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Wei ZR, Jiao D, Wehenkel CA, Wei XX, Wang XQ. Phylotranscriptomic and ecological analyses reveal the evolution and morphological adaptation of Abies. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 39152659 DOI: 10.1111/jipb.13760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/19/2024]
Abstract
Coniferous forests are under severe threat of the rapid anthropogenic climate warming. Abies (firs), the fourth-largest conifer genus, is a keystone component of the boreal and temperate dark-coniferous forests and harbors a remarkably large number of relict taxa. However, the uncertainty of the phylogenetic and biogeographic history of Abies significantly impedes our prediction of future dynamics and efficient conservation of firs. In this study, using 1,533 nuclear genes generated from transcriptome sequencing and a complete sampling of all widely recognized species, we have successfully reconstructed a robust phylogeny of global firs, in which four clades are strongly supported and all intersectional relationships are resolved, although phylogenetic discordance caused mainly by incomplete lineage sorting and hybridization was detected. Molecular dating and ancestral area reconstruction suggest a Northern Hemisphere high-latitude origin of Abies during the Late Cretaceous, but all extant firs diversified during the Miocene to the Pleistocene, and multiple continental and intercontinental dispersals took place in response to the late Neogene climate cooling and orogenic movements. Notably, four critically endangered firs endemic to subtropical mountains of China, including A. beshanzuensis, A. ziyuanensis, A. fanjingshanensis and A. yuanbaoshanensis from east to west, have different origins and evolutionary histories. Moreover, three hotspots of species richness, including western North America, central Japan, and the Hengduan Mountains, were identified in Abies. Elevation and precipitation, particularly precipitation of the coldest quarter, are the most significant environmental factors driving the global distribution pattern of fir species diversity. Some morphological traits are evolutionarily constrained, and those linked to elevational variation (e.g., purple cone) and cold resistance (e.g., pubescent branch and resinous bud) may have contributed to the diversification of global firs. Our study sheds new light on the spatiotemporal evolution of global firs, which will be of great help to forest management and species conservation in a warming world.
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Affiliation(s)
- Zhou-Rui Wei
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan Jiao
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Christian Anton Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico
| | - Xiao-Xin Wei
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Xiao-Quan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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Ji HY, Ye C, Chen YQ, Li JW, Hidayat A, Miao JL, Li JH, Wu JY, Zhai JW, Lan SR, Jin XH. Phylogenomics and biogeographical diversification of Collabieae (Orchidaceae) and its implication in the reconstruction of the dynamic history of Asian evergreen broadleaved forests. Mol Phylogenet Evol 2024; 196:108084. [PMID: 38688440 DOI: 10.1016/j.ympev.2024.108084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 02/16/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
The tribe Collabieae (Epidendroideae, Orchidaceae) comprises approximately 500 species. Generic delimitation within Collabieae are confusing and phylogenetic interrelationships within the Collabieae have not been well resolved. Plastid genomes and nuclear internal transcribed spacer (ITS) sequences were used to estimate the phylogenetic relationships, ancestral ranges, and diversification rates of Collabieae. The results showed that Collabieae was subdivided into nine clades with high support. We proposed to combine Ancistrochilus and Pachystoma into Spathoglottis, merge Collabium and Chrysoglossum into Diglyphosa, and separate Pilophyllum and Hancockia as distinctive genera. The diversification of the nine clades of Collabieae might be associated with the uplift of the Himalayas during the Late Oligocene/Early Miocene. The enhanced East Asian summer monsoon in the Late Miocene may have promoted the rapid diversification of Collabieae at a sustained high diversification rate. The increased size of terrestrial pseudobulbs may be one of the drivers of Collabieae diversification. Our results suggest that the establishment and development of evergreen broadleaved forests facilitated the diversification of Collabieae.
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Affiliation(s)
- Hong-Yu Ji
- State Key Laboratory of Plant Diversity and Speciality Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chao Ye
- State Key Laboratory of Plant Diversity and Speciality Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yan-Qiong Chen
- College of Geography and Oceanography, Minjiang University, Fuzhou, China
| | - Jian-Wu Li
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Arief Hidayat
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong, Indonesia
| | - Jiang-Lin Miao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Jian-Yong Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), China
| | - Jun-Wen Zhai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Si-Ren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Xiao-Hua Jin
- State Key Laboratory of Plant Diversity and Speciality Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China; China National Botanical Garden, Beijing, China.
