.2022.1023595
Stöcklin, Jürg, & (2022). Carl Friedrich Hagenbach (1771-1849) und seine “Basler Flora” im historischen Kontext. Bauhinia, 28, 87–102. https://botges.ch/file/con/113/87_102_BAUHINIA_28_2022_WEB_stoecklin_de_vos.pdf
Lucek, Kay, Bouaouina, Selim, Jospin, Amanda, Grill, Andrea, & (2021). Prevalence and relationship of endosymbiotic Wolbachia in the butterfly genus Erebia. BMC ecology and evolution, 21(1), 95. https://doi.org/10.1186/s12862-021-01822-9
Messerschmid, Thibaud F. E., Wehling, Judith, Bobon, Nadine, Kahmen, Ansgar, Klak, Cornelia, Los, Jessica A., Nelson, Daniel B., dos Santos, Patricia, , & Kadereit, Gudrun. (2021). Carbon isotope composition of plant photosynthetic tissues reflects a Crassulacean Acid Metabolism (CAM) continuum in the majority of CAM lineages. Perspectives in Plant Ecology Evolution and Systematics, 51, ARTN 125619. https://doi.org/10.1016/j.ppees.2021.125619
Mora-Carrera, Emiliano, Stubbs, Rebecca L., Keller, Barbara, Léveillé-Bourret, Étienne, , Szövényi, Peter, & Conti, Elena. (2021). Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species. Molecular Ecology, 27. https://doi.org/10.1111/mec.16270
Pitman, Nigel C. A., Suwa, Tomomi, Ulloa Ulloa, Carmen, Miller, James, Solomon, James, Philipp, Juliana, Vriesendorp, Corine F., Derby Lewis, Abigail, Perk, Sinem, Bonnet, Pierre, Joly, Alexis, Tobler, Mathias W., Best, Jason H., Janovec, John P., Nixon, Kevin C., Thiers, Barbara M., Tulig, Melissa, Gilbert, Edward E., Campostrini Forzza, Rafaela, et al. (2021). Identifying gaps in the photographic record of the vascular plant flora of the Americas. Nature Plants, 7(8), 1010–1014. https://doi.org/10.1038/s41477-021-00974-2
, Augustijnen, Hannah, Baetscher, Livio, & Lucek, Kay. (2020). Speciation through chromosomal fusion and fission in Lepidoptera. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1806), 20190539. https://doi.org/10.1098/rstb.2019.0539
Pegoraro, Luca, , Cozzolino, Salvatore, & Scopece, Giovanni. (2019). Shift in flowering time allows diploid and autotetraploid Anacamptis pyramidalis (Orchidaceae) to coexist by reducing competition for pollinators. Botanical Journal of the Linnean Society, 191(2), 274–284. https://doi.org/10.1093/botlinnean/boz043
de Vos, J. M., Keller, B., Zhang, L.-R., Nowak, M. D., & Conti, E. (2018). Mixed mating in homostylous species: Genetic and experimental evidence from an alpine plant with variable herkogamy, primula halleri. International Journal of Plant Sciences, 179(2), 87–99. https://doi.org/10.1086/695527
Goolsby, Eric W., Moore, Abigail J., Hancock, Lillian P., , & Edwards, Erika J. (2018). Molecular evolution of key metabolic genes during transitions to C-4 and CAM photosynthesis. American Journal of Botany, 105(3), 602–613. https://doi.org/10.1002/ajb2.1051
Hancock, Lillian P., Obbens, Frank, Moore, Abigail J., Thiele, Kevin, , West, Judy, Holtum, Joseph A. M., & Edwards, Erika J. (2018). Phylogeny, evolution, and biogeographic history of Calandrinia (Montiaceae). American Journal of Botany, 105(6), 1021–1034. https://doi.org/10.1002/ajb2.1110
Moore, Abigail J., , Hancock, Lillian P., Goolsby, Eric, & Edwards, Erika J. (2018). Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo Clade (Caryophyllales). Systematic Biology, 67(3), 367–383. https://doi.org/10.1093/sysbio/syx078
