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Jin P, Zhang M, Du B, Zhang J, Sun B. A new gnetalean macrofossil from the Lower Cretaceous of the Laiyang Basin, eastern China. PLANT DIVERSITY 2024; 46:678-682. [PMID: 39290879 PMCID: PMC11403114 DOI: 10.1016/j.pld.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 02/22/2024] [Accepted: 03/05/2024] [Indexed: 09/19/2024]
Abstract
•A new species Laiyangia compacta gen. et sp. nov. with unusual female spikes was described from the Laiyang Formation.•This species shows transitional morphology between early ephedroid and modern gnetoid.•The epidermal microstructural character of this species provides a driver paleoclimate of Laiyang area in Early Cretaceous.
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Affiliation(s)
- Peihong Jin
- Key Laboratory of Petroleum Resources, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Gansu Province, Lanzhou 730000, China
| | - Mingzhen Zhang
- Key Laboratory of Petroleum Resources, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Gansu Province, Lanzhou 730000, China
| | - Baoxia Du
- Key Laboratory Western China's Mineral Resources of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Jing Zhang
- Key Laboratory Western China's Mineral Resources of Gansu Province, Lanzhou University, Lanzhou 730000, China
| | - Bainian Sun
- Key Laboratory Western China's Mineral Resources of Gansu Province, Lanzhou University, Lanzhou 730000, China
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2
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Coiro M, Roberts EA, Hofmann CC, Seyfullah LJ. Cutting the long branches: Consilience as a path to unearth the evolutionary history of Gnetales. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1082639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Gnetales are one of the most fascinating groups within seed plants. Although the advent of molecular phylogenetics has generated some confidence in their phylogenetic placement of Gnetales within seed plants, their macroevolutionary history still presents many unknowns. Here, we review the reasons for such unknowns, and we focus the discussion on the presence of “long branches” both in their molecular and morphological history. The increased rate of molecular evolution and genome instability as well as the numerous unique traits (both reproductive and vegetative) in the Gnetales have been obstacles to a better understanding of their evolution. Moreover, the fossil record of the Gnetales, though relatively rich, has not yet been properly reviewed and investigated using a phylogenetic framework. Despite these apparent blocks to progress we identify new avenues to enable us to move forward. We suggest that a consilience approach, involving different disciplines such as developmental genetics, paleobotany, molecular phylogenetics, and traditional anatomy and morphology might help to “break” these long branches, leading to a deeper understanding of this mysterious group of plants.
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3
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Yang M, Wan T, Dai C, Zou XC, Liu F, Gong YB. Modern honey bees disrupt the pollination of an ancient gymnosperm, Gnetum luofuense. Ecology 2021; 102:e03497. [PMID: 34314038 DOI: 10.1002/ecy.3497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/28/2021] [Accepted: 06/10/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Min Yang
- State Key Laboratory of Hybrid Rice, Department of Ecology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Tao Wan
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, 430074, China.,Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, 518004, China
| | - Can Dai
- School of Resources and Environmental Science, Hubei University, Wuhan, 430062, China
| | - Xiao-Chun Zou
- State Key Laboratory of Hybrid Rice, Department of Ecology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Fan Liu
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, 430074, China.,Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yan-Bing Gong
- State Key Laboratory of Hybrid Rice, Department of Ecology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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M. Van Waveren I. A morphometric analysis of Tobleriabicuspis, a Voltziales seed cone from the early Permian Jambi palaeoflora, Sumatra (Indonesia). PHYTOKEYS 2019; 119:67-95. [PMID: 31015778 PMCID: PMC6443619 DOI: 10.3897/phytokeys.119.29555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/21/2019] [Indexed: 06/09/2023]
Abstract
Tobleriabicuspis, a coniferophyte seed cone, is described from the Jambi Palaeoflora, Sumatra of Asselian (early Permian) age. A morphometric analysis based on cones, paired fertile units, and fertile and sterile scales, demonstrates their close relationship. Small paired fertile units occur mainly in cones. Medium-sized paired fertile units occur mainly on scales. And large paired fertile units are mainly dispersed. The cones are considered female and the paired fertile units are considered to represent the seeds. The cones are composed of helicoidal, bilaterally symmetrical and deeply incised scales with paired seeds. A comparison can be made with the Voltziales female taxon Schizolepis from the Triassic and Jurassic. Tobleria is regarded as having a voltzian Voltziales affinity and dates from approximately 16 to 26 million years before any other such cones.