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Wu Y, Yang K, Wen X, Sun Y. Genetic Differentiation and Relationship among Castanopsis chinensis, C. qiongbeiensis, and C. glabrifolia (Fagaceae) as Revealed by Nuclear SSR Markers. PLANTS (BASEL, SWITZERLAND) 2024; 13:1486. [PMID: 38891296 PMCID: PMC11175008 DOI: 10.3390/plants13111486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024]
Abstract
Castanopsis chinensis (Spreng.) Hance is widespread in the subtropical forests of China. Castanopsis qiongbeiensis G.A. Fu and Castanopsis glabrifolia J. Q. Li & Li Chen are limited to the coastal beaches of Wenchang county in the northeast of Hainan Island, and have similar morphological characteristics to C. chinensis. It is supposed that C. qiongbeiensis and C. glabrifolia are closely related to C. chinensis. In the present study, the genetic differentiation, gene flow, and genetic relationship of C. chinensis, C. qiongbeiensis, and C. glabrifolia were investigated by using 15 nuclear microsatellite markers; a total of 308 individuals from 17 populations were sampled in the three species. The allelic variation of nuclear microsatellites revealed moderate but significant genetic differentiation (FCT = 0.076) among C. chinensis, C. qiongbeiensis, and C. glabrifolia, and genetic differentiation between C. chinensis and C. glabrifolia was larger than that between C. chinensis and C. qiongbeiensis. Demographic simulations revealed unidirectional gene flow from C. chinensis to C. glabrifolia and C. qiongbeiensis, which highlight dispersal from mainland to island. The isolation effect of Qiongzhou Strait increased the genetic differentiation of species on both sides of the strait; however, the differentiation was diminished by gene flow that occurred during the historical period when Hainan Island was connected to mainland China. Our results supported the argument that C. glabrifolia should be considered an independent species and argued that C. qiongbeiensis should be regarded as an incipient species and independent conservation unit.
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Affiliation(s)
- Yang Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.W.); (K.Y.)
| | - Kai Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.W.); (K.Y.)
| | - Xiangying Wen
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ye Sun
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.W.); (K.Y.)
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Kuo HC, Schoneman T, Gao LM, Gruezo WS, Amoroso VB, Yang Y, Yang KC, Chien CT, Möller M, Wang CN. A leading-edge scenario in the phylogeography and evolutionary history of East Asian insular Taxus in Taiwan and the Philippines. Front Genet 2024; 15:1372309. [PMID: 38756448 PMCID: PMC11096487 DOI: 10.3389/fgene.2024.1372309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/15/2024] [Indexed: 05/18/2024] Open
Abstract
The cool temperate origin of gymnosperm Taxus species in East Asia is specifically diverse and widespread. Certain lineages have managed to extend their distribution further south to subtropical and tropical islands such as Taiwan and the Philippines. To address questions including whether these insular lineages, recently identified as T. phytonii, have become genetically distinct from each other and from their continental relatives, and when and how they colonized their residing islands, we sampled over 11 populations, covering 179 Taxus individuals from Taiwan and the Philippines. Using four cpDNA and one nuclear marker, we showed in population genetic and genealogical analyses that the two insular lineages were genetically distinct from each other and also from other continental Taxus and that they represented each other's closest relative. Estimated with the coalescent-based multi-type tree (MTT) analyses, we inferred an origin of Taiwanese T. phytonii more ancient than 2.49 Mya and that of Philippine T. phytonii more ancient than 1.08 Mya. In addition, the divergence demographic history revealed by both MTT and isolation with migration (IM) analyses indicated the presence of recent post-split migrations from a continental taxon, T. mairei, to Taiwanese T. phytonii, as well as from Taiwanese T. phytonii to Philippine T. phytonii. Overall, this study suggests Taiwan as a stepping stone through which the temperate-origin yew trees can extend their distributions to tropical regions such as the Philippines.
