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Nguyen AT, Atkinson BA. Cretaceous and Paleocene fossils reveal an extinct higher clade within Cornales, the dogwood order. AMERICAN JOURNAL OF BOTANY 2024; 111:e16372. [PMID: 39010697 DOI: 10.1002/ajb2.16372] [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: 11/09/2023] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 07/17/2024]
Abstract
PREMISE Characterization and phylogenetic integration of fossil angiosperms with uncertain affinities is relatively limited, which may obscure the diversity of extinct higher taxa in the flowering plant tree of life. The order Cornales contains a diversity of extinct taxa with uncertain familial affinities that make it an ideal group for studying turnover in angiosperms. Here, we describe a new extinct genus of Cornales unassignable to an extant family and conduct a series of phylogenetic analyses to reconstruct relationships of fossils across the order. METHODS Two permineralized endocarps were collected from the Cedar District Formation (Campanian, 82-80 Ma) of Sucia Island, State of Washington, United States. Fossils were sectioned with the cellulose acetate peel technique and incorporated into a morphological dataset. To assess the utility of this dataset to accurately place taxa in their respective clades, we used a series of phylogenetic pseudofossilization analyses. We then conducted a total-evidence analysis and a scaffold-based approach to determine relationships of fossils. RESULTS Based on their unique combination of characters, the fossils represent a new genus, Fenestracarpa washingtonensis gen. nov. et sp. nov. Pseudofossilization analyses indicate that our morphological dataset can be used to accurately recover taxa at the major clade to family level, generally with moderate to high support. The total-evidence and scaffold-based analyses recovered Fenestracarpa and other fossil genera in an entirely extinct clade within Cornales. CONCLUSIONS Our findings increase the reported diversity of extinct Cornales and indicate that the order's initial radiation likely included the divergence of an extinct higher clade that endured the end-Cretaceous Mass extinction but perished during the Cenozoic.
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Affiliation(s)
- Austin T Nguyen
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, 66045, KS, USA
- Biodiversity Institute, University of Kansas, Lawrence, 66045, KS, USA
| | - Brian A Atkinson
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, 66045, KS, USA
- Biodiversity Institute, University of Kansas, Lawrence, 66045, KS, USA
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2
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Naware D, Benson R. Patterns of variation in fleshy diaspore size and abundance from Late Triassic-Oligocene. Biol Rev Camb Philos Soc 2024; 99:430-457. [PMID: 38081480 DOI: 10.1111/brv.13029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 03/06/2024]
Abstract
Vertebrate-mediated seed dispersal is a common attribute of many living plants, and variation in the size and abundance of fleshy diaspores is influenced by regional climate and by the nature of vertebrate seed dispersers among present-day floras. However, potential drivers of large-scale variation in the abundance and size distributions of fleshy diaspores through geological time, and the importance of geographic variation, are incompletely known. This knowledge gap is important because fleshy diaspores are a key mechanism of energy transfer from photosynthesis to animals and may in part explain the diversification of major groups within birds and mammals. Various hypotheses have been proposed to explain variation in the abundance and size distribution of fleshy diaspores through time, including plant-frugivore co-evolution, angiosperm diversification, and changes in vegetational structure and climate. We present a new data set of more than 800 georeferenced fossil diaspore occurrences spanning the Triassic-Oligocene, across low to mid- to high palaeolatitudes. We use this to quantify patterns of long-term change in fleshy diaspores, examining the timing and geographical context of important shifts as a test of the potential evolutionary and climatic explanations. We find that the fleshy fruit sizes of angiosperms increased for much of the Cretaceous, during the early diversification of angiosperms from herbaceous ancestors with small fruits. Nevertheless, this did not cause a substantial net change in the fleshy diaspore size distributions across seed plants, because gymnosperms had achieved a similar size distribution by at least the Late Triassic. Furthermore, gymnosperm-dominated Mesozoic ecosystems were mostly open, and harboured low proportions of specialised frugivores until the latest Cretaceous, suggesting that changes in vegetation structure and plant-frugivore co-evolution were probably not important drivers of fleshy diaspore size distributions over long timescales. Instead, fleshy diaspore size distributions may be largely constrained by physical or life-history limits that are shared among groups and diversify as a plant group expands into different growth forms/sizes, habitats, and climate regimes. Mesozoic gymnosperm floras had a low abundance of fleshy diaspores (<50% fleshy diaspore taxa), that was surpassed by some low-latitude angiosperm floras in the Cretaceous. Eocene angiosperm floras show a mid- to high latitude peak in fleshy fruit abundance, with very high proportions of fleshy fruits that even exceed those seen at low latitudes both in the Eocene and today. Mid- to high latitude proportions of fleshy fruits declined substantially over the Eocene-Oligocene transition, resulting in a shift to more modern-like geographic distributions with the highest proportion of fleshy fruits occurring in low-latitude tropical assemblages. This shift was coincident with global cooling and the onset of Southern Hemisphere glaciation, suggesting that rapid cooling at mid- and high latitudes caused a decrease in availability of the climate conditions most favourable for fleshy fruits in angiosperms. Future research could be focused on examining the environmental niches of modern fleshy fruits, and the potential effects of climate change on fleshy fruit and frugivore diversity.
