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Lian L, Peng HW, Erst AS, Ortiz RDC, Jabbour F, Chen ZD, Wang W. Bayesian tip-dated phylogeny and biogeography of Cissampelideae (Menispermaceae): Mitigating the effects of homoplastic morphological characters. Cladistics 2024; 40:391-410. [PMID: 38469932 DOI: 10.1111/cla.12573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
The integration of morphological and molecular data is essential to understand the affinities of fossil taxa and spatio-temporal evolutionary processes of organisms. However, homoplastic morphological characters can mislead the placement of fossil taxa and impact downstream analyses. Here, we provide an example of how to mitigate effectively the effect of morphological homoplasy on the placement of fossil taxa and biogeographic inferences of Cissampelideae. We assembled three data types, morphological data only, morphological data with a molecular scaffold and combined morphological and molecular data. By removing high-level homoplastic morphological data or reweighting the morphological characters, we conducted 15 parsimony, 12 undated Bayesian and four dated Bayesian analyses. Our results show that the 14 selected Cissampelideae fossil taxa are placed poorly when based only on morphological data, but the addition of molecular scaffold and combination of morphological and molecular data greatly improve the resolution of fossil nodes. We raise the monotypic Stephania subg. Botryodiscia to generic status and discover that three fossils previously assigned to Stephania should be members of Diploclisia. The Bayesian tip-dated tree recovered by removing homoplastic morphological characters with a Rescaled Consistency Index <0.25 has the highest stratigraphic fit and consequently generates more reasonable biogeographic reconstruction for Cissampelideae. Cissampelideae began to diversify in Asia in the latest Cretaceous and subsequently dispersed to South America around the Cretaceous-Palaeogene boundary. Two dispersal events from Asia to Africa occurred in the Early Eocene and the Late Eocene-Late Oligocene, respectively. These findings provide guidelines and practical methods for mitigating the effects of homoplastic morphological characters on fossil placements and Bayesian tip-dating, as well as insights into the past tropical floristic exchanges among different continents.
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Affiliation(s)
- Lian Lian
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Huan-Wen Peng
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Andrey S Erst
- Central Siberian Botanical Garden, Siberian Branch of Russian Academy of Sciences, Zolotodolinskaya str. 101, Novosibirsk, 630090, Russia
| | - Rosa Del C Ortiz
- Missouri Botanical Garden, 4344 Shaw Blvd, St Louis, Missouri, 63110, USA
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, Université des Antilles, EPHE, 57 rue Cuvier, CP39, Paris, 75005, France
| | - Zhi-Duan Chen
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Wang
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Capobianco A, Friedman M. Fossils indicate marine dispersal in osteoglossid fishes, a classic example of continental vicariance. Proc Biol Sci 2024; 291:20241293. [PMID: 39137888 DOI: 10.1098/rspb.2024.1293] [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: 02/05/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 08/15/2024] Open
Abstract
The separation of closely related terrestrial or freshwater species by vast marine barriers represents a biogeographical riddle. Such cases can provide evidence for vicariance, a process whereby ancient geological events like continental rifting divided ancestral geographical ranges. With an evolutionary history extending tens of millions of years, freshwater ecology, and distribution encompassing widely separated southern landmasses, osteoglossid bonytongue fishes are a textbook case of vicariance attributed to Mesozoic fragmentation of the Gondwanan supercontinent. Largely overlooked fossils complicate the clean narrative invoked for extant species by recording occurrences on additional continents and in marine settings. Here, we present a new total-evidence phylogenetic hypothesis for bonytongue fishes combined with quantitative models of range evolution and show that the last common ancestor of extant osteoglossids was likely marine, and that the group colonized freshwater settings at least four times when both extant and extinct lineages are considered. The correspondence between extant osteoglossid relationships and patterns of continental fragmentation therefore represents a striking example of biogeographical pseudocongruence. Contrary to arguments against vicariance hypotheses that rely only on temporal or phylogenetic evidence, these results provide direct palaeontological support for enhanced dispersal ability early in the history of a group with widely separated distributions in the modern day.
