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Liu Y, Wang Y, Willett SD, Zimmermann NE, Pellissier L. Escarpment evolution drives the diversification of the Madagascar flora. Science 2024; 383:653-658. [PMID: 38330102 DOI: 10.1126/science.adi0833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 01/04/2024] [Indexed: 02/10/2024]
Abstract
Madagascar exhibits high endemic biodiversity that has evolved with sustained and stable rates of speciation over the past several tens of millions of years. The topography of Madagascar is dominated by a mountainous continental rift escarpment, with the highest plant diversity and rarity found along the steep, eastern side of this geographic feature. Using a process-explicit model, we show that precipitation-driven erosion and landward retreat of this high-relief topography creates transient habitat organization through multiple mechanisms, including catchment expansion, isolation of highland remnants, and formation of topographic barriers. Habitat isolation and reconnection on a million-year timescale serves as an allopatric speciation pump creating the observed biodiversity.
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Affiliation(s)
- Yi Liu
- Swiss Federal Research Institute (WSL), 8903 Birmensdorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
| | - Yanyan Wang
- Department of Earth Sciences, ETH Zürich, 8092 Zürich, Switzerland
| | - Sean D Willett
- Department of Earth Sciences, ETH Zürich, 8092 Zürich, Switzerland
| | - Niklaus E Zimmermann
- Swiss Federal Research Institute (WSL), 8903 Birmensdorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
| | - Loïc Pellissier
- Swiss Federal Research Institute (WSL), 8903 Birmensdorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
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2
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Francisconi AF, Marroquín JAM, Cauz-Santos LA, van den Berg C, Martins KKM, Costa MF, Picanço-Rodrigues D, de Alencar LD, Zanello CA, Colombo CA, Hernández BGD, Amaral DT, Lopes MTG, Veasey EA, Zucchi MI. Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns. Sci Rep 2023; 13:20635. [PMID: 37996522 PMCID: PMC10667357 DOI: 10.1038/s41598-023-44631-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 10/10/2023] [Indexed: 11/25/2023] Open
Abstract
The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C. prunifera, worldwide known for wax utilization; and Syagrus romanzoffiana, of great ornamental potential. Copernicia spp. showed the largest chloroplast genomes (C. prunifera: 157,323 bp and C. alba: 157,192 bp), while S. romanzoffiana and B. gasipaes var. gasipaes presented the smallest (155,078 bp and 155,604 bp). Structurally, great synteny was detected among palms. Conservation was also observed in the distribution of single sequence repeats (SSR). Copernicia spp. presented less dispersed repeats, without occurrence in the small single copy (SSC). All RNA editing sites were C (cytidine) to U (uridine) conversions. Overall, closely phylogenetically related species shared more sites. Almost all nodes of the phylogenetic analysis showed a posterior probability (PP) of 1.0, reaffirming the close relationship between Acrocomia species. These results elucidate the conservation among palm chloroplast genomes, but point to subtle structural changes, providing support for the evolutionary dynamics of the Arecaceae family.
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Affiliation(s)
- Ana Flávia Francisconi
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Jonathan Andre Morales Marroquín
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Luiz Augusto Cauz-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Wien, Austria
| | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina S/N-Novo Horizonte, Feira de SantanaFeira de Santana, Bahia, CEP 44036-900, Brazil
| | - Kauanne Karolline Moreno Martins
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Marcones Ferreira Costa
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
- Universidade Federal do Piauí, BR-343 Km 3.5, Floriano, Piauí, CEP 64808-605, Brazil
| | - Doriane Picanço-Rodrigues
- Departamento de Biologia, Universidade Federal do Amazonas, Avenida Gen. Rodrigo Octávio Jordão Ramos, 3000-Coroado I-Campus Universitário-Senador Arthur Virgílio Filho-Setor Sul, Bloco H, Manaus, Amazonas, CEP 69077-000, Brazil
| | - Luciano Delmodes de Alencar
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Cesar Augusto Zanello
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Carlos Augusto Colombo
- Instituto Agronômico, Av. Theodureto de Almeida Camargo, 1500, Campinas, São Paulo, CEP 13075-630, Brazil
| | | | - Danilo Trabuco Amaral
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal do ABC, Avenida dos Estados, 5001, Santo André, São Paulo, CEP 09040-040, Brazil
| | - Maria Teresa Gomes Lopes
- Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Avenida Rodrigo Otávio Ramos, 3000-Bairro Coroado, Manaus, Amazonas, CEP 69077-000, Brazil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Avenida Pádua Dias, 11-Bairro São Dimas, Piracicaba, São Paulo, CEP 13418-900, Brazil
| | - Maria Imaculada Zucchi
- Agência Paulista de Tecnologia dos Agronegócios (APTA), Polo Centro Sul, Rodovia SP 127 Km 30, CP 28, Piracicaba, São Paulo, CEP 13400-970, Brazil.
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Wölke FJR, Cabral A, Lim JY, Kissling WD, Onstein RE. Africa as an evolutionary arena for large fruits. THE NEW PHYTOLOGIST 2023; 240:1574-1586. [PMID: 37334569 DOI: 10.1111/nph.19061] [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: 10/14/2022] [Accepted: 05/14/2023] [Indexed: 06/20/2023]
Abstract
Strong paleoclimatic change and few Late Quaternary megafauna extinctions make mainland Africa unique among continents. Here, we hypothesize that, compared with elsewhere, these conditions created the ecological opportunity for the macroevolution and geographic distribution of large fruits. We assembled global phylogenetic, distribution and fruit size data for palms (Arecaceae), a pantropical, vertebrate-dispersed family with > 2600 species, and integrated these with data on extinction-driven body size reduction in mammalian frugivore assemblages since the Late Quaternary. We applied evolutionary trait, linear and null models to identify the selective pressures that have shaped fruit sizes. We show that African palm lineages have evolved towards larger fruit sizes and exhibited faster trait evolutionary rates than lineages elsewhere. Furthermore, the global distribution of the largest palm fruits across species assemblages was explained by occurrence in Africa, especially under low canopies, and extant megafauna, but not by mammalian downsizing. These patterns strongly deviated from expectations under a null model of stochastic (Brownian motion) evolution. Our results suggest that Africa provided a distinct evolutionary arena for palm fruit size evolution. We argue that megafaunal abundance and the expansion of savanna habitat since the Miocene provided selective advantages for the persistence of African plants with large fruits.