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Affiliation(s)
- Hao-Chih Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Travis Schoneman
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - William Sm. Gruezo
- Plant Biology Division, College of Arts and Sciences, Institute of Biological Sciences, University of the Philippines at Los Baños, Laguna, Philippines
| | - Victor B. Amoroso
- Center for Biodiversity Research and Extension in Mindanao (CEBREM), Central Mindanao University, Mindanao, Philippines
| | - Yang Yang
- Tainan District Agricultural Research and Extension Station, Ministry of Agriculture, Tainan, Taiwan
| | - Kuo-Cheng Yang
- General Education Center, Providence University, Taichung, Taiwan
| | - Ching-Te Chien
- Botanical Garden Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Michael Möller
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
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Zhu H, Tan Y. The Origin of Evergreen Broad-Leaved Forests in East Asia from the Evidence of Floristic Elements. PLANTS (BASEL, SWITZERLAND) 2024; 13:1106. [PMID: 38674515 PMCID: PMC11054231 DOI: 10.3390/plants13081106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024]
Abstract
Arguments about the origin and evolution of the evergreen broad-leaved forests in East Asia exist generally, and are even contradictory in some cases. The origin and evolution of the flora of East Asia, especially in the evolutionary process, the formation time of the Asian monsoon, the implications of phylogenetic and biogeographic studies on some important taxa, and the implications of palaeobotanical evidence are debatable. Most research from different disciplines suggests that the monsoon in the Miocene was key to the diversification of East Asian flora and its evergreen broad-leaved forests. The common view is that the evergreen broad-leaved forests of East Asia are closely related to the monsoon's intensity and developments, which were caused by the uplift of Himalaya-Tibet during or after the mid-Miocene. Analysis of the floristic elements show that the present subtropical evergreen broad-leaved forests in East Asia could have an early or ancient tropical origin and a tropical Asian affinity, but that their species are dominated by endemic Chinese or East Asian ones, many of which have tropical Asian affinity or are tropical sister species. The time of Himalayan uplift and the intensity of the monsoon climate are believed to be key to the formation of the evergreen broad-leaved forests in East Asia. Combined with existing paleobotanical findings, the uplift of the Himalayas and the formation of the monsoon climate, as well as floristic elements of the subtropical evergreen broad-leaved forests, we believe that they evolved from an Asian tropical rainforest after the mid-Miocene in the southeastern region of East Asia, while the ancient subtropical evergreen broad-leaved forests in the southwestern region continuously evolved into the present subtropical ones.
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Affiliation(s)
- Hua Zhu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan International Joint Laboratory of Southeast Asia Biodiversity Conservation, Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Mengla 666303, China;
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Lv S, Chen J, Li B, Fu T, Song M, Zhang P, Liu K, Kou Y, Wang J. The complete chloroplast genome sequence of Pinus bhutanica (Pinaceae) and its phylogenetic implications. Mitochondrial DNA B Resour 2024; 9:182-185. [PMID: 38288249 PMCID: PMC10823889 DOI: 10.1080/23802359.2024.2305710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/10/2024] [Indexed: 01/31/2024] Open
Abstract
Pinus bhutanica is a critically endangered conifer and occurs only in central Bhutan, northwestern Yunnan and southeastern Xizang in China. In this study, the complete chloroplast genome of Pinus bhutanica was first assembled based on next-generation sequencing. The genome sequence was 116,919 bp in length with an overall GC content of 38.75%. A total of 106 functional genes were detected in the genome, including 72 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. The phylogenetic tree reconstructed by 12 chloroplast genomes revealed that P. bhutanica is most closely related to Pinus wangii in subsection Strobus of Pinus.