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Affiliation(s)
- Alessio Capobianco
- GeoBio-Center LMU, Ludwig-Maximilians-Universität München , Munich, Germany
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München , Munich, Germany
- Department of Earth and Environmental Sciences, University of Michigan , Ann Arbor, MI, USA
- Museum of Paleontology, University of Michigan , Ann Arbor, MI, USA
| | - Matt Friedman
- Department of Earth and Environmental Sciences, University of Michigan , Ann Arbor, MI, USA
- Museum of Paleontology, University of Michigan , Ann Arbor, MI, USA
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3
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Li E, Wang Y, Liu K, Liu Y, Xu C, Dong W, Zhang Z. Historical climate change and vicariance events contributed to the intercontinental disjunct distribution pattern of ash species (Fraxinus, Oleaceae). Commun Biol 2024; 7:603. [PMID: 38769470 PMCID: PMC11106067 DOI: 10.1038/s42003-024-06296-1] [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: 01/18/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
The Northern Hemisphere temperate forests exhibit a disjunct distributional pattern in Europe, North America, and East Asia. Here, to reveal the promoter of intercontinental disjunct distribution, Fraxinus was used as a model organism to integrate abundant fossil evidence with high-resolution phylogenies in a phytogeographic analysis. We constructed a robust phylogenetic tree using genomic data, reconstructed the geographic ancestral areas, and evaluated the effect of incorporating fossil information on the reconstructed biogeographic history. The phylogenetic relationships of Fraxinus were highly resolved and divided into seven clades. Fraxinus originated in western North America during Eocene, and six intercontinental dispersal events and five intercontinental vicariance events were occured. Results suggest that climate change and vicariance contributed to the intercontinental disjunct distribution pattern of Fraxinus. Moreover, results highlight the necessity of integrating phylogenetic relationship and fossil to improve the reliability of inferred biogeographic events and our understanding of the processes underlying disjunct distributions.
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Affiliation(s)
- Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yushuang Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Kangjia Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yanlei Liu
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
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4
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Zhang Q, Folk RA, Mo ZQ, Ye H, Zhang ZY, Peng H, Zhao JL, Yang SX, Yu XQ. Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae). Mol Phylogenet Evol 2023; 188:107912. [PMID: 37648181 DOI: 10.1016/j.ympev.2023.107912] [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: 03/06/2023] [Revised: 08/09/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
Gene tree discordance is a significant legacy of biological evolution. Multiple factors can result in incongruence among genes, such as introgression, incomplete lineage sorting (ILS), gene duplication or loss. Resolving the background of gene tree discordance is a critical way to uncover the process of species diversification. Camellia, the largest genus in Theaceae, has controversial taxonomy and systematics due in part to a complex evolutionary history. We used 60 transcriptomes of 55 species, which represented 15 sections of Camellia to investigate its phylogeny and the possible causes of gene tree discordance. We conducted gene tree discordance analysis based on 1,617 orthologous low-copy nuclear genes, primarily using coalescent species trees and polytomy tests to distinguish hard and soft conflict. A selective pressure analysis was also performed to assess the impact of selection on phylogenetic topology reconstruction. Our results detected different levels of gene tree discordance in the backbone of Camellia, and recovered rapid diversification as one of the possible causes of gene tree discordance. Furthermore, we confirmed that none of the currently proposed sections of Camellia was monophyletic. Comparisons among datasets partitioned under different selective pressure regimes showed that integrating all orthologous genes provided the best phylogenetic resolution of the species tree of Camellia. The findings of this study reveal rapid diversification as a major source of gene tree discordance in Camellia and will facilitate future investigation of reticulate relationships at the species level in this important plant genus.
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Affiliation(s)
- Qiong Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, MS 39762, United States
| | - Zhi-Qiong Mo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hang Ye
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Forestry Research Institute, Nanning 530002, Guangxi, China
| | - Zhao-Yuan Zhang
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Forestry Research Institute, Nanning 530002, Guangxi, China
| | - Hua Peng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jian-Li Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China.
| | - Shi-Xiong Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Xiang-Qin Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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5
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Almeida EAB, Bossert S, Danforth BN, Porto DS, Freitas FV, Davis CC, Murray EA, Blaimer BB, Spasojevic T, Ströher PR, Orr MC, Packer L, Brady SG, Kuhlmann M, Branstetter MG, Pie MR. The evolutionary history of bees in time and space. Curr Biol 2023; 33:3409-3422.e6. [PMID: 37506702 DOI: 10.1016/j.cub.2023.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/04/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023]
Abstract
Bees are the most significant pollinators of flowering plants. This partnership began ca. 120 million years ago, but the uncertainty of how and when bees spread across the planet has greatly obscured investigations of this key mutualism. We present a novel analysis of bee biogeography using extensive new genomic and fossil data to demonstrate that bees originated in Western Gondwana (Africa and South America). Bees likely originated in the Early Cretaceous, shortly before the breakup of Western Gondwana, and the early evolution of any major bee lineage is associated with either the South American or African land masses. Subsequently, bees colonized northern continents via a complex history of vicariance and dispersal. The notable early absences from large landmasses, particularly in Australia and India, have important implications for understanding the assembly of local floras and diverse modes of pollination. How bees spread around the world from their hypothesized Southern Hemisphere origin parallels the histories of numerous flowering plant clades, providing an essential step to studying the evolution of angiosperm pollination syndromes in space and time.