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Affiliation(s)
- Friederike J R Wölke
- Evolution and Adaptation, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
| | - Andressa Cabral
- Evolution and Adaptation, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
| | - Jun Ying Lim
- Department of Biological Sciences, National University of Singapore, Block S16, 6 Science Drive 2, Singapore City, 117546, Singapore
| | - W Daniel Kissling
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Sciencepark 904, 1098 XH, Amsterdam, the Netherlands
| | - Renske E Onstein
- Evolution and Adaptation, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, the Netherlands
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4
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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: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [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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Kadam SK, Tamboli AS, Mane RN, Yadav SR, Choo YS, Burgos-Hernández M, Pak JH. Revised molecular phylogeny, global biogeography, and diversification of palms subfamily Coryphoideae (Arecaceae) based on low copy nuclear and plastid regions. JOURNAL OF PLANT RESEARCH 2023; 136:159-177. [PMID: 36520246 DOI: 10.1007/s10265-022-01425-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Coryphoideae are palmate-leaved palms from the family Arecaceae consisting of 46 genera representing 421 species. Although several phylogenetic analyses based on different genomic regions have been carried out on Coryphoideae, a fully resolved molecular phylogenetic tree has not been reported yet. To achieve this, we applied two phylogenetic reconstruction methods: Maximum Likelihood and Bayesian Inference, using amplified sampling by retrieving chloroplast and nuclear DNA sequences from NCBI and adding newly produced sequences from Indian accession into the dataset. The same dataset (chloroplast + nuclear DNA sequences) was used to estimate divergence times and the evolutionary history of Coryphoideae with a Bayesian uncorrelated, lognormal relaxed-clock approach and a Statistical Divergence-Vicariance Analysis method, respectively. The phylogenetic analyses based on a combined chloroplast and nuclear DNA sequence dataset showed well-resolved relationships within the subfamily. Both phylogenetic trees divide Coryphoideae into two main groups: CSPT (Crysophileae, Sabaleae, Phoeniceae, and Trachycarpeae) and the Syncarpous group. These main groups are segregated into eight tribes (Trachycarpeae, Phoeniceae, Sabaleae, Crysophileae, Borasseae, Corypheae, Caryoteae, and Chuniophoeniceae) and four subtribes (Rhapidine, Livistoninae, Hyphaeninae, and Lataniinae) with strong support-values. Most previously unresolved and doubtful relationships within tribes Trachycarpeae and Crysophilieae are now resolved and well-supported. The reconstructed phylogenetic trees support all previous systematic revisions of the subfamily. All Indian sampled species of Arenga, Bentinckia, Hyphaene, and Trachycarpus show close relation with their respective congeneric species. Molecular dating results and integration of biogeography suggest that Coryphoideae originated in Laurasia at ~95.12 Ma and then diverged into the tropical and subtropical regions of the whole world. This study offers the correct combination of nuclear and plastid regions to test the current and future systematic revisions.
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Affiliation(s)
- Suhas K Kadam
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Asif S Tamboli
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Rohit N Mane
- Angiosperm Taxonomy Laboratory, Department of Botany, Shivaji University, Kolhapur, 416004, Maharashta, India
- Department of Botany, Rayat Shikshan Sansthas, Balwant College, Vita, 415311, Sangli, India
| | - Shrirang R Yadav
- Angiosperm Taxonomy Laboratory, Department of Botany, Shivaji University, Kolhapur, 416004, Maharashta, India
| | - Yeon-Sik Choo
- Department of Biology, School of Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Mireya Burgos-Hernández
- Department of Botany, Colegio de Postgraduados, Km 36, Federal Highway Mexico-Texcoco, Montecillo, Texcoco, 56264, Mexico.
| | - Jae Hong Pak
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Cytogenetics, Typification, Molecular Phylogeny and Biogeography of Bentinckia (Arecoideae, Arecaceae), an Unplaced Indian Endemic Palm from Areceae. BIOLOGY 2023; 12:biology12020233. [PMID: 36829510 PMCID: PMC9952971 DOI: 10.3390/biology12020233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023]
Abstract
Bentinckia is a genus of flowering plants which is an unplaced member of the tribe Areceae (Arecaceae). Two species are recognized in the genus, viz. B. condapanna Berry ex Roxb. from the Western Ghats, India, and B. nicobarica (Kurz) Becc. from the Nicobar Islands. This work constitutes taxonomic revision, cytogenetics, molecular phylogeny, and biogeography of the Indian endemic palm genus Bentinckia. The present study discusses the ecology, morphology, taxonomic history, distribution, conservation status, and uses of Bentinckia. A neotype was designated for the name B. condapanna. Cytogenetical studies revealed a new cytotype of B. condapanna representing 2n = 30 chromosomes. Although many phylogenetic reports of the tribe Areceae are available, the relationship within the tribe is still ambiguous. To resolve this, we carried out Bayesian Inference (BI) and Maximum Likelihood (ML) analysis using an appropriate combination of chloroplast and nuclear DNA regions. The same phylogeny was used to study the evolutionary history of Areceae. Phylogenetic analysis revealed that Bentinckia forms a clade with other unplaced members, Clinostigma and Cyrostachys, and together they show a sister relationship with the subtribe Arecinae. Biogeographic analysis shows Bentinckia might have originated in Eurasia and India.
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Schley RJ, Pellicer J, Ge X, Barrett C, Bellot S, Guignard MS, Novák P, Suda J, Fraser D, Baker WJ, Dodsworth S, Macas J, Leitch AR, Leitch IJ. The ecology of palm genomes: repeat-associated genome size expansion is constrained by aridity. THE NEW PHYTOLOGIST 2022; 236:433-446. [PMID: 35717562 PMCID: PMC9796251 DOI: 10.1111/nph.18323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Genome size varies 2400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat 'communities' are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective. We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically informed linear models to explore relationships between repeat dynamics and environmental factors. We show that palm genome size and repeat 'community' composition are best explained by aridity. Specifically, Ty3-gypsy and TIR elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. By contrast, Ty1-copia and LINE elements were more abundant in drier environments. Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements that may associate with stress-response genes (e.g. Ty1-copia) have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat 'communities'.
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Affiliation(s)
- Rowan J. Schley
- University of ExeterLaver Building, North Park RoadExeterDevonEX4 4QEUK
- Royal Botanic GardensKewSurreyTW9 3ABUK
| | - Jaume Pellicer
- Royal Botanic GardensKewSurreyTW9 3ABUK
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)Passeig del Migdia sn08038BarcelonaSpain
| | - Xue‐Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhou510650China
| | - Craig Barrett
- Department of BiologyWest Virginia UniversityMorgantownWV26506USA
| | | | | | - Petr Novák
- Biology Centre, Institute of Plant Molecular BiologyCzech Academy of Sciences370 05České BudějoviceCzech Republic
| | | | | | | | - Steven Dodsworth
- School of Biological SciencesUniversity of PortsmouthPortsmouthHampshirePO1 2DYUK
| | - Jiří Macas
- Biology Centre, Institute of Plant Molecular BiologyCzech Academy of Sciences370 05České BudějoviceCzech Republic
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Chen DJ, Landis JB, Wang HX, Sun QH, Wang Q, Wang HF. Plastome structure, phylogenomic analyses and molecular dating of Arecaceae. FRONTIERS IN PLANT SCIENCE 2022; 13:960588. [PMID: 36237503 PMCID: PMC9552784 DOI: 10.3389/fpls.2022.960588] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/08/2022] [Indexed: 05/29/2023]
Abstract
Arecaceae is a species-rich clade of Arecales, while also being regarded as a morphologically diverse angiosperm family with numerous species having significant economic, medicinal, and ornamental value. Although in-depth studies focused on the chloroplast structure of Arecaceae, as well as inferring phylogenetic relationships using gene fragments, have been reported in recent years, a comprehensive analysis of the chloroplast structure of Arecaceae is still needed. Here we perform a comprehensive analysis of the structural features of the chloroplast genome of Arecaceae, compare the variability of gene sequences, infer phylogenetic relationships, estimate species divergence times, and reconstruct ancestral morphological traits. In this study, 74 chloroplast genomes of Arecaceae were obtained, covering five subfamilies. The results show that all chloroplast genomes possess a typical tetrad structure ranging in size between 153,806-160,122 bp, with a total of 130-137 genes, including 76-82 protein-coding genes, 29-32 tRNA genes, and 4 rRNA genes. Additionally, the total GC content was between 36.9-37.7%. Analysis of the SC/IR boundary indicated that the IR region underwent expansion or contraction. Phylogenetic relationships indicate that all five subfamilies in Arecaceae are monophyletic and that Ceroxyloideae and Arecoideae are sister groups (BS/PP = 100/1). The results of molecular dating indicate that the age of the crown group of Arecaceae is likely to be 96.60 [84.90-107.60] Ma, while the age of the stem group is 102.40 [93.44-111.17] Ma. Reconstruction of ancestral traits indicate that the ancestral characteristics of the family include monoecious plants, one seed, six stamens, and a smooth pericarp.