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Affiliation(s)
- Shiqi Lv
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Jiao Chen
- Xifeng Experimental Station on Soil and Water Conservation of Yellow River Conservancy Commission, Qingyang, China
| | - Bingbing Li
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Taotao Fu
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Mingliang Song
- Conservation Center of Shahe National Wetland Park, Luohe, China
| | - Pengtao Zhang
- Conservation Center of Shahe National Wetland Park, Luohe, China
| | - Kang Liu
- Conservation Center of Shahe National Wetland Park, Luohe, China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Jing Wang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
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Wang XC, Zhang ZK, Zhuang WY. Species Diversity of Penicillium in Southwest China with Discovery of Forty-Three New Species. J Fungi (Basel) 2023; 9:1150. [PMID: 38132751 PMCID: PMC10744262 DOI: 10.3390/jof9121150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023] Open
Abstract
Penicillium species are ubiquitous in all kinds of environments, and they are of industrial, agricultural and clinical importance. In this study, soil fungal diversity in Southwestern China was investigated, and that of Penicillium turned out to be unexpectedly high. The survey included a total of 179 cultures of the genus isolated from 33 soil samples. Three-locus phylogenetic analyses and morphological comparisons were carried out. The examinations revealed that they belonged to two subgenera (Aspergilloides and Penicillium), 11 sections (Aspergilloides, Canescentia, Citrina, Exilicaulis, Fasciculata, Gracilenta, Lanata-Divaricata, Penicillium, Ramosum, Robsamsonia, and Sclerotiorum), 25 series, and 74 species. Forty-three species were discovered as new to science, and a new series, Simianshanica, was established in sect. Aspergilloides. Additionally, 11 species were recorded for the first time in China. Species isolation frequency and distribution of the group were also discussed.
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Affiliation(s)
- Xin-Cun Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Zhi-Kang Zhang
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Wen-Ying Zhuang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
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Overson RP, Johnson MG, Bechen LL, Kinosian SP, Douglas NA, Fant JB, Hoch PC, Levin RA, Moore MJ, Raguso RA, Wagner WL, Skogen KA, Wickett NJ. A phylogeny of the evening primrose family (Onagraceae) using a target enrichment approach with 303 nuclear loci. BMC Ecol Evol 2023; 23:66. [PMID: 37974080 PMCID: PMC10655384 DOI: 10.1186/s12862-023-02151-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/16/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The evening primrose family (Onagraceae) includes 664 species (803 taxa) with a center of diversity in the Americas, especially western North America. Ongoing research in Onagraceae includes exploring striking variation in floral morphology, scent composition, and breeding system, as well as the role of these traits in driving diversity among plants and their interacting pollinators and herbivores. However, these efforts are limited by the lack of a comprehensive, well-resolved phylogeny. Previous phylogenetic studies based on a few loci strongly support the monophyly of the family and the sister relationship of the two largest tribes but fail to resolve several key relationships. RESULTS We used a target enrichment approach to reconstruct the phylogeny of Onagraceae using 303 highly conserved, low-copy nuclear loci. We present a phylogeny for Onagraceae with 169 individuals representing 152 taxa sampled across the family, including extensive sampling within the largest tribe, Onagreae. Deep splits within the family are strongly supported, whereas relationships among closely related genera and species are characterized by extensive conflict among individual gene trees. CONCLUSIONS This phylogenetic resource will augment current research projects focused throughout the family in genomics, ecology, coevolutionary dynamics, biogeography, and the evolution of characters driving diversification in the family.
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Affiliation(s)
- Rick P Overson
- Arizona State University, PO Box 875502, Tempe, AZ, 85287, USA
| | | | - Lindsey L Bechen
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL, 60022, USA
- Whitehead Institute for Biomedical Research, 455 Main St, Cambridge, MA, 02142, USA
| | - Sylvia P Kinosian
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL, 60022, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, PO Box 210088, Tucson, AZ, 85721, USA
| | - Norman A Douglas
- University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Jeremie B Fant
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL, 60022, USA
- Northwestern University, 2205 Tech Dr, Evanston, IL, 60208, USA
| | - Peter C Hoch
- Missouri Botanical Garden, 4344 Shaw Blvd, St. Louis, MO, 63110, USA
| | | | | | | | - Warren L Wagner
- Smithsonian Institution, MRC-166, PO Box 37012, Washington, DC, 20013, USA
| | - Krissa A Skogen
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL, 60022, USA
- Northwestern University, 2205 Tech Dr, Evanston, IL, 60208, USA
- Clemson University, 132 Long Hall, Clemson, SC, 29634, USA
| | - Norman J Wickett
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL, 60022, USA.
- Northwestern University, 2205 Tech Dr, Evanston, IL, 60208, USA.
