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Yao G, Zhang YQ, Barrett C, Xue B, Bellot S, Baker WJ, Ge XJ. A plastid phylogenomic framework for the palm family (Arecaceae). BMC Biol 2023; 21:50. [PMID: 36882831 PMCID: PMC9993706 DOI: 10.1186/s12915-023-01544-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/14/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Over the past decade, phylogenomics has greatly advanced our knowledge of angiosperm evolution. However, phylogenomic studies of large angiosperm families with complete species or genus-level sampling are still lacking. The palms, Arecaceae, are a large family with ca. 181 genera and 2600 species and are important components of tropical rainforests bearing great cultural and economic significance. Taxonomy and phylogeny of the family have been extensively investigated by a series of molecular phylogenetic studies in the last two decades. Nevertheless, some phylogenetic relationships within the family are not yet well-resolved, especially at the tribal and generic levels, with consequent impacts for downstream research. RESULTS Plastomes of 182 palm species representing 111 genera were newly sequenced. Combining these with previously published plastid DNA data, we were able to sample 98% of palm genera and conduct a plastid phylogenomic investigation of the family. Maximum likelihood analyses yielded a robustly supported phylogenetic hypothesis. Phylogenetic relationships among all five palm subfamilies and 28 tribes were well-resolved, and most inter-generic phylogenetic relationships were also resolved with strong support. CONCLUSIONS The inclusion of nearly complete generic-level sampling coupled with nearly complete plastid genomes strengthened our understanding of plastid-based relationships of the palms. This comprehensive plastid genome dataset complements a growing body of nuclear genomic data. Together, these datasets form a novel phylogenomic baseline for the palms and an increasingly robust framework for future comparative biological studies of this exceptionally important plant family.
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Affiliation(s)
- Gang Yao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Yu-Qu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Present Address: College of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Craig Barrett
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Bine Xue
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | | | | | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.
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Onstein RE, Kissling WD, Linder HP. The megaherbivore gap after the non-avian dinosaur extinctions modified trait evolution and diversification of tropical palms. Proc Biol Sci 2022; 289:20212633. [PMID: 35414237 PMCID: PMC9006001 DOI: 10.1098/rspb.2021.2633] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The Cretaceous-Palaeogene (K-Pg) extinction of the non-avian dinosaurs (66 Ma) led to a 25 million year gap of megaherbivores (>1000 kg) before the evolution of megaherbivorous mammals in the Late Eocene (40 Ma). The botanical consequences of this 'Palaeocene megaherbivore gap' (PMHG) remain poorly explored. We hypothesize that the absence of megaherbivores should result in changes in the diversification and trait evolution of associated plant lineages. We used phylogenetic time- and trait-dependent diversification models with palms (Arecaceae) and show that the PMHG was characterized by speciation slowdowns, decreased evolution of armature and increased evolution of megafaunal (≥4 cm) fruits. This suggests that the absence of browsing by megaherbivores during the PMHG may have led to a loss of defence traits, but the absence of megaherbivorous seed dispersers did not lead to a loss of megafaunal fruits. Instead, increases in PMHG fruit sizes may be explained by simultaneously rising temperatures, rainforest expansion, and the subsequent radiation of seed-dispersing birds and mammals. We show that the profound impact of the PMHG on plant diversification can be detected even with the overwriting of adaptations by the subsequent Late Eocene opening up of megaherbivore-associated ecological opportunities. Our study provides a quantitative, comparative framework to assess diversification and adaptation during one of the most enigmatic periods in angiosperm history.