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Affiliation(s)
- Da-Juan Chen
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Haikou, China
| | - Jacob B. Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, United States
| | - Hong-Xin Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Zhai Mingguo Academician Work Station, Sanya University, Sanya, China
| | - Qing-Hui Sun
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Qiao Wang
- Hainan Shengda Modern Agriculture Development Co., Ltd., Qionghai, China
| | - Hua-Feng Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Haikou, China
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9
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The likely extinction of hundreds of palm species threatens their contributions to people and ecosystems. Nat Ecol Evol 2022; 6:1710-1722. [PMID: 36163257 DOI: 10.1038/s41559-022-01858-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 07/24/2022] [Indexed: 02/07/2023]
Abstract
Protecting nature's contributions to people requires accelerating extinction risk assessment and better integrating evolutionary, functional and used diversity with conservation planning. Here, we report machine learning extinction risk predictions for 1,381 palm species (Arecaceae), a plant family of high socio-economic and ecological importance. We integrate these predictions with published assessments for 508 species (covering 75% of all palm species) and we identify top-priority regions for palm conservation on the basis of their proportion of threatened evolutionarily distinct, functionally distinct and used species. Finally, we explore palm use resilience to identify non-threatened species that could potentially serve as substitutes for threatened used species by providing similar products. We estimate that over a thousand palms (56%) are probably threatened, including 185 species with documented uses. Some regions (New Guinea, Vanuatu and Vietnam) emerge as top ten priorities for conservation only after incorporating machine learning extinction risk predictions. Potential substitutes are identified for 91% of the threatened used species and regional use resilience increases with total palm richness. However, 16 threatened used species lack potential substitutes and 30 regions lack substitutes for at least one of their threatened used palm species. Overall, we show that hundreds of species of this keystone family face extinction, some of them probably irreplaceable, at least locally. This highlights the need for urgent actions to avoid major repercussions on palm-associated ecosystem processes and human livelihoods in the coming decades.
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Song A, Liu J, Liang SQ, Van Do T, Nguyen HB, Deng WYD, Jia LB, Del Rio C, Srivastava G, Feng Z, Zhou ZK, Huang J, Su T. Leaf fossils of Sabalites (Arecaceae) from the Oligocene of northern Vietnam and their paleoclimatic implications. PLANT DIVERSITY 2022; 44:406-416. [PMID: 35967257 PMCID: PMC9363516 DOI: 10.1016/j.pld.2021.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 05/30/2023]
Abstract
Recent paleobotanical investigations in Vietnam provide a good opportunity to improve our understanding of the biodiversity and paleoclimatic conditions in the geological past of Southeast Asia. Palms (Arecaceae) are a diverse family of typical thermophilous plants with a relatively low tolerance for freezing. In this study, we describe well-preserved fossil palm leaves from the Oligocene Dong Ho Formation of Hoanh Bo Basin, northern Vietnam. Characters of the fossil leaves, such as a fan-shaped costapalmate lamina, an unarmed petiole, a costa slightly enlarged at the base that then tapers distally into the blade, and well-preserved amphistomatic leaves with cuticles, suggest that they represent a new fossil species, which we herein designate Sabalites colaniae A. Song, T. Su, T. V. Do et Z.K. Zhou sp. nov. Together with other paleontological and palaeoclimatic evidence, we conclude that a warm climate prevailed in northern Vietnam and nearby areas during the Oligocene.
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Affiliation(s)
- Ai Song
- Institute of Palaeontology, Yunnan Key Laboratory for Palaeobiology, MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Yunnan Key Laboratory of Earth System Science, Yunnan University, Kunming, 650500, China
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Jia Liu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Shui-Qing Liang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Truong Van Do
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Viet Nam
- Graduate Academy of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Viet Nam
| | - Hung Ba Nguyen
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Viet Nam
| | - Wei-Yu-Dong Deng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Lin-Bo Jia
- CAS Key Laboratory of Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Cédric Del Rio
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | | | - Zhuo Feng
- Institute of Palaeontology, Yunnan Key Laboratory for Palaeobiology, MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Yunnan Key Laboratory of Earth System Science, Yunnan University, Kunming, 650500, China
| | - Zhe-Kun Zhou
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Jian Huang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Tao Su
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
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11
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Pinanga palms revisited 20 years on: what can changes in Pinanga species populations tell us about rainforest understory palm persistence? JOURNAL OF TROPICAL ECOLOGY 2022. [DOI: 10.1017/s0266467422000256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Borneo is the centre of diversity of the palm genus Pinanga. At least 13 understory species have been recorded in the Ulu Temburong National Park in Brunei, but little is known of their persistence. Changes in populations of Pinanga understory palms may be indicative of more widespread changes due to climate change, such as changes in rainfall, which may be important for the palm diversity in the protected area. However, we know little about the population dynamics of these palms, how persistent their populations are or if they behave similarly over long time frames. In 1998, populations of five co-occurring species of Pinanga at several locations in the Ulu Temburong National Park were documented. This project aimed to undertake a comprehensive resurvey of the original five Pinanga palm species populations in order to assess if they showed similar population changes across sites and species after two decades. Overall, most species maintained their population size in the surveyed region but not consistently among sites, and one species significantly declined in abundance. There was considerable variation in population growth rate (R) within and among species and sites that was significantly correlated with density and the percentage of multi-stemmed plants. There was evidence of pulsed recruitment in some species and or sites rather than steady or exponential patterns of population growth.
