An integrative approach clarifies species delimitation and biogeographic history of Debregeasia (Urticaceae)

doi:10.1016/j.pld.2024.11.004

Plant Diversity ›› 2025, Vol. 47 ›› Issue (02): 229-243.DOI: 10.1016/j.pld.2024.11.004

• Articles • Previous Articles Next Articles

An integrative approach clarifies species delimitation and biogeographic history of Debregeasia (Urticaceae)

Amos Kipkoech^a,c, Ke Li^a,d, Richard I. Milne^e, Oyetola Olusegun Oyebanji^f,g, Moses C. Wambulwa^h, Xiao-Gang Fu^a,c, Dennis A. Wakhungu^b,c, Zeng-Yuan Wu^a, Jie Liu^a,b

a. Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
b. CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
c. University of Chinese Academy of Sciences, Beijing 100093, China;
d. School of Ecology and Environment Science, Yunnan University, Kunming, China;
e. Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK;
f. Department of Biology, University of Louisiana, Lafayette, LA, USA;
g. Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA;
h. Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui, Kenya

Received:2024-04-03 Revised:2024-11-19 Online:2025-04-03 Published:2025-03-25
Contact: Zeng-Yuan Wu,E-mail:wuzengyuan@mail.kib.ac.cn;Jie Liu,E-mail:liujie@mail.kib.ac.cn
Supported by:
This research was funded by the National Natural Science Foundation of China (42171071, 42211540718), Key Research Program of Frontier Sciences, CAS (ZDBS-LY-7001), Yunnan Fundamental Research Projects (202401AT070190, 202201BC070001), Top-notch Young Talents Project of Yunnan Provincial “Ten Thousand Talents Program” (YNWR-QNBJ-2018-146, YNWR-QNBJ-2020-293), and CAS “Light of West China” Program. Jie Liu and Zeng-Yuan Wu were also supported by the China Scholarship Council (202304910135 and 202304910138) for a one-year study at the University of Toronto, Canada.

An integrative approach clarifies species delimitation and biogeographic history of Debregeasia (Urticaceae)

Amos Kipkoech^a,c, Ke Li^a,d, Richard I. Milne^e, Oyetola Olusegun Oyebanji^f,g, Moses C. Wambulwa^h, Xiao-Gang Fu^a,c, Dennis A. Wakhungu^b,c, Zeng-Yuan Wu^a, Jie Liu^a,b

a. Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
b. CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
c. University of Chinese Academy of Sciences, Beijing 100093, China;
d. School of Ecology and Environment Science, Yunnan University, Kunming, China;
e. Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK;
f. Department of Biology, University of Louisiana, Lafayette, LA, USA;
g. Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA;
h. Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui, Kenya

通讯作者: Zeng-Yuan Wu,E-mail:wuzengyuan@mail.kib.ac.cn;Jie Liu,E-mail:liujie@mail.kib.ac.cn
作者简介:Amos Kipkoech,E-mail:pkoech160@gmail.com;Ke Li,E-mail:like@mail.kib.ac.cn;Richard I.Milne,E-mail:R.Milne@ed.ac.uk;Oyetola Olusegun Oyebanji,E-mail:oyebanjioyetola@gmail.com;Moses C.Wambulwa,E-mail:mcwambulwa@gmail.com;Xiao-Gang Fu,E-mail:fuxiaogang@mail.kib.ac.cn;Dennis A.Wakhungu,E-mail:dennis@mail.kib.ac.cn
基金资助:
This research was funded by the National Natural Science Foundation of China (42171071, 42211540718), Key Research Program of Frontier Sciences, CAS (ZDBS-LY-7001), Yunnan Fundamental Research Projects (202401AT070190, 202201BC070001), Top-notch Young Talents Project of Yunnan Provincial “Ten Thousand Talents Program” (YNWR-QNBJ-2018-146, YNWR-QNBJ-2020-293), and CAS “Light of West China” Program. Jie Liu and Zeng-Yuan Wu were also supported by the China Scholarship Council (202304910135 and 202304910138) for a one-year study at the University of Toronto, Canada.