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Affiliation(s)
- Duhita Naware
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, OX1 3AN, UK
| | - Roger Benson
- American Museum of Natural History, 200 Central Park West, New York, NY, 10024-5102, USA
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Coiro M. Embracing uncertainty: The way forward in plant fossil phylogenetics. AMERICAN JOURNAL OF BOTANY 2024; 111:e16282. [PMID: 38334302 DOI: 10.1002/ajb2.16282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 02/10/2024]
Abstract
Although molecular phylogenetics remains the most widely used method of inferring the evolutionary history of living groups, the last decade has seen a renewed interest in morphological phylogenetics, mostly driven by the promises that integrating the fossil record in phylogenetic trees offers to our understanding of macroevolutionary processes and dynamics and the possibility that the inclusion of fossil taxa could lead to more accurate phylogenetic hypotheses. The plant fossil record presents some challenges to its integration in a phylogenetic framework. Phylogenies including plant fossils often retrieve uncertain relationships with low support, or lack of resolution. This low support is due to the pervasiveness of morphological convergence among plant organs and the fragmentary nature of many plant fossils, and it is often perceived as a fundamental weakness reducing the utility of plant fossils in phylogenetics. Here I discuss the importance of uncertainty in morphological phylogenetics and how we can identify important information from different patterns and types of uncertainty. I also review a set of methodologies that can allow us to understand the causes underpinning uncertainty and how these practices can help us to further our knowledge of plant fossils. I also propose that a new visual language, including the use of networks instead of trees, represents an improvement on the old visualization based on consensus trees and more adequately serves phylogeneticists working with plant fossils. This set of methods and visualization tools represents an important way forward in a fundamental field for our understanding of the evolutionary history of plants.
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Affiliation(s)
- Mario Coiro
- Department of Palaeontology, University of Vienna, Vienna, Austria
- Ronin Institute for Independent Scholarship, Montclair, NJ, USA
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Wu X, Simpson SA, Youngblood RC, Liu XF, Scheffler BE, Rinehart TA, Alexander LW, Hulse-Kemp AM. Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea ( Hydrangea macrophylla) and insights into Asterid evolution. HORTICULTURE RESEARCH 2023; 10:uhad217. [PMID: 38130599 PMCID: PMC10734616 DOI: 10.1093/hr/uhad217] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/07/2023] [Indexed: 12/23/2023]
Abstract
The Hydrangea genus belongs to the Hydrangeaceae family, in the Cornales order of flowering plants, which early diverged among the Asterids, and includes several species that are commonly used ornamental plants. Of them, Hydrangea macrophylla is one of the most valuable species in the nursery trade, yet few genomic resources are available for this crop or closely related Asterid species. Two high-quality haplotype-resolved reference genomes of hydrangea cultivars 'Veitchii' and 'Endless Summer' [highest quality at 2.22 gigabase pairs (Gb), 396 contigs, N50 22.8 megabase pairs (Mb)] were assembled and scaffolded into the expected 18 pseudochromosomes. Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants, nuclear data were found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids. Genetic mapping with an F1 hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape, CYP78A5 located on chromosome 4, and a novel gene, BAM3 located on chromosome 17, for causing double flower. Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contribute to understanding the largest group of flowering plants, the Asterids.
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Affiliation(s)
- Xingbo Wu
- Department of Environmental Horticulture, Tropical Research and Education Center, University of Florida, Homestead, FL 33031, United States
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC 27695, United States
| | - Sheron A Simpson
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, United States
| | - Ramey C Youngblood
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS 39762, United States
| | - Xiaofen F Liu
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, United States
| | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, United States
| | - Timothy A Rinehart
- Crop Production and Protection, USDA-ARS, Beltsville, MD 20705, United States
| | - Lisa W Alexander
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, USDA-ARS, McMinnville, TN 37110, United States
| | - Amanda M Hulse-Kemp
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC 27695, United States
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, United States
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Atkinson BA. Icacinaceae fossil provides evidence for a Cretaceous origin of the lamiids. NATURE PLANTS 2022; 8:1374-1377. [PMID: 36376504 DOI: 10.1038/s41477-022-01275-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/10/2022] [Indexed: 05/12/2023]
Abstract
Today the asterids comprise over 80,000 species of flowering plants; however, relatively little is known about the timing of their early diversification. This is particularly true for the diverse lamiid clade, which comprises half of asterid diversity. Here, a lamiid fossil fruit assigned to Icacinaceae from the Campanian of western North America provides important macrofossil evidence indicating that lamiids diverged at least 80 million years ago and sheds light on potential Cretaceous rainforest-like ecosystems.