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Affiliation(s)
- Eduardo A B Almeida
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-901, Brazil.
| | - Silas Bossert
- Department of Entomology, Washington State University, Pullman, WA 99164, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
| | - Bryan N Danforth
- Department of Entomology, Cornell University, Comstock Hall, Ithaca, NY 14853, USA
| | - Diego S Porto
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-901, Brazil; Finnish Museum of Natural History - LUOMUS, University of Helsinki, Helsinki 00014, Finland
| | - Felipe V Freitas
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-901, Brazil; Department of Entomology, Washington State University, Pullman, WA 99164, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA
| | - Elizabeth A Murray
- Department of Entomology, Washington State University, Pullman, WA 99164, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Bonnie B Blaimer
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, 10115 Berlin, Germany
| | - Tamara Spasojevic
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Life Sciences, Natural History Museum Basel, 4051 Basel, Switzerland; Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Patrícia R Ströher
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná 81531-990, Brazil; Department of Anthropology and Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Michael C Orr
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, 70191 Stuttgart, Germany; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Laurence Packer
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Michael Kuhlmann
- Zoological Museum, University of Kiel, Hegewischstr. 3, 24105 Kiel, Germany
| | - Michael G Branstetter
- U.S. Department of Agriculture, Agricultural Research Service, Pollinating Insects Research Unit, Utah State University, Logan, UT 84322, USA
| | - Marcio R Pie
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná 81531-990, Brazil; Department of Biology, Edge Hill University, St Helens Rd, Ormskirk, Lancashire L39 4QP, UK
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6
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Yang X, Zhang X, Xue T, Zhang X, Yang F, Yu J, Janssens SB, Bussmann RW, Yu S. Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification. Proc Biol Sci 2023; 290:20230659. [PMID: 37491959 PMCID: PMC10369024 DOI: 10.1098/rspb.2023.0659] [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: 03/21/2023] [Accepted: 07/03/2023] [Indexed: 07/27/2023] Open
Abstract
Demonstrating the process of transregional biogeography and mechanisms underlying evolutionary radiations is crucial to understanding biological evolution. Here, we use Hydrangeeae (Hydrangeaceae), a tribe with a unique disjunct distribution and complex trait variations, using a solid phylogenetic framework, to investigate how geographical and climatic factors interact with functional traits to trigger plant evolutionary radiations. We constructed the first highly supported and dated phylogenetic framework using 79 protein-coding genes obtained from 81 plastomes, representing 63 species and all major clades, and found that most extant species originated from asynchronous diversification of two lineages undergoing repeated expansion and retraction, at middle and high latitudes of the Northern Hemisphere between East Asia and North America, during the Eocene to Pleistocene (driven by geologic and climatic dynamics). In accordance with these drivers, interactions of flora between central-eastern China and Japan occurred frequently after the Late Tertiary. We found that resource limitation and range fragmentation probably accelerated the diversification of Hydrangeeae, which supports the resource-use hypothesis. Our study sheds light on the evolutionary radiation and assembly of flora within East Asia, and the East Asian-North American disjunction, through integration of phylogenomic and biogeographic data with functional trait and ecological data.
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Affiliation(s)
- Xudong Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, People's Republic of China
| | - Tiantian Xue
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xiaoxia Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Fusheng Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Jianghong Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
- College of Forestry, Guizhou University, Guiyang 550025, People's Republic of China
| | - Steven B. Janssens
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium
| | - Rainer W. Bussmann
- Institute of Botany and Bakuriani Alpine Botanical Garden, Ilia State University, Botanical Street 1, 0105 Tbilisi, Georgia
- Department of Botany, State Museum for Natural History Karlsruhe, Erbprinzenstraße 13, 76133 Karlsruhe, Germany
| | - Shengxiang Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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Wan X, Zhang L, Lehtonen S, Tuomisto H, Zhang DW, Gao XF, Zhang LB. Five long-distance dispersals shaped the major intercontinental disjunctions in Tectariaceae s.l. (Polypodiales, Polypodiopsida). Mol Phylogenet Evol 2023:107845. [PMID: 37301485 DOI: 10.1016/j.ympev.2023.107845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/02/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
Intercontinental disjunct distributions can arise either from vicariance, from long-distance dispersal, or through extinction of an ancestral population with a broader distribution. Tectariaceae s.l., a clade of ferns in Polypodiales with ca. 300 species mainly distributed in the tropics and subtropics, provide an excellent opportunity to investigate global distribution patterns. Here, we assembled a dataset of eight plastid markers and one nuclear marker of 636 (92% increase of the earlier largest sampling) accessions representing ca. 210 species of all eight genera in Tectariaceae s.l. (Arthropteridaceae, Pteridryaceae, and Tectariaceae s.s.) and 35 species of other families of eupolypods Ⅰ. A new phylogeny is reconstructed to study the biogeography and trait-associated diversification. Our major results include: (1) a distinct lineage of Tectaria sister to the rest of the American Tectaria is identified; (2) Tectariaceae s.l., and the three families: Arthropteridaceae (Arthropteris), Pteridryaceae (Draconopteris, Malaifilix, Polydictyum, Pteridrys), and Tectariaceae s.s. (Hypoderris, Tectaria, and Triplophyllum), might have all originated in late Cretaceous; (3) only five intercontinental dispersals occurred in Pteridryaceae and Tectariaceae s.s. giving rise to their current intercontinental disjunction; (4) we provide the second evidence in ferns that a long-distance dispersal between Malesia and Americas during the Paleocene to Eocene led to the establishment/origin of a new genus (Draconopteris); and (5) diversification rate of each state of leaf dissection is different, and the lowest is in the simple-leaved taxa.