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12
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Carrete M, Hiraldo F, Romero-Vidal P, Blanco G, Hernández-Brito D, Sebastián-González E, Díaz-Luque JA, Tella JL. Worldwide Distribution of Antagonistic-Mutualistic Relationships Between Parrots and Palms. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.790883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Palms, like all plants, show coevolutionary relationships with animals that have been traditionally categorized as mutualistic (seed dispersers and pollinators) or antagonistic (seed predators). This dual perspective, however, has prevented a full understanding of their true interactions with some animal groups, mainly those that do not ingest entire fruits. One clear example is parrots, which have been described to use palm species as feeding resources, while their role as seed dispersers has been largely neglected. Here, we combined fieldwork data with information from the literature and citizen science (i.e., naturalists and nature photographers) on parrot foraging ecology worldwide to evaluate the spatial and taxonomic extent of parrot-palm interactions and to identify the eco-evolutionary factors involved. We identified 1,189 interactions between 135 parrots and 107 palm species in more than 50 countries across the six realms where palms are present as natives or introduced. Combining this information, we identified 427 unique parrot-palm interacting pairs (i.e., a parrot species interacting with a palm species). Pure antagonistic interactions (i.e., parrots just preying on seeds or eating or destroying their non-reproductive parts) were less common (5%) than mutualistic ones (i.e., parrots benefiting by partially preying on the seed or fruit or consuming the pulp of the fruit or the flower but also contributing to seed dispersal and, potentially, pollination; 89%). After controlling for phylogeny, the size of consumed seeds and parrot body mass were positively related. Seed dispersal distances varied among palm species (range of estimated median dispersal distances: 9–250 m), with larger parrots dispersing seeds at greater distances, especially large fruits commonly categorized as megafauna anachronisms (>4 cm length). Although parrot-palm interactions are widespread, several factors (e.g., social behavior, predation fear, food availability, or seasonality) may affect the actual position of parrots on the antagonism-mutualism continuum for different palm species and regions, deserving further research. Meanwhile, the pervasiveness of parrot-palm mutualistic interactions, mainly involving seed dispersal and pollination, should not be overlooked in studies of palm ecology and evolution.
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13
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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] [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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14
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Dias MC, Clement CR, Fraga HPDF, Silva RSD, Rodrigues DP, Vieira LDN. The complete plastid genome of Bactris riparia (Arecaceae) and a comparative analysis in Bactridinae (Cocoseae, Arecaceae). Genet Mol Biol 2022; 45:e20210305. [DOI: 10.1590/1678-4685-gmb-2021-0305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 09/24/2022] [Indexed: 11/09/2022] Open
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15
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Lehtonen S, Muscarella R, Moulatlet G, Balslev H, Tuomisto H. Edaphic heterogeneity and the evolutionary trajectory of Amazonian plant communities. Ecol Evol 2021; 11:17672-17685. [PMID: 35003631 PMCID: PMC8717337 DOI: 10.1002/ece3.8477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 11/10/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
We investigated how the phylogenetic structure of Amazonian plant communities varies along an edaphic gradient within the non-inundated forests. Forty localities were sampled on three terrain types representing two kinds of soil: clayey soils of a high base cation concentration derived from the Solimões formation, and loamy soils with lower base cation concentration derived from the Içá formation and alluvial terraces. Phylogenetic community metrics were calculated for each locality for ferns and palms both with ferns as one group and for each of three fern clades with a crown group age comparable to that of palms. Palm and fern communities showed significant and contrasting phylogenetic signals along the soil gradient. Fern species richness increased but standard effect size of mean pairwise distance (SES.MPD) and variation of pairwise distances (VPD) decreased with increasing soil base cation concentration. In contrast, palm communities were more species rich on less cation-rich soils and their SES.MPD increased with soil base cation concentration. Species turnover between the communities reflected the soil gradient slightly better when based on species occurrences than when phylogenetic distances between the species were considered. Each of the three fern subclades behaved differently from each other and from the entire fern clade. The fern clade whose phylogenetic patterns were most similar to those of palms also resembled palms in being most species-rich on cation-poor soils. The phylogenetic structuring of local plant communities varies along a soil base cation concentration gradient within non-inundated Amazonian rain forests. Lineages can show either similar or different phylogenetic community structure patterns and evolutionary trajectories, and we suggest this to be linked to their environmental adaptations. Consequently, geological heterogeneity can be expected to translate into a potentially highly diverse set of evolutionarily distinct community assembly pathways in Amazonia and elsewhere.
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Affiliation(s)
| | - Robert Muscarella
- Plant Ecology and EvolutionEvolutionary Biology CenterUppsala UniversityUppsalaSweden
| | - Gabriel Moulatlet
- Facultad de Ciencias de la Tierra y AguaUniversidad Regional Amazónica IkiamTenaEcuador
| | - Henrik Balslev
- Section for Ecoinformatics & BiodiversityDepartment of BioscienceAarhus UniversityAarhusDenmark
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16
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Palm functional trait responses to local environmental factors in the Colombian Amazon. JOURNAL OF TROPICAL ECOLOGY 2021. [DOI: 10.1017/s0266467421000493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractFunctional traits play a key role in driving plant community effects on ecosystem function. We examined nine functional traits in various palm (Arecaceae) species and their relationships with moisture, tree-fall gaps, slope, and forest type at 29 transects (500×5 m) in the northeastern region of the Colombian Amazon. Redundancy analysis of mean trait values of species within a plot weighted by their abundance and Pearson correlations were used to evaluate the relationships between traits and environmental factors. The community trait composition was correlated with local environmental factors, which explained 23% of the trait variance. We detected functional dominance of the tallest palms in soils with high moisture and in floodplain forests (p ≤0.05). Palms with relatively long leaves were dominant in the flooded forests. Acaulescent and small palms were dominant on high slopes, and in terra firme forests, long-petioled palms were dominant in forest gaps. The number of seeds per fruit was not correlated with any environmental variable. Thus, hydrology is one of the main drivers of the functional composition of neotropical palm communities at the local scale, segregating tall palms with competitive and evasive strategies from small understory palms, which are mainly stress tolerant.