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Affiliation(s)
- Renske E. Onstein
- Evolution and Adaptation, German Centre for Integrative Biodiversity Research (iDiv) Halle–Jena–Leipzig, Leipzig 04103 Germany
| | - W. Daniel Kissling
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, Noord-Holland, The Netherlands
| | - H. Peter Linder
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, ZH Switzerland
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de Oliveira DM, de Oliveira DBC, Nunes YRF, de Almeida Alves TM, Kohlhoff M, Andrade AA, Cota BB. Natural Occurring Phenolic Derivatives from Mauritia flexuosa (Buriti) Stems and Their Potential Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus (MRSA). Chem Biodivers 2022; 19:e202100788. [PMID: 35146890 DOI: 10.1002/cbdv.202100788] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/13/2022] [Indexed: 11/12/2022]
Abstract
Mauritia flexuosa Linnaeus filius (buriti or aguage; Arecaceae) is a palm used by traditional medicine in Brazil to treat dysentery and diarrhea. Our group showed that the soluble dichloromethane (CH2 Cl2 ) fraction from EtOH extract from M. flexuosa stems inhibited the growth of methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA) and it is rich in phenolic compounds. This study aimed to isolate new phenolic compounds from CH2 Cl2 fraction from M. flexuosa stems with in vitro antibacterial activity. The crude CH2 Cl2 fraction was fractionated by gel permeation chromatography (GPC) followed by semi-preparative RP-HPLC. The antibacterial activity was evaluated using the broth microdilution method against MSSA (ATCC 29213) and MRSA (clinical isolate 155). All compounds were also tested against Gram-negative (Escherichia coli; ATCC 35218) bacteria and two fungi species (Candida albicans; ATCC 14053 and Trichophyton rubrum; ATCC MYA 4438). The chemical structures of isolated compounds were determined by analysis and comparison with literature data of their NMR and HRMS spectra and optical activity. The chemical investigation yielded seven aromatic compounds, of which four, (2S,15S)-2,15-dimethyl-2,15-dioxa-1,8(1,4)-dibenzenacyclotetradecaphane (1), (2S,5S)-1-(4-hydroxyphenyl)hexane-2,5-diol (3), bruguierol E (4), and buritin (5) were previously unreported and three are known compounds identified as 6-(4'-hydroxyphenyl) hexan-2-one (2), (+)-(2R,3R)-dihydrokaempferol (6), and (+)-(2R)-naringenin (7). Compounds 1 and 7 showed antibacterial activity against MRSA and MSSA with minimum inhibitory concentrations (MICs) of between 62.5 and 31.3 μg/mL, respectively. Our preliminary findings support that CH2 Cl2 fraction from buriti, a typical species of flooded areas of Brazilian savanna, and its aromatic phenolic compounds are active against MSSA and MRSA contributing with understanding about the traditional use of this species.
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Affiliation(s)
- Djalma Menezes de Oliveira
- Department of Science and Technology, State University of Bahia Southwest, José Moreira Sobrinho Avenue, 45206-191, Jequié, Bahia, Brazil
| | - Diego Batista Carneiro de Oliveira
- Laboratory of Microbiology, Federal University of Triângulo Mineiro, Pça Manoel Terra, 330, Abadia, 38025-015, Uberaba, Minas Gerais, Brazil
| | - Yule Roberta Ferreira Nunes
- Ecology Laboratory and Plant Propagation, Department of General Biology, Estadual University of Montes Claros, University Campus Prof. Darcy Ribeiro, 39401-089, Montes Claros, Minas Gerais, Brazil
| | - Tânia Maria de Almeida Alves
- Laboratory of Chemistry Bioactive Natural Products, René Rachou Institute, Oswaldo Cruz Foundation, Augusto de Lima Avenue, 1715, Barro Preto, 30190-002, Belo Horizonte, Minas Gerais, Brazil
| | - Markus Kohlhoff
- Laboratory of Chemistry Bioactive Natural Products, René Rachou Institute, Oswaldo Cruz Foundation, Augusto de Lima Avenue, 1715, Barro Preto, 30190-002, Belo Horizonte, Minas Gerais, Brazil
| | - Anderson Assunção Andrade
- Laboratory of Microbiology, Federal University of Triângulo Mineiro, Pça Manoel Terra, 330, Abadia, 38025-015, Uberaba, Minas Gerais, Brazil
| | - Betania Barros Cota
- Laboratory of Chemistry Bioactive Natural Products, René Rachou Institute, Oswaldo Cruz Foundation, Augusto de Lima Avenue, 1715, Barro Preto, 30190-002, Belo Horizonte, Minas Gerais, Brazil
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Ibrahim MA, Al-Shomrani BM, Alharbi SN, Elliott TA, Alsuabeyl MS, Alqahtani FH, Manee MM. Genome-wide comparative analysis of transposable elements in Palmae genomes. Front Biosci (Landmark Ed) 2021; 26:1119-1131. [PMID: 34856758 DOI: 10.52586/5014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/07/2021] [Accepted: 11/11/2021] [Indexed: 11/09/2022]
Abstract