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Affiliation(s)
- Brian A Atkinson
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.
- Biodiversity Institute, University of Kansas, Lawrence, KS, USA.
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Wang J, Zou H, Liu M, Wang Y, Ru J, Guo C. The Phylogenetic Significance of Fruit Structures in the Family Cornaceae of China and Related Taxa. PLANTS (BASEL, SWITZERLAND) 2022; 11:2591. [PMID: 36235457 PMCID: PMC9573492 DOI: 10.3390/plants11192591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The fruit morphological structures of the Cornaceae of China and related taxa were studied using the wax GMA semi-thin section method and other methods to identify characters useful in delimiting clades circumscribed in previous molecular phylogenetic studies. Maximum parsimony analyses of 27 fruit structural characters resulted in a generally poorly resolved strict consensus tree, yet one whose major clades matched those revealed previously. Cornaceae of China and related taxa are recognized in four significant clades with the following fruit structural features: (1) Helwingia, fruits lack trichome, the abdominal vascular bundles are close to the endocarp, and the endocarp sclereid is elongated; (2) Aucuba, single-cell lanceolate trichomes, pericarp without secretory structure; (3) Torricellia, polygon and elongated sclereids in the endocarp, pericarp without crystal and tannin; and (4) Cornus sensu lato, the trichome is T-shaped, the abdominal ventral bundle is absent, and the endocarp sclereid is nearly round. In Cornus sensu lato, this document supported that the cornelian cherries (CC, subg. Cornus) and the big-bracted dogwoods (BB, subg. Syncarpea) are sister groups. The dwarf dogwoods (DW, subg. Arctocrania) are sister to them, and the blue- or white-fruited dogwoods (BW, subg. Kraniopsis, subg. Yinquania, and subg. Mesomora) are the base of the Cornus sensu lato clade. The number of cell layers of endocarps and the types of crystals afford sound evidence for identifying their relationship. This study indicated that the fruit structures of Cornaceae might provide morphological and anatomical evidence for molecular phylogeny.
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Affiliation(s)
- Jingru Wang
- Key Laboratory of Molecular Cytogenetic and Genetic Breeding of Heilongjiang Province, Department of Life Sciences, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Hui Zou
- Key Laboratory of Molecular Cytogenetic and Genetic Breeding of Heilongjiang Province, Department of Life Sciences, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Mei Liu
- Key Laboratory of Molecular Cytogenetic and Genetic Breeding of Heilongjiang Province, Department of Life Sciences, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Yuting Wang
- Key Laboratory of Molecular Cytogenetic and Genetic Breeding of Heilongjiang Province, Department of Life Sciences, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Jian Ru
- Department of Life Sciences, College of Life Science and Technology, Shangrao Normal University, Shangrao 334001, China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetic and Genetic Breeding of Heilongjiang Province, Department of Life Sciences, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
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Bippus AC, Flores JR, Hyvönen J, Tomescu AMF. The role of paleontological data in bryophyte systematics. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4273-4290. [PMID: 35394022 DOI: 10.1093/jxb/erac137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
Systematics reconstructs tempo and mode in biological evolution by resolving the phylogenetic fabric of biodiversity. The staggering duration and complexity of evolution, coupled with loss of information (extinction), render exhaustive reconstruction of the evolutionary history of life unattainable. Instead, we sample its products-phenotypes and genotypes-to generate phylogenetic hypotheses, which we sequentially reassess and update against new data. Current consensus in evolutionary biology emphasizes fossil integration in total-evidence analyses, requiring in-depth understanding of fossils-age, phenotypes, and systematic affinities-and a detailed morphological framework uniting fossil and extant taxa. Bryophytes present a special case: deep evolutionary history but sparse fossil record and phenotypic diversity encompassing small dimensional scales. We review how these peculiarities shape fossil inclusion in bryophyte systematics. Paucity of the bryophyte fossil record, driven primarily by phenotypic (small plant size) and ecological constraints (patchy substrate-hugging populations), and incomplete exploration, results in many morphologically isolated, taxonomically ambiguous fossil taxa. Nevertheless, instances of exquisite preservation and pioneering studies demonstrate the feasibility of including bryophyte fossils in evolutionary inference. Further progress will arise from developing extensive morphological matrices for bryophytes, continued exploration of the fossil record, re-evaluation of previously described fossils, and training specialists in identification and characterization of bryophyte fossils, and in bryophyte morphology.