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17
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Earth history events shaped the evolution of uneven biodiversity across tropical moist forests. Proc Natl Acad Sci U S A 2021; 118:2026347118. [PMID: 34599095 PMCID: PMC8501849 DOI: 10.1073/pnas.2026347118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2021] [Indexed: 02/07/2023] Open
Abstract
Tropical moist forests harbor much of the world’s biodiversity, but this diversity is not evenly distributed globally, with tropical moist forests in the Neotropics and Indomalaya generally exhibiting much greater diversity than in the Afrotropics. Here, we assess the ubiquity of this “pantropical diversity disparity” (PDD) using the present-day distributions of over 150,000 species of plants and animals, and we compare these distributions with a spatial model of diversification combined with reconstructions of plate tectonics, temperature, and aridity. Our study demonstrates that differences in paleoenvironmental dynamics between continents, including mountain building, aridification, and global temperature fluxes, can explain the PDD by shaping spatial and temporal patterns of species origination and extinction, providing a close match to observed distributions of plants and animals. Far from a uniform band, the biodiversity found across Earth’s tropical moist forests varies widely between the high diversity of the Neotropics and Indomalaya and the relatively lower diversity of the Afrotropics. Explanations for this variation across different regions, the “pantropical diversity disparity” (PDD), remain contentious, due to difficulty teasing apart the effects of contemporary climate and paleoenvironmental history. Here, we assess the ubiquity of the PDD in over 150,000 species of terrestrial plants and vertebrates and investigate the relationship between the present-day climate and patterns of species richness. We then investigate the consequences of paleoenvironmental dynamics on the emergence of biodiversity gradients using a spatially explicit model of diversification coupled with paleoenvironmental and plate tectonic reconstructions. Contemporary climate is insufficient in explaining the PDD; instead, a simple model of diversification and temperature niche evolution coupled with paleoaridity constraints is successful in reproducing the variation in species richness and phylogenetic diversity seen repeatedly among plant and animal taxa, suggesting a prevalent role of paleoenvironmental dynamics in combination with niche conservatism. The model indicates that high biodiversity in Neotropical and Indomalayan moist forests is driven by complex macroevolutionary dynamics associated with mountain uplift. In contrast, lower diversity in Afrotropical forests is associated with lower speciation rates and higher extinction rates driven by sustained aridification over the Cenozoic. Our analyses provide a mechanistic understanding of the emergence of uneven diversity in tropical moist forests across 110 Ma of Earth’s history, highlighting the importance of deep-time paleoenvironmental legacies in determining biodiversity patterns.
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18
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Escobar S, Helmstetter AJ, Montúfar R, Couvreur TLP, Balslev H. Phylogenomic relationships and historical biogeography in the South American vegetable ivory palms (Phytelepheae). Mol Phylogenet Evol 2021; 166:107314. [PMID: 34592464 DOI: 10.1016/j.ympev.2021.107314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 01/06/2023]
Abstract
The palm tribe Phytelepheae form a clade of three genera and eight species whose phylogenetic relationships and historical biogeography are not fully understood. Based on morphological similarities and phylogenetic relatedness, it has been suggested that Phytelephas seemannii and Phytelephas schottii are synonyms of Phytelephas macrocarpa, implying the existence of only six species within the Phytelepheae. In addition, uncertainty in their phylogenetic relationships in turn results in blurred biogeographic history. We inferred the phylogenomic relationships in the Phytelepheae by target-capturing 176 nuclear genes and estimated divergence times by using four fossils for time calibration. We lastly explored the biogeographic history of the tribe by inferring its ancestral range evolution. Our phylogenomic trees showed that P. seemannii and P. schottii are not closely related with P. macrocarpa, and therefore, support the existence of eight species in the Phytelepheae. The ancestor of the tribe was widely-distributed in the Chocó, Magdalena, and Amazonia during the Miocene at 19.25 Ma. Early diversification in Phytelephas at 5.27 Ma could have occurred by trans-Andean vicariance after the western Andes uplifted rapidly at ∼ 10 Ma. Our results show the utility of phylogenomic approaches to shed light on species relationships and their biogeographic history.
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Affiliation(s)
- Sebastián Escobar
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, DK 8000 Aarhus C, Denmark.
| | | | - Rommel Montúfar
- Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Thomas L P Couvreur
- IRD, UMR DIADE, University of Montpellier, Montpellier, France; Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Henrik Balslev
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, DK 8000 Aarhus C, Denmark
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19
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Cássia-Silva C, Freitas CG, Jardim L, Bacon CD, Collevatti RG. In situ radiation explains the frequency of dioecious palms on islands. ANNALS OF BOTANY 2021; 128:205-215. [PMID: 33949659 PMCID: PMC8324027 DOI: 10.1093/aob/mcab056] [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: 01/30/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS Dioecy has evolved up to 5000 times in angiosperms, despite the potentially high intrinsic costs to unisexuality. Dioecy prevents inbreeding, which is especially relevant on isolated islands when gene pools are small. Dioecy is also associated with certain dispersal traits, such as fruit size and type. However, the influence of dioecy on other life history traits and island distribution remains poorly understood. Here, we test the effect of dioecy on palm (Arecaceae) speciation rates, fruit size and frequency on islands. METHODS We used phylogenetic comparative methods to estimate the ancestral state of the sexual system and its impact on speciation rates and fruit size. Frequency of sexual systems, effect of insularity on the probability of being dioecious, and phylogenetic clustering of island dioecious vs. mainland species were inferred. Lastly, we determined the interplay of insularity and sexual system on speciation rates. KEY RESULTS Palms repeatedly evolved different sexual systems (dioecy, monoecy and polygamy) from a hermaphrodite origin. Differences in speciation rates and fruit size among the different sexual systems were not identified. An effect of islands on the probability of the palms being dioecious was also not found. However, we found a high frequency and phylogenetic clustering of dioecious palms on islands, which were not correlated with higher speciation rates. CONCLUSIONS The high frequency and phylogenetic clustering may be the result of in situ radiation and suggest an 'island effect' for dioecious palms, which was not explained by differential speciation rates. This island effect also cannot be attributed to long-distance dispersal due to the lack of fruit size difference among sexual systems, and particularly because palm dispersal to islands is highly constrained by the interaction between the sizes of fruit and frugivores. Taken together, we suggest that trait flexibility in sexual system evolution and the in situ radiation of dioecious lineages are the underlying causes of the outstanding distribution of palms on islands.
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Affiliation(s)
- Cibele Cássia-Silva
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Cíntia G Freitas
- Pós-Graduação em Ecologia e Conservação, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Lucas Jardim
- Laboratório de Ecologia Teórica e Síntese, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Rosane G Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
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20
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Ghosh Dasgupta M, Dev SA, Muneera Parveen AB, Sarath P, Sreekumar VB. Draft genome of Korthalsia laciniosa (Griff.) Mart., a climbing rattan elucidates its phylogenetic position. Genomics 2021; 113:2010-2022. [PMID: 33862180 DOI: 10.1016/j.ygeno.2021.04.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 03/21/2021] [Accepted: 04/11/2021] [Indexed: 12/28/2022]
Abstract
Korthalsia laciniosa (Griff.) Mart. is a climbing rattan used as a source of durable and flexible cane. In the present study, the draft genome of K. laciniosa was sequenced, de novo assembled and annotated. Genome-wide identification of MADS-Box transcription factors revealed loss of Mβ, and Mγ genes belonging to Type I subclass in the rattan lineage. Mining of the genome revealed presence of 13 families of lignin biosynthetic pathway genes and expression profiling of nine major genes documented relatively lower level of expression in cirrus when compared to leaflet and petiole. The chloroplast genome was re-constructed and analysis revealed the phylogenetic relatedness of this genus to Eugeissona, in contrast with its present taxonomic position. The genomic resource generated in the present study will accelerate population structure analysis, genetic resource conservation, phylogenomics and facilitate understanding the unique developmental processes like gender expression at molecular level.
