Zheng, W.F.*, D.F. Morales-Briones*, Z.J Zhang*, J.Y. Tian, Y. Hu, X.M. Wei, W.D Zhang, N. Zhang, D.Y. Chen, X. Hemu, C.H. Huang, L.Y. Chen. 2026. Phylogenomics provides insights into the phylogeny of Liliales and the evolution of colchicine biosynthesis genes. Molecular Phylogenetics and Evolution 16 : 108506 *equal contribution. Link Data
Chen, L.Y., J.L. Wang, Y. Cao, H. Chen, T. Yuan, W.D. Zhang, D.F. Morales-Briones, S.Y. Zhao, N.H. Tan, C.H. Huang, T. Wan, Q.F. Wang. 2026. The convergent genomic dynamism for aquatic adaptation in vascular plants. Current Biology 36: 1–13 Link Data
Žerdoner Čalasan A., D.F. Morales-Briones, G. Kadereit, K. Shepherd. 2026. Evolutionary history of Australian samphires (Salicornieae, Amaranthaceae). Annals of Botany 137(1): 247–266 Link
Buono D., G. Kadereit, A Liston, S. Zarre, D.F. Morales-Briones. 2025. Building a robust backbone for Astragalus (Fabaceae) using a clade-specific target enrichment bait set. American Journal of Botany. Open Access Data
Buono D., G. Kadereit, D.F. Morales-Briones. 2025. Astragalean819: An Astragalean clade-specific bait set to resolve Astragalus phylogenetic relationships. Applications in Plant Sciences 13(5): e70024 Open Access Data
Zhang, L.*, D.F. Morales-Briones*, J. Sun, X. Guo, P. Guo, K. Zhang, H. Wang, Y. Wang, X. Wang, F. Shang. 2025. Nuclear phylogeny of Malus with increased sampling provides new insights into biogeography and character evolution. BMC Plant Biology 25, 1267. *equal contribution Open Access
Kiedaisch T., G. Kadereit, A. Žerdoner Čalasan, D.F. Morales-Briones. 2025. Advancing phylogenomics in Amaranthaceae sensu stricto: Development and application of a new nuclear target enrichment bait set. Applications in Plant Sciences 13(5): e70019 Open Access Data
Huang, X., L. Yang, X. Ma, Z. Yang, Q. Wang, H. Wang, Y. Yang, D.F. Morales-Briones, B. Zhong. 2025. Phylogenomic discordance is mainly driven by pervasive ancient hybridization and incomplete lineage sorting during the early divergence of major angiosperm lineages. Plant Communications 6(11): 101529. Open Access Data
Rodewald S.E., D.P. Klein, R. Shtein, G.F. Smith, E. Joyce, D.F. Morales-Briones, S. Bernhard, R. Letsara, H. Mertes, P. Huehn, G. Kadereit. 2025. A new phylogenetic framework for the genus Kalanchoe (Crassulaceae) and implications for infrageneric classification. Annals of Botany 135(7): 1311–1328 Open Access
Wang, G.Q., D.F. Morales‐Briones, J.B. Landis, H.X. Wang, H.F. Wang. 2025. Progress in molecular systematics of Caprifoliaceae. Taxon 74(1): 5–12. Link
Zhu W., L. Chen, X.M. van der Burgt, P.M. Haba, D. Garaeva, P. Lau, D.F. Morales-Briones, MC. Veranso-Libalah. 2025. Rediscovery and phylogenomic placement of Feliciadamia stenocarpa (Feliciadamieae, Melastomataceae): Assessing gene tree discordance. Botanical Journal of the Linnean Society boaf047. Link
Wang, X.X.*, C.H. Huang*, D.F. Morales-Briones*, N. Zhang, Y. Hu, P.G. Zhao, X.M. Wei, K. Wei, X.Y. Hemu, N. Tan, Q.F. Wang, Chen, L.Y. Phylotranscriptomics reveals the phylogeny of Asparagales and the evolution of allium flavor biosynthesis. 2024. Nature Communications 15, 9663. *equal contribution. Open Access Data
Yang, X.L., Q.H. Sun, D.F. Morales-Briones, J.B. Landis, D.J. Chen, H.X. Wang, J. Wen, H.F. Wang. 2024. New insights into intergeneric relationships of Lonicera (Caprifoliaceae) revealed by nuclear ribosomal DNA cistron data and plastid phylogenomics. Journal of Systematics and Evolution 62 (3): 333–357. Link
Wang, H.X., D.F. Morales-Briones, J.B. Landis, J. Wen, H.F. Wang. 2024. Biogeographic analysis based on phylogenomic data supports that multiple ancient dispersals facilitated the eastern Asia - North America - Mexico disjunction in the subfamily Linnaeoideae (Caprifoliaceae). Journal of Systematics and Evolution 62 (5): 1025–1036. Link
