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 mcaf004 Link
G.Q Wang, 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
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. Link 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. Target Enrichment Data Uncovers Rapid Radiation, Whole Genome Duplication, and Extensive Hybridization in Slipper Orchid Genus Cypripedium L. Annals of Botany 134(7): 1229–1250. Link 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 Gene 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
Buono D., G. Kadereit, A Liston, S. Zarre, D.F. Morales-Briones. Building a robust backbone for Astragalus (Fabaceae) using a clade-specific target enrichment bait set. bioRxiv 2024.11.19.624276 Link
Buono D., G. Kadereit, D.F. Morales-Briones. Astragalean819: An Astragalean clade-specific bait set to resolve Astragalus phylogenetic relationships.
Kiedaisch T., G. Kadereit, A. Žerdoner Čalasan, D.F. Morales-Briones. Advancing phylogenomics in Amaranthaceae sensu stricto: Development and application of a new nuclear target enrichment bait set.
Žerdoner Čalasan A., D.F. Morales-Briones, G. Kadereit, K. Shepherd. Evolutionary history of Australian samphires (Salicornieae, Amaranthaceae).
Yang, L., X. Ma, Z. Yang, Q. Wang, H. Wang, Y. Yang, D.F. Morales-Briones, B. Zhong. Phylogenomic analyses reveal deep reticulation and incomplete lineage sorting obscuring the phylogeny of Mesangiospermae.
Zheng W.F.*, C.H. Huang*, D.F. Morales-Briones*, K.H Wei, Y. Hu, X.M. Wei, X.X. Wang, W.D. Zhang, J.L. Wang, D.Y. Chen, G.Y. Xie, X. Hemu, N.H Tan, L.Y. Chen, C. Dai. Has colchicine induced chromosome doubling in Colchicaceae and the genes involved in colchicine biosynthesis? An evolutionary perspective. *equal contribution.
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
Zhu W., L. Chen, X.M. van der Burgt, P.M. Haba, D. Garaeva, P. Lau, D.F. Morales-Briones, MC. Veranso-Libalah. Rediscovery and Phylogenomic Placement of Feliciadamia stenocarpa (Feliciadamieae, Melastomataceae): Assessing Gene Tree Discordance.
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.
Sun, K., E. Lyakh, D.F. Morales-Briones, F. Weitkämper, S. Werth. Insights into the molecular phylogeny of the Eurasian montane riparian genus Myricaria based on Angiosperms353 phylogenomic data
Zhang, L.*, D.F. Morales-Briones*, J. Sun, X. Guo, P. Guo, K. Zhang, H. Wang, Y. Wang, X. Wang, F. Shang. Nuclear phylogeny of Malus with increased sampling provides new insights into biogeography and character evolution. *equal contribution.