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Roeble L, van Benthem KJ, Weigelt P, Kreft H, Knope ML, Mandel JR, Vargas P, Etienne RS, Valente L. Island biogeography of the megadiverse plant family Asteraceae. Nat Commun 2024; 15:7276. [PMID: 39179568 PMCID: PMC11343744 DOI: 10.1038/s41467-024-51556-7] [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: 12/19/2023] [Accepted: 08/09/2024] [Indexed: 08/26/2024] Open
Abstract
The megadiverse plant family Asteraceae forms an iconic component of island floras including many spectacular radiations, but a global picture of its insular diversity is lacking. Here, we uncover the global biogeographical and evolutionary patterns of Asteraceae on islands to reveal the magnitude and potential causes of their evolutionary success. We compile a global checklist of Asteraceae species native and endemic to islands and combine it with macroecological analyses and a phylogenetic review of island radiations. Asteraceae have a global distribution on islands, comprising approximately 6,000 native island species, with 58% endemics. While diversity of the family on islands is lower than expected given its overall diversity, Asteraceae are the most diverse family on oceanic islands, suggesting an exceptional ability to thrive in isolation. In agreement with island biogeography predictions, native Asteraceae diversity increases with area and decreases with isolation, while endemism increases with both. We identify 39 confirmed island radiations and 69 putative radiations, exceeding numbers for other iconic insular groups. Our results reveal Asteraceae offer immense potential for research in ecology and evolution, given their close tracking of island biogeography expectations, large number of both species and radiations, cosmopolitan distribution, and numerous undiscovered radiations.
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Affiliation(s)
- Lizzie Roeble
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands.
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands.
| | - Koen J van Benthem
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Patrick Weigelt
- Biodiversity, Macroecology and Biogeography, University of Göttingen, 37077, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Göttingen, Germany
- Campus Institute Data Science, Göttingen, Germany
| | - Holger Kreft
- Biodiversity, Macroecology and Biogeography, University of Göttingen, 37077, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Göttingen, Germany
- Campus Institute Data Science, Göttingen, Germany
| | - Matthew L Knope
- University of Hawai'i at Hilo, Dept. of Biology, 200 W. Kawili St., Hilo, HI, 96720, USA
| | - Jennifer R Mandel
- Department of Biological Sciences, University of Memphis, Memphis, TN, USA
| | - Pablo Vargas
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Luis Valente
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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Liu X, Luo J, Chen H, Li T, Qu T, Tang M, Fu Z. Comparative analysis of complete chloroplast genomes of Synotis species (Asteraceae, Senecioneae) for identification and phylogenetic analysis. BMC Genomics 2024; 25:769. [PMID: 39112930 PMCID: PMC11308156 DOI: 10.1186/s12864-024-10663-x] [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: 07/09/2023] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND The Synotis (C. B. Clarke) C. Jeffrey & Y. L. Chen is an ecologically important genus of the tribe Senecioneae, family Asteraceae. Because most species of the genus bear similar morphology, traditional morphological identification methods are very difficult to discriminate them. Therefore, it is essential to develop a reliable and effective identification method for Synotis species. In this study, the complete chloroplast (cp.) genomes of four Synotis species, S. cavaleriei (H.Lév.) C. Jeffrey & Y.L. Chen, S. duclouxii (Dunn) C. Jeffrey & Y.L. Chen, S. nagensium (C.B. Clarke) C. Jeffrey & Y.L. Chen and S. erythropappa (Bureau & Franch.) C. Jeffrey & Y. L. Chen had been sequenced using next-generation sequencing technology and reported here. RESULTS These four cp. genomes exhibited a typical quadripartite structure and contained the large single-copy regions (LSC, 83,288 to 83,399 bp), the small single-copy regions (SSC, 18,262 to 18,287 bp), and the inverted repeat regions (IR, 24,837 to 24,842 bp). Each of the four cp. genomes encoded 134 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (ycf1 and rps19). The highly variable regions (trnC-GCA-petN, ccsA-psaC, trnE-UUC-rpoB, ycf1, ccsA and petN) may be used as potential molecular barcodes. The complete cp. genomes sequence of Synotis could be used as the potentially effective super-barcode to accurately identify Synotis species. Phylogenetic analysis demonstrated that the four Synotis species were clustered into a monophyletic group, and they were closed to the Senecio, Crassocephalum and Dendrosenecio in tribe Senecioneae. CONCLUSIONS This study will be useful for further species identification, evolution, genetic diversity and phylogenetic studies within this genus Synotis and the tribe Senecioneae.
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Affiliation(s)
- Xiaofeng Liu
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest (Sichuan Normal University), Ministry of Education, Chengdu, 610066, China
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Junjia Luo
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Hui Chen
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Tingyu Li
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Tianmeng Qu
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Ming Tang
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Zhixi Fu
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest (Sichuan Normal University), Ministry of Education, Chengdu, 610066, China.
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China.
- Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University, Chengdu, 610101, China.
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Heads M, Saldivia P. The challenging biogeography of the Juan Fernández Islands and Coast Range of central Chile explained by new models of East Pacific tectonics. Biol Rev Camb Philos Soc 2024. [PMID: 39032008 DOI: 10.1111/brv.13121] [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: 12/05/2023] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 07/22/2024]
Abstract
Biogeographers have often been puzzled by several unusual features in the Juan Fernández Islands (JFI) biota. These include the very high endemism density, multiple endemics that are older than the current islands, close biogeographic affinities with the central and West Pacific, and affinities with the diverse Coast Range of central Chile. We review aspects of biogeography in the JFI and the Coast Range in light of recent geological studies. These have examined the mantle below the East Pacific and South America, and have produced radical, new ideas on tectonic history. A long-lived, intraoceanic archipelago ~9000 km long is now thought to have existed in the East Pacific (passing between the JFI hotspot and mainland Chile) until the mid-Cretaceous. At this time, South America, which was moving westward with the opening of the Atlantic, collided with the archipelago. The assumption that the JFI biota is no older than its current islands is questionable, as taxa would have survived on prior islands produced at the JFI hotspot. We propose a new interpretation of evolution in the region based on tectonics rather than on island age and incorporating the following factors: the newly described East Pacific Archipelago; a long history for the JFI hotspot; metapopulation dynamics, including metapopulation vicariance; and formation of the Humboldt Current in the Cretaceous. The model accounts for many distinctive features of the JFI and Coast Range biota.
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Affiliation(s)
- Michael Heads
- Buffalo Museum of Science, 1020 Humboldt Parkway, Buffalo, NY, 14211-1293, USA
| | - Patricio Saldivia
- Biota Ltda, Miguel Claro 1224, Providencia, Santiago, Chile
- Museo Regional de Aysén, Km. 3 camino a Coyhaique Alto, Coyhaique, Chile
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Chen H, Li T, Chen X, Qu T, Zheng X, Luo J, Li B, Zhang G, Fu Z. Insights into comparative genomics, structural features, and phylogenetic relationship of species from Eurasian Aster and its related genera (Asteraceae: Astereae) based on complete chloroplast genome. FRONTIERS IN PLANT SCIENCE 2024; 15:1367132. [PMID: 38736446 PMCID: PMC11082289 DOI: 10.3389/fpls.2024.1367132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/25/2024] [Indexed: 05/14/2024]
Abstract
Aster L. is an economically and phylogenetically important genus in the tribe Astereae. Here, the complete plastomes of the eight Aster species were assembled and characterized using next-generation sequencing datasets. The results indicated the complete plastomes of Aster had a quadripartite structure. These genomes were 152,045-152,729 bp in length and contained 132-133 genes, including 87 protein-coding genes, 37-38 tRNA genes, and eight rRNA genes. Expansion or contraction of inverted repeat regions and forward, palindromic, complement, and reverse repeats were detected in the eight Aster species. Additionally, our analyses showed the richest type of simple sequence repeats was A/T mononucleotides, and 14 highly variable regions were discovered by analyzing the border regions, sequence divergence, and hotspots. Phylogenetic analyses indicated that 27 species in Astereae were clustered into six clades, i.e., A to D, North American, and outgroup clades, and supported that the genera Heteropappus, Kalimeris, and Heteroplexis are nested within Aster. The results indicated the clades B to D might be considered as genera. Divergence time estimate showed the clades A, B, C, and D diverged at 23.15 Mya, 15.13 Mya, 24.29 Mya, and 21.66 Mya, respectively. These results shed light on the phylogenetic relationships of Aster and provided new information on species identification of Aster and its related genera.
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Affiliation(s)
- Hui Chen
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Tingyu Li
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
| | - Xinyu Chen
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
| | - Tianmeng Qu
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
| | - Xinyi Zheng
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
| | - Junjia Luo
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
| | - Bo Li
- Sichuan Environmental Monitoring Center, Chengdu, China
| | - Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Zhixi Fu
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
- Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University, Chengdu, China
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5
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Sage RF, Gilman IS, Smith JAC, Silvera K, Edwards EJ. Atmospheric CO2 decline and the timing of CAM plant evolution. ANNALS OF BOTANY 2023; 132:753-770. [PMID: 37642245 PMCID: PMC10799994 DOI: 10.1093/aob/mcad122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/19/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND AND AIMS CAM photosynthesis is hypothesized to have evolved in atmospheres of low CO2 concentration in recent geological time because of its ability to concentrate CO2 around Rubisco and boost water use efficiency relative to C3 photosynthesis. We assess this hypothesis by compiling estimates of when CAM clades arose using phylogenetic chronograms for 73 CAM clades. We further consider evidence of how atmospheric CO2 affects CAM relative to C3 photosynthesis. RESULTS Where CAM origins can be inferred, strong CAM is estimated to have appeared in the past 30 million years in 46 of 48 examined clades, after atmospheric CO2 had declined from high (near 800 ppm) to lower (<450 ppm) values. In turn, 21 of 25 clades containing CAM species (but where CAM origins are less certain) also arose in the past 30 million years. In these clades, CAM is probably younger than the clade origin. We found evidence for repeated weak CAM evolution during the higher CO2 conditions before 30 million years ago, and possible strong CAM origins in the Crassulaceae during the Cretaceous period prior to atmospheric CO2 decline. Most CAM-specific clades arose in the past 15 million years, in a similar pattern observed for origins of C4 clades. CONCLUSIONS The evidence indicates strong CAM repeatedly evolved in reduced CO2 conditions of the past 30 million years. Weaker CAM can pre-date low CO2 and, in the Crassulaceae, strong CAM may also have arisen in water-limited microsites under relatively high CO2. Experimental evidence from extant CAM species demonstrates that elevated CO2 reduces the importance of nocturnal CO2 fixation by increasing the contribution of C3 photosynthesis to daily carbon gain. Thus, the advantage of strong CAM would be reduced in high CO2, such that its evolution appears less likely and restricted to more extreme environments than possible in low CO2.
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Affiliation(s)
- Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Ian S Gilman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - J Andrew C Smith
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Katia Silvera
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
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Zhao LC, Chen R, Yu ZY, Tang M, Yang QE. Synotisjinpingensis (Asteraceae, Senecioneae), a new species with white ray florets from southeastern Yunnan, China. PHYTOKEYS 2023; 235:199-210. [PMID: 38033623 PMCID: PMC10682980 DOI: 10.3897/phytokeys.235.112230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/22/2023] [Indexed: 12/02/2023]
Abstract
Synotisjinpingensis (Asteraceae, Senecioneae), a new species from Jinping county in southeastern Yunnan province, China, is described and illustrated. This species is distinguished by having white ray florets in the genus Synotis, in which only species with yellow ray florets have been hitherto known. In habit and leaf shape S.jinpingensis is most closely similar to S.duclouxii, a species occurring in southwestern Guizhou, southern Sichuan and northeastern Yunnan, China, but differs, in addition to the color of ray florets, by having fewer lateral veins of leaves, obviously longer bracts of calyculus, and larger phyllaries. The membership of the new species within Synotis is strongly corroborated by evidence from floral micromorphology and phylogenetic analyses based on ITS sequence data. Color photographs of living plants, a distribution map, and provisional IUCN status of S.jinpingensis are provided.