Background: Transposable elements (TEs) are the largest component of the genetic material of most eukaryotes and can play roles in shaping genome architecture and regulating phenotypic variation; thus, understanding genome evolution is only possible if we comprehend the contributions of TEs. However, the quantitative and qualitative contributions of TEs can vary, even between closely related lineages. For palm species, in particular, the dynamics of the process through which TEs have differently shaped their genomes remains poorly understood because of a lack of comparative studies. Materials and methods: We conducted a genome-wide comparative analysis of palm TEs, focusing on identifying and classifying TEs using the draft assemblies of four palm species: Phoenix dactylifera, Cocos nucifera, Calamus simplicifolius, and Elaeis oleifera. Our TE library was generated using both de novo structure-based and homology-based methodologies. Results: The generated libraries revealed the TE component of each assembly, which varied from 41-81%. Class I retrotransposons covered 36-75% of these species' draft genome sequences and primarily consisted of LTR retroelements, while non-LTR elements covered about 0.56-2.31% of each assembly, mainly as LINEs. The least represented were Class DNA transposons, comprising 1.87-3.37%. Conclusion: The current study contributes to a detailed identification and characterization of transposable elements in Palmae draft genome assemblies.
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Affiliation(s)
- Mohanad A Ibrahim
- National Centre for Bioinformatics, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia
| | - Badr M Al-Shomrani
- National Centre for Bioinformatics, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia
| | - Sultan N Alharbi
- National Centre for Bioinformatics, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia
| | - Tyler A Elliott
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Mohammed S Alsuabeyl
- National Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia
| | - Fahad H Alqahtani
- National Centre for Bioinformatics, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia
| | - Manee M Manee
- National Centre for Bioinformatics, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia.,National Center for Agricultural Technology, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia
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Agostini-Costa TDS. Bioactive compounds and health benefits of some palm species traditionally used in Africa and the Americas - A review. J Ethnopharmacol 2018; 224:202-229. [PMID: 29842962 DOI: 10.1016/j.jep.2018.05.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE According to previous ethno-medicinal reviews, Cocos nucifera, Elaeis guineensis and Phoenix dactylifera are among the main palms which are often used on the American and African continents to treat infections, infestations and disorders in the digestive, respiratory, genito-urinary, dermal, endocrine, cardiovascular, muscular-skeletal, mental and neural systems, as well as neoplasms, dental issues and metabolic and nutritional disorders. In addition, one or more species of the wild genera Acrocomia, Areca, Astrocaryum, Attalea, Bactris, Borassus, Calamus, Chamaedorea, Chamaerops, Euterpe, Hyphaene, Mauritia, Oenocarpus and Syagrus have a high number of records of these ethno-medicinal uses. The most used parts of the palm tree are the fruits, followed by roots, seeds, leaves and flower sap. AIM OF THE STUDY This review discusses the phytochemical composition and the pharmacological properties of these important ethno-medicinal palms, aiming to provide a contribution to future research prospects. MATERIALS AND METHODS Significant information was compiled from an electronic search in widely used international scientific databases (Google Scholar, Science Direct, SciFinder, Web of Science, PubMed, Wiley on line Library, Scielo, ACS Publications), and additional information was obtained from dissertations, theses, books and other relevant websites. RESULTS Palms, in general, are rich in oils, terpenoids and phenolic compounds. Fruits of many species are notable for their high content of healthy oils and fat-soluble bioactive compounds, mainly terpenoids, such as pigment carotenoids (and provitamin A), phytosterols, triterpene pentacyclics and tocols (and vitamin E), while other species stood out for their phenolic compounds derived from benzoic and cinnamic acids, along with flavan-3-ol, flavone, flavonol, and stilbene compounds or anthocyanin pigments. In addition to fruits, other parts of the plant such as seeds, leaves, palm heart, flowers and roots are also sources of many bioactive compounds. These compounds are linked to the ethno-medicinal use of many palms that improve human health against infections, infestations and disorders of human systems. CONCLUSIONS Palms have provided bioactive samples that validate their effectiveness in traditional medicine. However, the intensive study of all palm species related to ethno-medicinal use is needed, along with selection of the most appropriate palm accessions, ripe stage of the fruit and /or part of the plant. Furthermore, the complete profiles of all phytochemicals, their effects on animal models and human subjects, and toxicological and clinical trials are suggested, which, added to the incorporation of improved technological processes, should represent a significant advance for the implementation of new opportunities with wide benefits for human health.