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Affiliation(s)
- Modhumita Ghosh Dasgupta
- Institute of Forest Genetics and Tree Breeding, Forest Campus, R.S. Puram, Coimbatore Pincode-641002, India
| | - Suma Arun Dev
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi P. O, Thrissur, Kerala 680653, India
| | - Abdul Bari Muneera Parveen
- Institute of Forest Genetics and Tree Breeding, Forest Campus, R.S. Puram, Coimbatore Pincode-641002, India
| | - Paremmal Sarath
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi P. O, Thrissur, Kerala 680653, India; Ph.D. Scholar, Forest Research Institute Deemed to be University, Dehradun, Uttarakhand, India
| | - V B Sreekumar
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi P. O, Thrissur, Kerala 680653, India
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21
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Matsunaga KK, Smith SY. Fossil palm reading: using fruits to reveal the deep roots of palm diversity. AMERICAN JOURNAL OF BOTANY 2021; 108:472-494. [PMID: 33624301 PMCID: PMC8048450 DOI: 10.1002/ajb2.1616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/22/2020] [Indexed: 05/11/2023]
Abstract
PREMISE Fossils are essential for understanding evolutionary history because they provide direct evidence of past diversity and geographic distributions. However, resolving systematic relationships between fossils and extant taxa, an essential step for many macroevolutionary studies, requires extensive comparative work on morphology and anatomy. While palms (Arecaceae) have an excellent fossil record that includes numerous fossil fruits, many are difficult to identify due in part to limited comparative data on modern fruit structure. METHODS We studied fruits of 207 palm species, representing nearly every modern genus, using X-ray microcomputed tomography. We then developed a morphological data set to test whether the fossil record of fruits can improve our understanding of palm diversity in the deep past. To evaluate the accuracy with which this data set recovers systematic relationships, we performed phylogenetic pseudofossilization analyses. We then used the data set to investigate the phylogenetic relationships of five previously published fossil palm fruits. RESULTS Phylogenetic analyses of fossils and pseudofossilization of extant taxa show that fossils can be placed accurately to the tribe and subtribe level with this data set, but node support must be considered. The phylogenetic relationships of the fossils suggest origins of many modern lineages in the Cretaceous and early Paleogene. Three of these fossils are suitable as new node calibrations for palms. CONCLUSIONS This work improves our knowledge of fruit structure in palms, lays a foundation for applying fossil fruits to macroevolutionary studies, and provides new insights into the evolutionary history and early diversification of Arecaceae.
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Affiliation(s)
- Kelly K.S. Matsunaga
- Department of Earth and Environmental Sciences & Museum of PaleontologyUniversity of MichiganAnn ArborMI48109USA
- Present address:
Department of Ecology and Evolutionary Biology & Biodiversity InstituteUniversity of KansasLawrenceKS66045USA
| | - Selena Y. Smith
- Department of Earth and Environmental Sciences & Museum of PaleontologyUniversity of MichiganAnn ArborMI48109USA
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Kuhnhäuser BG, Bellot S, Couvreur TLP, Dransfield J, Henderson A, Schley R, Chomicki G, Eiserhardt WL, Hiscock SJ, Baker WJ. A robust phylogenomic framework for the calamoid palms. Mol Phylogenet Evol 2021; 157:107067. [PMID: 33412273 DOI: 10.1016/j.ympev.2020.107067] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 01/11/2023]
Abstract
Well-supported phylogenies are a prerequisite for the study of the evolution and diversity of life on earth. The subfamily Calamoideae accounts for more than one fifth of the palm family (Arecaceae), occurs in tropical rainforests across the world, and supports a billion-dollar industry in rattan products. It contains ca. 550 species in 17 genera, 10 subtribes and three tribes, but their phylogenetic relationships remain insufficiently understood. Here, we sequenced almost one thousand nuclear genomic regions for 75 systematically selected Calamoideae, representing the taxonomic diversity within all calamoid genera. Our phylogenomic analyses resolved a maximally supported phylogenetic backbone for the Calamoideae, including several higher-level relationships not previously inferred. In-depth analysis revealed low gene tree conflict for the backbone but complex deep evolutionary histories within several subtribes. Overall, our phylogenomic framework sheds new light on the evolution of palms and provides a robust foundation for future comparative studies, such as taxonomy, systematics, biogeography, and macroevolutionary research.
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Affiliation(s)
- Benedikt G Kuhnhäuser
- Department of Plant Sciences, University of Oxford, United Kingdom; Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | | | | | | | - Rowan Schley
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, United Kingdom; Department of Biology, Aarhus University, Denmark
| | - Simon J Hiscock
- Department of Plant Sciences, University of Oxford, United Kingdom
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Velazco SJE, Svenning J, Ribeiro BR, Laureto LMO. On opportunities and threats to conserve the phylogenetic diversity of Neotropical palms. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13215] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Santiago José Elías Velazco
- Instituto de Biología Subtropical Universidad Nacional de Misiones‐CONICET Puerto Iguazú Misiones N3370BFAArgentina
| | - Jean‐Christian Svenning
- Section of Ecoinformatics and Biodiversity, Department of Bioscience Aarhus University AarhusDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE) Department of Bioscience, Aarhus University AarhusDK‐8000Denmark
| | - Bruno R. Ribeiro
- Programa de Pós‐Graduaçao Ecología e Evolução Instituto de Ciências Biológicas V, Universidade Federal de Goiás Goiânia Goiás 74.690‐900Brazil
| | - Livia Maira Orlandi Laureto
- Theoretical, Metacommunity and Landscape Ecology Laboratory Instituto de Ciências Biológicas V, Universidade Federal de Goiás Goiânia Goiás 74.690‐900Brazil
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Li T, Liu D, Yang Y, Guo J, Feng Y, Zhang X, Cheng S, Feng J. Phylogenetic supertree reveals detailed evolution of SARS-CoV-2. Sci Rep 2020; 10:22366. [PMID: 33353955 PMCID: PMC7755913 DOI: 10.1038/s41598-020-79484-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023] Open
Abstract
Corona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-2 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, yet limited progress was obtained, principally owing to the disability of these methods to reasonably integrate phylogenetic information from all genes of SARS-CoV-2. Supertree method based on multiple trees can produce the overall reasonable phylogenetic tree. However, the supertree method has been barely used for phylogenetic analysis of viruses. Here we applied the matrix representation with parsimony (MRP) pseudo-sequence supertree analysis to study the origin and evolution of SARS-CoV-2. Compared with other phylogenetic analysis methods, the supertree method showed more resolution power for phylogenetic analysis of coronaviruses. In particular, the MRP pseudo-sequence supertree analysis firmly disputes bat coronavirus RaTG13 be the last common ancestor of SARS-CoV-2, which was implied by other phylogenetic tree analysis based on viral genome sequences. Furthermore, the discovery of evolution and mutation in SARS-CoV-2 was achieved by MRP pseudo-sequence supertree analysis. Taken together, the MRP pseudo-sequence supertree provided more information on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.