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Affiliation(s)
- Liao-Chen Zhao
- College of Forestry, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, China
| | - Ren Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, Guangdong, China
| | - Zhi-Yong Yu
- Center of Conservation Biology, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, Guangdong, China
| | - Ming Tang
- College of Forestry, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, China
| | - Qin-Er Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, Guangdong, China
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Skopalíková J, Leong-Škorničková J, Šída O, Newman M, Chumová Z, Zeisek V, Jarolímová V, Poulsen AD, Dantas-Queiroz MV, Fér T, Záveská E. Ancient hybridization in Curcuma (Zingiberaceae)-Accelerator or brake in lineage diversifications? THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:773-785. [PMID: 37537754 DOI: 10.1111/tpj.16408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023]
Abstract
Hybridization is a widespread phenomenon in the evolution of plants and exploring its role is crucial to understanding diversification processes of many taxonomic groups. Recently, more attention is focused on the role of ancient hybridization that has repeatedly been shown as triggers of evolutionary radiation, although in some cases, it can prevent further diversification. The causes, frequency, and consequences of ancient hybridization remain to be explored. Here, we present an account of several events of ancient hybridization in turmeric, the economically important plant genus Curcuma (Zingiberaceae), which harbors about 130 known species. We analyzed 1094 targeted low-copy genes and plastomes obtained by next-generation sequencing of 37 species of Curcuma, representing the known genetic diversity and spanning the geographical distribution of the genus. Using phylogenetic network analysis, we show that the entire genus Curcuma as well as its most speciose lineage arose via introgression from the genus Pyrgophyllum and one of the extinct lineages, respectively. We also document a single event of ancient hybridization, with C. vamana as a product, that represents an evolutionary dead end. We further discuss distinct circumstances of those hybridization events that deal mainly with (in)congruence in chromosome counts of the parental lineages.
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Affiliation(s)
- Jana Skopalíková
- Department of Botany, Charles University, Prague, Czech Republic
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Jana Leong-Škorničková
- The Herbarium, Singapore Botanic Gardens, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Otakar Šída
- Department of Botany, National Museum in Prague, Prague, Czech Republic
| | - Mark Newman
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK
| | - Zuzana Chumová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Vojtěch Zeisek
- Department of Botany, Charles University, Prague, Czech Republic
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Vlasta Jarolímová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | | | | | - Tomáš Fér
- Department of Botany, Charles University, Prague, Czech Republic
| | - Eliška Záveská
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
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Escobari B, Borsch T, Kilian N. Generic concepts and species diversity within the Gynoxyoid clade (Senecioneae, Compositae). PHYTOKEYS 2023; 234:61-106. [PMID: 37860599 PMCID: PMC10582726 DOI: 10.3897/phytokeys.234.107750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/19/2023] [Indexed: 10/21/2023]
Abstract
The Gynoxyoid clade of the Senecioneae (Asteraceae) until now included the five genera Aequatorium, Gynoxys, Nordenstamia, Paracalia and Paragynoxys as diagnosed using selected morphological characters. In their pre-phylogenetic circumscription, the genera Aequatorium and Paragynoxys were considered to inhabit the northern Andes in contrast to Nordenstamia and Paracalia that occur in the central Andes. The most species-rich genus, Gynoxys, was believed to be distributed throughout the Andes. We use a recently established plastid phylogenomic framework that rendered Gynoxys paraphyletic to further evaluate the delimitation of genera in the Gynoxyoid clade. We examine the morphological variation of all members of the Gynoxyoid to identify characters potentially informative at genus level. This results in a matrix of eleven, mostly multistate characters, including those originally used to diagnose these genera. The ancestral character state inference displays a high level of homoplasy, but nevertheless supports the recognition of four genera. Aequatorium is characterised by white radiate capitula. Paracalia and Paragynoxys share white flowers and floral characteristics, such as flower opening and length of disc flowers lobes, as plesiomorphic states, but differ in habit (scandent shrubs vs. trees). Paracalia also retained white flowers, but its two species are characterised by the absence of outer phyllaries. The genera Gynoxys and Nordenstamia comprise species with yellow capitula which appear to be a derived feature in the Gynoxyoids. The genus Nordenstamia, with eight species, is synonymised under Gynoxys since molecular evidence shows its species nested within various parts of the Gynoxys subclade and the morphological variation of Nordenstamia falls well within that of Gynoxys. With the goal to assign all species to four genera (Aequatorium, Gynoxys, Paracalia and Paragynoxys), we assess the states for the eleven characters for all members of the Gynoxyoids and generate new ETS and ITS sequences for 171 specimens belonging to 49 species to further support their generic placement. We provide a taxonomic treatment for the four genera recognised here including amended diagnoses and morphological descriptions. Furthermore, a species-level taxonomic backbone is elaborated for all genera using electronic tools that list 158 currently accepted names and synonyms (209 names in total) with the respective protologue and type information, as well as notes on the current understanding of species limits. Eleven names are newly synonymised, two are lectotypified and eight are newly transferred to other genera.
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Affiliation(s)
- Belen Escobari
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin 14195, Germany
- Herbario Nacional de Bolivia, Universidad Mayor de San Andres, Casilla, La Paz, 10077, Bolivia
| | - Thomas Borsch
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin 14195, Germany
| | - Norbert Kilian
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin 14195, Germany
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Chen Z, Zhou Z, Guo ZM, Van Do T, Sun H, Niu Y. Historical development of karst evergreen broadleaved forests in East Asia has shaped the evolution of a hemiparasitic genus Brandisia (Orobanchaceae). PLANT DIVERSITY 2023; 45:501-512. [PMID: 37936821 PMCID: PMC10625920 DOI: 10.1016/j.pld.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/14/2023] [Accepted: 03/17/2023] [Indexed: 11/09/2023]
Abstract
Brandisia is a shrubby genus of about eight species distributed basically in East Asian evergreen broadleaved forests (EBLFs), with distribution centers in the karst regions of Yunnan, Guizhou, and Guangxi in southwestern China. Based on the hemiparasitic and more or less liana habits of this genus, we hypothesized that its evolution and distribution were shaped by the development of EBLFs there. To test our hypothesis, the most comprehensive phylogenies of Brandisia hitherto were constructed based on plastome and nuclear loci (nrDNA, PHYA and PHYB); then divergence time and ancestral areas were inferred using the combined nuclear loci dataset. Phylogenetic analyses reconfirmed that Brandisia is a member of Orobanchaceae, with unstable placements caused by nuclear-plastid incongruences. Within Brandisia, three major clades were well supported, corresponding to the three subgenera based on morphology. Brandisia was inferred to have originated in the early Oligocene (32.69 Mya) in the Eastern Himalayas-SW China, followed by diversification in the early Miocene (19.45 Mya) in karst EBLFs. The differentiation dates of Brandisia were consistent with the origin of keystone species of EBLFs in this region (e.g., Fagaceae, Lauraceae, Theaceae, and Magnoliaceae) and the colonization of other characteristic groups (e.g., Gesneriaceae and Mahonia). These findings indicate that the distribution and evolution of Brandisia were facilitated by the rise of the karst EBLFs in East Asia. In addition, the woody and parasitic habits, and pollination characteristics of Brandisia may also be the important factors affecting its speciation and dispersal.
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Affiliation(s)
- Zhe Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
| | - Zhuo Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
| | - Ze-Min Guo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Truong Van Do
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay 10000, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay 10000, Hanoi, Vietnam
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
| | - Yang Niu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, Yunnan, China
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10
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Liu TJ, Zhang SY, Wei L, Lin W, Yan HF, Hao G, Ge XJ. Plastome evolution and phylogenomic insights into the evolution of Lysimachia (Primulaceae: Myrsinoideae). BMC PLANT BIOLOGY 2023; 23:359. [PMID: 37452336 PMCID: PMC10347800 DOI: 10.1186/s12870-023-04363-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Lysimachia L., the second largest genus within the subfamily Myrsinoideae of Primulaceae, comprises approximately 250 species worldwide. China is the species diversity center of Lysimachia, containing approximately 150 species. Despite advances in the backbone phylogeny of Lysimachia, species-level relationships remain poorly understood due to limited genomic information. This study analyzed 50 complete plastomes for 46 Lysimachia species. We aimed to identify the plastome structure features and hypervariable loci of Lysimachia. Additionally, the phylogenetic relationships and phylogenetic conflict signals in Lysimachia were examined. RESULTS These fifty plastomes within Lysimachia had the typical quadripartite structure, with lengths varying from 152,691 to 155,784 bp. Plastome size was positively correlated with IR and intron length. Thirteen highly variable regions in Lysimachia plastomes were identified. Additionally, ndhB, petB and ycf2 were found to be under positive selection. Plastid ML trees and species tree strongly supported that L. maritima as sister to subg. Palladia + subg. Lysimachia (Christinae clade), while the nrDNA ML tree clearly placed L. maritima and subg. Palladia as a sister group. CONCLUSIONS The structures of these plastomes of Lysimachia were generally conserved, but potential plastid markers and signatures of positive selection were detected. These genomic data provided new insights into the interspecific relationships of Lysimachia, including the cytonuclear discordance of the position of L. maritima, which may be the result of ghost introgression in the past. Our findings have established a basis for further exploration of the taxonomy, phylogeny and evolutionary history within Lysimachia.
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Affiliation(s)
- Tong-Jian Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Shu-Yan Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Lei Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Lin
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, 510650, China
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11
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Julca I, Vargas P, Gabaldón T. Phylogenomics of the Olea europaea complex using 15 whole genomes supports recurrent genetic admixture together with differentiation into seven subspecies. BMC Biol 2023; 21:85. [PMID: 37069619 PMCID: PMC10111821 DOI: 10.1186/s12915-023-01583-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND The last taxonomic account of Olea recognises six subspecies within Olea europaea L., including the Mediterranean olive tree (subsp. europaea) and five other subspecies (laperrinei, guanchica, maroccana, cerasiformis, and cuspidata) distributed across the Old World, including Macaronesian islands. The evolutionary history of this monophyletic group (O. europaea complex) has revealed a reticulated scenario involving hybridization and polyploidization events, leading to the presence of a polyploid series associated with the subspecies. However, how the polyploids originated, and how the different subspecies contributed to the domestication of the cultivated olive are questions still debated. Tracing the recent evolution and genetic diversification of the species is key for the management and preservation of its genetic resources. To study the recent history of the O. europaea complex, we compared newly sequenced and available genomes for 27 individuals representing the six subspecies. RESULTS Our results show discordance between current subspecies distributions and phylogenomic patterns, which support intricate biogeographic patterns. The subspecies guanchica, restricted to the Canary Islands, is closely related to subsp. europaea, and shows a high genetic diversity. The subsp. laperrinei, restricted now to high mountains of the Sahara desert, and the Canarian subsp. guanchica contributed to the formation of the allotetraploid subsp. cerasiformis (Madeira islands) and the allohexaploid subsp. maroccana (western Sahara region). Our phylogenomic data support the recognition of one more taxon (subsp. ferruginea) for the Asian populations, which is clearly segregated from the African subsp. cuspidata. CONCLUSIONS In sum, the O. europaea complex underwent several processes of hybridization, polyploidy, and geographical isolation resulting in seven independent lineages with certain morphological traits recognised into subspecies.
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Affiliation(s)
- Irene Julca
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Pablo Vargas
- Department of Biodiversity and Conservation, Real Jardín Botánico de Madrid, Calle Claudio Moyano 1, 28014, Madrid, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain.
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain.
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12
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Liu Q, Gao Y, Dong W, Zhao L. Plastome evolution and phylogeny of the tribe Ruteae (Rutaceae). Ecol Evol 2023; 13:e9821. [PMID: 36789335 PMCID: PMC9911629 DOI: 10.1002/ece3.9821] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 01/15/2023] [Accepted: 01/23/2023] [Indexed: 02/12/2023] Open
Abstract
Rutaceae is a large family, and the genus-level classification in the subfamilies or tribes of this family is not unified based on different taxonomic treatments. Until now, phylogenetic relationships of some genera in traditional tribe Ruteae have not been clearly resolved. In this study, seven new complete plastomes of this tribe were sequenced, and a comparative analysis was performed to investigate their plastome characteristics and evolution. In addition, we inferred the phylogenetic relationships of Ruteae based on complete plastome and nuclear ITS data. All plastomes exhibited a typical quadripartite structure and were relatively conserved in their structure and gene arrangement. Their genome sizes ranged from 154,656 bp to 160,677 bp, and the size variation was found to be associated with differences in IR expansion and gene loss. A total of 112 to 114 genes were identified in the genomes, including 78 to 79 protein-coding genes, 30 tRNA genes, 4 rRNA genes, and 2 pseudogenes. Sequence divergence analysis indicated that non-coding regions exhibited a higher percentage of variable characters, and nine non-coding and six coding regions were identified as divergent hotspots. Phylogenetic results based on different datasets showed that this tribe was divided into three reciprocally exclusive groups. The phylogenetic analyses between plastome and nuclear ITS data were partly incongruent with each other. This study provides new insights into plastome evolution of Ruteae as well as Rutaceae. The availability of these plastomes provides useful genomic resources for molecular DNA barcodes and phylogenetically informative markers and deepens our understanding of the phylogeny in Ruteae.