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Sant’Anna-Santos BF, dos Santos SA, Nunes ELP, Francino DMT, Carvalho Júnior WGO. Does leaf anatomy aid in species identification of Butia (Arecaceae)? AoB Plants 2018; 10:ply046. [PMID: 30151095 PMCID: PMC6101567 DOI: 10.1093/aobpla/ply046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/26/2018] [Indexed: 05/25/2023]
Abstract
Butia is a neotropical genus whose identification is based mostly on characters from external morphology, which are sometimes variable or inadequate for species differentiation. We aimed to verify if leaf anatomy of 18 Butia species brings new characters suitable for species identification and if it corroborates the phylogenetic relationship within the genus. Moreover, we propose an anatomical key to assist in species identification. Pinnae were collected and subjected to the usual techniques for light and scanning electron microscopies. The anatomical key was created with the aid of Xper2 software, based on the importance of characters to distinguish species according to the Jaccard index. All species have isobilateral mirrored mesophyll, amphistomatic leaves and secondary vascular bundles with sclerenchymatic sheath reinforcement connected to the hypodermis. Among the species studied, B. marmorii and B. matogrossensis showed exclusive characters. For the other species, up to five characters are sufficient for delimitation. Our anatomical key presents relevant characters that allow the identification of the recognized species of Butia. Reliable anatomical characters of easy observation, especially the raphides, are valuable in species distinction. Leaf anatomy, already used to support new taxa in related genera like Allagoptera and Syagrus, can also be useful to validate questionable Butia species and differentiate between similar species but do not reflect the proposed relationship between Butia species.
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Affiliation(s)
- Bruno Francisco Sant’Anna-Santos
- Laboratório de Anatomia e Biomecânica Vegetal, Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, PR, Brazil
| | - Samuel Alves dos Santos
- Laboratório de Anatomia e Dendrologia, Universidade Federal de Minas Gerais (UFMG), Avenida Universitária, 1000, Bairro Universitário, Montes Claros, MG, Brazil
| | - Elaine L P Nunes
- Laboratório de Anatomia e Biomecânica Vegetal, Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, PR, Brazil
| | - Dayana Maria Teodoro Francino
- Departamento de Ciências Biológicas, Universidade Federal dos Vales do Jequitinhonha e Mucuri (UFVJM), Rodovia BR 367, Diamantina, MG, Brazil
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Osborne OG, De‐Kayne R, Bidartondo MI, Hutton I, Baker WJ, Turnbull CGN, Savolainen V. Arbuscular mycorrhizal fungi promote coexistence and niche divergence of sympatric palm species on a remote oceanic island. New Phytol 2018; 217:1254-1266. [PMID: 29034978 PMCID: PMC5813143 DOI: 10.1111/nph.14850] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/14/2017] [Indexed: 05/14/2023]
Abstract
Microbes can have profound effects on their hosts, driving natural selection, promoting speciation and determining species distributions. However, soil-dwelling microbes are rarely investigated as drivers of evolutionary change in plants. We used metabarcoding and experimental manipulation of soil microbiomes to investigate the impact of soil and root microbes in a well-known case of sympatric speciation, the Howea palms of Lord Howe Island (Australia). Whereas H. forsteriana can grow on both calcareous and volcanic soils, H. belmoreana is restricted to, but more successful on, volcanic soil, indicating a trade-off in adaptation to the two soil types. We suggest a novel explanation for this trade-off. Arbuscular mycorrhizal fungi (AMF) are significantly depleted in H. forsteriana on volcanic soil, relative to both H. belmoreana on volcanic soil and H. forsteriana on calcareous soil. This is mirrored by the results of survival experiments, where the sterilization of natural soil reduces Howea fitness in every soil-species combination except H. forsteriana on volcanic soil. Furthermore, AMF-associated genes exhibit evidence of divergent selection between Howea species. These results show a mechanism by which divergent adaptation can have knock-on effects on host-microbe interactions, thereby reducing interspecific competition and promoting the coexistence of plant sister species.