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Affiliation(s)
- Xia Wan
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China; University of Chinese Academy of Sciences, Beijing 100049, China; Missouri Botanical Garden, St. Louis, Missouri 63110, USA
| | - Liang Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Missouri Botanical Garden, St. Louis, Missouri 63110, USA
| | - Samuli Lehtonen
- Biodiversity Unit, University of Turku, FI-20014 Turku, Finland
| | - Hanna Tuomisto
- Department of Biology, University of Turku, FI-20014 Turku, Finland
| | - Da-Wei Zhang
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Xin-Fen Gao
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Li-Bing Zhang
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Missouri Botanical Garden, St. Louis, Missouri 63110, USA.
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Zan T, He YT, Zhang M, Yonezawa T, Ma H, Zhao QM, Kuo WY, Zhang WJ, Huang CH. Phylogenomic analyses of Camellia support reticulate evolution among major clades. Mol Phylogenet Evol 2023; 182:107744. [PMID: 36842731 DOI: 10.1016/j.ympev.2023.107744] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/08/2023] [Accepted: 02/21/2023] [Indexed: 02/28/2023]
Abstract
Camellia (Theaceae) is a morphologically highly diverse genus of flowering plants and includes many famous species with high economic value, and the phylogeny of this genus is not fully resolved. We used 95 transcriptomes from 87 Camellia species and identified 1481 low-copy genes to conduct a detailed analysis of the phylogeny of this genus according to various data-screening criteria. The results show that, very different from the two existing classification systems of Camellia, 87 species are grouped into 8 main clades and two independent species, and that all 8 clades except Clade 8 were strongly supported by almost all the coalescent or concatenated trees using different gene subsets. However, the relationships among these clades were weakly supported and different from analyses using different gene subsets; furthermore, they do not agree with the phylogeny from chloroplast genomes of Camellia. Additional analyses support reticulate evolution (probably resulting from introgression or hybridization) among some major Camellia lineages, providing explanation for extensive gene tree conflicts. Furthermore, we inferred that together with the formation of East Asian subtropical evergreen broad-leaved forests, Camellia underwent a radiative divergence of major clades at 23 ∼ 19 Ma in the late Miocene then had a subsequent species burst at 10 ∼ 5 Ma. Principal component and cluster analyses provides new insights into morphological changes underlying the evolution of Camellia and a reference to further clarify subgenus and sections of this genus. The comprehensive study here including a nuclear phylogeny and other analyses reveal the rapid evolutionary history of Camellia.
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Affiliation(s)
- Ting Zan
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Yi-Tao He
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Min Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Takahiro Yonezawa
- Faculty of Agriculture, Tokyo University of Agriculture, Funako 1737, Atsugi, Kanagawa 14 243-0034, Japan.
| | - Hong Ma
- Department of Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
| | - Qiang-Min Zhao
- Guangzhou Zongke Horticulture Development Co., Ltd., Guangzhou 511300, China.
| | - Wen-Yu Kuo
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Wen-Ju Zhang
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Chien-Hsun Huang
- Ecological Engineering and State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
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Skema C, Jourdain-Fievet L, Dubuisson JY, Le Péchon T. Out of Madagascar, repeatedly: The phylogenetics and biogeography of Dombeyoideae (Malvaceae s.l.). Mol Phylogenet Evol 2023; 182:107687. [PMID: 36581141 DOI: 10.1016/j.ympev.2022.107687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/23/2022] [Accepted: 12/22/2022] [Indexed: 12/27/2022]
Abstract
Dispersals have been shown to be critical to the evolution of the long isolated but megadiverse flora of Madagascar and the surrounding islands of the western Indian Ocean, but we are just beginning to understand the directionality of these dispersals. With more than half of its species occurring in the western Indian Ocean region (WIOR), the paleotropical subfamily Dombeyoideae provides a particularly useful case study through which to better understand the biogeography of the WIOR, and yet its biogeography is poorly understood. Here we sampled six molecular markers from all 20 genera in the Dombeyoideae to reconstruct the most complete phylogeny to date for the subfamily. From this, divergence times, calibrated with three fossils (two dombeyoid, one malvoid), and ancestral range estimations were hypothesized. Biogeographic stochastic mapping (BSM) analyses on the maximum clade credibility tree were completed and compared to BSM analyses on 1,000 trees randomly sampled from the posterior distribution of trees resulting from the dating analysis. We found the Dombeyoideae crown node diverged ca. 53 million years ago out of a broad ancestral range involving all three major areas of its distribution: Madagascar, Africa, and Asia. The majority of diversification and dispersals in the subfamily occurred within the last ca. 10 million years, mostly from the Pliocene onwards. There were roughly five dispersals from Madagascar to Africa (and only one in reverse), at least six from Madagascar to surrounding islands of the WIOR (Mascarenes and Comoros), and one dispersal from Madagascar to Asia (and ca. 1 in reverse). Other long-distance dispersals included one from Africa to St. Helena and one from Africa to Australasia, both from within the most widespread clade, the Cheirolaena & allies clade, and one dispersal from Asia to Africa. Critically, the Dombeyoideae provide strong evidence for considering the island of Madagascar as a source for the colonization of continents, as well as the surrounding islands of the WIOR. Furthermore, narrow sympatry was a key process in the evolution of the subfamily, particularly in Madagascar and the Mascarenes.