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Affiliation(s)
- Qiaoyun Liu
- School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Yongwei Gao
- School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Wenpan Dong
- School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Liangcheng Zhao
- Museum of Beijing Forestry University, Beijing Forestry UniversityBeijingChina
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Sciuto K, Wolf MA, Sfriso A, Brancaleoni L, Iberite M, Iamonico D. Molecular and Morphometric Update on Italian Salicornia (Chenopodiaceae), with a Focus on the Species S. procumbens s. l. PLANTS (BASEL, SWITZERLAND) 2023; 12:375. [PMID: 36679088 PMCID: PMC9860865 DOI: 10.3390/plants12020375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
Salicornia is a highly taxonomically problematic genus due to the reduced morphological observable characters. Ten Eurasian species are currently recognized: S. alpini, S. europaea, S. fruticosa, S. hispanica, S. lagascae, S. perennans, S. perennis, S. persica, S. procumbens, and S. pruinosa. In addition, eleven subspecies are accepted, mainly based on their distribution areas. Along the Venetian coasts and in Sardinia, in the past, an endemic species called S. veneta was recognized, but this name was later synonymized with S. procumbens subsp. procumbens. The aim of the present research is investigating different Italian Salicornia populations by a molecular point of view, using the nuclear ribosomal external transcribed spacer ETS and the plastid psbA-trnH intergenic spacer. A particular focus is on the comparison between Venetian (including those occurring in locus classicus of S. veneta) and Sardinian S. procumbens and other Italian populations of this species. The molecular analyses based on the plastid marker highlight that the Italian S. procumbens populations form two well distinct groups. In particular, some of the Venetian (Locus classicus of S. veneta) and all the Sardinian specimens are genetically distinct (=plastid haplotype 1) from the other investigated populations (=plastid haplotype 2). This indicates that the psbA-trnH haplotype 1 glassworts represent a distinct entity, which we suppose to coincide with the former S. veneta. Therefore, we suggest to recognize this taxonomic entity at the subspecies rank, as S. procumbens subsp. veneta comb. and stat. nov. However, contrary to the results found with the plastid psbA-trnH intergenic spacer, the ETS locus does not show a separation into two distinct clades for S. procumbens, probably due to a different evolution of the two loci. Nevertheless, in the ETS phylogenetic reconstruction, the Sardinian specimens (=ribotypes 2 and 3) are placed, together with a Moroccan sample, in a subclade separated from all the other S. procumbens. These results suggest that the Sardinian populations can represent a subspecies/incipient speciation process, probably due to geographic isolation. In the light of this, morphometric analyses (k-means, MANOVA, PCA, DA, and Box-Plot) have been carried out on the Sardinian and Venetian populations to verify if this distinction is detectable also by a morphological point of view. The morphometric analyses highlight the existence of two groups, concerning both the nuclear and plastid trees. Six characters were found to be diagnostic.
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Affiliation(s)
- Katia Sciuto
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Marion A. Wolf
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Adriano Sfriso
- Department of Environmental Sciences, Informatics and Statistics, Ca’Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy
| | - Lisa Brancaleoni
- Department of Environment and Prevention Sciences, University of Ferrara, C.so Ercole I D’Este 32, 44121 Ferrara, Italy
| | - Mauro Iberite
- Department of Environmental Biology, Sapienza University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Duilio Iamonico
- Ce.R.S.I.Te.S., Sapienza University of Rome, Via XXIV Maggio 7, 04100 Latina, Italy
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14
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Siu TY, Kong BLH, Wong KH, Wu HY, But GWC, Shaw PC, Lau DTW. Characterization and phylogenetic analysis of the complete chloroplast genome of Emilia sonchifolia (L.) DC. Mitochondrial DNA B Resour 2023; 8:20-22. [PMID: 36620323 PMCID: PMC9815244 DOI: 10.1080/23802359.2022.2055980] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Emilia sonchifolia is a herb with antioxidant, anti-inflammatory, antitumor, and wound healing properties. The complete chloroplast genome (cp genome) of the genus Emilia was sequenced for the first time. The cp genome of E. sonchifolia is 151,474 bp in length. It contained a large single-copy (LSC) region (84,004 bp), and small single-copy (SSC) region (17,980 bp), and two inverted repeats (IRs, 24,745 bp). Phylogenetic analysis of 24 species was conducted. E. sonchifolia was found to be closely related to Pericallis hybrida and Dendrosenecio spp. The sequenced cp genome would be useful to understand the phylogeny and genomic studies of the genus Emilia.
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Affiliation(s)
- Tin-Yan Siu
- School of Life Sciences, Shiu-Ying Hu Herbarium, The Chinese University of Hong Kong, Hong Kong
| | - Bobby Lim-Ho Kong
- Li Dak Sum Yip Yio Chin R&D Centre for Chinese Medicines, The Chinese University of Hong Kong, Hong Kong,School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Kwan-Ho Wong
- School of Life Sciences, Shiu-Ying Hu Herbarium, The Chinese University of Hong Kong, Hong Kong
| | - Hoi-Yan Wu
- Li Dak Sum Yip Yio Chin R&D Centre for Chinese Medicines, The Chinese University of Hong Kong, Hong Kong
| | | | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R&D Centre for Chinese Medicines, The Chinese University of Hong Kong, Hong Kong,School of Life Sciences, The Chinese University of Hong Kong, Hong Kong,State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants (CUHK) and Institute of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong
| | - David Tai-Wai Lau
- School of Life Sciences, Shiu-Ying Hu Herbarium, The Chinese University of Hong Kong, Hong Kong,Li Dak Sum Yip Yio Chin R&D Centre for Chinese Medicines, The Chinese University of Hong Kong, Hong Kong,CONTACT David Tai-Wai Lau School of Life Sciences, Shiu-Ying Hu Herbarium, The Chinese University of Hong Kong, Hong Kong
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15
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Lei JQ, Liu CK, Cai J, Price M, Zhou SD, He XJ. Evidence from Phylogenomics and Morphology Provide Insights into the Phylogeny, Plastome Evolution, and Taxonomy of Kitagawia. PLANTS (BASEL, SWITZERLAND) 2022; 11:3275. [PMID: 36501315 PMCID: PMC9740501 DOI: 10.3390/plants11233275] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Kitagawia Pimenov is one of the segregate genera of Peucedanum sensu lato within the Apiaceae. The phylogenetic position and morphological delimitation of Kitagawia have been controversial. In this study, we used plastid genome (plastome) and nuclear ribosomal DNA (nrDNA) sequences to reconstruct the phylogeny of Kitagawia, along with comparative plastome and morphological analyses between Kitagawia and related taxa. The phylogenetic results identified that all examined Kitagawia species were divided into Subclade I and Subclade II within the tribe Selineae, and they were all distant from the representative members of Peucedanum sensu stricto. The plastomes of Kitagawia and related taxa showed visible differences in the LSC/IRa junction (JLA) and several hypervariable regions, which separated Subclade I and Subclade II from other taxa. Fruit anatomical and micromorphological characteristics, as well as general morphological characteristics, distinguished the four Kitagawia species within Subclade I from Subclade II and other related genera. This study supported the separation of Kitagawia from Peucedanum sensu lato, confirmed that Kitagawia belongs to Selineae, and two species (K. praeruptora and K. formosana) within Subclade II should be placed in a new genus. We believe that the "core" Kitagawia should be limited to Subclade I, and this genus can be distinguished by the association of a series of morphological characteristics. Overall, our study provides new insights into the phylogeny, plastome evolution, and taxonomy of Kitagawia.
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Affiliation(s)
- Jia-Qing Lei
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Chang-Kun Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jing Cai
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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16
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Cai J, Qin HH, Lei JQ, Liu CK, He XJ, Zhou SD. The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data. BMC PLANT BIOLOGY 2022; 22:534. [PMID: 36380268 PMCID: PMC9667662 DOI: 10.1186/s12870-022-03919-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The genus Seseli L., which consists of 125-140 species distributed in the Old World from western Europe and northwestern Africa to China and Japan, is one of the largest and most taxonomically difficult genera of Apiaceae Lindl. Although several previous studies have been conducted on Seseli based on limited morphological characteristics and molecular fragments, a robust and comprehensive phylogeny of Seseli remains elusive. Plastomes provide abundant genetic information and have been widely used in studying plant phylogeny and evolution. Consequently, we newly generated the complete plastomes of eleven Seseli taxa. We combined plastome data and morphological characteristics to investigate the phylogeny of Seseli. RESULTS In our study, we observed that the genome length, gene numbers, IR/SC borders, and repeat composition of the eleven Seseli plastomes were variable. Several appropriate mutation hotspot regions may be developed as candidate DNA barcodes for evolution, phylogeny, and species identification of Seseli. The phylogenetic results identified that Seseli was not a monophyletic group. Moreover, the eleven newly sequenced Seseli taxa did not cluster with S. tortuosum (the type species of Seseli, belonging to the tribe Selineae), where S. delavayi clustered with Eriocycla belonging to the tribe Echinophoreae and the other ten belonged to Selineae. The comparative plastome and morphological characteristics analyses confirmed the reliability of the phylogenetic analyses and implied the complex evolution of Seseli. CONCLUSION Combining molecular and morphological data is efficient and useful for studying the phylogeny of Seseli. We suggest that "a narrow sense" of Seseli will be meaningful for further study and the current taxonomic system of Seseli needs to be revised. In summary, our study can provide new insights into the phylogenetic relationships and taxonomic framework of Seseli.
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Affiliation(s)
- Jing Cai
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Huan-Huan Qin
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jia-Qing Lei
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chang-Kun Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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17
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Crameri S, Fior S, Zoller S, Widmer A. A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae). Mol Ecol Resour 2022; 22:3087-3105. [PMID: 35689779 PMCID: PMC9796917 DOI: 10.1111/1755-0998.13666] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/29/2022] [Accepted: 06/01/2022] [Indexed: 01/07/2023]
Abstract
Understanding the genetic changes associated with the evolution of biological diversity is of fundamental interest to molecular ecologists. The assessment of genetic variation at hundreds or thousands of unlinked genetic loci forms a sound basis to address questions ranging from micro- to macroevolutionary timescales, and is now possible thanks to advances in sequencing technology. Major difficulties are associated with (i) the lack of genomic resources for many taxa, especially from tropical biodiversity hotspots; (ii) scaling the numbers of individuals analysed and loci sequenced; and (iii) building tools for reproducible bioinformatic analyses of such data sets. To address these challenges, we developed target capture probes for genomic studies of the highly diverse, pantropically distributed and economically significant rosewoods (Dalbergia spp.), explored the performance of an overlapping probe set for target capture across the legume family (Fabaceae), and built the general purpose bioinformatic pipeline CaptureAl. Phylogenomic analyses of Malagasy Dalbergia species yielded highly resolved and well supported hypotheses of evolutionary relationships. Population genomic analyses identified differences between closely related species and revealed the existence of a potentially new species, suggesting that the diversity of Malagasy Dalbergia species has been underestimated. Analyses at the family level corroborated previous findings by the recovery of monophyletic subfamilies and many well-known clades, as well as high levels of gene tree discordance, especially near the root of the family. The new genomic and bioinformatic resources, including the Fabaceae1005 and Dalbergia2396 probe sets, will hopefully advance systematics and ecological genetics research in legumes, and promote conservation of the highly diverse and endangered Dalbergia rosewoods.
