2026
Chen, L., M.C. Veranso-Libalah, J.P. Quakenbush, F.A. Michelangeli, D.F. Morales-Briones, G. Kadereit. 2026. Integrative utilization of genomic resources for improved phylogenetic resolution in Sonerileae (Melastomataceae). American Journal of Botany 113: e70216. https://doi.org/10.1002/ajb2.70216
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): 80–92. https://doi.org/10.1016/j.cub.2025.11.026
Kadereit, G., A. Höwener, D. Garaeva, D.F. Morales-Briones. 2026. Phylogenomics and systematics of African Sesuvium (Aizoaceae). Taxon 75(3): e70160. https://doi.org/10.1002/tax.70160
Liu, P.F., Y.X. He, Y.X. Di, W.L. Yang, 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. 2026. The uplift of the Qinghai–Xizang Plateau and global climate cooling triggered spatiotemporal evolution of Lonicera (Caprifoliaceae). Journal of Systematics and Evolution. https://doi.org/10.1111/jse.70061
Romoleroux, K., C.J. Rodríguez E., D.F. Morales-Briones. 2026. Lachemilla santurbanensis (Rosaceae), a new species from Colombia. Brittonia. https://doi.org/10.1007/s12228-026-09887-w
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. https://doi.org/10.1093/aob/mcaf232
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 216: 108506. https://doi.org/10.1016/j.ympev.2025.108506 *equal contribution.
Zhu, W., L. Chen, X.M. van der Burgt, P.M. Haba, D. Garaeva, P. Lau, D.F. Morales-Briones, M.C. Veranso-Libalah. 2026. Rediscovery and phylogenomic flacement of Feliciadamia stenocarpa (Feliciadamieae, Melastomataceae): assessing gene tree discordance. Botanical Journal of the Linnean Society 210(20): 127–142. https://doi.org/10.1093/botlinnean/boaf047
2025
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. https://doi.org/10.1002/aps3.70024
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 112(8): e70084. http://doi.org/10.1002/ajb2.70084
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. https://doi.org/10.1016/j.xplc.2025.101529
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. http://doi.org/10.1002/aps3.70019
Rodewald, S.E., D.P. Klein, R. Shtein, G.F. Smith, E. Joyce, D.F. Morales-Briones, S. Bernhard, R. Letsara, H. Mertes, P. Hühn, G. Kadereit. 2025. A new phylogenetic framework for the genus Kalanchoe (Crassulaceae) and implications for infrageneric classification. Annals of Botany 135(7): 1311–1328. https://doi.org/10.1093/aob/mcaf004
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. https://doi.org/10.1002/tax.13279
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. https://doi.org/10.1186/s12870-025-07311-1 *equal contribution.
2024
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 L. Annals of Botany 134(7): 1229–1250. https://doi.org/10.1093/aob/mcae161
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. https://doi.org/10.1111/jse.13036
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, L.Y. Chen. 2024. Phylotranscriptomics reveals the phylogeny of Asparagales and the evolution of allium flavor biosynthesis. Nature Communications 15: 9663. https://doi.org/10.1038/s41467-024-53943-6 *equal contribution.
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. https://doi.org/10.1111/jse.13014
2023
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. https://doi.org/10.1093/dnares/dsad011
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. https://doi.org/10.18061/bssb.v2i3.8992
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 of subgenus Chamaecerasus of Lonicera (Caprifoliaceae). Molecular Phylogenetics and Evolution 184: 107808. https://doi.org/10.1016/j.ympev.2023.107808
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. https://doi.org/10.1111/nph.19175 *equal contribution.
2022
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 shed light into the adaptation to aquatic environments in Alismatales. Molecular Biology and Evolution 39(5): msac079. https://doi.org/10.1093/molbev/msac079 *equal contribution.
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. https://doi.org/10.1111/jse.12815
Morales-Briones, D.F., B. Gehrke, C.H. Huang, A. Liston, M. Hong, 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. https://doi.org/10.1093/sysbio/syab032
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. https://doi.org/10.1002/ajb2.1860
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. https://doi.org/10.1093/aob/mcab139
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. https://doi.org/10.1111/nph.18098
2021
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. https://doi.org/10.1093/sysbio/syaa066
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. https://doi.org/10.1111/jse.12745 *equal contribution.
2019
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. https://doi.org/10.1093/bioinformatics/btz620
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. https://doi.org/10.1002/aps3.11294
Morales-Briones, D.F., D.C. Tank. 2019. Extensive allopolyploidy in the neotropical genus Lachemilla (Rosaceae) revealed by incomplete concerted evolution of the nuclear ribosomal DNA cistron and plastid phylogenomics. American Journal of Botany 106(3): 415–437. https://doi.org/10.1002/ajb2.1253
Morales-Briones, D.F., K. Romoleroux, D.C. Tank. 2019. Three new species of Lachemilla (Rosaceae) from South America. PhytoKeys 127: 93–119. https://doi.org/10.3897/phytokeys.127.36324
2018
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. https://doi.org/10.1002/aps3.1156
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. https://doi.org/10.1111/nph.15099
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. https://doi.org/10.1600/036364418X696897
2017
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. https://doi.org/10.3732/apps.1700020
2016
Morales-Briones, D.F. 2016. Lachemilla mexiquense (Rosaceae), a new species from Mexico. PhytoKeys 62: 25–32. https://doi.org/10.3897/phytokeys.62.7953
2012
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. https://doi.org/10.1111/j.1756-1051.2011.01413.x
Accepted (in press)