- Clemson University, 132 Long Hall, Clemson, SC, 29634, USA.
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Wang S, Gao J, Li Z, Chen K, Pu W, Feng C. Phylotranscriptomics supports numerous polyploidization events and phylogenetic relationships in Nicotiana. FRONTIERS IN PLANT SCIENCE 2023; 14:1205683. [PMID: 37575947 PMCID: PMC10421670 DOI: 10.3389/fpls.2023.1205683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023]
Abstract
Introduction Nicotiana L. (Solanaceae) is of great scientific and economic importance, and polyploidization has been pivotal in shaping this genus. Despite many previous studies on the Nicotiana phylogenetic relationship and hybridization, evidence from whole genome data is still lacking. Methods In this study, we obtained 995 low-copy genes and plastid transcript fragments from the transcriptome datasets of 26 Nicotiana species, including all sections. We reconstructed the phylogenetic relationship and phylogenetic network of diploid species. Results The incongruence among gene trees showed that the formation of N. sylvestris involved incomplete lineage sorting. The nuclear-plastid discordance and nuclear introgression absence indicated that organelle capture from section Trigonophyllae was involved in forming section Petunioides. Furthermore, we analyzed the evolutionary origin of polyploid species and dated the time of hybridization events based on the analysis of PhyloNet, sequence similarity search, and phylogeny of subgenome approaches. Our results highly evidenced the hybrid origins of five polyploid sections, including sections Nicotiana, Repandae, Rusticae, Polydicliae, and Suaveolentes. Notably, we provide novel insights into the hybridization event of section Polydicliae and Suaveolentes. The section Polydicliae formed from a single hybridization event between maternal progenitor N. attenuata and paternal progenitor N. undulata; the N. sylvestris (paternal progenitor) and the N. glauca (maternal progenitor) were involved in the formation of section Suaveolentes. Discussion This study represents the first exploration of Nicotiana polyploidization events and phylogenetic relationships using the high-throughput RNA-seq approach. It will provide guidance for further studies in molecular systematics, population genetics, and ecological adaption studies in Nicotiana and other related species.
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Affiliation(s)
- Shuaibin Wang
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Junping Gao
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Zhaowu Li
- Puai Medical College, Shaoyang University, Shaoyang, China
| | - Kai Chen
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Wenxuan Pu
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Chen Feng
- Jiangxi Provincial Key Laboratory of ex-situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
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Huang L, Li S, Huang W, Xiang H, Jin J, Oskolski AA. Glacial expansion of cold-tolerant species in low latitudes: megafossil evidence and species distribution modelling. Natl Sci Rev 2023; 10:nwad038. [PMID: 36960221 PMCID: PMC10029839 DOI: 10.1093/nsr/nwad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
Fossil wood of Chinese white pine (Pinus armandii Franch.) from the Late Pleistocene deposits of Maoming Basin of South China provides the first megafossil evidence for glacial expansion of the range of a cold-tolerant species in low latitudes.
