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RRC ID 89539
Author Li J, Jia S, Wu D, Tao W, Ruhsam M, Mao K.
Title Phylogenomics reveals the reticulate evolution and biogeographic history of New World cypresses, Hesperocyparis (Cupressaceae).
Journal Cladistics
Abstract Deciphering the evolutionary history of lineages shaped by rapid radiation, hybridization and incomplete lineage sorting (ILS) remains a major challenge in phylogenetics. Previous studies of Hesperocyparis (Cupressaceae) relied on limited markers and yielded inconsistent results. Here, we applied target enrichment sequencing across multiple individuals per species to generate comprehensive genomic datasets, including 2628 nuclear single-copy genes and nearly complete plastid genomes. We reconstructed robust phylogenies, assessed gene flow and reticulation and inferred the spatiotemporal and ecological niche evolution of Hesperocyparis. Our analyses resolved the genus into three clades-Macrocarpa, Arizonica and the basal H. bakeri-and strongly supported its monophyly within the HCX clade (Hesperocyparis, Callitropsis, Xanthocyparis). However, significant cytonuclear discordance was observed, reflecting the influence of ancient hybridization and ILS. Molecular dating placed the origin of Hesperocyparis in the late Eocene (~39.2 Ma), with most diversification occurring during the Oligocene and Miocene. Ancestral range and state reconstructions support a northwestern North American origin, followed by complex southward and eastward dispersal patterns likely driven by climatic shifts towards increased aridity. This study highlights the utility of genome-scale data in resolving complex evolutionary relationships and underscores hybridization, climate-driven dispersal and ecological adaptation as key drivers of diversification in Hesperocyparis.
Volume 42(2)
Pages 109-127
Published 2025-12-22
DOI 10.1111/cla.70021
Description J-OBIS data were referenced. BiodiC-J data were referenced.
PMID 41427622
MeSH Biological Evolution* Evolution, Molecular Gene Flow Genome, Plant Genome, Plastid Phylogeny* Phylogeography
Resource
GBIF Spermatophyte collection of Himeji City Science Museum Fish collection of the Kagoshima University Museum Vascular Plant Collection of Natural History Museum and Institute, Chiba Herbarium Specimens of Museum of Nature and Human Activities, Hyogo Pref., Japan Spermatophyta collection of Museum of Natural and Environmental History, Shizuoka Ibaraki Nature Museum, Vascular Plants collection Vascular plant collection of The University Museum, The University of Tokyo Plant specimens of Toyota City Nature Sanctuary Vascular plant specimens of National Museum of Nature and Science (TNS) Plant Specimens of Kurashiki Museum of Natural History Herbarium Specimens of Tokushima Prefectural Museum, Japan Plant specimens of Tochigi Prefectural Museum Herbarium of Kitakyushu Museum of Natural History and Human History Fish Collection of Natural History Museum and Institute, Chiba Herbarium Specimens of The Kagoshima University Museum (KAG) Plant Specimens of Lake Biwa Museum Spermatophyta specimens of Iwate Prefectural Museum Japanese Woody Plants Asia-Pacific Dataset Vascular Plants Collection of Sagamihara City Museum Plant specimens in the Museum of Nature and Human Activities, Hyogo Vascular plant specimens of the herbarium of the Tohoku University (TUS) Plant specimens deposited in Osaka Museum of Natural History, Japan Vascular Plant Specimens of Kochi Prefectural Makino Botanical Garden Botanical collection of Gifu Prefecture Museum Plant Specimens of The Shimane Nature Museum of Mt. Sanbe Vascular Plant Specimen database of Kanagawa Prefectural Museum of Natural History Plant Specimen Database of Tama Forest Science Garden, Forestry and Forest Products Research Institute, Japan Gunma Museum of Natural History, Vascular Plant Specimen Plant specimens of Otaru Museum Gunma Museum of Natural History, Mammal Specimen Insect Collection of Natural History Museum and Institute, Chiba Fungi specimen database of Kanagawa Prefectural Museum of Natural History Vascular plants collection of Hiratsuka City Museum Vascular Plant Specimens of the URO Herbarium (Faculty of Education, University of the Ryukyus) Plant specimens of Kushiro City Museum Plant specimens of Horaiji-san Museum of Natural History Kiichi T. collection Spermatophytes collection of Okinawa Prefectural Museum & Art Museum Fossil Specimens of Ibaraki Nature Museum Fossil Specimens of Komatsu City Museum Vascular Plant Specimens of the RYU Herbarium (Faculty of Science, University of the Ryukyus) Insect specimens of Hokkaido University Herbarium Specimens of Bonin and Ryukyu Islands Vascular plant collection of The University of Tokyo (Botanical Garden) Vascular plant specimens of Sugadaira Research Station, Mountain Science Center, University of Tsukuba Vascular plant collection of J.F. Oberlin University Herbarium of Shinshu University Plant specimens of Parthenon Tama Museum (PTHM) Plant specimens of Obihiro Centennial City Museum Vascular plant specimens of Nagano Environmental Conservation Research Institute, Nagano Prefecture Botanical Specimens of Kaizuka City Museum of Natural History (KCMN) Tracheophyta collection of Biodiversity Center of Japan, Ministry of the Environment Vascular plant specimens of The Shirakami Research Center for Environmental Sciences, Hirosaki University Vascular plant specimens of Aomori City Forestry Museum Asahikawa Educational College herbarium Plant specimens of Komatsu City Museum Plant specimens of the Museum of Yamagata University Plant specimens of Toyota City Nature Sanctuary (from non-museum circle) Plant specimens of Horaiji-san Museum of Natural History Toji K. collection Vascular plant specimens of Toyama Science Museum Plant specimens of Takatsuki Nature Museum (Aquapia Akutagawa) Vascular Plant Specimens of Yamagata Prefectural Museum Nagoya-Plants Entomological Specimens of Museum of Nature and Human Activities, Hyogo Pref., Japan Vascular plant specimens of Omachi Alpine Museum Plant Specimens collections of the Kyushu University Museum Vascular plant specimens of Akita Prefectural Museum Vascular plants database of Atsugi City Museum Herbarium, University Archives and Collections, Fukushima University, Japan (FKSE) Gymnospermatatophytina Collection of Saitama Museum of Natural History Insect Collection of Yokosuka City Museum Vascular plant specimens of Iida City Museum Plant specimens of Oiso Municipal Museum Herbarium of Hokkaido University Museum (SAPS)