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Affiliation(s)
- Isabel M. Van Waveren
- Naturalis Biodiversity Center, Postbus 9517, 2300 RA, Leiden, the NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
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5
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Benca JP, Duijnstee IAP, Looy CV. UV-B-induced forest sterility: Implications of ozone shield failure in Earth's largest extinction. SCIENCE ADVANCES 2018; 4:e1700618. [PMID: 29441357 PMCID: PMC5810612 DOI: 10.1126/sciadv.1700618] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 01/08/2018] [Indexed: 05/13/2023]
Abstract
Although Siberian Trap volcanism is considered a primary driver of the largest extinction in Earth history, the end-Permian crisis, the relationship between these events remains unclear. However, malformations in fossilized gymnosperm pollen from the extinction interval suggest biological stress coinciding with pulsed forest decline. These grains are hypothesized to have been caused by enhanced ultraviolet-B (UV-B) irradiation from volcanism-induced ozone shield deterioration. We tested this proposed mechanism by observing the effects of inferred end-Permian UV-B regimes on pollen development and reproductive success in living conifers. We find that pollen malformation frequencies increase fivefold under high UV-B intensities. Surprisingly, all trees survived but were sterilized under enhanced UV-B. These results support the hypothesis that heightened UV-B stress could have contributed not only to pollen malformation production but also to deforestation during Permian-Triassic crisis intervals. By reducing the fertility of several widespread gymnosperm lineages, pulsed ozone shield weakening could have induced repeated terrestrial biosphere destabilization and food web collapse without exerting a direct "kill" mechanism on land plants or animals. These findings challenge the paradigm that mass extinctions require kill mechanisms and suggest that modern conifer forests may be considerably more vulnerable to anthropogenic ozone layer depletion than expected.
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Affiliation(s)
- Jeffrey P. Benca
- Department of Integrative Biology and Museum of Paleontology, University of California, Berkeley, 3060 Valley Life Sciences Building, Berkeley, CA 94720–3140, USA
- Corresponding author.
| | - Ivo A. P. Duijnstee
- Department of Integrative Biology and Museum of Paleontology, University of California, Berkeley, 3060 Valley Life Sciences Building, Berkeley, CA 94720–3140, USA
| | - Cindy V. Looy
- Department of Integrative Biology and Museum of Paleontology, University of California, Berkeley, 3060 Valley Life Sciences Building, Berkeley, CA 94720–3140, USA
- University and Jepson Herbaria, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, CA 94720–2465, USA
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6
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Barker MS. A Gneato nuclear genome. NATURE PLANTS 2018; 4:63-64. [PMID: 29379154 DOI: 10.1038/s41477-018-0102-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
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7
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van Eldijk TJB, Wappler T, Strother PK, van der Weijst CMH, Rajaei H, Visscher H, van de Schootbrugge B. A Triassic-Jurassic window into the evolution of Lepidoptera. SCIENCE ADVANCES 2018; 4:e1701568. [PMID: 29349295 PMCID: PMC5770165 DOI: 10.1126/sciadv.1701568] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 12/04/2017] [Indexed: 06/02/2023]
Abstract
On the basis of an assemblage of fossilized wing scales recovered from latest Triassic and earliest Jurassic sediments from northern Germany, we provide the earliest evidence for Lepidoptera (moths and butterflies). The diverse scales confirm a (Late) Triassic radiation of lepidopteran lineages, including the divergence of the Glossata, the clade that comprises the vast multitude of extant moths and butterflies that have a sucking proboscis. The microfossils extend the minimum calibrated age of glossatan moths by ca. 70 million years, refuting ancestral association of the group with flowering plants. Development of the proboscis may be regarded as an adaptive innovation to sucking free liquids for maintaining the insect's water balance under arid conditions. Pollination drops secreted by a variety of Mesozoic gymnosperms may have been non-mutualistically exploited as a high-energy liquid source. The early evolution of the Lepidoptera was probably not severely interrupted by the end-Triassic biotic crisis.