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Affiliation(s)
- Luliang Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences/School of Ecology, Sun Yat-sen University, China
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, China
| | - Shufeng Li
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, China
| | - Weiye Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences/School of Ecology, Sun Yat-sen University, China
| | - Helanlin Xiang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences/School of Ecology, Sun Yat-sen University, China
| | | | - Alexei A Oskolski
- Department of Botany and Plant Biotechnology, University of Johannesburg, South Africa
- Botanical Museum, Komarov Botanical Institute of the Russian Academy of Sciences, Russia
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Luo D, Song MS, Xu B, Zhang Y, Zhang JW, Ma XG, Hao XJ, Sun H. A clue to the evolutionary history of modern East Asian flora: insights from phylogeography and diterpenoid alkaloid distribution pattern of the Spiraea japonica complex. Mol Phylogenet Evol 2023; 184:107772. [PMID: 36977458 DOI: 10.1016/j.ympev.2023.107772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/07/2023] [Accepted: 03/21/2023] [Indexed: 03/28/2023]
Abstract
Each subkingdom of East Asian flora (EAF) has a unique evolutionary history, but which has rarely been described based on phylogeographic studies of EAF species. The Spiraea japonica L. complex, which is widespread in East Asia (EA), has received considerable attention because of the presence of diterpenoid alkaloids (DAs). It provides a proxy for understanding the genetic diversity and DA distribution patterns of species under various environmental conditions associated with the geological background in EA. In the present study, the plastome and chloroplast/nuclear DNA of 71 populations belonging to the S. japonica complex and its congeners were sequenced, combined with DA identification, environmental analyses, and ecological niche modelling, to investigate their phylogenetic relationships, genetic and DAs distribution patterns, biogeography, and demographic dynamics. An "ampliative" S. japonica complex was put forward, comprising all species of Sect. Calospira Ser. Japonicae, of which three evolutionary units carrying their respective unique types of DAs were identified and associated with the regionalization of EAF (referring to the Hengduan Mountains, central China, and east China). Moreover, a transition belt in central China with its biogeographic significance was revealed by genetic and DA distribution patterns from the perspective of ecological adaptation. The origin and onset differentiation of the "ampliative" S. japonica complex was estimated in the early Miocene (22.01/19.44 Ma). The formation of Japanese populations (6.75 Ma) was facilitated by the land bridge, which subsequently had a fairly stable demographic history. The populations in east China have undergone a founder effect after the Last Glacial Maximum, which may have been promoted by the expansion potential of polyploidization. Overall, the in-situ origin and diversification of the "ampliative" S. japonica complex since the early Miocene is a vertical section of the formation and development of modern EAF and was shaped by the geological history of each subkingdom.
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Affiliation(s)
- Dong Luo
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Min-Shu Song
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Bo Xu
- College of Forestry, Southwest Forestry University, Kunming 650224, China
| | - Yu Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Jian-Wen Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Xiang-Guang Ma
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China
| | - Xiao-Jiang Hao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China.
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China.
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Ye JW, Tian B, Li DZ. Monsoon intensification in East Asia triggered the evolution of its flora. FRONTIERS IN PLANT SCIENCE 2022; 13:1046538. [PMID: 36507402 PMCID: PMC9733597 DOI: 10.3389/fpls.2022.1046538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION East Asia (EA), which falls within the region of the Asian monsoon that is composed of the East Asia monsoon (EAM) and the Indian monsoon (IM), is known for its high species diversity and endemism. This has been attributed to extreme physiographical heterogeneity in conjunction with climate and sea-level changes during the Pleistocene, this hypothesis has been widely proven by phylogeographic studies. Recently, dated phylogenies have indicated that the origins (stem age) of the flora occurred after the Oligocene-Miocene boundary and are related to the establishment of the EAM. METHODS Hence, this study further examined whether the strengthening of the monsoons triggered floral evolution via a meta-analysis of the tempo-spatial pattern of evolutionary radiation dates (crown ages) of 101 endemic seed plant genera. RESULTS Taxonomic diversification began during the late Eocene, whereas the accumulated number of diversifications did not significantly accelerate until the late Miocene. The distribution of the weighted mean and the average divergence times in the EAM, IM, or transitional regions all fall within the mid-late Miocene. Fossils of the Tertiary relict genera are mostly and widely distributed outside EA and only half of the earliest fossils in the EA region are not older than Miocene, while their divergence times are mostly after the late Miocene. The pattern of divergence time of monotypic and polytypic taxa suggest the climatic changes after the late Pliocene exert more influence on monotypic taxa. DISCUSSION The two key stages of floral evolution coincide with the intensifications of the EAM and IM, especially the summer monsoon which brings a humid climate. An integrated review of previous studies concerning flora, genus, and species levels further supports our suggestion that monsoon intensification in EA triggered the evolution of its flora.
