Publications from the lab, including access links.

2026

Chen, M., Xu, Z.-C., Liu, J.-X., Feng, X., Ye, X.-Y., Zhou, M.-Y.*, Li, D.-Z.*, 2026. Phylogenomics and taxonomic revision of the Himalayan endemic Thamnocalamus (Poaceae, Bambusoideae) from China based on syntenic nuclear genes and morphology. Journal of Systematics Evolution 64(1): 106-124. https://doi.org/10.1111/jse.70044

Feng, X, Xu, Z.-C., Liu, J.-X., Chen, M., Sokoloff, D.D., Fomichev, C.I., Zhou, M.-Y.*, Li, D.-Z.*, 2026. Phylogeny of Vietnamosasa (Poaceae, Bambusoideae) based on syntenic nuclear genes with description of a new species. PhytoKeys 273: 71-91. https://doi.org/10.3897/phytokeys.273.182677

Qin, S.-Y., Ree, R.H.*, Zuo, Z.-Y., Yu, C.-C., Xu, S.-X., Rong, J., Ma, P.-F.*, Li, D.-Z.*, 2026. Waves of range dynamics and gene flow characterize the biogeographic history of Litsea elongata, a dominant tree in East Asian evergreen broadleaved forests. Plants, People, Planet 1-15. https://nph.onlinelibrary.wiley.com/doi/10.1002/ppp3.70204

2025

Chen, M., Chen, Y.-J., Zhou, M.-Y., Xu, Z.-C., Zhang, Y.-X., Zhang, E.-X., Liu, J.-X.*, Li, D.-Z.*, 2025. Syntenic nuclear genes and morphology reveal unusual new climbing bamboo species of Melocalamus in the Gaoligong Mountains. Taxon 74(6): 1404-1420. https://doi.org/10.1002/tax.13385

Chen, Y.-J., Chen, M., Zhou, M.-Y., Xu, Z.-C., Zhang, Y.-X., Liu, J.-X.*, Li, D.-Z.*, 2025. Further investigation of Melocalamus (Poaceae, Bambusoideae) in China based on Skmer analysis and morphology. PhytoKeys 259: 177-198. https://doi.org/10.3897/phytokeys.259.151683

Deng, L.-J., Li, Y.-L., Wang, F.-Y., Sun, X.-Q., Milne, R.I., Liu, J.*, Wu, Z.-Y.*, 2025. Comparative metabolomics of two nettle species unveils distinct high-altitude adaptation mechanisms on the Tibetan Plateau. BMC Plant Biology 25: 640. https://doi.org/10.1186/s12870-025-06666-9

Fu, X.-G.#, Liu, J.#, Milne, R.I., Monro, A.K., Liu, S.-Y., Tian, Q., Stull, G.W., Kipkoech, A., Yi, T.-S.*, Li, D.-Z.*, Wu, Z.-Y.*, 2025. A robust phylogenomic framework supports a revised intrafamilial classification of Urticaceae. Plant Diversity https://doi.org/10.1016/j.pld.2025.12.003.

Khan, R.#, Wu, Z.-Y.#, Sun, Z.-Y., Mambo, W.W., Kipkoech, A., Ahmad, M., Luo, Y.-H., Li, Z.H., Li, D.Z., Liu, J., 2025. Heterogeneous landscape shaped the phylogeographical pattern of Debregeasia orientalis (Urticaceae) in southwestern China. Botanical Journal of the Linnean Society boaf094. https://doi.org/10.1093/botlinnean/boaf094

Kipkoech, A., Li, K., Milne, R.I., Oyebanji, O.O., Wambulwa, M.C., Fu, X.-G., Wakhungu, D.A., Wu, Z.-Y.*, Liu, J.*, 2025. An integrative approach clarifies species delimitation and biogeographic history of Debregeasia (Urticaceae). Plant Diversity 47(2): 229-243. https://doi.org/10.1016/j.pld.2024.11.004