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Affiliation(s)
- Alexander C Bippus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
- Department of Biological Sciences, California State Polytechnic University-Humboldt, Arcata, CA, USA
| | - Jorge R Flores
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
- Viikki Plant Science Center & Organismal & Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - Alexandru M F Tomescu
- Department of Biological Sciences, California State Polytechnic University-Humboldt, Arcata, CA, USA
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Flores JR, Bippus AC, Suárez GM, Hyvönen J. Defying death: incorporating fossils into the phylogeny of the complex thalloid liverworts (Marchantiidae, Marchantiophyta) confirms high order clades but reveals discrepancies in family-level relationships. Cladistics 2021; 37:231-247. [PMID: 34478198 DOI: 10.1111/cla.12442] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2020] [Indexed: 12/13/2022] Open
Abstract
In recent years, the use of extensive molecular and morphological datasets has clarified the phylogenetic relationships among the orders of complex thalloid liverworts (Marchantiidae). However, previous studies excluded extinct taxa; thereby, undersampling the actual taxonomic diversity of the group. Here, we conducted a total-evidence analysis of Marchantiidae incorporating fossils. The combined dataset consisted of 11 genes-sampled from the nuclear, mitochondrial and plastid genomes-and 128 morphological characters. Sixty-two species, representing all classes and orders within Marchantiophyta and genera within Marchantiidae were included in the analyses. Six fossils were scored from literature: two assigned to the outgroup (Metzgeriothallus sharonae and Pallaviciniites sandaolingensis) and four to the ingroup (Marchantites cyathodoides, M. huolinhensis, Ricciopsis ferganica and R. sandaolingensis). Tree searches were conducted using parsimony as the optimality criterion. Clade sensitivity was assessed across a wide range of weighting regimes. Also, we evaluated the influence of fossils on the inferred topologies and branch support. Our results were congruent with previously inferred clades above the order level: Neohodgsoniales was sister to a clade formed by Sphaerocarpales and Marchantiales. However, relationships among families within Marchantiales contradicted recent studies. For instance, a clade consisting of Monosoleniaceae, Wiesnerellaceae and Targioniaceae was sister to the morphologically simple taxa instead of being nested within them as in previous studies. Novel synapomorphies were found for several clades within Marchantiales. Outgroup fossils were more influential than Marchantiidae fossils on overall topologies and branch support values. Except for a single weighting scheme, sampling continuous characters and down-weighting characters improved fossil stability. Ultimately, our results challenge the widespread notion that bryophyte fossils are problematic for phylogenetic inference.
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Affiliation(s)
- Jorge R Flores
- Finnish Museum of Natural History (Botany), University of Helsinki, PO Box 7, Helsinki, FI-00014, Finland
| | - Alexander C Bippus
- Department of Botany and Plant Pathology, Oregon State University, 2701 SW Campus Way, Corvallis, OR, 97331, USA
| | - Guillermo M Suárez
- Unidad Ejecutora Lillo (CONICET - Fundación Miguel Lillo), Miguel Lillo 251, San Miguel de Tucumán, Tucumán, 4000, Argentina.,Facultad de Ciencias Naturales, Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, San Miguel de Tucumán, Tucumán, 4000, Argentina
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany), University of Helsinki, PO Box 7, Helsinki, FI-00014, Finland.,Organismal and Evolutionary Biology, Viikki Plant Science Centre, University of Helsinki, PO Box 65, Helsinki, FI-00014, Finland
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Thomas SK, Liu X, Du Z, Dong Y, Cummings A, Pokorny L, Xiang Q(J, Leebens‐Mack JH. Comprehending Cornales: phylogenetic reconstruction of the order using the Angiosperms353 probe set. AMERICAN JOURNAL OF BOTANY 2021; 108:1112-1121. [PMID: 34263456 PMCID: PMC8361741 DOI: 10.1002/ajb2.1696] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 05/12/2021] [Indexed: 05/08/2023]
Abstract
PREMISE Cornales is an order of flowering plants containing ecologically and horticulturally important families, including Cornaceae (dogwoods) and Hydrangeaceae (hydrangeas), among others. While many relationships in Cornales are strongly supported by previous studies, some uncertainty remains with regards to the placement of Hydrostachyaceae and to relationships among families in Cornales and within Cornaceae. Here we analyzed hundreds of nuclear loci to test published phylogenetic hypotheses and estimated a robust species tree for Cornales. METHODS Using the Angiosperms353 probe set and existing data sets, we generated phylogenomic data for 158 samples, representing all families in the Cornales, with intensive sampling in the Cornaceae. RESULTS We curated an average of 312 genes per sample, constructed maximum likelihood gene trees, and inferred a species tree using the summary approach implemented in ASTRAL-III, a method statistically consistent with the multispecies coalescent model. CONCLUSIONS The species tree we constructed generally shows high support values and a high degree of concordance among individual nuclear gene trees. Relationships among families are largely congruent with previous molecular studies, except for the placement of the nyssoids and the Grubbiaceae-Curtisiaceae clades. Furthermore, we were able to place Hydrostachyaceae within Cornales, and within Cornaceae, the monophyly of known morphogroups was well supported. However, patterns of gene tree discordance suggest potential ancient reticulation, gene flow, and/or ILS in the Hydrostachyaceae lineage and the early diversification of Cornus. Our findings reveal new insights into the diversification process across Cornales and demonstrate the utility of the Angiosperms353 probe set.