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Affiliation(s)
- Simon Crameri
- Institute of Integrative BiologyETH ZurichZürichSwitzerland
| | - Simone Fior
- Institute of Integrative BiologyETH ZurichZürichSwitzerland
| | - Stefan Zoller
- Institute of Integrative BiologyETH ZurichZürichSwitzerland,Genetic Diversity Centre (GDC)ETH ZurichZürichSwitzerland
| | - Alex Widmer
- Institute of Integrative BiologyETH ZurichZürichSwitzerland
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18
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Multiplex PCR Identification of Aspergillus cristatus and Aspergillus chevalieri in Liupao Tea Based on Orphan Genes. Foods 2022; 11:foods11152217. [PMID: 35892804 PMCID: PMC9332452 DOI: 10.3390/foods11152217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 11/21/2022] Open
Abstract
“Golden flower” fungi in dark tea are beneficial to human health. The rapid identification method of “golden flower” fungi can verify the quality of dark tea products and ensure food safety. In this study, 6 strains were isolated from Liupao tea. They were respectively identified as A. cristatus, A. chevalieri, and A. pseudoglaucus. A. pseudoglaucus was reported as Liupao tea “golden flower” fungus for the first time. It was found that the ITS and BenA sequences of A. cristatus and A. chevalieri were highly conserved. It is difficult to clearly distinguish these closely related species by ITS sequencing. To rapidly identify species, multiplex PCR species-specific primers were designed based on orphan genes screened by comparative genomics analysis. Multiplex PCR results showed that orphan genes were specific and effective for the identification of A. cristatus and A. chevalieri isolated from Liupao tea and Fu brick tea. We confirmed that orphan genes can be used for identification of closely related Aspergillus species. Validation showed that the method is convenient, rapid, robust, sequencing-free, and economical. This promising method will be greatly beneficial to the dark tea processing industry and consumers.
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19
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Li M, Xian X, Ren B, Wang H, Li W, Chen J. The complete chloroplast genome of Gynura japonica and its phylogenetic implications. Mitochondrial DNA B Resour 2022; 7:1392-1394. [PMID: 35923637 PMCID: PMC9341369 DOI: 10.1080/23802359.2022.2102443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Gynura japonica (Asteraceae) is a folk herbal medicine with multi-pharmacological functions involving analgesic, hemostatic and antiangiogenic activities. The study was conducted to assemble the complete chloroplast (cp) genome of G. japonica through a genome-skimming approach. The assembled cp genome was 151,023 bp in size, with 62.8% AT content, consisting of a large single copy (LSC) of 83,185 bp, two copies of inverted repeat (IRa and IRb) of 24,847 bp, and a small single copy (SSC) of 18,144 bp. The cp genome of G. japonica contained 133 genes, including eight ribosomal RNA genes (rRNAs), 37 transfer RNA genes (tRNAs), 86 protein-coding genes (PCGs), and two pseudogenes (ψycf1 and ψrps19). Our phylogenomic analysis based on whole plastid genomes strongly supports G. japonica is a sister to the clade including Crassocephalum crepidioides and Jacobaea vulgaris.
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Affiliation(s)
- Mimi Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xin Xian
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Bingru Ren
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Hongjiang Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Weilin Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Forestry College, Nanjing Forestry University, Nanjing, China
| | - Jian Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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20
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Li ZX, Guo XL, Price M, Zhou SD, He XJ. Phylogenetic position of Ligusticopsis (Apiaceae, Apioideae): evidence from molecular data and carpological characters. AOB PLANTS 2022; 14:plac008. [PMID: 35475242 PMCID: PMC9035215 DOI: 10.1093/aobpla/plac008] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 03/02/2022] [Indexed: 05/13/2023]
Abstract
Ligusticopsis (Apiaceae, Apioideae) is now considered to have an East-Asia and Sino-Himalaya distribution. The genus was not recognized as a natural and separate genus and was treated as a synonym of Ligusticum both in Flora Reipublicae Popularis Sinicae and Flora of China since first established, though Pimenov et al. have made many taxonomic revisions to Ligusticopsis, phylogenetic relationships between Ligusticopsis and Ligusticum have been in dispute. Thirty-four plastomes and 35 nrITS from Apioideae were analysed by RAxML and MrBayes to reconstruct the phylogenetic relationships, along with carpology of 10 species and comparative analyses of 17 plastomes to investigate the evidence supporting the independence of Ligusticopsis. As a result, nine species suggested to be Ligusticopsis formed a highly supported monophyletic branch (Subclade A) inside Selineae both in maximum likelihood and Bayesian inference; the results of the comparative analyses further supported the monophyly of Subclade A, mainly in the location of genes at the IRa/LSC boundary, the sequence diversity exhibited by various genes (e.g. trnH-GUG-psbA and ycf2) and same codon biases in terminator TAA (relative synonymous codon usage = 1.75). Species in Subclade A also had shared characters in mericarps, combined with other characters of the plant, 'base clothed in fibrous remnant sheaths, pinnate bracts, pinnate bracteoles longer than rays of umbellule, mericarps strongly compressed dorsally, median and lateral ribs filiform or keeled, marginal ribs winged, and numerous vittae in commissure and each furrow' should be the most important and diagnostic characters of Ligusticopsis. Our phylogenetic trees and other analyses supported the previous taxonomic treatments of Pimenov et al. that Ligusticopsis should be a natural and separate genus rather than a synonym of Ligusticum.
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Affiliation(s)
- Zi-Xuan Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
| | - Xian-Lin Guo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
| | - Megan Price
- Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
- Corresponding authors’ e-mail addresses: ;
| | - Xing-Jin He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
- Corresponding authors’ e-mail addresses: ;
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21
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Jin XJ, Huang Y, Wei YK, Ma Q, Liu LX, Fu ZX, Wu GF, Zhang YH, Li P. Elsholtziazhongyangii (Lamiaceae), a new species from Sichuan, China. PHYTOKEYS 2022; 193:77-88. [PMID: 36760841 PMCID: PMC9849022 DOI: 10.3897/phytokeys.193.80327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/05/2022] [Indexed: 06/18/2023]
Abstract
Elsholtziazhongyangii (Lamiaceae), a new species from Sichuan Province, China, is described and illustrated. The new species is morphologically similar to E.feddeif.feddei, but it can be easily distinguished from E.feddeif.feddei by smaller corolla (3.2-3.5 mm vs. 4.5-5.3 mm), bract indumentum (glabrous, except margin ciliate vs. villous, especially on veins abaxially, glabrous adaxially) and bract stalked (ca. 1.2 mm vs. sessile). Phylogenetic analyses, based on two nuclear ribosomal (ETS, ITS) and five plastid (rbcL, matK, trnL-F, ycf1, ycf1-rps15) regions, confirmed that the new species formed a monophyletic clade with robust support. The new species is currently known from western Sichuan.
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Affiliation(s)
- Xin-Jie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, ChinaWenzhou UniversityWenzhouChina
| | - Yue Huang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, ChinaWenzhou UniversityWenzhouChina
| | - Yu-Kun Wei
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical GardenShanghaiChina
| | - Qing Ma
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, ChinaZhejiang Shuren UniversityHangzhouChina
| | - Lu-Xian Liu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475001, ChinaHenan UniversityKaifengChina
| | - Zhi-Xi Fu
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, ChinaSichuan Normal UniversityChengduChina
| | - Gui-Fang Wu
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, ChinaWenzhou UniversityWenzhouChina
| | - Yong-Hua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, ChinaWenzhou UniversityWenzhouChina
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, ChinaZhejiang UniversityHangzhouChina
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22
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Wang Y, Huang J, Li E, Xu S, Zhan Z, Zhang X, Yang Z, Guo F, Liu K, Liu D, Shen X, Shang C, Zhang Z. Phylogenomics and Biogeography of Populus Based on Comprehensive Sampling Reveal Deep-Level Relationships and Multiple Intercontinental Dispersals. FRONTIERS IN PLANT SCIENCE 2022; 13:813177. [PMID: 35185985 PMCID: PMC8855119 DOI: 10.3389/fpls.2022.813177] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Populus not only has significant economic and ecological values, but also serves as a model tree that is widely used in the basic research of tree growth, physiology, and genetics. However, high levels of morphological variation and extensive interspecific hybridization of Populus pose an obstacle for taxonomy, and also to the understanding of phylogenetic interspecific relationships and biogeographical history. In this study, a total of 103 accessions representing almost all the wild species of Populus were collected and whole-genome re-sequenced to examine the phylogenetic relationships and biogeography history. On the basis of 12,916,788 nuclear single nucleotide polymorphisms (SNPs), we reconstructed backbone phylogenies using concatenate and coalescent methods, we highly disentangled the species relationships of Populus, and several problematic taxa were treated as species complexes. Furthermore, the phylogeny of the chloroplast genome showed extensive discordance with the trees from the nuclear genome data, and due to extensive chloroplast capture and hybridization of Populus species, plastomes could not accurately evaluate interspecies relationships. Ancient gene flow between clades and some hybridization events were also identified by ABBA-BABA analysis. The reconstruction of chronogram and ancestral distributions suggested that North America was the original region of this genus, and subsequent long dispersal and migration across land bridges were contributed to the modern range of Populus. The diversification of Populus mainly occurred in East Asia in recent 15 Ma, possibly promoted by the uplift of the Tibetan Plateau. This study provided comprehensive evidence on the phylogeny of Populus and proposed a four-subgeneric classification and a new status, subgenus Abaso. Meanwhile, ancestral distribution reconstruction with nuclear data advanced the understanding of the biogeographic history of Populus.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Ce Shang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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23
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Zhang GQ, Chen GZ, Chen LJ, Zhai JW, Huang J, Wu XY, Li MH, Peng DH, Rao WH, Liu ZJ, Lan SR. Phylogenetic incongruence in Cymbidium orchids. PLANT DIVERSITY 2021; 43:452-461. [PMID: 35024514 PMCID: PMC8720702 DOI: 10.1016/j.pld.2021.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 06/14/2023]
Abstract
Cymbidium, which includes approximately 80 species, is one of the most ornamental and cultivated orchid genera. However, a lack of markers and sparse sampling have posed great challenges to resolving the phylogenetic relationships within the genus. In the present study, we reconstructed the phylogenetic relationships by utilizing one nuclear DNA (nrITS) and seven plastid genes (rbcL, trnS, trnG, matK, trnL, psbA, and atpI) from 70 species (varieties) in Cymbidium. We also examined the occurrence of phylogenetic conflict between nuclear (nrITS) and plastid loci and investigated how phylogenetic conflict bears on taxonomic classification within the genus. We found that phylogenetic conflict and low support values may be explained by hybridization and a lack of informative characteristics. Our results do not support previous classification of the subgenera and sections within Cymbidium. Discordance between gene trees and network analysis indicate that reticulate evolution occurred in the genus Cymbidium. Overall, our study indicates that Cymbidium has undergone a complex evolution.
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Affiliation(s)
- Guo-Qiang Zhang
- Forestry College of Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Gui-Zhen Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Li-Jun Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, 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, 350002, China
| | - Jie Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Xin-Yi Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dong-Hui Peng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wen-Hui Rao
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Si-Ren Lan
- Forestry College of Fujian Agriculture and Forestry University, Fuzhou, 350002, 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, 350002, China
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24
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Guo X, Fang D, Sahu SK, Yang S, Guang X, Folk R, Smith SA, Chanderbali AS, Chen S, Liu M, Yang T, Zhang S, Liu X, Xu X, Soltis PS, Soltis DE, Liu H. Chloranthus genome provides insights into the early diversification of angiosperms. Nat Commun 2021; 12:6930. [PMID: 34836973 PMCID: PMC8626473 DOI: 10.1038/s41467-021-26922-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
Chloranthales remain the last major mesangiosperm lineage without a nuclear genome assembly. We therefore assemble a high-quality chromosome-level genome of Chloranthus spicatus to resolve enigmatic evolutionary relationships, as well as explore patterns of genome evolution among the major lineages of mesangiosperms (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales). We find that synteny is highly conserved between genomic regions of Amborella, Vitis, and Chloranthus. We identify an ancient single whole-genome duplication (WGD) (κ) prior to the divergence of extant Chloranthales. Phylogenetic inference shows Chloranthales as sister to magnoliids. Furthermore, our analyses indicate that ancient hybridization may account for the incongruent phylogenetic placement of Chloranthales + magnoliids relative to monocots and eudicots in nuclear and chloroplast trees. Long genes and long introns are found to be prevalent in both Chloranthales and magnoliids compared to other angiosperms. Overall, our findings provide an improved context for understanding mesangiosperm relationships and evolution and contribute a valuable genomic resource for future investigations.