Thomson, Scott A., Pyle, Richard L., Ahyong, Shane T., Alonso-Zarazaga, Miguel, Ammirati, Joe, Araya, Juan Francisco, Ascher, John S., Audisio, Tracy Lynn, Azevedo-Santos, Valter M., Bailly, Nicolas, Baker, William J., Balke, Michael, Barclay, Maxwell V. L., Barrett, Russell L., Benine, Ricardo C., Bickerstaff, James R. M., Bouchard, Patrice, Bour, Roger, Bourgoin, Thierry, et al. (2018). Taxonomy based on science is necessary for global conservation. Plos Biology, 16(3), e2005075. https://doi.org/10.1371/journal.pbio.2005075
Pérez-Escobar, O. A., Chomicki, G., Condamine, F. L., De Vos, J. M., Martins, A. C., Smidt, E. C., Klitgård, B., Gerlach, G., & Heinrichs, J. (2017). Multiple Geographical Origins of Environmental Sex Determination enhanced the diversification of Darwin’s Favourite Orchids. Scientific Reports, 7(1). https://doi.org/10.1038/s41598-017-12300-y
Keller, B., de Vos, J. M., Schmidt-Lebuhn, A. N., Thomson, J. D., & Conti, E. (2016). Both morph- and species-dependent asymmetries affect reproductive barriers between heterostylous species. Ecology and Evolution, 6(17), 6223–6244. https://doi.org/10.1002/ece3.2293
Edwards, E. J., De Vos, J. M., & Donoghue, M. J. (2015). Doubtful pathways to cold tolerance in plants. Nature, 521(7552), E5–E6. https://doi.org/10.1038/nature14393
De Vos, J. M., Joppa, L. N., Gittleman, J. L., Stephens, P. R., & Pimm, S. L. (2015). Estimating the normal background rate of species extinction. Conservation Biology, 29(2), 452–462. https://doi.org/10.1111/cobi.12380
Haller, B. C., De Vos, J. M., Keller, B., Hendry, A. P., & Conti, E. (2014). A tale of two morphs: Modeling pollen transfer, magic traits, and reproductive isolation in parapatry. PLoS ONE, 9(9). https://doi.org/10.1371/journal.pone.0106512
de Vos, J. M., Hughes, C. E., Schneeweiss, G. M., Moore, B. R., & Conti, E. (2014). Heterostyly accelerates diversification via reduced extinction in primroses. Proceedings of the Royal Society B: Biological Sciences, 281(1784). https://doi.org/10.1098/rspb.2014.0075
Abrahamczyk, S., de Vos, J. M., Sedivy, C., Gottleuber, P., & Kessler, M. (2014). A humped latitudinal phylogenetic diversity pattern of orchid bees (Hymenoptera: Apidae: Euglossini) in western Amazonia: Assessing the influence of climate and geologic history. Ecography, 37(5), 500–508. https://doi.org/10.1111/j.1600-0587.2013.00417.x
de Vos, J. M., Wüest, R. O., & Conti, E. (2014). Small and ugly? Phylogenetic analyses of the “selfing syndrome” reveal complex evolutionary fates of monomorphic primrose flowers. Evolution, 68(4), 1042–1057. https://doi.org/10.1111/evo.12331
Koenen, E.J.M., , Atchison, G.W., Simon, M.F., Schrire, B.D., de Souza, E.R., de Queiroz, L.P., & Hughes, C.E. (2013). Exploring the tempo of species diversification in legumes. South African Journal of Botany, 89, 19–30. https://doi.org/10.1016/j.sajb.2013.07.005
Schirrmeister, B. E., De Vos, J. M., Antonelli, A., & Bagheri, H. C. (2013). Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event. Proceedings of the National Academy of Sciences of the United States of America, 110(5), 1791–1796. https://doi.org/10.1073/pnas.1209927110