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Affiliation(s)
- Timo J. B. van Eldijk
- Department of Earth Sciences, Marine Palynology and Paleoceanography, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, Netherlands
| | - Torsten Wappler
- Natural History Department, Hessisches Landesmuseum Darmstadt, Friedensplatz 1, 64283 Darmstadt, Germany
| | - Paul K. Strother
- Department of Earth and Environmental Science, Weston Observatory, Boston College, 381 Concord Road, Weston, MA 02493–1340, USA
| | - Carolien M. H. van der Weijst
- Department of Earth Sciences, Marine Palynology and Paleoceanography, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, Netherlands
| | - Hossein Rajaei
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Henk Visscher
- Department of Earth Sciences, Marine Palynology and Paleoceanography, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, Netherlands
| | - Bas van de Schootbrugge
- Department of Earth Sciences, Marine Palynology and Paleoceanography, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, Netherlands
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8
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Puebla GG, Iglesias A, Gómez MA, Prámparo MB. Fossil record of Ephedra in the Lower Cretaceous (Aptian), Argentina. JOURNAL OF PLANT RESEARCH 2017; 130:975-988. [PMID: 28528483 DOI: 10.1007/s10265-017-0953-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 04/21/2017] [Indexed: 06/07/2023]
Abstract
Fossil plants from the Lower Cretaceous (upper Aptian) of the La Cantera Formation, Argentina, are described. The fossils studied represent a leafy shooting system with several orders of articulated and striated axes and attached leaves with unequivocal ephedroid affinity. We also found associated remains of ovulate cones with four whorls of sterile bracts, which contain two female reproductive units (FRU). Ovulate cone characters fit well within the genus Ephedra. Special characters in the ovulate cones including an outer seed envelope with two types of trichomes, allowed us to consider our remains as a new Ephedra species. Abundant dispersed ephedroid pollen obtained from the macrofossil-bearing strata also confirms the abundance of Ephedraceae in the basin. The co-occurrence of abundant fossil of Ephedra (adapted to dry habitats) associated with thermophilic cheirolepideacean conifer pollen (Classopollis) in the unit would suggest marked seasonality at the locality during the Early Cretaceous. Furthermore, the floristic association is linked to dry sensitive rocks in the entire section. The macro- and microflora from San Luis Basin are similar in composition to several Early Cretaceous floras from the Northern Gondwana floristic province, but it may represent one of the southernmost records of an arid biome in South America.
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Affiliation(s)
- Gabriela G Puebla
- Unidad de Paleopalinología, Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales Centro Científico Tecnológico, UNCuyo-CONICET, Av. Adrián Ruiz Leal s/n-C.C.131, 5500, Mendoza, Argentina.
| | - Ari Iglesias
- Instituto de Investigaciones en Biodiversidad y Medioambiente UNCO-CONICET, Quintral 1250, 8400, San Carlos de Bariloche, Río Negro, Argentina
| | - María A Gómez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis CONICET, Chacabuco 913, 5700, San Luis, Argentina
| | - Mercedes B Prámparo
- Unidad de Paleopalinología, Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales Centro Científico Tecnológico, UNCuyo-CONICET, Av. Adrián Ruiz Leal s/n-C.C.131, 5500, Mendoza, Argentina
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9
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Yang J, Chen X, Bai J, Fang D, Qiu Y, Jiang W, Yuan H, Bian C, Lu J, He S, Pan X, Zhang Y, Wang X, You X, Wang Y, Sun Y, Mao D, Liu Y, Fan G, Zhang H, Chen X, Zhang X, Zheng L, Wang J, Cheng L, Chen J, Ruan Z, Li J, Yu H, Peng C, Ma X, Xu J, He Y, Xu Z, Xu P, Wang J, Yang H, Wang J, Whitten T, Xu X, Shi Q. The Sinocyclocheilus cavefish genome provides insights into cave adaptation. BMC Biol 2016; 14:1. [PMID: 26728391 PMCID: PMC4698820 DOI: 10.1186/s12915-015-0223-4] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/17/2015] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. RESULTS The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. CONCLUSION As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.