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Affiliation(s)
- Owen G. Osborne
- Department of Life SciencesImperial College LondonAscotSL5 7PYUK
| | - Rishi De‐Kayne
- Department of Life SciencesImperial College LondonAscotSL5 7PYUK
| | - Martin I. Bidartondo
- Department of Life SciencesImperial College LondonAscotSL5 7PYUK
- Royal Botanic Gardens, KewRichmondTW9 3DSUK
| | - Ian Hutton
- Lord Howe Island MuseumLord Howe IslandNSW2898Australia
| | | | | | - Vincent Savolainen
- Department of Life SciencesImperial College LondonAscotSL5 7PYUK
- Royal Botanic Gardens, KewRichmondTW9 3DSUK
- University of JohannesburgAuckland ParkJohannesburg2006South Africa
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Bacon CD, Moraes R M, Jaramillo C, Antonelli A. Endemic palm species shed light on habitat shifts and the assembly of the Cerrado and Restinga floras. Mol Phylogenet Evol 2017; 110:127-133. [PMID: 28288942 DOI: 10.1016/j.ympev.2017.03.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 03/07/2017] [Accepted: 03/09/2017] [Indexed: 11/19/2022]
Abstract
Species expansions into new habitats are often associated with physiological adaptations, for instance when rain forest lineages colonize dry habitats. Although such shifts have been documented for the Brazilian savanna (Cerrado), little is known about the biogeographic origin of species occupying an extreme South American habitat type, the coastal dunes (Restinga). We examined the formation of this poorly known, endangered habitat by reconstructing the evolutionary history of two endemic species. Due to the proposed recency and uniqueness of this habitat, we hypothesized that Restinga species of the palm genus Allagoptera to be recently evolved and to present derived morphological characters. To detect habit shifts in absolute time, we used one plastid and nine nuclear genes to reconstruct the phylogenetic and biogeographic history of Allagoptera. We used light microscopy and stable isotope analysis to explore whether morphological adaptations occurred concomitantly with habitat shifts. Phylogenetic relationships were well supported and we found ancestral lineages of Allagoptera to be widely distributed throughout habitats that are currently occupied by extant species. Over the last ca. 7Ma Allagoptera has shifted its preference to increasingly dry habitats. Coincident with the colonization of the Cerrado and Restinga, morphological adaptations also evolved, including subterranean stems that are fire-resistant and long underground stem and root systems that facilitate water access. We did not find differences in metabolic pathway or modifications to pollen morphology when compared to other palm lineages. Assuming that the evolutionary history of Allagoptera is indicative of the habitat in which it occurs, our results infer a recent origin for Cerrado species. Although little is known about the formation of the Restinga habitat, our results also suggest a longer history than currently proposed; with an origin of Restinga habitats dating back to the Late Pliocene.