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Affiliation(s)
- Xing Guo
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Dongming Fang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Sunil Kumar Sahu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Shuai Yang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Xuanmin Guang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Ryan Folk
- grid.260120.70000 0001 0816 8287Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762 United States of America
| | - Stephen A. Smith
- grid.214458.e0000000086837370Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 United States of America
| | - Andre S. Chanderbali
- grid.15276.370000 0004 1936 8091Florida Museum of Natural History, University of Florida, Gainesville, FL United States of America
| | - Sisi Chen
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China ,grid.9227.e0000000119573309South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650 China
| | - Min Liu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Ting Yang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Shouzhou Zhang
- grid.9227.e0000000119573309Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen, Chinese Academy of Sciences, Shenzhen, 518004 China
| | - Xin Liu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China ,grid.21155.320000 0001 2034 1839BGI-Fuyang, BGI-Shenzhen, Fuyang, 236009 China
| | - Xun Xu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China ,grid.21155.320000 0001 2034 1839Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518083 China
| | - Pamela S. Soltis
- grid.15276.370000 0004 1936 8091Florida Museum of Natural History, University of Florida, Gainesville, FL United States of America
| | - Douglas E. Soltis
- grid.15276.370000 0004 1936 8091Florida Museum of Natural History, University of Florida, Gainesville, FL United States of America ,grid.15276.370000 0004 1936 8091Department of Biology, University of Florida, Gainesville, FL 32611 United States of America
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China. .,Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark.
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25
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Escobari B, Borsch T, Quedensley TS, Gruenstaeudl M. Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif-based sequence alignment amid low genetic distances. AMERICAN JOURNAL OF BOTANY 2021; 108:2235-2256. [PMID: 34636417 DOI: 10.1002/ajb2.1775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The genus Gynoxys and relatives form a species-rich lineage of Andean shrubs and trees with low genetic distances within the sunflower subtribe Tussilaginineae. Previous molecular phylogenetic investigations of the Tussilaginineae have included few, if any, representatives of this Gynoxoid group or reconstructed ambiguous patterns of relationships for it. METHODS We sequenced complete plastid genomes of 21 species of the Gynoxoid group and related Tussilaginineae and conducted detailed comparisons of the phylogenetic relationships supported by the gene, intron, and intergenic spacer partitions of these genomes. We also evaluated the impact of manual, motif-based adjustments of automatic DNA sequence alignments on phylogenetic tree inference. RESULTS Our results indicate that the inclusion of all plastid genome partitions is needed to infer well-supported phylogenetic trees of the Gynoxoid group. Whole plastome-based tree inference suggests that the genera Gynoxys and Nordenstamia are polyphyletic and form the core clade of the Gynoxoid group. This clade is sister to a clade of Aequatorium and Paragynoxys and also includes some but not all representatives of Paracalia. CONCLUSIONS The concatenation and combined analysis of all plastid genome partitions and the construction of manually-curated, motif-based DNA sequence alignments are found to be instrumental in the recovery of well-supported relationships of the Gynoxoid group. We demonstrate that the correct assessment of homology in genome-level plastid sequence data sets is crucial for subsequent phylogeny reconstruction and that the manual post-processing of multiple sequence alignments improves the reliability of such reconstructions amid low genetic distances between taxa.
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Affiliation(s)
- Belen Escobari
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, 14195, Germany
- Herbario Nacional de Bolivia, Universidad Mayor de San Andres, Casilla, La Paz, 10077, Bolivia
| | - Thomas Borsch
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, 14195, Germany
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
| | - Taylor S Quedensley
- Department of Biology, Texas Christian University, Fort Worth, TX, 76109, USA
| | - Michael Gruenstaeudl
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
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26
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Li ZZ, Lehtonen S, Martins K, Wang QF, Chen JM. Complete genus-level plastid phylogenomics of Alismataceae with revisited historical biogeography. Mol Phylogenet Evol 2021; 166:107334. [PMID: 34715331 DOI: 10.1016/j.ympev.2021.107334] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/19/2022]
Abstract
Alismataceae, an ancient lineage of monocots, has attracted attention due to its complex evolutionary history, ornamental value, and ecological role. However, the phylogenetic relationships and evolutionary history of the family have not been conclusively resolved. Here, we constructed the first complete genus-level plastid phylogeny of Alismataceae by using 78 genes and updated the historical biogeography based on the phylogenomic tree. Our results divide the Alismataceae into three major clades with robust support values; one clade comprises the former Limnocharitaceae, and the second clade includes the mainly temperate genera Alisma, Baldellia, Damasonium and Luronium, and the monotypic African genus Burnatia as a sister of the temperate genera. The remaining genera are either tropical or have some temperate species in addition to tropical ones, and they constitute the third major clade. Molecular dating and biogeographic analyses suggest that Alismataceae arose in Neotropical, West Palearctic, and Afrotropical regions during the Cretaceous, followed by the split into three main clades due to a combination of vicariance and dispersal events. Unlike earlier studies, we inferred that the mainly temperate clade likely originated from Afrotropical and West Palearctic regions during the Eocene. The most recent common ancestor of the other two clades lived in the Neotropical area during the Late Cretaceous. Long-distance dispersal and vicariance together seem to contribute to the transoceanic distribution of this family.
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Affiliation(s)
- Zhi-Zhong Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Samuli Lehtonen
- Herbarium, Biodiversity Unit, University of Turku, Turku 20014, Finland
| | - Karina Martins
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba 18052-780, Brazil
| | - Qing-Feng Wang
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jin-Ming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China.
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27
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Górniak M, Szlachetko DL, Olędrzyńska N, Naczk AM, Mieszkowska A, Boss L, Ziętara MS. Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on Paphiopedilum Pfitz. (Orchidaceae). Int J Mol Sci 2021; 22:ijms222111393. [PMID: 34768824 PMCID: PMC8583834 DOI: 10.3390/ijms222111393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022] Open
Abstract
The phylogeny of the genus Paphiopedilum based on the plastome is consistent with morphological analysis. However, to date, none of the analyzed nuclear markers has confirmed this. Topology incongruence among the trees of different nuclear markers concerns entire sections of the subgenus Paphiopedilum. The low-copy nuclear protein-coding gene PHYC was obtained for 22 species representing all sections and subgenera of Paphiopedilum. The nuclear-based phylogeny is supported by morphological characteristics and plastid data analysis. We assumed that an incongruence in nuclear gene trees is caused by ancestral homoploid hybridization. We present a model for inferring the phylogeny of the species despite the incongruence of the different tree topologies. Our analysis, based on six low-copy nuclear genes, is congruent with plastome phylogeny and has been confirmed by phylogenetic network analysis.
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Affiliation(s)
- Marcin Górniak
- Department of Evolutionary Genetics and Biosystematics, University of Gdańsk, 80-309 Gdańsk, Poland; (A.M.N.); (A.M.); (M.S.Z.)
- Correspondence:
| | - Dariusz L. Szlachetko
- Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, 80-309 Gdańsk, Poland; (D.L.S.); (N.O.)
| | - Natalia Olędrzyńska
- Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, 80-309 Gdańsk, Poland; (D.L.S.); (N.O.)
| | - Aleksandra M. Naczk
- Department of Evolutionary Genetics and Biosystematics, University of Gdańsk, 80-309 Gdańsk, Poland; (A.M.N.); (A.M.); (M.S.Z.)
| | - Agata Mieszkowska
- Department of Evolutionary Genetics and Biosystematics, University of Gdańsk, 80-309 Gdańsk, Poland; (A.M.N.); (A.M.); (M.S.Z.)
| | - Lidia Boss
- Department of Bacterial Molecular Genetics, University of Gdańsk, 80-309 Gdańsk, Poland;
| | - Marek S. Ziętara
- Department of Evolutionary Genetics and Biosystematics, University of Gdańsk, 80-309 Gdańsk, Poland; (A.M.N.); (A.M.); (M.S.Z.)
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28
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Zhang C, Huang CH, Liu M, Hu Y, Panero JL, Luebert F, Gao T, Ma H. Phylotranscriptomic insights into Asteraceae diversity, polyploidy, and morphological innovation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1273-1293. [PMID: 33559953 DOI: 10.1111/jipb.13078] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/08/2021] [Indexed: 05/29/2023]
Abstract
Biodiversity is not evenly distributed among related groups, raising questions about the factors contributing to such disparities. The sunflower family (Asteraceae, >26,000 species) is among the largest and most diverse plant families, but its species diversity is concentrated in a few subfamilies, providing an opportunity to study the factors affecting biodiversity. Phylotranscriptomic analyses here of 244 transcriptomes and genomes produced a phylogeny with strong support for the monophyly of Asteraceae and the monophyly of most subfamilies and tribes. This phylogeny provides a reference for detecting changes in diversification rates and possible factors affecting Asteraceae diversity, which include global climate shifts, whole-genome duplications (WGDs), and morphological evolution. The origin of Asteraceae was estimated at ~83 Mya, with most subfamilies having diverged before the Cretaceous-Paleocene boundary. Phylotranscriptomic analyses supported the existence of 41 WGDs in Asteraceae. Changes to herbaceousness and capitulescence with multiple flower-like capitula, often with distinct florets and scaly pappus/receptacular bracts, are associated with multiple upshifts in diversification rate. WGDs might have contributed to the survival of early Asteraceae by providing new genetic materials to support morphological transitions. The resulting competitive advantage for adapting to different niches would have increased biodiversity in Asteraceae.
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Affiliation(s)
- Caifei Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennslyvania, 16802, USA
| | - Mian Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yi Hu
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennslyvania, 16802, USA
| | - Jose L Panero
- Department of Integrative Biology, The University of Texas, University Station C0930, Austin, Texas, 78712, USA
| | - Federico Luebert
- Institut für Bodiversität der Pflanzen, Universität Bonn, Bonn, D - 53115, Germany
- Department of Silviculture and Nature Conservation, University of Chile, Santiago, 9206, Chile
| | - Tiangang Gao
- State Key Laboratory of Evolutionary and Systematic Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Hong Ma
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennslyvania, 16802, USA
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Ren C, Wang L, Nie ZL, Johnson G, Yang QE, Wen J. Development and phylogenetic utilities of a new set of single-/low-copy nuclear genes in Senecioneae (Asteraceae), with new insights into the tribal position and the relationships within subtribe Tussilagininae. Mol Phylogenet Evol 2021; 162:107202. [PMID: 33992786 DOI: 10.1016/j.ympev.2021.107202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/13/2021] [Accepted: 05/06/2021] [Indexed: 11/26/2022]
Abstract
The tribe Senecioneae is one of the largest tribes in Asteraceae, with a nearly cosmopolitan distribution. Despite great efforts devoted to elucidate the evolution of Senecioneae, many questions still remain concerning the systematics of this group, from the tribal circumscription and position to species relationships in many genera. The hybridization-based target enrichment method of next-generation sequencing has been accepted as a promising approach to resolve phylogenetic problems. We herein develop a set of single-/low-copy genes for Senecioneae, and test their phylogenetic utilities. Our results demonstrate that these genes work highly efficiently for Senecioneae, with a high average gene recovery of 98.8% across the tribe and recovering robust phylogenetic hypotheses at different levels. In particular, the delimitation of the Senecioneae has been confirmed to include Abrotanella and exclude Doronicum, with the former sister to core Senecioneae and the latter shown to be more closely related to Calenduleae. Moreover, Doronicum and Calenduleae are inferred to be the closest relatives of Senecioneae, which is a new hypothesis well supported by statistical topology tests, morphological evidence, and the profile of pyrrolizidine alkaloids, a special kind of chemical characters generally used to define Senecioneae. Furthermore, this study suggests a complex reticulation history in the diversification of Senecioneae, accounting for the prevalence of polyploid groups in the tribe. With subtribe Tussilagininae s.str. as a case study showing a more evident pattern of gene duplication, we further explored reconstructing the phylogeny in the groups with high ploidy levels. Our results also demonstrate that tree topologies based on sorted paralogous copies are stable across different methods of phylogenetic inference, and more congruent with the morphological evidence and the results of previous phylogenetic studies.