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Affiliation(s)
- Tingting Li
- Institute of Immunology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Dongxia Liu
- Institute of Pathology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yadi Yang
- Institute of Immunology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jiali Guo
- The Second Clinical Medical School, Lanzhou University, Lanzhou, 730000, China
| | - Yujie Feng
- The Second Clinical Medical School, Lanzhou University, Lanzhou, 730000, China
| | - Xinmo Zhang
- The Second Clinical Medical School, Lanzhou University, Lanzhou, 730000, China
| | - Shilong Cheng
- The First Clinical Medical School, Lanzhou University, Lanzhou, 730000, China
| | - Jie Feng
- Institute of Pathology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China.
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25
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Cássia-Silva C, Freitas CG, Lemes LP, Paterno GB, Dias PA, Bacon CD, Collevatti RG. Higher evolutionary rates in life-history traits in insular than in mainland palms. Sci Rep 2020; 10:21125. [PMID: 33273647 PMCID: PMC7713303 DOI: 10.1038/s41598-020-78267-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/17/2020] [Indexed: 12/28/2022] Open
Abstract
Isolated islands, due to the reduced interspecific competition compared to mainland habitats, present ecological opportunities for colonizing lineages. As a consequence, island lineages may be expected to experience higher rates of trait evolution than mainland lineages. However, island effects on key life-history traits of vascular plants remain underexplored at broad spatiotemporal scales, even for emblematic island clades such as palms. Here, we used phylogenetic comparative methods to evaluate potential differences in size and macroevolutionary patterns of height and fruit diameter among mainland, continental, and volcanic island palms. Further, phylogenetic beta-diversity was used to determine if lineage turnover supported an adaptive radiation scenario on volcanic islands. Volcanic island palms were taller than their continental island and mainland counterparts, whereas continental island palms exhibited smaller fruit size. Height and fruit size of palms evolved under evolutionary constraints towards an optimal value. However, scenarios of adaptive radiation and niche conservatism were not supported for the height and fruit size of volcanic and mainland palm clades, respectively, as expected. Instead, continental island palms exhibited higher evolutionary rates for height and fruit size. Insular palm assemblages (continental and volcanic) are composed of unique lineages. Beyond representing evolutionary sources of new palm lineages, our results demonstrate that insular habitats are important in shaping palm trait diversity. Also, the higher phenotypic evolutionary rates of continental island palms suggest disparate selection pressures on this habitat type, which can be an important driver of trait diversification over time. Taken together, these results stress the importance of insular habitats for conservation of functional, phylogenetic, and taxonomic diversity of palms.
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Affiliation(s)
- Cibele Cássia-Silva
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74001-970, Brazil.
| | - Cíntia G Freitas
- Pós-Graduação em Ecologia e Conservação, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR, 81531-990, Brazil
| | - Larissa Pereira Lemes
- Laboratório de Ecologia Teórica e Síntese, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74001-970, Brazil
| | - Gustavo Brant Paterno
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
- Chair of Restoration Ecology, School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 6, 85354, Freising, Germany
| | - Priscila A Dias
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74001-970, Brazil
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden
| | - Rosane G Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74001-970, Brazil
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26
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Bellot S, Bayton RP, Couvreur TLP, Dodsworth S, Eiserhardt WL, Guignard MS, Pritchard HW, Roberts L, Toorop PE, Baker WJ. On the origin of giant seeds: the macroevolution of the double coconut (Lodoicea maldivica) and its relatives (Borasseae, Arecaceae). THE NEW PHYTOLOGIST 2020; 228:1134-1148. [PMID: 32544251 PMCID: PMC7590125 DOI: 10.1111/nph.16750] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 05/29/2020] [Indexed: 05/25/2023]
Abstract
Seed size shapes plant evolution and ecosystems, and may be driven by plant size and architecture, dispersers, habitat and insularity. How these factors influence the evolution of giant seeds is unclear, as are the rate of evolution and the biogeographical consequences of giant seeds. We generated DNA and seed size data for the palm tribe Borasseae (Arecaceae) and its relatives, which show a wide diversity in seed size and include the double coconut (Lodoicea maldivica), the largest seed in the world. We inferred their phylogeny, dispersal history and rates of change in seed size, and evaluated the possible influence of plant size, inflorescence branching, habitat and insularity on these changes. Large seeds were involved in 10 oceanic dispersals. Following theoretical predictions, we found that: taller plants with fewer-branched inflorescences produced larger seeds; seed size tended to evolve faster on islands (except Madagascar); and seeds of shade-loving Borasseae tended to be larger. Plant size and inflorescence branching may constrain seed size in Borasseae and their relatives. The possible roles of insularity, habitat and dispersers are difficult to disentangle. Evolutionary contingencies better explain the gigantism of the double coconut than unusually high rates of seed size increase.
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Affiliation(s)
| | - Ross P. Bayton
- Royal Botanic Gardens, KewRichmond, SurreyTW9 3AEUK
- Department of Biological SciencesUniversity of ReadingWhiteknightsPO Box 217Reading, BerkshireRG6 6AHUK
| | | | - Steven Dodsworth
- Royal Botanic Gardens, KewRichmond, SurreyTW9 3AEUK
- School of Life SciencesUniversity of BedfordshireLutonLU1 3JUUK
| | - Wolf L. Eiserhardt
- Royal Botanic Gardens, KewRichmond, SurreyTW9 3AEUK
- Department of BiologyAarhus UniversityNy Munkegade 116Aarhus C8000Denmark
| | | | - Hugh W. Pritchard
- Royal Botanic Gardens, KewWakehurst Place, Wellcome Trust Millennium BuildingArdinglyWest SussexRH17 6TNUK
| | - Lucy Roberts
- Department of ZoologyUniversity of CambridgeDowning StreetCambridgeCB2 3EJUK
| | - Peter E. Toorop
- Royal Botanic Gardens, KewWakehurst Place, Wellcome Trust Millennium BuildingArdinglyWest SussexRH17 6TNUK
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27
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Nascimento LFD, Guimarães PR, Onstein RE, Kissling WD, Pires MM. Associated evolution of fruit size, fruit colour and spines in Neotropical palms. J Evol Biol 2020; 33:858-868. [PMID: 32198956 DOI: 10.1111/jeb.13619] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/23/2020] [Accepted: 03/10/2020] [Indexed: 11/29/2022]
Abstract
Understanding how ecological interactions have shaped the evolutionary dynamics of species traits remains a challenge in evolutionary ecology. Combining trait evolution models and phylogenies, we analysed the evolution of characters associated with seed dispersal (fruit size and colour) and herbivory (spines) in Neotropical palms to infer the role of these opposing animal-plant interactions in driving evolutionary patterns. We found that the evolution of fruit colour and fruit size was associated in Neotropical palms, supporting the adaptive interpretation of seed-dispersal syndromes and highlighting the role of frugivores in shaping plant evolution. Furthermore, we revealed a positive association between fruit size and the presence of spines on palm leaves, bracteas and stems. We hypothesize that interactions between palms and large-bodied frugivores/herbivores may explain the evolutionary relationship between fruit size and spines. Large-bodied frugivores, such as extinct megafauna, besides consuming the fruits and dispersing large seeds, may also have consumed the leaves or damaged the plants, thus simultaneously favouring the evolution of large fruits and defensive structures. Our findings show how current trait patterns can be understood as the result of the interplay between antagonistic and mutualistic interactions that have happened throughout the evolutionary history of a clade.