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Affiliation(s)
- Shawn K. Thomas
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
- Division of Biological SciencesUniversity of MissouriColumbiaMO65203USA
| | - Xiang Liu
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNC27695USA
- SyngentaResearch Triangle ParkNC27709USA
| | - Zhi‐Yuan Du
- Wuhan Botanical GardenThe Chinese Academy of SciencesWuhanHubei430074China
| | - Yibo Dong
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNC27695USA
- Global Health Infectious Disease ResearchCollege of Public HealthUniversity of South FloridaTampaFL33612USA
| | - Amanda Cummings
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
| | - Lisa Pokorny
- Royal Botanic Gardens, KewRichmondLondonTW9 3AEUK
- Computational/Systems Biology and Genomics ProgramCentre for Plant Biotechnology and GenomicsUPM‐INIA‐CSICPozuelo de Alarcón (Madrid)28223Spain
| | - Qui‐Yun (Jenny) Xiang
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNC27695USA
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Schönenberger J, von Balthazar M, López Martínez A, Albert B, Prieu C, Magallón S, Sauquet H. Phylogenetic analysis of fossil flowers using an angiosperm-wide data set: proof-of-concept and challenges ahead. AMERICAN JOURNAL OF BOTANY 2020; 107:1433-1448. [PMID: 33026116 PMCID: PMC7702048 DOI: 10.1002/ajb2.1538] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/08/2020] [Indexed: 05/29/2023]
Abstract
PREMISE Significant paleobotanical discoveries in recent decades have considerably improved our understanding of the early evolution of angiosperms and their flowers. However, our ability to test the systematic placement of fossil flowers on the basis of phylogenetic analyses has remained limited, mainly due to the lack of an adequate, angiosperm-wide morphological data set for extant taxa. Earlier attempts to place fossil flowers phylogenetically were, therefore, forced to make prior qualitative assessments of the potential systematic position of fossils and to restrict phylogenetic analyses to selected angiosperm subgroups. METHODS We conduct angiosperm-wide molecular backbone analyses of 10 fossil flower taxa selected from the Cretaceous record. Our analyses make use of a floral trait data set built within the framework of the eFLOWER initiative. We provide an updated version of this data set containing data for 28 floral and two pollen traits for 792 extant species representing 372 angiosperm families. RESULTS We find that some fossils are placed congruently with earlier hypotheses while others are found in positions that had not been suggested previously. A few take up equivocal positions, including the stem branches of large clades. CONCLUSIONS Our study provides an objective approach to test for the phylogenetic position of fossil flowers across angiosperms. Such analyses may provide a complementary tool for paleobotanical studies, allowing for a more comprehensive understanding of fossil phylogenetic relationships in angiosperms. Ongoing work focused on extending the sampling of extant taxa and the number of floral traits will further improve the applicability and accuracy of our approach.
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Affiliation(s)
- Jürg Schönenberger
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14ViennaA‐1030Austria
| | - Maria von Balthazar
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14ViennaA‐1030Austria
| | - Andrea López Martínez
- Instituto de BiologíaUniversidad Nacional Autónoma de MéxicoCircuito Exterior, Ciudad Universitaria, CoyoacánMéxico City04510Mexico
| | - Béatrice Albert
- Ecologie Systématique EvolutionUniv. Paris‐SudCNRSAgroParisTechUniversité Paris‐SaclayOrsay91400France
| | - Charlotte Prieu
- Ecologie Systématique EvolutionUniv. Paris‐SudCNRSAgroParisTechUniversité Paris‐SaclayOrsay91400France
| | - Susana Magallón
- Instituto de BiologíaUniversidad Nacional Autónoma de MéxicoCircuito Exterior, Ciudad Universitaria, CoyoacánMéxico City04510Mexico
| | - Hervé Sauquet
- Ecologie Systématique EvolutionUniv. Paris‐SudCNRSAgroParisTechUniversité Paris‐SaclayOrsay91400France
- National Herbarium of New South Wales (NSW)Royal Botanic Gardens and Domain TrustSydneyNSW2000Australia
- Evolution and Ecology Research CentreSchool of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyAustralia
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11
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Nowicki M, Houston LC, Boggess SL, Aiello AS, Payá‐Milans M, Staton ME, Hayashida M, Yamanaka M, Eda S, Trigiano RN. Species diversity and phylogeography of Cornus kousa (Asian dogwood) captured by genomic and genic microsatellites. Ecol Evol 2020; 10:8299-8312. [PMID: 32788980 PMCID: PMC7417245 DOI: 10.1002/ece3.6537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/09/2020] [Indexed: 01/01/2023] Open
Abstract
Cornus kousa (Asian dogwood), an East Asia native tree, is the most economically important species of the dogwood genus, owing to its desirable horticultural traits and ability to hybridize with North America-native dogwoods. To assess the species genetic diversity and to better inform the ongoing and future breeding efforts, we assembled an herbarium and arboretum collection of 131 noncultivated C. kousa specimens. Genotyping and capillary electrophoresis analyses of our C. kousa collection with the newly developed genic and published nuclear genomic microsatellites permitted assessment of genetic diversity and evolutionary history of the species. Regardless of the microsatellite type used, the study yielded generally similar insights into the C. kousa diversity with subtle differences deriving from and underlining the marker used. The accrued evidence pointed to the species distinct genetic pools related to the plant country of origin. This can be helpful in the development of the commercial cultivars for this important ornamental crop with increased pyramided utility traits. Analyses of the C. kousa evolutionary history using the accrued genotyping datasets pointed to an unsampled ancestor population, possibly now extinct, as per the phylogeography of the region. To our knowledge, there are few studies utilizing the same gDNA collection to compare performance of genomic and genic microsatellites. This is the first detailed report on C. kousa species diversity and evolutionary history inference.