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Affiliation(s)
- Cynthia Skema
- Morris Arboretum of the University of Pennsylvania, 100 E. Northwestern Avenue, Philadelphia, PA 19118, USA.
| | - Lucile Jourdain-Fievet
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, Université des Antilles, CP 48, 57 rue Cuvier, 75005 Paris, France; Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
| | - Jean-Yves Dubuisson
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, Université des Antilles, CP 48, 57 rue Cuvier, 75005 Paris, France
| | - Timothée Le Péchon
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium; Fédération Wallonie-Bruxelles, Service Général de l'Enseignement supérieur et de la Recherche scientifique, 1 rue A. Lavallée, 1080 Bruxelles, Belgium
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Qin SY, Zuo ZY, Guo C, Du XY, Liu SY, Yu XQ, Xiang XG, Rong J, Liu B, Liu ZF, Ma PF, Li DZ. Phylogenomic insights into the origin and evolutionary history of evergreen broadleaved forests in East Asia under Cenozoic climate change. Mol Ecol 2023; 32:2850-2868. [PMID: 36847615 DOI: 10.1111/mec.16904] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 02/09/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
The evergreen versus deciduous leaf habit is an important functional trait for adaptation of forest trees and has been hypothesized to be related to the evolutionary processes of the component species under paleoclimatic change, and potentially reflected in the dynamic history of evergreen broadleaved forests (EBLFs) in East Asia. However, knowledge about the shift of evergreen versus deciduous leaf with the impact of paleoclimatic change using genomic data remains rare. Here, we focus on the Litsea complex (Lauraceae), a key lineage with dominant species of EBLFs, to gain insights into how evergreen versus deciduous trait shifted, providing insights into the origin and historical dynamics of EBLFs in East Asia under Cenozoic climate change. We reconstructed a robust phylogeny of the Litsea complex using genome-wide single-nucleotide variants (SNVs) with eight clades resolved. Fossil-calibrated analyses, diversification rate shifts, ancestral habit, ecological niche modelling and climate niche reconstruction were employed to estimate its origin and diversification pattern. Taking into account studies on other plant lineages dominating EBLFs of East Asia, it was revealed that the prototype of EBLFs in East Asia probably emerged in the Early Eocene (55-50 million years ago [Ma]), facilitated by the greenhouse warming. As a response to the cooling and drying climate in the Middle to Late Eocene (48-38 Ma), deciduous habits were evolved in the dominant lineages of the EBLFs in East Asia. Up to the Early Miocene (23 Ma), the prevailing of East Asian monsoon increased the extreme seasonal precipitation and accelerated the emergence of evergreen habits of the dominant lineages, and ultimately shaped the vegetation resembling that of today.
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Affiliation(s)
- Sheng-Yuan Qin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Yu Zuo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xin-Yu Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shui-Yin Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiang-Qin Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Guo Xiang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Centre for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Jun Rong
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Centre for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Zhi-Fang Liu
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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11
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Guo C, Luo Y, Gao LM, Yi TS, Li HT, Yang JB, Li DZ. Phylogenomics and the flowering plant tree of life. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:299-323. [PMID: 36416284 DOI: 10.1111/jipb.13415] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.