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Affiliation(s)
- Jun-Wei Ye
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Bin Tian
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Habib S, Gong Y, Dong S, Lindstrom A, William Stevenson D, Liu Y, Wu H, Zhang S. Phylotranscriptomics reveal the spatio-temporal distribution and morphological evolution of Macrozamia, an Australian endemic genus of Cycadales. ANNALS OF BOTANY 2022; 130:671-685. [PMID: 36111957 PMCID: PMC9670756 DOI: 10.1093/aob/mcac117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/14/2022] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Cycads are regarded as an ancient lineage of living seed plants, and hold important clues to understand the early evolutionary trends of seed plants. The molecular phylogeny and spatio-temporal diversification of one of the species-rich genera of cycads, Macrozamia, have not been well reconstructed. METHODS We analysed a transcriptome dataset of 4740 single-copy nuclear genes (SCGs) of 39 Macrozamia species and two outgroup taxa. Based on concatenated (maximum parsimony, maximum likelihood) and multispecies coalescent analyses, we first establish a well-resolved phylogenetic tree of Macrozamia. To identify cyto-nuclear incongruence, the plastid protein coding genes (PCGs) from transcriptome data are extracted using the software HybPiper. Furthermore, we explore the biogeographical history of the genus and shed light on the pattern of floristic exchange between three distinct areas of Australia. Six key diagnostic characters are traced on the phylogenetic framework using two comparative methods, and infra-generic classification is investigated. KEY RESULTS The tree topologies of concatenated and multi-species coalescent analyses of SCGs are mostly congruent with a few conflicting nodes, while those from plastid PCGs show poorly supported relationships. The genus contains three major clades that correspond to their distinct distributional areas in Australia. The crown group of Macrozamia is estimated to around 11.80 Ma, with a major expansion in the last 5-6 Myr. Six morphological characters show homoplasy, and the traditional phenetic sectional division of the genus is inconsistent with this current phylogeny. CONCLUSIONS This first detailed phylogenetic investigation of Macrozamia demonstrates promising prospects of SCGs in resolving phylogenetic relationships within cycads. Our study suggests that Macrozamia, once widely distributed in Australia, underwent major extinctions because of fluctuating climatic conditions such as cooling and mesic biome disappearance in the past. The current close placement of morphologically distinct species in the phylogenetic tree may be related to neotenic events that occurred in the genus.
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Affiliation(s)
- Sadaf Habib
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yiqing Gong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Anders Lindstrom
- Global Biodiversity Conservancy 144/124 Moo 3, Soi Bua Thong, Bangsalae, Sattahip, Chonburi 20250, Thailand
| | | | - Yang Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Hong Wu
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shouzhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
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Shao YZ, Yuan ZL, Liu YY, Liu FQ, Xiang RC, Zhang YY, Ye YZ, Chen Y, Wen Q. Glacial Expansion or Interglacial Expansion? Contrasting Demographic Models of Four Cold-Adapted Fir Species in North America and East Asia. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.844354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding and forecasting species’ response to climate change is a critical need for future conservation and management. Two expansion hypotheses, the glacial expansion versus the interglacial expansion, have been proposed to interpret how cold-adapted organisms in the northern hemisphere respond to Quaternary climatic fluctuations. To test these two hypotheses, we originally used two pairs of high-low elevation firs from North America (Abies lasiocarpa and Abies balsamea) and East Asia (Abies chensiensis and Abies nephrolepis). Abies lasiocarpa and Abies chensiensis are widely distributed in high-elevation regions of western North America and central China. Abies balsamea and Abies nephrolepis occur in central North America and northeast China, with much lower elevations. These fir species are typical cold-adapted species and sensitive to climate fluctuations. Here, we integrated the mtDNA and cpDNA polymorphisms involving 44 populations and 585 individuals. Based on phylogeographic analyses, recent historical range expansions were indicated in two high-elevation firs (Abies lasiocarpa and Abies chensiensis) during the last glaciation (43.8–28.4 or 21.9–14.2 kya, 53.1–34.5 or 26.6–17.2 kya). Such glacial expansions in high-elevation firs were further confirmed by the evidence of species distribution modelling, geographic-driven genetic patterns, palynological records, and current distribution patterns. Unlike the north American firs, the SDM models indicated unremarkable expansion or contraction in East Asia firs for its much more stable conditions during different historical periods. Taken together, our findings highly supported that high-elevation firs experienced glacial expansion during the Quaternary climate change in East Asia and North America, as interglacial expansion within low-elevation firs. Under this situation, the critically endangered fir species distributed in high elevation would have no enough higher elevational space to migrate. Facing the increasing global warming, thus we proposed ex-situ conservation of defining conservation units as the most meaningful strategy.
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