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Affiliation(s)
- Marcin Nowicki
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
| | - Logan C. Houston
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
| | - Sarah L. Boggess
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
| | | | - Miriam Payá‐Milans
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
- Present address:
Centro de Biotecnología y Genómica de PlantasUPM‐INIAMadridSpain
| | - Margaret E. Staton
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
| | | | - Masahiro Yamanaka
- Department of Pharmaceytical SciencesInternational University of Health and WelfareOhtawaraJapan
| | - Shigetoshi Eda
- Department of Forestry, Wildlife and FisheriesCenter for Wildlife Health ORUKnoxvilleTNUSA
- Department of MicrobiologyCenter for Wildlife Health ORUKnoxvilleTNUSA
| | - Robert N. Trigiano
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTNUSA
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12
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Stull GW, Soltis PS, Soltis DE, Gitzendanner MA, Smith SA. Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages. AMERICAN JOURNAL OF BOTANY 2020; 107:790-805. [PMID: 32406108 DOI: 10.1002/ajb2.1468] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 02/26/2020] [Indexed: 05/14/2023]
Abstract
PREMISE Discordance between nuclear and organellar phylogenies (cytonuclear discordance) is a well-documented phenomenon at shallow evolutionary levels but has been poorly investigated at deep levels of plant phylogeny. Determining the extent of cytonuclear discordance across major plant lineages is essential not only for elucidating evolutionary processes, but also for evaluating the currently used framework of plant phylogeny, which is largely based on the plastid genome. METHODS We present a phylogenomic examination of a major angiosperm clade (Asteridae) based on sequence data from the nuclear, plastid, and mitochondrial genomes as a means of evaluating currently accepted relationships inferred from the plastome and exploring potential sources of genomic conflict in this group. RESULTS We recovered at least five instances of well-supported cytonuclear discordance concerning the placements of major asterid lineages (i.e., Ericales, Oncothecaceae, Aquifoliales, Cassinopsis, and Icacinaceae). We attribute this conflict to a combination of incomplete lineage sorting and hybridization, the latter supported in part by previously inferred whole-genome duplications. CONCLUSIONS Our results challenge several long-standing hypotheses of asterid relationships and have implications for morphological character evolution and for the importance of ancient whole-genome duplications in early asterid evolution. These findings also highlight the value of reevaluating broad-scale angiosperm and green-plant phylogeny with nuclear genomic data.