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Affiliation(s)
- Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | | | - Jie Bai
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,Fauna & Flora International, Cambridge, CB1 2JD, UK.
| | - Dongming Fang
- BGI-Shenzhen, Shenzhen, 518083, China. .,Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Ying Qiu
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,China National Genebank, Shenzhen, 518083, China.
| | - Wansheng Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Hui Yuan
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Chao Bian
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Jiang Lu
- BGI-Shenzhen, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shiyang He
- BGI-Shenzhen, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiaofu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Yaolei Zhang
- BGI-Shenzhen, Shenzhen, 518083, China. .,School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
| | - Xiaoai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xinxin You
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | | | - Ying Sun
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National Genebank, Shenzhen, 518083, China.
| | | | - Yong Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
| | | | - He Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xiaoyong Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xinhui Zhang
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Lanping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | | | - Le Cheng
- China National Genebank, Shenzhen, 518083, China. .,BGI-Yunnan, Kunming, 650106, China.
| | - Jieming Chen
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Zhiqiang Ruan
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Jia Li
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hui Yu
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chao Peng
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Xingyu Ma
- Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen, 518083, China. .,Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., Zhenjiang, 212000, China.
| | - Junmin Xu
- Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen, 518083, China. .,Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., Zhenjiang, 212000, China.
| | - You He
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201204, China.
| | - Zhengfeng Xu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210029, China.
| | - Pao Xu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China. .,James D. Watson Institute of Genome Science, Hangzhou, 310008, China.
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China. .,James D. Watson Institute of Genome Science, Hangzhou, 310008, China.
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, 518083, China. .,Department of Biology, Ole Maaløes Vej 5, University of Copenhagen, DK-2200, Copenhagen, Denmark.
| | - Tony Whitten
- Fauna & Flora International, Cambridge, CB1 2JD, UK.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Qiong Shi
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen, 518083, China. .,Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., Zhenjiang, 212000, China.
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11
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Yang Y, Lin L, Wang Q. Chengia laxispicata gen. et sp. nov., a new ephedroid plant from the Early Cretaceous Yixian Formation of western Liaoning, Northeast China: evolutionary, taxonomic, and biogeographic implications. BMC Evol Biol 2013; 13:72. [PMID: 23530702 PMCID: PMC3626868 DOI: 10.1186/1471-2148-13-72] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/20/2013] [Indexed: 11/10/2022] Open
Abstract
Background The extant Gnetales include three monotypic families, namely, Ephedraceae (Ephedra), Gnetaceae (Gnetum), and Welwitschiaceae (Welwitschia), all of which possess compound female cones that comprise a main axis and 1 to multiple pairs/whorls of bracts subtending a female reproductive unit or having lower pairs/whorls of bracts sterile. However, the evolutionary origin of such a reproductive architecture in Gnetales is controversial in the light of the competing anthophyte versus gnetifer hypotheses of seed plant relationships. Hence, macrofossils demonstrating the structure of compound female cones of the Gnetales should be important to decipher the early evolution of the order. Results A new ephedroid plant Chengia laxispicata gen. et sp. nov. is described from the Early Cretaceous Yixian Formation of western Liaoning, Northeast China. The fossil represents a part of a leafy shooting system with reproductive organs attached. The main shoot bears internodes and swollen nodes, from which lateral branches arise oppositely. Reproductive organs consist of female spikes terminal to twigs or axillary to linear leaves. Spikes are loosely arranged, having prominent nodes and internodes. Bracts of the spikes are decussately opposite and comprise 4—8 pairs of bracts. Each bract subtends an ellipsoid seed. Seeds are sessile, with a thin outer envelope and a distal micropylar tube. Conclusions Chengia laxispicata gen. et sp. nov. provides a missing link between archetypal fertile organs in the crown lineage of the Gnetales and compound female cones of the extant Ephedraceae. Combined with a wealth of Ephedra and ephedroid macrofossils from the Early Cretaceous, we propose a reduction and sterilization hypothesis that the female cone of the extant Ephedraceae may have stemmed from archetypal fertile organs in the crown lineage of the Gnetales. These have undergone sequentially intermediate links similar to female cones of Cretaceous Siphonospermum, Chengia, and Liaoxia by reduction and sterilization of the lower fertile bracts, shortenings of internodes and peduncles as well as loss of reproductive units in all inferior bracts. The basal family Ephedraceae including Ephedra of the extant Gnetales was demonstrated to have considerable diversity by the Early Cretaceous, so an emended familial diagnosis is given here. The Jehol Biota in Northeast China and adjacent areas contains a plethora of well-preserved macrofossils of Ephedra and ephedroids that show different evolutionary stages including primitive and derived characters of Ephedraceae, so Northeast China and adjacent areas may represent either the centre of origination or one of the centres for early diversification of the family.