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Affiliation(s)
- Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.
| | - Monica Moraes R
- Herbario Nacional de Bolivia, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, Bolivia
| | | | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden; Gothenburg Botanical Garden, Göteborg, Sweden
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Faurby S, Eiserhardt WL, Baker WJ, Svenning JC. An all-evidence species-level supertree for the palms (Arecaceae). Mol Phylogenet Evol 2016; 100:57-69. [PMID: 27060018 DOI: 10.1016/j.ympev.2016.03.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 02/19/2016] [Accepted: 03/01/2016] [Indexed: 11/24/2022]
Abstract
Several attempts have been made to generate complete species-level phylogenies for large clades, enabling comprehensive analyses of ecological or evolutionary hypotheses at the species level. No such phylogeny has, however, been generated for any major plant group yet, but here we generate such a phylogeny for the palm family (Arecaceae). We do this using a novel Bayesian approach, estimating the validity of intra-generic taxonomic groupings as topological constraints to assist in placing species without genetic or morphological data. From these we implement those that are supported by genetic or morphological data for a given genus or for related genera. The intergeneric relationships in our new phylogeny are surprisingly different from earlier phylogenies in the placement of genera within tribes, but largely identical to previous findings in the deeper branches in the phylogeny, pointing to the need for incorporating phylogenetic uncertainty in analyses based on this phylogeny. Initial analyses of the new phylogeny suggest non-constancy in diversification rates over time within genera, with an apparent increase in diversification rate over time, but no evidence for any geographic variation in the magnitude of this increase. We hope that our study will stimulate further evolutionary or ecological studies using palms as study organisms as well as discussions of the optimal way to place the many species without genetic or morphological data.
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Affiliation(s)
- Søren Faurby
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark; Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, CSIC, Calle José Gutiérrez Abascal 2, Madrid 28006, Spain.
| | - Wolf L Eiserhardt
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark; Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - William J Baker
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Jens-Christian Svenning
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
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10
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Barrett CF, Baker WJ, Comer JR, Conran JG, Lahmeyer SC, Leebens-Mack JH, Li J, Lim GS, Mayfield-Jones DR, Perez L, Medina J, Pires JC, Santos C, Wm Stevenson D, Zomlefer WB, Davis JI. Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots. New Phytol 2016; 209:855-70. [PMID: 26350789 DOI: 10.1111/nph.13617] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 07/23/2015] [Indexed: 05/03/2023]
Abstract
Despite progress based on multilocus, phylogenetic studies of the palms (order Arecales, family Arecaceae), uncertainty remains in resolution/support among major clades and for the placement of the palms among the commelinid monocots. Palms and related commelinids represent a classic case of substitution rate heterogeneity that has not been investigated in the genomic era. To address questions of relationships, support and rate variation among palms and commelinid relatives, 39 plastomes representing the palms and related family Dasypogonaceae were generated via genome skimming and integrated within a monocot-wide matrix for phylogenetic and molecular evolutionary analyses. Support was strong for 'deep' relationships among the commelinid orders, among the five palm subfamilies, and among tribes of the subfamily Coryphoideae. Additionally, there was extreme heterogeneity in the plastid substitution rates across the commelinid orders indicated by model based analyses, with c. 22 rate shifts, and significant departure from a global clock. To date, this study represents the most comprehensively sampled matrix of plastomes assembled for monocot angiosperms, providing genome-scale support for phylogenetic relationships of monocot angiosperms, and lays the phylogenetic groundwork for comparative analyses of the drivers and correlates of such drastic differences in substitution rates across a diverse and significant clade.
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Affiliation(s)
- Craig F Barrett
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | | | - Jason R Comer
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - John G Conran
- Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, 5005, Australia
| | - Sean C Lahmeyer
- Herbarium, The Huntington Library, Art Collection, and Botanical Gardens, San Marino, CA, 91108, USA
| | | | - Jeff Li
- Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA, 92521, USA
| | - Gwynne S Lim
- L. H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Dustin R Mayfield-Jones
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
- Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Leticia Perez
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
| | - Jesus Medina
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
| | - J Chris Pires
- Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Cristian Santos
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
| | - Dennis Wm Stevenson
- Pfizer Laboratory of Molecular Systematics, New York Botanical Garden, Bronx, NY, 10458, USA
| | - Wendy B Zomlefer
- Herbarium, The Huntington Library, Art Collection, and Botanical Gardens, San Marino, CA, 91108, USA
| | - Jerrold I Davis
- L. H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
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