Zhao, Y., Milne, R., Liu, J., Li, Z.-P., Fu, X.-G., Li, K., Kipkoech, A., Wu, Z.-Y.*, 2025. An integrated study of ramie (Boehmeria nivea), and its wild, cultivated, and feral forms. Ecology and Evolution 15(3): e71126. https://doi.org/10.1002/ece3.71126

Zuo, Z.-Y., Rouhan, G., Dong, S.-Y., Liu, H.-M., Du, X.-Y., Zhang, L.-B. *, Lu, J.-M.*, 2025. A revised classification of Dryopteridaceae based on plastome phylogenomics and morphological evidence, with the description of a new genus, Pseudarachniodes. Plant Diversity 47(1): 34-52. https://doi.org/10.1016/j.pld.2024.07.010

2024

Liu, J.-X., Guo, C., Ma, P.-F., Zhou, M.-Y., Luo, Y.-H., Zhu, G.-F., Xu, Z.-C., Richard, I.M., Maria, S.V., Li, D.-Z.*, 2024. The origin and morphological character evolution of the paleotropical woody bamboos. Journal of Integrative Plant Biology 66: 2242-2261. https://doi.org/10.1111/jipb.13751

Liu Y.-L. #, Gao S.-Y. #, Jin G. #, Zhou M.-Y. #, Gao Q.-J. #, Guo C., Yang Y.- Z., Niu L.-Z., Xia E., Guo Z.-H., Ma P.-F.*, Li D.-Z.*, 2024. BambooBase: A comprehensive database of bamboo omics and systematics, Molecular Plant 17(5): 682-685.https://doi.org/10.1016/j.molp.2024.02.017

Ma, P.-F.#, Liu, Y.-L. #, Guo, C. #, Jin, G. #, Guo, Z.-H. #, Mao, L., Yang, Y.-Z., Niu, L.-Z., Wang, Y.-J., Clark, L.G., Kellogg, E.A., Xu, Z.-C., Ye, X.-Y., Liu, J.-X., Zhou, M.-Y., Luo, Y., Yang, Y., Soltis, D.E., Bennetzen, J.L., Soltis, P.S., Li, D.-Z.*, 2024. Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance. Nature Genetics 56(6): 710-720. https://doi.org/10.1038/s41588-024-01683-0

Qin, S.-Y., Zuo, Z.-Y., Xu S.-X., Liu, J., Yang, F.-M., Luo, Y.-H., Ye, J.-W., Zhao, Y., Rong, J., Liu, B., Ma, P.-F.*, Li, D.-Z.*, 2024. Anthropogenic disturbance driving population decline of a dominant tree in East Asia evergreen broadleaved forests over the last 11,000 years. Conservation Biology 38(1): e14180. https://doi.org/10.1111/cobi.14180

Wu H., Li D.-Z., Ma P.-F., 2024. Unprecedented variation pattern of plastid genomes and the potential role in adaptive evolution in Poales. BMC Biology 22(1): 97. https://doi.org/10.1186/s12915-024-01890-5

Wu, Z.-Y., Chapman, M.A., Liu, J.*, Milne, R.I., Zhao, Y., Luo, Y.-H., Zhu, G.-F., Cadotte, M.W., Luan, M.-B.*, Fan, P.-Z., Monro A.K., Li, Z.-P., Corlett, R.T., Li, D.-Z.*, 2024. Genomic variation, environmental adaptation, and feralization in ramie, an ancient fiber crop. Plant Communications 5(8): 100942. https://doi.org/10.1016/j.xplc.2024.100942

Zhao, Y., Milne, R., Li, Z.-P., Kipkoech, A., Wu, Z.-Y.*, 2024. Boehmeria nivea var. strigosa (Urticaceae), a new variety from southwest China. Guihaia 44(9): 1617-1624. http://doi.org/10.11931/guihaia.gxzw202311013

2023

Liu, J.-X., Xu, Z.-C., Zhang, Y.-X., Zhou, M.-Y., Li, D.-Z. *, 2023. The identity of Dinochloa species and enumeration of Melocalamus (Poaceae: Bambusoideae) in China. Plant Diversity 45(2): 133-146. https://doi.org/10.1016/j.pld.2022.07.001