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Affiliation(s)
- Gregory W Stull
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
- Department of Botany, Smithsonian Institution, Washington, D.C., 20013, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
| | | | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
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Acuña Castillo R, Luebert F, Henning T, Weigend M. Major lineages of Loasaceae subfam. Loasoideae diversified during the Andean uplift. Mol Phylogenet Evol 2019; 141:106616. [PMID: 31520779 DOI: 10.1016/j.ympev.2019.106616] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/14/2022]
Abstract
The Loasoideae is the largest clade in the Loasaceae. This subfamily is widespread throughout the Neotropics and centered in the Andes, presenting an excellent opportunity to study diversification across much of temperate and mid to high-elevation areas of South America. Despite that, no studies have addressed the historical biogeography of the Loasoideae to date, leaving an important knowledge gap in this plant group. Here, we used four plastid markers (i.e., trnL-trnF, matK, trnS-trnG, and rps16) and sequenced 170 accessions (134 ingroup taxa) to infer the phylogeny of Loasoideae. We then used this phylogeny as basis to estimate divergence times using an uncorrelated relaxed molecular clock approach and seven fossils as primary calibration points. We employed the Dispersal-Extinction-Cladogenesis (DEC) approach to reconstruct the ancestral ranges of the subfamily. Our results indicate that stem Loasoideae diverged from its sister group in the Late Cretaceous to Early Paleocene (ca. 83-62 Ma). The crown node of the whole clade goes back to the Middle Paleocene to Middle Eocene (ca. 60-45 Ma), corresponding to the earliest diversification events of the extant groups, prior to most of the Andean orogeny and roughly coinciding with the Paleocene-Eocene Thermal Maximum. On the other hand, the crown nodes of most genera appear to have originated in the Oligocene and Miocene (median ages: 28-10 Ma). The diversification of some extant lineages appears to have happened in parallel to Andean uplift pulses that seem to have had an effect on the orogeny and concomitant establishment of new habitats and latitudinal corridors. The most likely ancestral areas retrieved for crown Loasoideae, are the tropical Andes and Pacific arid coast. Most of the extant clades have remained restricted to their ancestral areas. Transoceanic Long Distance Dispersal appears to have been involved in the arrival of Loasoid ancestors to South America, and in the distribution of the small clades Kissenia in Africa and Plakothira on the Marquesas Archipelago. The results presented here suggest that the historical biogeography of the continental scale radiation of Loasoideae, follows the sequence and timing of the development of temperate and mid to high-elevation habitats across South America during the Tertiary.
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Affiliation(s)
- Rafael Acuña Castillo
- Universität Bonn, Nees-Institut für Biodiversität der Pflanzen, Meckenheimer Allee 170, 53115 Bonn, Germany; Universidad de Costa Rica, Escuela de Biología, Apdo. Postal: 11501-2060 San Pedro de Montes de Oca, Costa Rica.
| | - Federico Luebert
- Universität Bonn, Nees-Institut für Biodiversität der Pflanzen, Meckenheimer Allee 170, 53115 Bonn, Germany; Universidad de Chile, Departamento de Silvicultura y Conservación de la Naturaleza, Santiago, Chile
| | - Tilo Henning
- Freie Universität Berlin, Botanischer Garten Botanisches Museum, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - Maximilian Weigend
- Universität Bonn, Nees-Institut für Biodiversität der Pflanzen, Meckenheimer Allee 170, 53115 Bonn, Germany
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14
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Atkinson BA, Martínez C, Crepet WL. Cretaceous asterid evolution: fruits of Eydeia jerseyensis sp. nov. (Cornales) from the upper Turonian of eastern North America. ANNALS OF BOTANY 2019; 123:451-460. [PMID: 30212854 PMCID: PMC6377102 DOI: 10.1093/aob/mcy170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND AND AIMS The asterids (>80 000 extant species) appear in the fossil record with considerable diversity near the Turonian-Coniacian boundary (~90 Ma; Late Cretaceous) and are strongly represented in the earliest diverging lineage, Cornales. These early asterid representatives have so far been reported from western North America and eastern Asia. In this study, we characterize a new cornalean taxon based on charcoalified fruits from the upper Turonian of eastern North America, a separate landmass from western North America at the time, and identify early palaeobiogeographical patterns of Cornales during the Cretaceous. METHODS Fossils were studied and imaged using scanning electron microscopy and micro-computed tomography (micro-CT) scanning. To assess the systematic affinities of the fossils, phylogenetic analyses were conducted using maximum parsimony. KEY RESULTS The charcoalified fruits are represented by tri-locular woody endocarps with dorsal apically opening germination valves. Three septa intersect to form a robust central axis. Endocarp ground tissue consists of two zones: an outer endocarp composed of isodiametric sclereids and an inner endocarp containing circum-locular fibres. Central vasculature is absent; however, there are several small vascular bundles scattered within the septa. Phylogenetic analysis places the new taxon within the extinct genus Eydeia. DISCUSSION Thick-walled endocarps with apically opening germination valves, no central vascular bundle and one seed per locule are indicative of the order Cornales. Comparative analysis suggests that the fossils represent a new species, Eydeia jerseyensis sp. nov. This new taxon is the first evidence of Cornales in eastern North America during the Cretaceous and provides insights into the palaeobiogeography and initial diversification of the order.