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Affiliation(s)
- Yong Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
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12
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Abstract
• Plants have utterly transformed the planet, but testing hypotheses of causality requires a reliable time-scale for plant evolution. While clock methods have been extensively developed, less attention has been paid to the correct interpretation and appropriate implementation of fossil data. • We constructed 17 calibrations, consisting of minimum constraints and soft maximum constraints, for divergences between model representatives of the major land plant lineages. Using a data set of seven plastid genes, we performed a cross-validation analysis to determine the consistency of the calibrations. Six molecular clock analyses were then conducted, one with the original calibrations, and others exploring the impact on divergence estimates of changing maxima at basal nodes, and prior probability densities within calibrations. • Cross-validation highlighted Tracheophyta and Euphyllophyta calibrations as inconsistent, either because their soft maxima were overly conservative or because of undetected rate variation. Molecular clock analyses yielded estimates ranging from 568-815 million yr before present (Ma) for crown embryophytes and from 175-240 Ma for crown angiosperms. • We reject both a post-Jurassic origin of angiosperms and a post-Cambrian origin of land plants. Our analyses also suggest that the establishment of the major embryophyte lineages occurred at a much slower tempo than suggested in most previous studies. These conclusions are entirely compatible with current palaeobotanical data, although not necessarily with their interpretation by palaeobotanists.
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Affiliation(s)
- John T Clarke
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Rachel C M Warnock
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, UK
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Whole fossil plants of Ephedra and their implications on the morphology, ecology and evolution of Ephedraceae (Gnetales). ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s11434-010-3069-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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14
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Hibbett DS, Matheny PB. The relative ages of ectomycorrhizal mushrooms and their plant hosts estimated using Bayesian relaxed molecular clock analyses. BMC Biol 2009; 7:13. [PMID: 19284559 PMCID: PMC2660285 DOI: 10.1186/1741-7007-7-13] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Accepted: 03/10/2009] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Ectomycorrhizae (ECM) are symbioses formed by polyphyletic assemblages of fungi (mostly Agaricomycetes) and plants (mostly Pinaceae and angiosperms in the rosid clade). Efforts to reconstruct the evolution of the ECM habit in Agaricomycetes have yielded vastly different results, ranging from scenarios with many relatively recent origins of the symbiosis and no reversals to the free-living condition; a single ancient origin of ECM and many subsequent transitions to the free-living condition; or multiple gains and losses of the association. To test the plausibility of these scenarios, we performed Bayesian relaxed molecular clock analyses including fungi, plants, and other eukaryotes, based on the principle that a symbiosis cannot evolve prior to the origin of both partners. As we were primarily interested in the relative ages of the plants and fungi, we did not attempt to calibrate the molecular clock using the very limited fossil record of Agaricomycetes. RESULTS Topologically constrained and unconstrained analyses suggest that the root node of the Agaricomycetes is much older than either the rosids or Pinaceae. The Agaricomycetidae, a large clade containing the Agaricales and Boletales (collectively representing 70% of Agaricomycetes), is also significantly older than the rosids. The relative age of Agaricomycetidae and Pinaceae, however, is sensitive to tree topology, and the inclusion or exclusion of the gnetophyte Welwitschia mirabilis. CONCLUSION The ancestor of the Agaricomycetes could not have been an ECM species because it existed long before any of its potential hosts. Within more derived clades of Agaricomycetes, there have been at least eight independent origins of ECM associations involving angiosperms, and at least six to eight origins of associations with gymnosperms. The first ECM symbioses may have involved Pinaceae, which are older than rosids, but several major clades of Agaricomycetes, such as the Boletales and Russulales, are young enough to have been plesiomorphically associated with either rosids or Pinaceae, suggesting that some contemporary ECM partnerships could be of very ancient origin.