Lagou, L.J., G. Kadereit, D.F. Morales-Briones. 2024. Phylogenomic analysis of target enrichment and transcriptome data uncovers rapid radiation and extensive hybridization in the slipper orchid genus Cypripedium. Annals of Botany 134(7): 1229–1250. Open Access Data
Morales-Briones, D.F., G. Kadereit. 2023. Exploring the possible role of hybridization in the evolution of photosynthetic pathways in Flaveria (Asteraceae), the prime model of C4 photosynthesis evolution. Bulletin of the Society of Systematic Biologists 2(3):1–16. Open Access Data
Zhang, L.*, D.F. Morales-Briones*, H. Wang, C.H. Huang, F. Shang, Y. Wang, H. Ma. 2023. Nuclear phylogenomics reveals rapid diversification and morphological innovations in the apple tribe (Maleae, Rosaceae). New Phytologist 240(5):2102–2120. *equal contribution. Link Data
Sun, Q.H., D.F. Morales-Briones, H.X. Wang, J.B. Landis, J. Wen, H.F. Wang. 2023. Target sequence capture data shed light on the deeper evolutionary relationship on the subgenus Chamaecerasus of Lonicera (Caprifoliaceae). Molecular Phylogenetics and Evolution 184:107808. Link
Ma, X., D. Ru, D.F. Morales-Briones, F. Mei, J. Wu, J. Liu, S. Wu. 2023. Genome sequence and salinity adaptation of the desert shrub Nitraria sibirica (Nitrariaceae, Sapindales). DNA Research 30(3):dsad011. Open Access Data
Morales-Briones, D.F., B. Gehrke, C.H. Huang, A. Liston, H. Ma, H.E. Marx, D.C. Tank, Y. Yang. 2022. Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae). Systematic Biology 71(1):190–207. Open Access Data
Sun, Q.H., D.F. Morales-Briones, H.X. Wang, J.B. Landis, J. Wen, H.F. Wang. 2022. Phylogenomic analyses of the East Asian endemic Abelia (Caprifoliaceae) shed insights into the temporal and spatial diversification history with widespread hybridization. Annals of Botany 129(2):201–216. Link Data
Ke, X.R., D.F. Morales-Briones, H.X. Wang, Q.H., Sun, J.B. Landis, J. Wen, H.F. Wang. 2022. Nuclear and plastid phylogenomic analyses provide insights into the reticulate evolution, species delimitation, and biogeography of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae). Journal of Systematics and Evolution 60(6):1331–1343. Link Data
Tefarikis, D.T., D.F. Morales-Briones, Y. Yang, G. Edwards, G. Kadereit. 2022. On the hybrid origin of the C2 Salsola divaricata agg. (Amaranthaceae) from C3 and C4 parental lineages. New Phytologist 234(5):1876–1890. Open Access Data
Chen, L.Y.*, B. Liu*, D.F. Morales-Briones*, M.L. Moody, F. Liu, G.W. Hu, C.H. Huang, J.M. Chen, Q.F. Wang. 2022. Phylogenomic analyses of Alismatales shed light into adaptations to aquatic environments. Molecular Biology and Evolution 39(5):msac079. *equal contribution. Open Access Data
Morales-Briones, D.F., N. Lin, E.Y. Huang, D.L. Grossenbacher, J.M, Sobel, C.D. Gilmore, D.C. Tank, Y. Yang. 2022. Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades. American Journal of Botany 109(6):1035–1046. Open Access Data
Morales-Briones, D.F., G. Kadereit, D.T. Tefarikis, M.J. Moore, S.A. Smith, S.F. Brockington, A.Timoneda, W.C. Yim, J.C. Cushman, Y. Yang. 2021. Disentangling sources of tene tree discordance in phylogenomic data sets: Testing ancient hybridizations in Amaranthaceae s.l. Systematic Biology 70(2): 219–235. Open Access Data
Wang, H.X.*, D.F. Morales-Briones*, M.J. Moore, J. Wen, H.F. Wang. 2021. A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily. Journal of Systematics and Evolution 59(5):897–914. *equal contribution. Link Data
Morales-Briones, D.F., T. Arias, V.S. Di Stilio, D.C Tank. 2019. Chloroplast primers for clade-wide phylogenetic studies of Thalictrum. Applications in Plant Sciences 7(10): e11294. Open Access Data