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Affiliation(s)
- Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Long Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Qin-Er Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China; Key Laboratory of Digital Botanical Garden of Guangdong Province, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China.
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
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Cordobés FM, Robbiati FO, Anton AM, Scrivanti LR. Phylogeny, evolution and ecological speciation analyses of Imperata (Poaceae: Andropogoneae) in the Neotropics. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1887959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Fernando Moro Cordobés
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad Nacional de Córdoba, Córdoba, Prov. de Córdoba, Argentina
| | - Federico Omar Robbiati
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad Nacional de Córdoba, Córdoba, Prov. de Córdoba, Argentina
| | - Ana María Anton
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad Nacional de Córdoba, Córdoba, Prov. de Córdoba, Argentina
| | - Lidia Raquel Scrivanti
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad Nacional de Córdoba, Córdoba, Prov. de Córdoba, Argentina
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Muasya AM, Larridon I. Delimiting the genera of the Ficinia Clade (Cypereae, Cyperaceae) based on molecular phylogenetic data. PeerJ 2021; 9:e10737. [PMID: 33569253 PMCID: PMC7845527 DOI: 10.7717/peerj.10737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/18/2020] [Indexed: 11/20/2022] Open
Abstract
Generic delimitations in the Ficinia Clade of tribe Cypereae are revisited. In particular, we aim to establish the placement of annual species currently included in Isolepis of which the phylogenetic position is uncertain. Phylogenetic inference is based on two nuclear markers (ETS, ITS) and five plastid markers (the genes matK, ndhF, rbcL and rps16, the trnL intron and trnL-F spacer) data, analyzed using model based methods. Topologies based on nuclear and plastid data show incongruence at the backbone. Therefore, the results are presented separately. The monophyly of the smaller genera (Afroscirpoides, Dracoscirpoides, Erioscirpus, Hellmuthia, Scirpoides) is confirmed. However, Isolepis is paraphyletic as Ficinia is retrieved as one of its clades. Furthermore, Ficinia is paraphyletic if I. marginata and allies are excluded. We take a pragmatic approach based on the nuclear topology, driven by a desire to minimize taxonomic changes, to recircumscribe Ficinia to include the annual Isolepis species characterized by cartilaginous glumes and formally include all the Isolepis species inferred outside the core Isolepis clade. Consequently, the circumscription of Isolepis is narrowed to encompass only those species retrieved as part of the core Isolepis clade. Five new combinations are made (Ficinia neocapensis, Ficinia hemiuncialis, Ficinia incomtula, Ficinia leucoloma, Ficinia minuta). We present nomenclatural summary at genus level, identification keys and diagnostic features.
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Affiliation(s)
- A Muthama Muasya
- Department of Biological Sciences, Bolus Herbarium, University of Cape Town, Rondebosch, Cape Town, South Africa.,Identification and Naming, Royal Botanic Gardens Kew, Richmond, Surrey, UK
| | - Isabel Larridon
- Identification and Naming, Royal Botanic Gardens Kew, Richmond, Surrey, UK.,Department of Biology, Systematic and Evolutionary Botany Lab, Ghent University, Gent, Belgium
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Meng KK, Chen SF, Xu KW, Zhou RC, Li MW, Dhamala MK, Liao WB, Fan Q. Phylogenomic analyses based on genome-skimming data reveal cyto-nuclear discordance in the evolutionary history of Cotoneaster (Rosaceae). Mol Phylogenet Evol 2021; 158:107083. [PMID: 33516804 DOI: 10.1016/j.ympev.2021.107083] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 12/16/2020] [Accepted: 01/12/2021] [Indexed: 11/19/2022]
Abstract
As a consequence of hybridization, polyploidization, and apomixis, the genus Cotoneaster (Rosaceae) represents one of the most complicated and controversial lineages in Rosaceae, with ca. 370 species which have been classified into two subgenera and several sections, and is notorious for its taxonomic difficulty. The infrageneric relationships and taxonomy of Cotoneaster have remained poorly understood. Previous studies have focused mainly on natural hybridization involving only several species, and phylogeny based on very limited markers. In the present study, the sequences of complete chloroplast genomes and 204 low-copy nuclear genes of 72 accessions, representing 69 species as ingroups, were used to conduct the most comprehensive phylogenetic analysis so far for Cotoneaster. Based on the sequences of complete chloroplast genomes and many nuclear genes, our analyses yield two robust phylogenetic trees respectively. Chloroplast genome and nuclear data confidently resolved relationships of this genus into two major clades which largely supported current classification based on morphological evidence. However, conflicts between the chloroplast genome and low-copy nuclear phylogenies were observed in both the species level and clade level. Cyto-nuclear discordance in the phylogeny could be caused by frequent hybridization events and incomplete sorting lineage (ILS). In addition, our divergence-time analysis revealed an evolutionary radiation of the genus from late Miocene to date.
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Affiliation(s)
- Kai-Kai Meng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Su-Fang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ke-Wang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Ren-Chao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ming-Wan Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Man Kumar Dhamala
- Central Department of Environmental Science, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Wen-Bo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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Lee YS, Kim J, Woo S, Park JY, Park HS, Shim H, Choi HI, Kang JH, Lee TJ, Sung SH, Yang TJ, Kang KB. Assessing the genetic and chemical diversity of Taraxacum species in the Korean Peninsula. PHYTOCHEMISTRY 2021; 181:112576. [PMID: 33166748 DOI: 10.1016/j.phytochem.2020.112576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/19/2020] [Accepted: 10/24/2020] [Indexed: 05/12/2023]
Abstract
The genetic relationship between Taraxacum species, also known as the dandelion, is complicated because of asexual and mixed sexual apomictic reproduction. The usage of Taraxacum species in traditional medicines make their specialized metabolism important, but interspecific chemical difference has rarely been reported for the genus. In this study, we assembled the chloroplast genome and 45S rDNA of six Taraxacum species that occur in Korea (T. campylodes, T. coreanum, T. erythrospermum, T. mongolicum, T. platycarpum, and T. ussuriense), and performed a comparative analysis, which revealed their phylogenetic relationships and possible natural hybridity. We also performed a liquid chromatography-mass spectrometry-based phytochemical analysis to reveal interspecific chemical diversity. The comparative metabolomics analysis revealed that Taraxacum species could be separated into three chemotypes according to their major defensive specialized metabolites, which were the sesquiterpene lactones, the phenolic inositols, and chlorogenic acid derivatives. The CP DNA- and 45S rDNA-based phylogenetic trees showed a tangled relationship, which supports the notion of ongoing hybridization of wild Taraxacum species. The untargeted LC-MS analysis revealed that each Taraxacum plant exhibits species-specific defensive specialized metabolism. Moreover, 45S rDNA-based phylogenetic tree correlated with the hierarchical cluster relied on metabolite compositions. Given the coincidence between these analyses, we represented that 45S rDNA could well reflect overall nuclear genome variation in Taraxacum species.
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Affiliation(s)
- Yun Sun Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jinkyung Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sunmin Woo
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Jung Hwa Kang
- Hantaek Botanical Garden, Yongin, 17183, Republic of Korea
| | - Taek Joo Lee
- Hantaek Botanical Garden, Yongin, 17183, Republic of Korea
| | - Sang Hyun Sung
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Kyo Bin Kang
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea; Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, 04310, Republic of Korea.
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Lai YJ, Han Y, Schuiteman A, Chase MW, Xu SZ, Li JW, Wu JY, Yang BY, Jin XH. Diversification in Qinghai-Tibet Plateau: Orchidinae (Orchidaceae) clades exhibiting pre-adaptations play critical role. Mol Phylogenet Evol 2020; 157:107062. [PMID: 33387648 DOI: 10.1016/j.ympev.2020.107062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 11/28/2022]
Abstract
We explore the origins of the extraordinary plant diversity in the Qinghai-Tibetan Plateau (QTP) using Orchidinae (Orchidaceae) as a model. Our results indicate that six major clades in Orchidinae exhibited substantial variation in the temporal and spatial sequence of diversification. Our time-calibrated phylogenetic model suggests that the species-richness of Orchidinae arose through a combination of in situ diversification, colonisation, and local recruitment. There are multiple origins of species-richness of Orchidinae in the QTP, and pre-adaptations in clades from North Temperate and alpine regions were crucial for in situ diversification. The geographic analysis identified 29 dispersals from Asia, Africa and Europe into the QTP and 15 dispersals out. Most endemic species of Orchidinae evolved within the past six million years.
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Affiliation(s)
- Yang-Jun Lai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, China
| | - Yu Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, China
| | - Andre Schuiteman
- Identification and Naming Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Mark W Chase
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102, Australia
| | - Song-Zhi Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, China
| | - Jian-Wu Li
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun Township, Mengla County, Yunnan 666303, China.
| | - Jian-Yong Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), China
| | - Bo-Yun Yang
- School of Life Sciences, Nanchang University, Nanchang 330031, China.
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, China.
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Yao J, Zhao F, Xu Y, Zhao K, Quan H, Su Y, Hao P, Liu J, Yu B, Yao M, Ma X, Liao Z, Lan X. Complete Chloroplast Genome Sequencing and Phylogenetic Analysis of Two Dracocephalum Plants. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4374801. [PMID: 33457408 PMCID: PMC7787725 DOI: 10.1155/2020/4374801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/26/2020] [Accepted: 12/18/2020] [Indexed: 11/17/2022]
Abstract
Dracocephalum tanguticum and Dracocephalum moldavica are important herbs from Lamiaceae and have great medicinal value. We used the Illumina sequencing technology to sequence the complete chloroplast genome of D. tanguticum and D. moldavica and then conducted de novo assembly. The two chloroplast genomes have a typical quadripartite structure, with the gene's lengths of 82,221 bp and 81,450 bp, large single-copy region's (LSC) lengths of 82,221 bp and 81,450 bp, and small single-copy region's (SSC) lengths of 17,363 bp and 17,066 bp, inverted repeat region's (IR) lengths of 51,370 bp and 51,352 bp, respectively. The GC content of the two chloroplast genomes was 37.80% and 37.83%, respectively. The chloroplast genomes of the two plants encode 133 and 132 genes, respectively, among which there are 88 and 87 protein-coding genes, respectively, as well as 37 tRNA genes and 8 rRNA genes. Among them, the rps2 gene is unique to D. tanguticum, which is not found in D. moldavica. Through SSR analysis, we also found 6 mutation hotspot regions, which can be used as molecular markers for taxonomic studies. Phylogenetic analysis showed that Dracocephalum was more closely related to Mentha.