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Affiliation(s)
- Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
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Yuan B, Yuan JK, Huang CG, Lian JR, Li YH, Fan XM, Yuan DY. Pseudopollen in Camellia oleifera and its implications for pollination ecology and taxonomy. FRONTIERS IN PLANT SCIENCE 2022; 13:1032187. [PMID: 36466242 PMCID: PMC9712735 DOI: 10.3389/fpls.2022.1032187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/24/2022] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS In 1997, Tsou described the special differentiation of the connective tissues of some species of Theaceae to produce single-celled powders with unique patterns called pseudopollen. The purpose of this study was to investigate the morphological structure of the pseudopollen of Camellia oleifera (Theaceae) and to study the morphology of pseudopollen in seven other Camellia species. METHODS Scanning electron microscopy, paraffin section, light microscopy, transmission electron microscopy, histochemistry. KEY RESULT C. oleifera pseudopollen was similar to normal pollen in macroscopic morphology but different microscopically. The normal pollen was starch-rich and yellow, with mostly reticulate exine ornamentation. In contrast, the pseudopollen was a white powder, single-celled and rich in protein, with parallel unbranched ridge lines on the outer wall, and originated from the parenchyma of the connective tissues. There are also differences in the micro-characteristics of normal and pseudopollen among different species in Camellia. CONCLUSION There are great differences in morphological structure between C. oleifera and other species in Camellia normal pollen and pseudopollen; these results may indicate that the pseudopollen can be used as a taxonomic basis for Camellia, and the macroscopic similarity between pseudopollen and pollen and histochemical characteristics of pseudopollen can be a pollination strategy.
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Affiliation(s)
- Bin Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha, China
| | - Jing-Kun Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha, China
| | - Cheng-Gong Huang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha, China
| | - Jia-Rui Lian
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha, China
| | - Yi-Huan Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha, China
| | - Xiao-Ming Fan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha, China
| | - De-Yi Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha, China
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Zhu X, Liang H, Jiang H, Kang M, Wei X, Deng L, Shi Y. Phylogeographic structure of Heteroplexis (Asteraceae), an endangered endemic genus in the limestone karst regions of southern China. FRONTIERS IN PLANT SCIENCE 2022; 13:999964. [PMID: 36388513 PMCID: PMC9647136 DOI: 10.3389/fpls.2022.999964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Though the karst regions in south and southwest China are plant diversity hotspots, our understanding of the phylogeography and evolutionary history of the plants there remains limited. The genus Heteroplexis (Asteraceae) is one of the typical representative plants isolated by karst habitat islands, and is also an endangered and endemic plant to China. In this study, species-level phylogeographic analysis of the genus Heteroplexis was conducted using restriction site-associated DNA sequencing (RADseq). The genetic structure showed a clear phylogeographic structure consistent with the current species boundaries in the H. microcephala, H. incana, H. vernonioides, H. sericophylla, and H. impressinervia. The significant global (R = 0.37, P < 0.01) and regional (R = 0.650.95, P < 0.05) isolation by distance (IBD) signals among species indicate strong geographic isolation in the karst mountains, which may result in chronically restricted gene flow and increased genetic drift and differentiation. Furthermore, the phylogeographic structure of Heteroplexis suggested a southward migration since the last glacial period. Demographic analysis revealed the karst mountains as a refuge for Heteroplexis species. Finally, both Treemix and ABBA-BABA statistic detected significant historical gene flow between species. Significant historical gene flow and long-term stability of effective population size (Ne) together explain the high genome-wide genetic diversity among species (π = 0.05370.0838). However, the recent collapse of Ne, widespread inbreeding within populations, and restricted contemporary gene flow suggest that Heteroplexis species are probably facing a high risk of genetic diversity loss. Our results help to understand the evolutionary history of karst plants and guide conservation.
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Affiliation(s)
- Xianliang Zhu
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Hui Liang
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
- College of Life Science, Guangxi Normal University, Guilin, China
| | - Haolong Jiang
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Ming Kang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiao Wei
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Lili Deng
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Yancai Shi
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
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14
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Cheng L, Li M, Han Q, Qiao Z, Hao Y, Balbuena TS, Zhao Y. Phylogenomics Resolves the Phylogeny of Theaceae by Using Low-Copy and Multi-Copy Nuclear Gene Makers and Uncovers a Fast Radiation Event Contributing to Tea Plants Diversity. BIOLOGY 2022; 11:biology11071007. [PMID: 36101388 PMCID: PMC9311850 DOI: 10.3390/biology11071007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary The Theaceae includes more than 300 species of great morphological diversity and has immense economic, cultural, and ornamental values. However, the evolutionary history of this family remains elusive. We integrated 91 genomes and transcriptome datasets of Theaceae and successfully resolved the phylogeny of Theaceae including relatives of cultivated tea plants from both extensive low-copy and multi-copy nuclear gene markers. Bayes-based molecular dating revealed that the ancestor of the tea family originated slightly earlier than the K-Pg boundary (Mass extinction events including the extinction of dinosaurs) with early diversification of three tribes associated with the Early Eocene Climatic Optimum. Further speciation analysis suggested a sole significant diversification shift rate in the common ancestor of Camellia associated with the Mid-Miocene Climatic Optimum. Collectively, polyploidy events, and key morphological innovation characters, such as pericarp with seed coat hardening, could possibly contribute to the Theaceae species diversity. Abstract Tea is one of the three most popular nonalcoholic beverages globally and has extremely high economic and cultural value. Currently, the classification, taxonomy, and evolutionary history of the tea family are largely elusive, including phylogeny, divergence, speciation, and diversity. For understanding the evolutionary history and dynamics of species diversity in Theaceae, a robust phylogenetic framework based on 1785 low-copy and 79,103 multi-copy nuclear genes from 91 tea plant genomes and transcriptome datasets had been reconstructed. Our results maximumly supported that the tribes Stewartieae and Gordonieae are successive sister groups to the tribe Theeae from both coalescent and super matrix ML tree analyses. Moreover, in the most evolved tribe, Theeae, the monophyletic genera Pyrenaria, Apterosperma, and Polyspora are the successive sister groups of Camellia. We also yield a well-resolved relationship of Camellia, which contains the vast majority of Theaceae species richness. Molecular dating suggests that Theaceae originated in the late L-Cretaceous, with subsequent early radiation under the Early Eocene Climatic Optimal (EECO) for the three tribes. A diversification rate shift was detected in the common ancestors of Camellia with subsequent acceleration in speciation rate under the climate optimum in the early Miocene. These results provide a phylogenetic framework and new insights into factors that likely have contributed to the survival of Theaceae, especially a successful radiation event of genus Camellia members to subtropic/tropic regions. These novel findings will facilitate the efficient conservation and utilization of germplasm resources for breeding cultivated tea and oil-tea. Collectively, these results provide a foundation for further morphological and functional evolutionary analyses across Theaceae.