Keller, B., De Vos, J. M., & Conti, E. (2012). Decrease of sexual organ reciprocity between heterostylous primrose species, with possible functional and evolutionary implications. Annals of Botany, 110(6), 1233–1244. https://doi.org/10.1093/aob/mcs199
Schmidt-Lebuhn, A. N., de Vos, J. M., Keller, B., & Conti, E. (2012). Phylogenetic analysis of Primula section Primula reveals rampant non-monophyly among morphologically distinct species. Molecular Phylogenetics and Evolution, 65(1), 23–34. https://doi.org/10.1016/j.ympev.2012.05.015
de Vos, J. M., Keller, B., Isham, S. T., Kelso, S., & Conti, E. (2012). Reproductive implications of herkogamy in homostylous primroses: Variation during anthesis and reproductive assurance in alpine environments. Functional Ecology, 26(4), 854–865. https://doi.org/10.1111/j.1365-2435.2012.02016.x
, & Breteler, F.J. (2009). A revision of the african genera paropsiopsis and smeathmannia (passifloraceae paropsieae), including a new species of paropsiopsis from cameroon. Edinburgh Journal of Botany, 66(1), 27–49. https://doi.org/10.1017/S0960428609005174
Other Publications
De Vos, J., Woudstra, Y., Leitch, I., & Hidalgo, O. (2024). Assessing male reproductive investment in Papaveraceae using flow cytometry reveals lineage-specific trajectories to pollen-to-ovule ratio reduction [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.08.23.609364
de Vos, J. M., Streiff, S. J. R., Bachelier, J. B., Epitawalage, N., Maurin, O., Forest, F., & Baker, W. J. (2024). Phylogenomics of the pantropical Connaraceae: revised infrafamilial classification and the evolution of heterostyly [Journal-article]. Plant Systematics and Evolution, 310(4). https://doi.org/10.1007/s00606-024-01909-y
, & Stöcklin, Jürg. (2023). A second Renaissance of herbarium-based research, almost five centuries after their invention [Journal-article]. BAUHINIA – Zeitschrift Der Basler Botanischen Gesellschaft, 29, 3–6. https://doi.org/10.12685/bauhinia.1345
Grall, Aurélie, Guggisberg, Alessia, Nyffeler, Reto, & (2023). Towards digitizing the botanical legacy of Fritz and Paul Sarasin in Basel and Zurich [Journal-article]. BAUHINIA – Zeitschrift Der Basler Botanischen Gesellschaft, 29. https://doi.org/10.12685/bauhinia.1363
Kahmen, Ansgar, Nelson, Daniel B., , & Basler, David. (2023). Stable isotopes from herbarium specimens reveal physiological responses of plants to global change [Journal-article]. BAUHINIA – Zeitschrift Der Basler Botanischen Gesellschaft, 29, 121–122. https://doi.org/10.12685/bauhinia.1364
Stöcklin, Jürg, & (2023). Caspar Bauhin’s life (1560–1624) – Academic career, achievements as a botanist and his herbarium [Journal-article]. BAUHINIA – Zeitschrift Der Basler Botanischen Gesellschaft, 29, 7–16. https://doi.org/10.12685/bauhinia.1346
Augustijnen, Hannah, Bätscher, Livio, Cesanek, Martin, Chkhartishvili, Tinatin, Dincă, Vlad, Iankoshvili, Giorgi, Ogawa, Kota, Vila, Roger, Klopfstein, Seraina, , & Lucek, Kay. (2023). A macroevolutionary role for chromosomal fusion and fission in Erebia butterflies [Posted-content]. https://doi.org/10.1101/2023.01.16.524200
Moore, A. J., de Vos, J. M., Hancock, L. P., Goolsby, E., & Edwards, E. J. (2017). Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo (Caryophyllales) [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/145995