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Affiliation(s)
- Brian A Atkinson
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Biodiversity Institute and Museum of Natural History, University of Kansas, Lawrence, KS, USA
| | - Camila Martínez
- L. H. Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - William L Crepet
- L. H. Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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15
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Hayes RF, Smith SY, Montellano-Ballesteros M, Álvarez-Reyes G, Hernandez-Rivera R, Fastovsky DE. Cornalean affinities, phylogenetic significance, and biogeographic implications of Operculifructus infructescences from the Late Cretaceous (Campanian) of Mexico. AMERICAN JOURNAL OF BOTANY 2018; 105:1911-1928. [PMID: 30359466 DOI: 10.1002/ajb2.1179] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/07/2018] [Indexed: 06/08/2023]
Abstract
Premise of the Study Cretaceous Cornales provide a crucial record of the early history of asterids. Most lineages of the order are well represented in the fossil record, but South African families of Curtisiaceae and Grubbiaceae remain poorly understood. Seventy-three specimens of a fossil infructescence belonging to the genus Operculifructus Estrada-Ruiz & Cevallos-Ferriz emend. Hayes & Smith from the Late Cretaceous (Campanian) El Gallo Formation, Baja California, Mexico bear previously undescribed characters that suggest a relationship to Grubbiaceae. Methods Microstructures of the fossils were examined through light microscopy and x-ray microcomputed tomography (microCT) scanning. Modern Grubbia tomentosa (Thunb.) Harms fruits were scanned for comparison to the fossil material. Phylogenetic analyses using the 77 fruit characters of Atkinson () were performed to test relationships of the fossil to major lineages of the order. Several analyses applied topological constraints to the extant taxa, based on various genetically supported hypotheses of relationship within Cornales. Key Results Novel structures of Operculifructus newly observed here include (1) anatropous ovules, (2) drupaceous fruits, (3) an epigynous disc, (4) and a stylar canal in the center of the disc aligned with the micropylar protrusion of the seed. Phylogenetic analysis consistently resolves Operculifructus as sister to Grubbiaceae. Conclusions Operculifructus provides direct evidence for the occurrence of Grubbiaceae in the Late Cretaceous, much older than previous Eocene evidence. The phylogeny of Atkinson () indicates that the new phylogenetic position recovered for Operculifructus also establishes the presence of the most basal drupaceous cornalean fruits in North America by the Campanian. RESUMEN EN ESPAÑOL Hipótesis de la Investigación Cornales cretácicos representan un registro esencial en la historia de los astéridos. Casi todos los linajes del orden están bien representados en el registro fósil, pero las familias africanas sureñas Curtisiaceae y Grubbiaceae permanecen pobremente entendidas. Setenta y tres ejemplares de una infrutescencia fósil perteneciente al género Operculifructus Estrada-Ruiz & Cevallos-Ferriz emend. Hayes & Smith de la formación campaniana (Cretácico Tardío) El Gallo, Baja California, México, poseen caracteres no descritos previamente y sugieren una relación con Grubbiaceae. Metodología Microestructuras de los fósiles fueron examinadas con microscopio de luz y microtomografía computarizada (micro-CT) de rayos X. Frutos actuales de Grubbia tomentosa (Thunb.) Harms fueron escaneados para su comparación con el material fósil. Se realizaron análisis filogenéticos usando los 77 caracteres de frutos de Atkinson () para probar las relaciones de los fósiles con los linajes principales del orden. En algunos análisis se aplicaron restricciones topológicas a los taxa actuales basándose en varias hipótesis, soportadas genéticamente, de las relaciones dentro de Cornales. Resultados Centrales (Cruciales) Las estructuras novedosas de Operculifructus, recientemente observadas aquí, incluyen (1) óvulos anátropos; (2) frutos drupáceos; (3) disco epígino; y (4) un canal estilar en el centro del disco alineado con la protuberancia micropilar de la semilla. Los análisis filogenéticos consistentemente dan como resultado que Operculifructus es hermano de Grubbiaceae. Conclusiones Operculifructus proporciona evidencia directa de la presencia de Grubbiaceae en el Cretácico Tardío, mucho antes que la previa evidencia en el Eoceno. La filogenia de Atkinson () indica que la nueva posición filogenética recuperada para Operculifructus también resalta la presencia de frutos drupáceos cornaleanos más basales en Norteamérica durante el Campaniano.
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Affiliation(s)
- Reilly F Hayes
- Department of Geosciences, University of Rhode Island, Kingston, Rhode Island, 02881, USA
| | - Selena Y Smith
- Department of Earth & Environmental Sciences and Museum of Paleontology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Marisol Montellano-Ballesteros
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, México, CDMX, 04510, Mexico
| | - Gerardo Álvarez-Reyes
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, México, CDMX, 04510, Mexico
| | - René Hernandez-Rivera
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, México, CDMX, 04510, Mexico
| | - David E Fastovsky
- Department of Geosciences, University of Rhode Island, Kingston, Rhode Island, 02881, USA
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16
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Rothwell GW, Escapa IH, Tomescu AMF. Tree of death: The role of fossils in resolving the overall pattern of plant phylogeny. AMERICAN JOURNAL OF BOTANY 2018; 105:1239-1242. [PMID: 30114314 DOI: 10.1002/ajb2.1138] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 07/16/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Gar W Rothwell
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331, USA
| | - Ignacio H Escapa
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Museo Paleontologico Egidio Feruglio, Avenida Fontana 140, Trelew, Chubut, 9100, Argentina
| | - Alexandru M F Tomescu
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA
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