Qin, S.-Y., Chen, K., Zhang, W.-J., Xiang, X.-G., Zuo, Z.-Y., Guo, C., Yao, Z., Li, L.-F., Wang, Y.-G., Song, Z.-P., Ji, Y., Yang, X.-Q., Zhang, J., Jin, W.-T., Wen, Q., Zhao, S.-Z., Chen, J.-K., Li, D.-Z., Rong, J., 2023. Phylogenomic insights into the reticulate evolution of Camellia sect. Paracamellia Sealy (Theaceae). Journal of Systematics and Evolution 62(1): 38-54. https://doi.org/10.1111/jse.12948

Qin, S.-Y., Zuo, Z.-Y., Guo, C., Du, X.-Y., Liu, S.-Y., Yu, X.-Q., Xiang, X.-G., Rong, J., Liu, B., Liu, Z.-F., Ma, P.-F.*, Li, D.-Z.*, 2023. Phylogenomic insights into the origin and evolutionary history of evergreen broadleaved forests in East Asia under Cenozoic climate change. Molecular Ecology 32(11): 2850-2868. https://doi.org/10.1111/mec.16904

Rakotonasolo, R.A., Dransfield, S., Haevermans, T., Ralimanana, H., Vorontsova, M.S., Zhou, M.-Y.*, Li, D.-Z.*, 2023. New insights into intergeneric relationships of Hickeliinae (Poaceae: Bambusoideae) revealed by complete plastid genomes. Plant Diversity 45(2): 125-132. https://doi.org/10.1016/j.pld.2022.06.001

Wu, Z.-Y., Milne, R.I., Liu, J., Nathan, R.*, Corlett, R.T., Li, D.-Z.*, 2023. The establishment of plants following long-distance dispersal. Trends in Ecology & Evolution 38(3): 289-300. https://doi.org/10.1016/j.tree.2022.11.003

2022

Du, X.-Y., Kuo, L.-Y., Zuo, Z.-Y., Li, D.-Z. *, Lu, J.-M. *, 2022. Structural variation of plastomes provides key insight into the deep phylogeny of ferns. Frontiers in Plant Science 13: 862772. https://doi.org/10.3389/fpls.2022.862772

Lu, J.-M.# *, Du, X.-Y.#, Kuo, L.-Y., Ebihara, A., Perrie, L.R., Zuo, Z.-Y., Shang, H., Chang, Y.-H., Li, D.-Z. *, 2022. Plastome phylogenomic analysis reveals evolutionary divergences of Polypodiales suborder Dennstaedtiineae. BMC Plant Biology 22: 511. https://doi.org/10.1186/s12870-022-03886-1

Ogoma, C.A., Liu, J., Stull, G.W., Wambulwa, M.C., Oyebanji, O., Milne, R.I., Monro, A.K., Zhao, Y., Li, D.-Z.*, Wu, Z.-Y.*, 2022. Deep insights into the plastome evolution and phylogenetic relationships of the tribe Urticeae (family Urticaceae). Frontiers in Plant Science 13: 870949. https://doi.org/10.3389/fpls.2022.870949

Wu H., Yang J.-B., Liu J.-X., Li D.-Z., Ma P.-F.*, 2022. Organelle phylogenomics and extensive conflicting phylogenetic signals in the monocot order Poales. Frontiers in Plant Science 12: 824672. https://doi.org/10.3389/fpls.2021.824672

Wu, Z.-Y., Milne, R.I., Liu, J., Slik, F., Yu, Y., Luo, Y.-H., Monro, A.K., Wang, W.-T., Wang, H., Kessler, P.J.A., Cadotte, M.W., Nathan, R., Li, D.-Z., 2022. Phylogenomics and evolutionary history of Oreocnide (Urticaceae) shed light on recent geological and climatic events in SE Asia. Molecular Phylogenetics and Evolution 175: 107555. https://doi.org/10.1016/j.ympev.2022.107555