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Affiliation(s)
- Junjun Yao
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
| | - Fangyu Zhao
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
| | - Yuanjiang Xu
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
- Key Laboratory of Forest Ecology in Tibet Plateau (Tibet Agricultural & Animal Husbandry University), Ministry of Education, Nyingchi, Tibet 860000, China
| | - Kaihui Zhao
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
| | - Hong Quan
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
- Key Laboratory of Forest Ecology in Tibet Plateau (Tibet Agricultural & Animal Husbandry University), Ministry of Education, Nyingchi, Tibet 860000, China
| | - Yanjie Su
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
| | - Peiyu Hao
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
| | - Jiang Liu
- Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China
| | - Benxia Yu
- Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China
| | - Min Yao
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiaojing Ma
- Jiangxi Institute for Drug Control, NMPA Key Laboratory of Quality Evaluation of Traditional Chinese Patent Medicine, Nanchang, Jiangxi 330029, China
| | - Zhihua Liao
- Key Laboratory of Eco-Environments in the Three Gorges Reservoir Region, Ministry of Education, Chongqing Engineering and Technology Research Center for Sweetpotato, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiaozhong Lan
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet 860000, China
- Jiangxi Institute for Drug Control, NMPA Key Laboratory of Quality Evaluation of Traditional Chinese Patent Medicine, Nanchang, Jiangxi 330029, China
- Key Laboratory of Eco-Environments in the Three Gorges Reservoir Region, Ministry of Education, Chongqing Engineering and Technology Research Center for Sweetpotato, School of Life Sciences, Southwest University, Chongqing 400715, China
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Ren T, Li ZX, Xie DF, Gui LJ, Peng C, Wen J, He XJ. Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships. BMC PLANT BIOLOGY 2020; 20:519. [PMID: 33187470 PMCID: PMC7663912 DOI: 10.1186/s12870-020-02696-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/12/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND The genus Ligusticum consists of approximately 60 species distributed in the Northern Hemisphere. It is one of the most taxonomically difficult taxa within Apiaceae, largely due to the varied morphological characteristics. To investigate the plastome evolution and phylogenetic relationships of Ligusticum, we determined the complete plastome sequences of eight Ligusticum species using a de novo assembly approach. RESULTS Through a comprehensive comparative analysis, we found that the eight plastomes were similar in terms of repeat sequence, SSR, codon usage, and RNA editing site. However, compared with the other seven species, L. delavayi exhibited striking differences in genome size, gene number, IR/SC borders, and sequence identity. Most of the genes remained under the purifying selection, whereas four genes showed relaxed selection, namely ccsA, rpoA, ycf1, and ycf2. Non-monophyly of Ligusticum species was inferred from the plastomes and internal transcribed spacer (ITS) sequences phylogenetic analyses. CONCLUSION The plastome tree and ITS tree produced incongruent tree topologies, which may be attributed to the hybridization and incomplete lineage sorting. Our study highlighted the advantage of plastome with mass informative sites in resolving phylogenetic relationships. Moreover, combined with the previous studies, we considered that the current taxonomy system of Ligusticum needs to be improved and revised. In summary, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of Ligusticum species.
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Affiliation(s)
- Ting Ren
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zi-Xuan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Ling-Jian Gui
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chang Peng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jun Wen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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Julca I, Marcet-Houben M, Cruz F, Gómez-Garrido J, Gaut BS, Díez CM, Gut IG, Alioto TS, Vargas P, Gabaldón T. Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.). BMC Biol 2020; 18:148. [PMID: 33100219 PMCID: PMC7586694 DOI: 10.1186/s12915-020-00881-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 09/27/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most emblematic perennial crop for Mediterranean countries since its domestication around 6000 years ago in the Levant. Two taxonomic varieties are currently recognized: cultivated (var. europaea) and wild (var. sylvestris) trees. However, it remains unclear whether olive cultivars derive from a single initial domestication event followed by secondary diversification, or whether cultivated lineages are the result of more than a single, independent primary domestication event. To shed light into the recent evolution and domestication of the olive tree, here we analyze a group of newly sequenced and available genomes using a phylogenomics and population genomics framework. RESULTS We improved the assembly and annotation of the reference genome, newly sequenced the genomes of twelve individuals: ten var. europaea, one var. sylvestris, and one outgroup taxon (subsp. cuspidata)-and assembled a dataset comprising whole genome data from 46 var. europaea and 10 var. sylvestris. Phylogenomic and population structure analyses support a continuous process of olive tree domestication, involving a major domestication event, followed by recurrent independent genetic admixture events with wild populations across the Mediterranean Basin. Cultivated olives exhibit only slightly lower levels of genetic diversity than wild forms, which can be partially explained by the occurrence of a mild population bottleneck 3000-14,000 years ago during the primary domestication period, followed by recurrent introgression from wild populations. Genes associated with stress response and developmental processes were positively selected in cultivars, but we did not find evidence that genes involved in fruit size or oil content were under positive selection. This suggests that complex selective processes other than directional selection of a few genes are in place. CONCLUSIONS Altogether, our results suggest that a primary domestication area in the eastern Mediterranean basin was followed by numerous secondary events across most countries of southern Europe and northern Africa, often involving genetic admixture with genetically rich wild populations, particularly from the western Mediterranean Basin.
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Affiliation(s)
- Irene Julca
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- Universitat Autònoma de Barcelona (UAB), 08193, Barcelona, Spain
| | - Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- Present address: Barcelona Supercomputing Centre (BSC-CNS), and Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Brandon S Gaut
- Department Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | | | - Ivo G Gut
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Tyler S Alioto
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Pablo Vargas
- Royal Botanical Garden of Madrid. Consejo Superior de Investigaciones Científicas (CSIC), 28014, Madrid, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
- Present address: Barcelona Supercomputing Centre (BSC-CNS), and Institute for Research in Biomedicine (IRB), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
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Biogeography, phylogenetic relationships and morphological analyses of the South American genus Mutisia L.f. (Asteraceae) shows early connections of two disjunct biodiversity hotspots. ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-020-00454-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Rivero-Guerra AO. Diversidad y distribución de los endemismos de Asteraceae (Compositae) en la Flora del Ecuador. COLLECTANEA BOTANICA 2020. [DOI: 10.3989/collectbot.2020.v39.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
La familia Asteraceae está representada en la Flora de Ecuador por un total de 310 táxones endémicos. Están agrupadas en 4 subfamilias (Asteroideae, Barnadesioideae, Cichorioideae y Mutisioideae), 16 tribus y 89 géneros. Doscientas setenta y dos táxones (87,74%) restringen su hábitat a la región andina. Los niveles más altos de endemismos están asociados a los Andes, mayoritariamente desde el bosque andino alto hasta el páramo, y a las Islas Galápagos. Los géneros con mayor riqueza de endemismos son Mikania (26), Pentacalia (23), y Gynoxys (20). Tres géneros monotípicos son endémicos: Cyathomone, Idiopappus y Trigonopterum. Los géneros Darwiniothamnus, Kingianthus, Lecocarpus, y Scalesia también son endémicos. La diversidad de la familia se incrementa desde los 2000 m a 3000 m, alcanzando su mayor riqueza entre los 2900-3000 m, con dominancia de las plantas arbustivas (195 especies, 1 subespecie, 2 variedades) y herbáceas (97 especies). Ciento veinteseis especies tienen categoría de vulnerable, 90 están en peligro de extinción y 24 están en estado crítico de amenaza. Las temperaturas y precipitaciones medias anuales varían significativamente entre los sectores biogeográficos.
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Mosyakin S, Shiyan N. Nomenclatural and taxonomic notes on Jacobaea borysthenica (Asteraceae) and some related taxa. UKRAINIAN BOTANICAL JOURNAL 2019. [DOI: 10.15407/ukrbotj76.06.473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Maddison DR, Sproul JS, Mendel H. Origin and adaptive radiation of the exceptional and threatened bembidiine beetle fauna of St Helena (Coleoptera: Carabidae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The central peaks of the isolated island of St Helena (south Atlantic Ocean) are home to an extraordinary set of ground beetles of the tribe Bembidiini, which belong to three endemic genus-group taxa. These beetles are strikingly different in overall body form from the many bembidiines found elsewhere in the world. At least some of the St Helena species are likely to be extinct, and all are threatened by habitat destruction and invasive species. Through next-generation sequencing of historical museum specimens, we examine the phylogenetic relationships of the St Helena fauna. We find that, in spite of their morphological disparities, the endemic bembidiines of St Helena form a clade of genetically similar species, with their sister group being Bembidion alsium from the Indian Ocean island of La Réunion, and the sister group of this pair being the African subgenus Omotaphus. We propose that the St Helena Peaks Bembidion are an adaptive radiation that arose from a single dispersal event to St Helena from a now-extinct African lineage (sister to Omotaphus) and that this extinct lineage also served as the ancestral source of B. alsium. Given that the St Helena Peaks Bembidion are deeply nested in the genus Bembidion, we move the three taxa back in that genus as subgenera and provide a new name (Bembidion shepherdae) for the now-homonymous Bembidion wollastoni.
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Affiliation(s)
- David R Maddison
- Department of Integrative Biology, 3029 Cordley Hall, Oregon State University, Corvallis, OR, USA
| | - John S Sproul
- Department of Integrative Biology, 3029 Cordley Hall, Oregon State University, Corvallis, OR, USA
- Department of Biology, University of Rochester, Hutchison Hall, Rochester, NY, USA
| | - Howard Mendel
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, UK
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Han T, Li M, Li J, Lv H, Ren B, Chen J, Li W. Comparison of chloroplast genomes of Gynura species: sequence variation, genome rearrangement and divergence studies. BMC Genomics 2019; 20:791. [PMID: 31664913 PMCID: PMC6821010 DOI: 10.1186/s12864-019-6196-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/16/2019] [Indexed: 11/10/2022] Open
Abstract
Background Some Gynura species have been reported to be natural anti-diabetic plants. Improvement of their traits towards application relies on hybridization. Clearly, phylogenetic relationships could optimize compatible hybridizations. For flowerings plants, chloroplast genomes have been used to solve many phylogenetic relationships. To date, the chloroplast genome sequences of 4 genera of the tribe Senecioneae have been uploaded to GenBank. The internal relationships within the genus Gynura and the relationship of the genus Gynura with other genera in the tribe Senecioneae need further research. Results The chloroplast genomes of 4 Gynura species were sequenced, assembled and annotated. In comparison with those of 12 other Senecioneae species, the Gynura chloroplast genome features were analysed in detail. Subsequently, differences in the microsatellite and repeat types in the tribe were found. From the comparison, it was found that IR expansion and contraction are conserved in the genera Gynura, Dendrosenecio and Ligularia. Compared to other regions on the chloroplast genome, the region from 25,000 to 50,000 bp was not conserved. Seven ndh genes in this region are under purifying selection, with small changes in amino acids. The whole chloroplast genome sequences of 16 Senecioneae species were used to build a phylogenetic tree. Based on the oldest Artemisia pollen fossil, the divergence time was estimated. Conclusions Sequencing the chloroplast genomes of 4 Gynura species helps us to solve many problems. The phylogenetic relationships and divergence time among 4 Gynura and 16 Senecioneae species were evaluated by comparing their chloroplast genomes. The phylogenetic relationship of the genera Gynura and Ligularia was different from that observed previous work. In a previous phylogenetic tree, the genus Ligularia belonged to the Tussilagininae subtribe, which was in a lineage that diverged earlier than other genera. Further morphology and genome-wide analyses are needed to clarify the genus relationships.
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Affiliation(s)
- Tianyu Han
- Co-Innovation Center for Sustainable Forestry in Southern China, Forestry College, Nanjing Forestry University, Nanjing, 210037, China
| | - Mimi Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Jiawei Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Han Lv
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Bingru Ren
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Jian Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Forestry College, Nanjing Forestry University, Nanjing, 210037, China.
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Jones KE, Fér T, Schmickl RE, Dikow RB, Funk VA, Herrando‐Moraira S, Johnston PR, Kilian N, Siniscalchi CM, Susanna A, Slovák M, Thapa R, Watson LE, Mandel JR. An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. APPLICATIONS IN PLANT SCIENCES 2019; 7:e11295. [PMID: 31667023 PMCID: PMC6814182 DOI: 10.1002/aps3.11295] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/05/2019] [Indexed: 05/23/2023]
Abstract
PREMISE Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here. METHODS Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. RESULTS Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. DISCUSSION The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific.