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Affiliation(s)
- David S Hibbett
- Biology Department, Clark University, Worcester, Massachusetts 01610, USA
| | - P Brandon Matheny
- Biology Department, Clark University, Worcester, Massachusetts 01610, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
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Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategy. Mol Phylogenet Evol 2009; 52:115-24. [PMID: 19166950 DOI: 10.1016/j.ympev.2008.12.026] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 12/30/2008] [Accepted: 12/31/2008] [Indexed: 11/22/2022]
Abstract
The cpDNA of Welwitschia mirabilis (the only species of Welwitschiales) was recently reported to be the most reduced and compact among photosynthetic land plants. However, cpDNAs of the other two gnetophyte lineages (viz. Ephedrales and Gnetales) have not yet been studied. It remains unclear what underlining mechanisms have downsized the cpDNA. To pin down major factors for cpDNA reduction and compaction in gnetophytes, we have determined 4 complete cpDNAs, including one from each of the 3 gnetophyte orders, Ephedra equisetina, Gnetum parvifolium, and W. mirabilis, and one from the non-Pinus Pinaceae, Keteleeria davidiana. We report that the cpDNAs of E. equisetina (109,518bp) and G.parvifolium (114,914bp) are not only smaller but more compact than that of W. mirabilis (118,919bp). The gnetophyte cpDNAs have commonly lost at least 18 genes that are retained in other seed plants. Furthermore, they have significantly biased usages of AT-rich codons and shorter introns and intergenic spaces, which are largely due to more deletions at inter-operon than intra-operon spaces and removal of segment sequences rather than single-nucleotides. We show that the reduced gnetophyte cpDNAs clearly resulted from selection for economy by deletions of genes and non-coding sequences, which then led to the compactness and the accelerated substitution rates. The smallest C-values in gnetophyte nuclear DNAs and the competitive or resource-poor situations encountered by gnetophytes further suggest a critical need for an economic strategy.
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Wu CS, Wang YN, Liu SM, Chaw SM. Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plants. Mol Biol Evol 2007; 24:1366-79. [PMID: 17383970 DOI: 10.1093/molbev/msm059] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic relationships among the 5 groups of extant seed plants are presently unsettled. To reexamine this long-standing debate, we determine the complete chloroplast genome (cpDNA) of Cycas taitungensis and 56 protein-coding genes encoded in the cpDNA of Gnetum parvifolium. The cpDNA of Cycas is a circular molecule of 163,403 bp with 2 typical large inverted repeats (IRs) of 25,074 bp each. We inferred phylogenetic relationships among major seed plant lineages using concatenated 56 protein-coding genes in 37 land plants. Phylogenies, generated by the use of 3 independent methods, provide concordant and robust support for the monophylies of extant seed plants, gymnosperms, and angiosperms. Within the modern gymnosperms are 2 highly supported sister clades: Cycas-Ginkgo and Gnetum-Pinus. This result agrees with both the "gnetifer" and "gnepines" hypotheses. The sister relationships in Cycas-Ginkgo and Gnetum-Pinus clades are further reinforced by cpDNA structural evidence. Branch lengths of Cycas-Ginkgo and Gnetum were consistently the shortest and the longest, respectively, in all separate analyses. However, the Gnetum relative rate test revealed this tendency only for the 3rd codon positions and the transversional sites of the first 2 codon positions. A PsitufA located between psbE and petL genes is here first detected in Anthoceros (a hornwort), cycads, and Ginkgo. We demonstrate that the PsitufA is a footprint descended from the chloroplast tufA of green algae. The duplication of ycf2 genes and their shift into IRs should have taken place at least in the common ancestor of seed plants more than 300 MYA, and the tRNAPro-GGG gene was lost from the angiosperm lineage at least 150 MYA. Additionally, from cpDNA structural comparison, we propose an alternative model for the loss of large IR regions in black pine. More cpDNA data from non-Pinaceae conifers are necessary to justify whether the gnetifer or gnepines hypothesis is valid and to generate solid structural evidence for the monophyly of extant gymnosperms.