Zhou, M.-Y.#, Liu, J.-X.#, Ma, P.-F., Yang, J.-B., Li, D.-Z.*, 2022. Plastid phylogenomics shed light on intergeneric relationships and spatiotemporal evolutionary history of Melocanninae (Poaceae: Bambusoideae). Journal of Sytematics Evolution 60(3): 640-652. https://doi.org/10.1111/jse.12843

Zuo, Z.-Y., Zhao, T., Du, X.-Y., Xiong, Y., Lu, J.-M. *, Li, D.-Z. *, 2022. A revision of Dryopteris sect. Diclisodon (Dryopteridaceae) based on morphological and molecular evidence with description of a new species. Plant Diversity 44(2): 181-190. https://doi.org/10.1016/j.pld.2021.09.005

2021

Du, X.-Y.#, Lu, J.-M.# *, Zhang, L.-B., Wen, J., Kuo, L.-Y., Mynssen, M.C., Schneider, H. *, Li, D.-Z.*, 2021. Simultaneous diversification of Polypodiales and angiosperms in the Mesozoic. Cladistics 37: 518-539. https://doi.org/10.1111/cla.12457

Jin G. #, Ma P.-F. #, Wu X.-P., Gu L.-F., Long M.-Y.*, Zhang C.-J*., Li D.-Z.*, 2021. New genes interacted with recent whole-genome duplicates in the fast stem growth of bamboos, Molecular Biology and Evolution 38(12): 5752-5768. https://doi.org/10.1093/molbev/msab288

Jin G., Zhou Y.-L., Yang H., Hu Y.-T., Shi Y., Li L., Siddique A., Liu C.-N., Zhu A.-D., Zhang C.-J.*, Li D.-Z.*, 2021. Genetic innovations: Transposable element recruitment and de novo formation lead to the birth of orphan genes in the rice genome, Journal of Systematics and Evolution 59(2): 341-351. https://doi.org/10.1111/jse.12548

Ma P.-F.#, Liu Y.-L.#, Jin G.-H., Liu J.-X., Wu H., He J., Guo Z.-H., Li D.-Z.*, 2021. The Pharus latifolius genome bridges the gap of early grass evolution. The Plant Cell 33(4): 846-864. https://doi.org/10.1093/plcell/koab015

Wu H., Ma P.-F., Li H.-T., Hu G.-X., Li D.-Z.*, 2021. Comparative plastomic analysis and insights into the phylogeny of Salvia (Lamiaceae). Plant Diversity 43(1): 15-26. https://doi.org/10.1016/j.pld.2020.07.004

Xu, Z.-C., Liu, J.-X., Li, D.-Z.*, 2021. Gigantochloa glabrata (Poaceae, Bambusoideae), a new bamboo species from Yunnan, China. PhytoKeys 171: 37-45. https://doi.org/10.3897/phytokeys.171.59562

Before 2021

Liu, J.-X., Zhou, M.-Y., Yang, G.-Q., Zhang, Y.-X., Ma, P.-F., Guo, C., Vorontsova, M.S., Li, D.-Z.*, 2020. ddRAD analyses reveal a credible phylogenetic relationship of the four main genera of Bambusa- Dendrocalamus-Gigantochloa complex (Poaceae: Bambusoideae). Molecular Phylogenetics and Evolution 106758. https://doi.org/10.1016/j.ympev.2020.106758

Wang, R.-N., Milne, R.I., Du, X.-Y., Liu, J.*, Wu, Z.-Y.*, 2020. Characteristics and mutational hotspots of plastomes in Debregeasia (Urticaceae). Frontiers in Genetics 11: 729. https://doi.org/10.3389/fgene.2020.00729