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Affiliation(s)
- Katy E. Jones
- Botanischer Garten und Botanisches Museum BerlinFreie Universität BerlinKönigin‐Luise‐Str. 6–814195BerlinGermany
| | - Tomáš Fér
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2CZ 12800PragueCzech Republic
| | - Roswitha E. Schmickl
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2CZ 12800PragueCzech Republic
- Institute of BotanyThe Czech Academy of SciencesZámek 1CZ 25243PrůhoniceCzech Republic
| | - Rebecca B. Dikow
- Data Science LabOffice of the Chief Information OfficerSmithsonian InstitutionWashingtonD.C.20013‐7012USA
| | - Vicki A. Funk
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionWashingtonD.C.20013‐7012USA
| | | | - Paul R. Johnston
- Freie Universität BerlinEvolutionary BiologyBerlinGermany
- Berlin Center for Genomics in Biodiversity ResearchBerlinGermany
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB)BerlinGermany
| | - Norbert Kilian
- Botanischer Garten und Botanisches Museum BerlinFreie Universität BerlinKönigin‐Luise‐Str. 6–814195BerlinGermany
| | - Carolina M. Siniscalchi
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB‐CSIC‐ICUB)Pg. del Migdia s.n.ES 08038BarcelonaSpain
| | - Marek Slovák
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2CZ 12800PragueCzech Republic
- Plant Science and Biodiversity CentreSlovak Academy of SciencesSK‐84523BratislavaSlovakia
| | - Ramhari Thapa
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
| | - Linda E. Watson
- Department of Plant Biology, Ecology, and EvolutionOklahoma State UniversityStillwaterOklahoma74078USA
| | - Jennifer R. Mandel
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
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Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China. FORESTS 2019. [DOI: 10.3390/f10070587] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Quercus bawanglingensis Huang, Li et Xing, an endemic evergreen oak of the genus Quercus (Fagaceae) in China, is currently listed in the Red List of Chinese Plants as a vulnerable (VU) plant. No chloroplast (cp) genome information is currently available for Q. bawanglingensis, which would be essential for the establishment of guidelines for its conservation and breeding. In the present study, the cp genome of Q. bawanglingensis was sequenced and assembled into double-stranded circular DNA with a length of 161,394 bp. Two inverted repeats (IRs) with a total of 51,730 bp were identified, and the rest of the sequence was separated into two single-copy regions, namely, a large single-copy (LSC) region (90,628 bp) and a small single-copy (SSC) region (19,036 bp). The genome of Q. bawanglingensis contains 134 genes (86 protein-coding genes, 40 tRNAs and eight rRNAs). More forward (29) than inverted long repeats (21) are distributed in the cp genome. A simple sequence repeat (SSR) analysis showed that the genome contains 82 SSR loci, involving 84.15% A/T mononucleotides. Sequence comparisons among the nine complete cp genomes, including the genomes of Q. bawanglingensis, Q. tarokoensis Hayata (NC036370), Q. aliena var. acutiserrata Maxim. ex Wenz. (KU240009), Q. baronii Skan (KT963087), Q. aquifolioides Rehd. et Wils. (KX911971), Q. variabilis Bl. (KU240009), Fagus engleriana Seem. (KX852398), Lithocarpus balansae (Drake) A. Camus (KP299291) and Castanea mollissima Bl. (HQ336406), demonstrated that the diversity of SC regions was higher than that of IR regions, which might facilitate identification of the relationships within this extremely complex family. A phylogenetic analysis showed that Fagus engleriana and Trigonobalanus doichangensis form the basis of the produced evolutionary tree. Q. bawanglingensis and Q. tarokoensis, which belong to the group Ilex, share the closest relationship. The analysis of the cp genome of Q. bawanglingensis provides crucial genetic information for further studies of this vulnerable species and the taxonomy, phylogenetics and evolution of Quercus.
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Brian JI, Davy SK, Wilkinson SP. Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts. PeerJ 2019; 7:e7178. [PMID: 31289699 PMCID: PMC6598746 DOI: 10.7717/peerj.7178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/22/2019] [Indexed: 12/23/2022] Open
Abstract
Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondrion; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of next generation sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting or the presence of co-dominance, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.
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Affiliation(s)
- Joshua I Brian
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Shaun P Wilkinson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Nicola MV, Johnson LA, Pozner R. Unraveling patterns and processes of diversification in the South Andean-Patagonian Nassauvia subgenus Strongyloma (Asteraceae, Nassauvieae). Mol Phylogenet Evol 2019; 136:164-182. [PMID: 30858079 DOI: 10.1016/j.ympev.2019.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 02/11/2019] [Accepted: 03/07/2019] [Indexed: 12/26/2022]
Abstract
Congruence among different sources of data is highly desirable in phylogenetic analyses. However, plastid and nuclear DNA may record different evolutionary processes such that incongruence among results from these sources can help unravel complex evolutionary histories. That is the case of Nassauvia subgenus Strongyloma (Asteraceae), a taxon with five putative species distributed in the southern Andes and Patagonian steppe. Morphometric and phylogeographic information cast doubt on the integrity of its species, and previous molecular data even questioned the monophyly of the subgenus. We tested those questions using plastid and nuclear DNA sequences by the application of different methods such as phylogenetic trees, networks, a test of genealogical sorting, an analysis of population structure, calibration of the trees, and hybridization test, assembling non-synchronous incongruent results at subgenus and species levels in a single reconstruction. The integration of our molecular analyses and previous taxonomic, morphological, and molecular studies support subgenus Strongyloma as a monophyletic group. However, the topology of the nuclear trees and the evidence of polyploids within subgenus Nassauvia, suggest a hypothetical origin and initial radiation of Nassauvia related to an ancient hybridization event that occurred around 17-6.3 Myr ago near the Andes in west-central Patagonia. Plastid data suggest a recent diversification within subgenus Strongyloma, at most 9.8 Myr ago, towards the Patagonian steppe east of the Andes. These processes cause phylogenies to deviate from the species tree since each putative species lack exclusive ancestry. The non-monophyly of its species using both plastid and nuclear data is caused mainly by incomplete lineage sorting occurred since the Miocene. The final uplift of the Andes and Pliocene-Pleistocene glacial-interglacial and its consequences on the landscape and climate structured the genetic composition of this group of plants in the Patagonian steppe. The molecular data presented here agree with previous morphological studies, in that the five putative species typically accepted in this subgenus are not independent taxa. This study emphasizes that adding more than one sequence per species, not combining data with dissimilar inheritance patterns without first performed incongruence tests, exploring data through different methodologies, considering the timing of events, and searching for the causes of poorly resolved and/or incongruent phylogenies help to reveal complex biological underlying processes, which might otherwise remain hidden.
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Affiliation(s)
- Marcela V Nicola
- Instituto de Botánica Darwinion (CONICET-ANCEFN), Labardén 200, C.C. 22, B1642HYD, San Isidro, Provincia de Buenos Aires, Argentina.
| | - Leigh A Johnson
- Department of Biology and Bean Life Science Museum, 4102 LSB, Brigham Young University, Provo, UT 84602, USA
| | - Raúl Pozner
- Instituto de Botánica Darwinion (CONICET-ANCEFN), Labardén 200, C.C. 22, B1642HYD, San Isidro, Provincia de Buenos Aires, Argentina
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Huang J, Yang LQ, Yu Y, Liu YM, Xie DF, Li J, He XJ, Zhou SD. Molecular phylogenetics and historical biogeography of the tribe Lilieae (Liliaceae): bi-directional dispersal between biodiversity hotspots in Eurasia. ANNALS OF BOTANY 2018; 122:1245-1262. [PMID: 30084909 PMCID: PMC6324749 DOI: 10.1093/aob/mcy138] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/22/2018] [Indexed: 05/25/2023]
Abstract
Background and Aims The role played by the Qinghai-Tibet Plateau (QTP) in the organismal diversification and biogeography of plants in the Northern Hemisphere has attracted much attention from evolutionary biologists. Here we use tribe Lilieae (Liliaceae), including primarily temperate and alpine lineages with disjunct distributions in the North Temperate Zone, as a case study to shed light upon these processes. Methods Using 191 taxa (five outgroup taxa) comprising more than 60 % of extant Lilieae species across the entire geographical range, we analyse phylogenetic relationships based on three plastid markers (matK, rbcL, rpl16) and nuclear ITS. Divergence time estimation and ancestral range reconstruction were further inferred. Key Results The results support a monophyletic Lilieae divided into four clades. Lilium is nested within Fritillaria, which is paraphyletic and partitioned into two clades, New World and Old World, in the chloroplast DNA (cpDNA) analysis. Incongruences between the ITS and cpDNA trees may be explained by divergent ITS paralogues and hybridization. Lilieae originated around 40-49 (28-67) Mya and probably diversified in the QTP region with four major clades that were established during the Oligocene and the Early Miocene. Uplift of the QTP and climatic changes probably drove early diversification of Lilieae in the QTP region. A rapid radiation occurred during the Late Miocene and the Pleistocene, coinciding temporally with recent orogenic process in the QTP region and climatic oscillations. Several lineages dispersed out of the QTP. Conclusions Lineage persistence and explosive radiation were important processes for establishing high species diversity of Lilieae in the QTP region. Both long-distance dispersal and migration across Beringia probably contributed to the modern distribution range of Lilieae. Our study shows that biotic interchanges between the QTP region and Irano-Turanian region and the Mediterranean Basin were bi-directional, suggesting the latter was a secondary centre of diversity.
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Affiliation(s)
- Jiao Huang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
- College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Li-Qin Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Yan-Mei Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Juan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
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Peterson PM, Vega IS, Romaschenko K, Giraldo-Cañas D, Rodriguez NFR. Revision of Muhlenbergia (Poaceae, Chloridoideae, Cynodonteae, Muhlenbergiinae) in Peru: classification, phylogeny, and a new species, M.romaschenkoi. PHYTOKEYS 2018; 114:123-206. [PMID: 30627045 PMCID: PMC6323114 DOI: 10.3897/phytokeys.114.28799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/01/2018] [Indexed: 06/09/2023]
Abstract
A taxonomic treatment, phylogeny based on analysis of six DNA sequence markers (ITS, ndhA intron, rpl32-trnL, rps3, rps16 intron and rps16-trnK) and classification of Muhlenbergia for Peru is given. Seventeen species and one presumed hybrid are recognised. Muhlenbergiaromaschenkoi sp. nov. is newly described from the Río Huallaga Valley, northeast of Huánuco. The type of Podosemumangustatum [≡ Muhlenbergiaangustata] clearly aligns with what we had been referring to as the hybrid between this species and M.rigida. Therefore, we adopt the next available heterotypic name, Muhlenbergiacoerulea, for what we had been calling M.angustata and change the hybrid designation to M.coerulea × M.rigida. Lectotypes are designated for Epicampescoerulea Griseb., Muhlenbergiaaffinis Trin., Muhlenbergiaberlandieri Trin., Muhlenbergiabeyrichiana Kunth, Muhlenbergiaelegansvar.atroviolacea Kuntze, Muhlenbergiaelegansvar.subviridis Kuntze and Muhlenbergiaphragmitoides Griseb.
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Affiliation(s)
- Paul M. Peterson
- Department of Botany MRC-166, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USANational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Isidoro Sánchez Vega
- Departamento de Biología, Herbario CPUN, Universidad Nacional de Cajamarca Apartado 55, Cajamarca, PerúUniversidad Nacional de CajamarcaCajamarcaPeru
| | - Konstantin Romaschenko
- Department of Botany MRC-166, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USANational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Diego Giraldo-Cañas
- Herbario Nacional Colombiano, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá DC, ColombiaUniversidad Nacional de ColombiaBogotáColombia
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Phylogeography of western Mediterranean Cymbalaria (Plantaginaceae) reveals two independent long-distance dispersals and entails new taxonomic circumscriptions. Sci Rep 2018; 8:18079. [PMID: 30591708 PMCID: PMC6308241 DOI: 10.1038/s41598-018-36412-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 11/19/2018] [Indexed: 11/24/2022] Open
Abstract
The Balearic Islands, Corsica and Sardinia (BCS) constitute biodiversity hotspots in the western Mediterranean Basin. Oligocene connections and long distance dispersal events have been suggested to cause presence of BCS shared endemic species. One of them is Cymbalaria aequitriloba, which, together with three additional species, constitute a polyploid clade endemic to BCS. Combining amplified fragment length polymorphism (AFLP) fingerprinting, plastid DNA sequences and morphometrics, we inferred the phylogeography of the group and evaluated the species’ current taxonomic circumscriptions. Based on morphometric and AFLP data we propose a new circumscription for C. fragilis to additionally comprise a group of populations with intermediate morphological characters previously included in C. aequitriloba. Consequently, we suggest to change the IUCN category of C. fragilis from critically endangered (CR) to near threatened (NT). Both morphology and AFLP data support the current taxonomy of the single island endemics C. hepaticifolia and C. muelleri. The four species had a common origin in Corsica-Sardinia, and two long-distance dispersal events to the Balearic Islands were inferred. Finally, plastid DNA data suggest that interspecific gene flow took place where two species co-occur.
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Guo X, Thomas DC, Saunders RM. Gene tree discordance and coalescent methods support ancient intergeneric hybridisation between Dasymaschalon and Friesodielsia (Annonaceae). Mol Phylogenet Evol 2018; 127:14-29. [DOI: 10.1016/j.ympev.2018.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 03/23/2018] [Accepted: 04/09/2018] [Indexed: 01/10/2023]
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