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Affiliation(s)
- Lin Cheng
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Mengge Li
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Qunwei Han
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Zhen Qiao
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Yanlin Hao
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Tiago Santana Balbuena
- Department of Agricultural, Livestock and Environmental Biotechnology, Sao Paulo State University, Jaboticabal 14884-900, Brazil;
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
- College of Agriculture, Guizhou University, Guiyang 550025, China
- Correspondence:
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15
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Zhang Q, Zhao L, Folk RA, Zhao JL, Zamora NA, Yang SX, Soltis DE, Soltis PS, Gao LM, Peng H, Yu XQ. Phylotranscriptomics of Theaceae: generic-level relationships, reticulation and whole-genome duplication. ANNALS OF BOTANY 2022; 129:457-471. [PMID: 35037017 PMCID: PMC8944729 DOI: 10.1093/aob/mcac007] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/16/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Theaceae, with three tribes, nine genera and more than 200 species, are of great economic and ecological importance. Recent phylogenetic analyses based on plastomic data resolved the relationships among the three tribes and the intergeneric relationships within two of those tribes. However, generic-level relationships within the largest tribe, Theeae, were not fully resolved. The role of putative whole-genome duplication (WGD) events in the family and possible hybridization events among genera within Theeae also remain to be tested further. METHODS Transcriptomes or low-depth whole-genome sequencing of 57 species of Theaceae, as well as additional plastome sequence data, were generated. Using a dataset of low-copy nuclear genes, we reconstructed phylogenetic relationships using concatenated, species tree and phylogenetic network approaches. We further conducted molecular dating analyses and inferred possible WGD events by examining the distribution of the number of synonymous substitutions per synonymous site (Ks) for paralogues in each species. For plastid protein-coding sequences , phylogenies were reconstructed for comparison with the results obtained from analysis of the nuclear dataset. RESULTS Based on the 610 low-copy nuclear genes (858 606 bp in length) investigated, Stewartieae was resolved as sister to the other two tribes. Within Theeae, the Apterosperma-Laplacea clade grouped with Pyrenaria, leaving Camellia and Polyspora as sister. The estimated ages within Theaceae were largely consistent with previous studies based mainly on plastome data. Two reticulation events within Camellia and one between the common ancestor of Gordonia and Schima were found. All members of the tea family shared two WGD events, an older At-γ and a recent Ad-β; both events were also shared with the outgroups (Diapensiaceae, Pentaphylacaceae, Styracaceae and Symplocaceae). CONCLUSIONS Our analyses using low-copy nuclear genes improved understanding of phylogenetic relationships at the tribal and generic levels previously proposed based on plastome data, but the phylogenetic position of the Apterosperma-Laplacea clade needs more attention. There is no evidence for extensive intergeneric hybridization within Theeae or for a Theaceae-specific WGD event. Land bridges (e.g. the Bering land bridge) during the Late Oligocene may have permitted the intercontinental plant movements that facilitated the putative ancient introgression between the common ancestor of Gordonia and Schima.