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Affiliation(s)
- Chung-Shien Wu
- Research Center for Biodiversity, Academia Sinica, Taipei, Taiwan
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17
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Won H, Renner SS. Dating dispersal and radiation in the gymnosperm Gnetum (Gnetales)--clock calibration when outgroup relationships are uncertain. Syst Biol 2006; 55:610-22. [PMID: 16969937 DOI: 10.1080/10635150600812619] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Most implementations of molecular clocks require resolved topologies. However, one of the Bayesian relaxed clock approaches accepts input topologies that include polytomies. We explored the effects of resolved and polytomous input topologies in a rate-heterogeneous sequence data set for Gnetum, a member of the seed plant lineage Gnetales. Gnetum has 10 species in South America, 1 in tropical West Africa, and 20 to 25 in tropical Asia, and explanations for the ages of these disjunctions involve long-distance dispersal and/or the breakup of Gondwana. To resolve relationships within Gnetum, we sequenced most of its species for six loci from the chloroplast (rbcL, matK, and the trnT-trnF region), the nucleus (rITS/5.8S and the LEAFY gene second intron), and the mitochondrion (nad1 gene second intron). Because Gnetum has no fossil record, we relied on fossils from other Gnetales and from the seed plant lineages conifers, Ginkgo, cycads, and angiosperms to constrain a molecular clock and obtain absolute times for within-Gnetum divergence events. Relationships among Gnetales and the other seed plant lineages are still unresolved, and we therefore used differently resolved topologies, including one that contained a basal polytomy among gymnosperms. For a small set of Gnetales exemplars (n = 13) in which rbcL and matK satisfied the clock assumption, we also obtained time estimates from a strict clock, calibrated with one outgroup fossil. The changing hierarchical relationships among seed plants (and accordingly changing placements of distant fossils) resulted in small changes of within-Gnetum estimates because topologically closest constraints overrode more distant constraints. Regardless of the seed plant topology assumed, relaxed clock estimates suggest that the extant clades of Gnetum began diverging from each other during the Upper Oligocene. Strict clock estimates imply a mid-Miocene divergence. These estimates, together with the phylogeny for Gnetum from the six combined data sets, imply that the single African species of Gnetum is not a remnant of a once Gondwanan distribution. Miocene and Pliocene range expansions are inferred for the Asian subclades of Gnetum, which stem from an ancestor that arrived from Africa. These findings fit with seed dispersal by water in several species of Gnetum, morphological similarities among apparently young species, and incomplete concerted evolution in the nuclear ITS region.
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Affiliation(s)
- Hyosig Won
- Department of Biology, University of Missouri-St. Louis, 8001 Natural Bridge Road, St. Louis, Missouri 63121, USA.
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Rydin C, Pedersen KR, Crane PR, Friis EM. Former diversity of Ephedra (Gnetales): evidence from Early Cretaceous seeds from Portugal and North America. ANNALS OF BOTANY 2006; 98:123-40. [PMID: 16675607 PMCID: PMC2803531 DOI: 10.1093/aob/mcl078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2005] [Revised: 12/22/2005] [Accepted: 03/06/2006] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS The extant species of the seed plant group Gnetales (Ephedra, Gnetum and Welwitschia) have been considered a remnant of a much greater, now extinct, diversity due to the pronounced differences in form and ecology among the genera. Until recently, this hypothesis has not been supported by evidence from the fossil record. This paper adds to the expanding information on Gnetales from the Early Cretaceous and describes coalified seeds from Barremian-Albian localities in Portugal and USA. METHODS The fossils were extracted from sediment samples by sieving in water. Adhering mineral matrix was removed by chemical treatment. Seeds were investigated using light and scanning electron microscopy. Morphology and anatomy of the seeds were documented and compared with those of extant species. KEY RESULTS The fossils share characters with extant Ephedra, for example papillae on the inner surface of the seed envelope and in situ polyplicate pollen grains that shed the exine during germination. They differ from extant Ephedra seeds in morphological and anatomical details as well as in their smaller size. Two new species of Ephedra are described together with one species assigned to a new genus of Gnetales. Other Ephedra-like seeds, for which pollen and critical morphological details are currently unknown, are also present in the samples. CONCLUSIONS These Cretaceous seeds document that key reproductive characters and pollen germination processes have remained unchanged within Ephedra for about 120 million years or more. There is sufficient variety in details of morphology to suggest that a diversity of Ephedra and Ephedra-like species were present in the Early Cretaceous flora. Their presence in Portugal and eastern North America indicates that they were widespread on the Laurasian continent. The fossil seeds are similar to seeds of Erdtmanithecales and this supports the previously suggested relationship between Erdtmanithecales and Gnetales.
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Affiliation(s)
- Catarina Rydin
- Department of Palaeobotany, Swedish Museum of Natural History, Box 50007, S-104 05 Stockholm, Sweden.
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