Abstract

Abstract: Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades. Debregeasia (Urticaceae), an economically important genus, presents challenges in species delimitation due to its overlapping morphological traits and unstable taxonomic assignments. Here, we analyzed 14 morphological traits and generated 12 data matrices from the plastomes and nrDNA using genome skimming from the nine recognized morphospecies to clarify species boundaries and assess barcode performance in Debregeasia. We also used a universal set of 353 nuclear genes to explore reticulate evolution and biogeographic history of Debregeasia. Plastomes of Debregeasia exhibited the typical quadripartite structure with conserved gene content and marginal independent variations in the SC/IR boundary at inter- and intra-specific levels. Three Debregeasia species were non-monophyletic and could not be discerned by any barcode; however, ultra-barcodes identified the remaining six (67%), outperforming standard barcodes (56%). Our phylogenetic analyses placed Debregeasia wallichiana outside the genus and suggested six monophyletic clades in Debregeasia, although the placement between Debregeasia hekouensis and Debregeasia libera varied. There was extensive trait overlap in key morphologically diagnostic characters, with reticulation analysis showing potentially pervasive hybridization, likely influenced by speciation patterns and overlaps between species ranges. We inferred that Debregeasia crown diversification began at ca. 12.82 Ma (95% HPD: 11.54-14.63 Ma) in the mid-Miocene within Australia, followed by vicariance and later long-distance dispersal, mainly out of southern China. Our findings highlight the utility of genomic data with integrative lines of evidence to refine species delimitation and explore evolutionary relationships in complex plant lineages.

Key words: Debregeasia, Plastome, Phylogenomics, Reticulate evolution, Species delimitation, Ultra-barcodes

摘要： Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades. Debregeasia (Urticaceae), an economically important genus, presents challenges in species delimitation due to its overlapping morphological traits and unstable taxonomic assignments. Here, we analyzed 14 morphological traits and generated 12 data matrices from the plastomes and nrDNA using genome skimming from the nine recognized morphospecies to clarify species boundaries and assess barcode performance in Debregeasia. We also used a universal set of 353 nuclear genes to explore reticulate evolution and biogeographic history of Debregeasia. Plastomes of Debregeasia exhibited the typical quadripartite structure with conserved gene content and marginal independent variations in the SC/IR boundary at inter- and intra-specific levels. Three Debregeasia species were non-monophyletic and could not be discerned by any barcode; however, ultra-barcodes identified the remaining six (67%), outperforming standard barcodes (56%). Our phylogenetic analyses placed Debregeasia wallichiana outside the genus and suggested six monophyletic clades in Debregeasia, although the placement between Debregeasia hekouensis and Debregeasia libera varied. There was extensive trait overlap in key morphologically diagnostic characters, with reticulation analysis showing potentially pervasive hybridization, likely influenced by speciation patterns and overlaps between species ranges. We inferred that Debregeasia crown diversification began at ca. 12.82 Ma (95% HPD: 11.54-14.63 Ma) in the mid-Miocene within Australia, followed by vicariance and later long-distance dispersal, mainly out of southern China. Our findings highlight the utility of genomic data with integrative lines of evidence to refine species delimitation and explore evolutionary relationships in complex plant lineages.

关键词: Debregeasia, Plastome, Phylogenomics, Reticulate evolution, Species delimitation, Ultra-barcodes

Amos Kipkoech, Ke Li, Richard I. Milne, Oyetola Olusegun Oyebanji, Moses C. Wambulwa, Xiao-Gang Fu, Dennis A. Wakhungu, Zeng-Yuan Wu, Jie Liu. An integrative approach clarifies species delimitation and biogeographic history of Debregeasia (Urticaceae)[J]. Plant Diversity, 2025, 47(02): 229-243.

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An integrative approach clarifies species delimitation and biogeographic history of Debregeasia (Urticaceae)

An integrative approach clarifies species delimitation and biogeographic history of Debregeasia (Urticaceae)

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