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Affiliation(s)
- Qiong Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lei Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, MS, USA
| | - Jian-Li Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
| | - Nelson A Zamora
- National Herbarium of Costa Rica (CR), Natural History Department of National Museum of Costa Rica, San José, Costa Rica
| | - Shi-Xiong Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan Lijiang Forest Ecosystem National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, China
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Dong W, Liu Y, Li E, Xu C, Sun J, Li W, Zhou S, Zhang Z, Suo Z. Phylogenomics and biogeography of Catalpa (Bignoniaceae) reveal incomplete lineage sorting and three dispersal events. Mol Phylogenet Evol 2021; 166:107330. [PMID: 34687844 DOI: 10.1016/j.ympev.2021.107330] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/10/2021] [Accepted: 10/13/2021] [Indexed: 01/21/2023]
Abstract
Catalpa Scop. (Bignoniaceae) is a small genus (8 spp.) of trees that is disjunctly distributed among eastern Asia, eastern United States, and the West Indies. Catalpa bears beautiful inflorescences and have been cultivated as important ornamental trees for landscaping, gardening, and timber. However, the phylogenetic relationships and biogeographic history of the genus have remained unresolved. In this study, we used a large genomic dataset that includes data from the chloroplast (plastomes), and nuclear genomes (ITS and 5,759 single-copy nuclear genes) to reconstruct phylogenetic relationship within Catalpa, test interspecific gene flow events within the genus, and infer its biogeographic history. Our phylogenetic results indicate that Catalpa is monophyletic containing two main clades, section Catalpa and section Macrocatalpa. Section Catalpa is further divided into three subclades. While most relationships are congruent between the chloroplast and nuclear datasets, the position of C. ovata differs, likely due to incomplete lineage sorting. Interspecific gene flow events include C. bungei s.s. with vectors of inheritance from C. duclouxii and C. fargesii, supporting a combination of these three species and recognizing a broadly circumscribed C. bungei s.l. Our biogeographic study suggests three main dispersal events, two of which occurred during the Oligocene. The first dispersal event occurred from southwestern North America and Mexico into the Greater Antilles giving rise to the ancestor of the section of Macrocatalpa. The second dispersal event also occurred from southwestern North America and Mexico, but led to central and northern North America, subsequently reaching China through the Bering land bridge, and also reaching Europe through the North Atlantic land bridge. The third dispersal event took place in the Miocene from China to North America and gave rise to a clade composed of C. bignonioides and C. speciosa. This study uses a phylogenomic approach and biogeographical methods to infer the evolutionary history of Catalpa, highlighting issues associated with gene tree discordance, and suggesting that incomplete lineage sorting likely played an important role in the evolutionary history of Catalpa.
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Affiliation(s)
- Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China.
| | - Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Enze Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wenying Li
- Institute of Forestry New Technologies, Chinese Academy of Forestry, Beijing 100091, China
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Zhili Suo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Incorporating Topological and Age Uncertainty into Event-Based Biogeography of Sand Spiders Supports Paleo-Islands in Galapagos and Ancient Connections among Neotropical Dry Forests. DIVERSITY 2021. [DOI: 10.3390/d13090418] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Event-based biogeographic methods, such as dispersal-extinction-cladogenesis, have become increasingly popular for attempting to reconstruct the biogeographic history of organisms. Such methods employ distributional data of sampled species and a dated phylogenetic tree to estimate ancestral distribution ranges. Because the input tree is often a single consensus tree, uncertainty in topology and age estimates are rarely accounted for, even when they may affect the outcome of biogeographic estimates. Even when such uncertainties are taken into account for estimates of ancestral ranges, they are usually ignored when researchers compare competing biogeographic hypotheses. We explore the effect of incorporating this uncertainty in a biogeographic analysis of the 21 species of sand spiders (Sicariidae: Sicarius) from Neotropical xeric biomes, based on a total-evidence phylogeny including a complete sampling of the genus. Using a custom R script, we account for uncertainty in ages and topology by estimating ancestral ranges over a sample of trees from the posterior distribution of a Bayesian analysis, and for uncertainty in biogeographic estimates by using stochastic maps. This approach allows for counting biogeographic events such as dispersal among areas, counting lineages through time per area, and testing biogeographic hypotheses, while not overestimating the confidence in a single topology. Including uncertainty in ages indicates that Sicarius dispersed to the Galapagos Islands when the archipelago was formed by paleo-islands that are now submerged; model comparison strongly favors a scenario where dispersal took place before the current islands emerged. We also investigated past connections among currently disjunct Neotropical dry forests; failing to account for topological uncertainty underestimates possible connections among the Caatinga and Andean dry forests in favor of connections among Caatinga and Caribbean + Mesoamerican dry forests. Additionally, we find that biogeographic models including a founder-event speciation parameter (“+J”) are more prone to suffer from the overconfidence effects of estimating ancestral ranges using a single topology. This effect is alleviated by incorporating topological and age uncertainty while estimating stochastic maps, increasing the similarity in the inference of biogeographic events between models with or without a founder-event speciation parameter. We argue that incorporating phylogenetic uncertainty in biogeographic hypothesis-testing is valuable and should be a commonplace approach in the presence of rogue taxa or wide confidence intervals in age estimates, and especially when using models including founder-event speciation.
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