Chen, L-Y., D.F. Morales-Briones, C.N. Passow, Y. Yang. 2019. Performance of gene expression analyses using de novo assembled transcripts in polyploid species. Bioinformatics 35(21): 4314–4320. Link Data
Morales-Briones, D.F., K. Romoleroux, D.C. Tank. 2019. Three new species of Lachemilla (Rosaceae) from South America. PhytoKeys 127: 93–119. Open Access Data
Morales-Briones, D.F., D.C Tank. 2019. Extensive allopolyploidy in the neotropical genus Lachemilla (Rosaceae) revealed by PCR‐based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics. American Journal of Botany 106(3): 415–437. Link Data
Morales-Briones, D.F., A. Liston, D.C. Tank. 2018. Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae). New Phytologist 218(4): 1668–1684. Link Data
Morales-Briones, D.F., K. Romoleroux, F. Kolář, D.C. Tank. 2018. Phylogeny and evolution of the neotropical radiation of Lachemilla (Rosaceae): Uncovering a history of reticulate evolution and implications for infrageneric classification. Systematic Botany 43(1): 17–34. Link Data. 2020 American Society of Plant Taxonomist Grady L. and Barbara D. Webster Plant Systematics Publication Award
Blischak, P.D., M. Latvis, D.F. Morales-Briones, J.C. Johnson, V.S. Di Stilio, A.D Wolfe, D.C. Tank. 2018. Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons. Applications in Plant Sciences 6(6): e1156. Open Access Data
Latvis, M., S.M. Mortimer, D.F. Morales-Briones, S. Torpey, S. Uribe-Convers, S.J. Jacobs, S. Mathews, D.C Tank. 2017. Targeting the most variable parts of the plastome using genomic data: primers for Castilleja and their utility across Orobanchaceae. Applications in Plant Sciences 5(9): 1700020. Open Access
Morales-Briones, D.F. 2016. Lachemilla mexiquense (Rosaceae), a new species from Mexico. PhytoKeys 62: 25–32. Open Access
Romoleroux, K., D.F. Morales-Briones. 2012. Lachemilla jaramilloi and L. talamanquensis spp. nov. (Rosaceae) from Ecuador and Costa Rica. Nordic Journal of Botany 30(6): 732–736. Link
Liu, P.F., W.L. Yang, Y.X. He, G.Q. Wang, J.B. Landis, D.F. Morales-Briones, J.J. Ringelberg, Q. Li, L.K, Su, S.Y. Zou, J. Wen, H.F. Wang. Phylogenomic and ecological analyses of orthologous nuclear genes reveal the spatiotemporal evolution and biogeographic history of Lonicera.
Kadereit, G., A. Höwener, D. Garaeva, D.F. Morales-Briones. Phylogenomics and systematics of African Sesuvium (Aizoaceae). bioRxiv 2025.08.11.669638 Link
Kadereit, J.W., K. MacLeod, A.M. Putra, G. Kadereit, D.F. Morales-Briones. Ongoing climate-driven peripatric speciation with habitat divergence in Moehringia sect. Moehringia in the European Alps.
Romoleroux, K., Rodríguez E., C.J., D.F. Morales-Briones. Lachemilla santurbanensis (Rosaceae), a new species from Colombia.
Zuo, S.Y., Q.H. Sun, D.F. Morales-Briones, J.B. Landis, H.X. Wang, H.Y Li, H.Y. Dong, J. Wen, H.F. Wang. Target enrichment phylogenomics and biogeographic analyses unravel rapid radiation and reticulate evolution between Hainan-South China mainland -Vietnam in Section Nintooa (Lonicera, Caprifoliaceae). bioRxiv 2024.08.01.605766 Link
Sun, K., E. Lyakh, D.F. Morales-Briones, F. Weitkämper, S. Werth. Towards an understanding of the taxonomy of Eurasian montane riparian genus Myricaria (Tamaricaceae) through Angiosperms353 herbariomics.
Chen, L., MC. Veranso-Libalah, J.P. Quakenbush, F.A. Michenlangeli, D.F. Morales-Briones, G. Kadereit. Comprehensive and Sustainable Utilization of Genomic Resources: Integrating Target Enrichment, Genome Skimming, RNA-Seq, and Deep Genome Skimming for Improved Phylogenetic Resolution in Sonerileae (Melastomataceae).
Joyce, E.M., M. Iskander, R. Vilalta-Pérez, D. Velázquez, A.N. Muellner-Riehl, D.M. Crayn, A. Höwener, D.F. Morales-Briones, C.M. Pannell. The complex evolution of the mahogany family (Meliaceae), and a revised tribal classification compatible with its reticulate history.