Guo, Z.-H.#, Ma, P.-F.#, Yang, G.-Q.#, Hu, J.-Y.#, Liu, Y.-L.#, Xia, E.-H., Zhong, M.-C., Zhao, L., Sun, G.-L., Xu, Y.-X., Zhao, Y.-J., Zhang, Y.-C., Zhang, Y.-X., Zhang, X.-M., Zhou, M.-Y., Guo, Y., Guo, C., Liu, J.-X., Ye, X.-Y., Chen, Y.-M., Yang, Y., Han, B., Lin, C.-S.*, Lu, Y.*, Li, D.-Z.*, 2019. Genome sequences provide insights into the reticulate origin and unique traits of woody bamboos. Molecular Plant 12(10): 1353-1365. https://doi.org/10.1016/j.molp.2019.05.009

Wu, Z.-Y., Liu, J., Provan, J., Wang, H., Chen, C.J., Cadotte, M.W., Luo, Y.H., Amorim, B.S., Li, D.Z.*, Milne, R.I., 2018. Testing Darwin's transoceanic dispersal hypothesis for the inland nettle family (Urticaceae). Ecology Letters 21(10): 1515-1529. https://doi.org/10.1111/ele.13132

Zhou, M., Liu, J., Liang, Y., Li, D.*, 2017. Distribution of Holttumochloa (Poaceae: Bambusoideae) in China with description of a new species revealed by morphological and molecular evidence. Plant Diversity 39(3): 135-139. https://doi.org/10.1016/j.pld.2017.05.001

Zhou, M.-Y., Zhang, Y.-X., Haeverman, T., Li, D.-Z.*, 2017. Towards a complete generic level plastid phylogeny of the paleotropical woody bamboos (Poaceae: Bambusoideae). Taxon 66(3): 539-553.

秦声远, 戎俊*, 张文驹, 陈家宽, 2017. 油茶栽培历史与长江流域油茶遗传资源. 生物多样性 26(4): 384-395. https://doi.org/10.17520/biods.2017254

Wu, Z.-Y., Milne, R.I., Chen, C.-J., Liu, J., Wang, H., Li, D.-Z.*, 2015. Ancestral state reconstruction reveals rampant homoplasy of diagnostic morphological characters in Urticaceae, conflicting with current classification schemes. PLOS ONE 10(11): e0141821. https://doi.org/10.1371/journal.pone.0141821

Wu, Z.-Y., Monro, A.K., Milne, R.I., Wang, H., Yi, T.-S., Liu, J., Li, D.-Z.*, 2013. Molecular phylogeny of the nettle family (Urticaceae) inferred from multiple loci of three genomes and extensive generic sampling. Molecular Phylogenetics and Evolution 69(3): 814-827. https://doi.org/10.1016/j.ympev.2013.06.022

Wu, Z.-Y., Li, D.-Z., Wang, H., Wang, W.-T.*, 2013. Two new species and one new variety of Elatostema (Urticaceae) from China. Annales Botanici Fennici 50(1-2): 75-78. https://doi.org/10.5735/085.050.0113

Wu, Z.-Y., Li, D.-Z., Wang, H., Wang, W.-T.*, 2012. One new series with its only new species of Elatostema (Urticaceae) from southeast Yunnan, China. Plant Diversity and Resources 34(2): 151-154.

Wu, Z.-Y., Wang, H., Li, D.-Z.*, 2012. Supplementary description of inflorescences of three species in Elatostema (Urticaceae). Plant Diversity and Resources 34(1): 13.

Wu, Z.-Y., Wang, W.-T., Wang, H., Li, D.-Z., 2011. Two new species of Elatostema (Urticaceae) from southeast Yunnan, China. PhytoKeys (7): 57-62. https://doi.org/10.3897/phytokeys.7.2022

Wu, Z.-Y., Wang, W.-T., Wang, H., Li, D.-Z.*, 2011. Elatostema densistriolatum sp. nov., E. latistipulum sp. nov. and E. cyrtandrifolium var. hirsutum var. nov. (Urticaceae) from southwest China. Nordic Journal of Botany 29(2): 227-232. https://doi.org/10.1111/j.1756-1051.2011.01076.x