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Affiliation(s)
| | - Paulo R Guimarães
- Departamento de Ecologia, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Renske E Onstein
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - W Daniel Kissling
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Mathias M Pires
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
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28
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Tanentzap AJ, Igea J, Johnston MG, Larcombe MJ. Does Evolutionary History Correlate with Contemporary Extinction Risk by Influencing Range Size Dynamics? Am Nat 2020; 195:569-576. [PMID: 32097046 DOI: 10.1086/707207] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Extinction threatens many species yet is predicted by few factors across the plant tree of life (ToL). Taxon age is one factor that may associate with extinction if occupancy of geographic and adaptive zones varies with time, but evidence for such an association has been equivocal. Age-dependent occupancy can also influence diversification rates and thus extinction risk where new taxa have small range and population sizes. To test how age, diversification, and range size were correlated with extinction, we analyzed 639 well-sampled genera representing 8,937 species from across the plant ToL. We found a greater proportion of species were threatened by contemporary extinction in younger and faster-diversifying genera. When we directly tested how range size mediated this pattern in two large, well-sampled groups, our results varied. In conifers, potential range size was smaller in older species and was correlated with higher extinction risk. Age on its own had no direct effect on extinction when accounting for its influence on range size. In palm species, age was neither directly nor indirectly correlated with extinction risk. Our results suggest that range size dynamics may explain differing patterns of extinction risk across the ToL, with consequences for biodiversity conservation.
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29
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Sakulsathaporn A, Wonnapinij P, Suttangkakul A, Apisitwanich S, Vuttipongchaikij S. RNA editing in the chloroplast of Asian Palmyra palm (Borassus flabellifer). Genet Mol Biol 2020; 42:e20180371. [PMID: 31968044 PMCID: PMC7206934 DOI: 10.1590/1678-4685-gmb-2018-0371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 10/02/2019] [Indexed: 11/22/2022] Open
Abstract
We have identified 46 RNA editing sites located in 20 chloroplast (cp) genes of Borassus flabellifer (Asian Palmyra palm), family Arecaceae, and tested these genes for supporting phylogenetic study among the commelinids. Among the 46 sites, 43 sites were found to cause amino acid alterations, which were predicted to increase the hydrophobicity and transmembrane regions of the proteins, and one site was to cause a premature stop codon. Analysis of these editing sites with data obtained from seed plants showed that a number of shared-editing sites depend on the evolutionary relationship between plants. We reconstructed a deep phylogenetic relationship among the commelinids using seven RNA edited genes that are orthologous among monocots. This tree could represent the relationship among subfamilies of Arecaceae family, but was insufficient to represent the relationship among the orders of the commelinid. After adding eight gene sequences with high parsimony-informative characters (PICs), the tree topology was improved and could support the topology for the commelinid orders ((Arecales,Dasypogenaceae) (Zingiberales+Commelinales,Poales)). The result provides support for inherent RNA editing along the evolution of seed plants, and we provide an alternative set of loci for the phylogenetic tree reconstruction of Arecaceae's subfamilies.
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Affiliation(s)
- Arpakorn Sakulsathaporn
- Center for Agricultural Biotechnology, Kasetsart University,
Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
- Center of Excellence on Agricultural Biotechnology:
(AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- School of Natural Resource and Environmental Management,
Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai
Campus, Nong Khai 43000, Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart
University, 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900, Thailand
- Center of Advanced studies for Tropical Natural Resources,
Kasetsart University, Ngam Wong Wan, Chatuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health,
Kasetsart University (OmiKU), 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900,
Thailand
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart
University, 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900, Thailand
- Center of Advanced studies for Tropical Natural Resources,
Kasetsart University, Ngam Wong Wan, Chatuchak, Bangkok 10900, Thailand
| | - Somsak Apisitwanich
- Center for Agricultural Biotechnology, Kasetsart University,
Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
- Center of Excellence on Agricultural Biotechnology:
(AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Department of Genetics, Faculty of Science, Kasetsart
University, 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900, Thailand
- Center of Advanced studies for Tropical Natural Resources,
Kasetsart University, Ngam Wong Wan, Chatuchak, Bangkok 10900, Thailand
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart
University, 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900, Thailand
- Center of Advanced studies for Tropical Natural Resources,
Kasetsart University, Ngam Wong Wan, Chatuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health,
Kasetsart University (OmiKU), 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900,
Thailand
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30
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Kissling WD, Balslev H, Baker WJ, Dransfield J, Göldel B, Lim JY, Onstein RE, Svenning JC. PalmTraits 1.0, a species-level functional trait database of palms worldwide. Sci Data 2019; 6:178. [PMID: 31551423 PMCID: PMC6760217 DOI: 10.1038/s41597-019-0189-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/09/2019] [Indexed: 11/21/2022] Open
Abstract
Plant traits are critical to plant form and function -including growth, survival and reproduction- and therefore shape fundamental aspects of population and ecosystem dynamics as well as ecosystem services. Here, we present a global species-level compilation of key functional traits for palms (Arecaceae), a plant family with keystone importance in tropical and subtropical ecosystems. We derived measurements of essential functional traits for all (>2500) palm species from key sources such as monographs, books, other scientific publications, as well as herbarium collections. This includes traits related to growth form, stems, armature, leaves and fruits. Although many species are still lacking trait information, the standardized and global coverage of the data set will be important for supporting future studies in tropical ecology, rainforest evolution, paleoecology, biogeography, macroecology, macroevolution, global change biology and conservation. Potential uses are comparative eco-evolutionary studies, ecological research on community dynamics, plant-animal interactions and ecosystem functioning, studies on plant-based ecosystem services, as well as conservation science concerned with the loss and restoration of functional diversity in a changing world.
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Affiliation(s)
- W Daniel Kissling
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands.
| | - Henrik Balslev
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | | | | | - Bastian Göldel
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | - Jun Ying Lim
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Jens-Christian Svenning
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Bioscience, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
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31
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Speciation in Howea Palms Occurred in Sympatry, Was Preceded by Ancestral Admixture, and Was Associated with Edaphic and Phenological Adaptation. Mol Biol Evol 2019; 36:2682-2697. [DOI: 10.1093/molbev/msz166] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abstract
Howea palms are viewed as one of the most clear-cut cases of speciation in sympatry. The sister species Howea belmoreana and H. forsteriana are endemic to the oceanic Lord Howe Island, Australia, where they have overlapping distributions and are reproductively isolated mainly by flowering time differences. However, the potential role of introgression from Australian mainland relatives had not previously been investigated, a process that has recently put other examples of sympatric speciation into question. Furthermore, the drivers of flowering time-based reproductive isolation remain unclear. We sequenced an RNA-seq data set that comprehensively sampled Howea and their closest mainland relatives (Linospadix, Laccospadix), and collected detailed soil chemistry data on Lord Howe Island to evaluate whether secondary gene flow had taken place and to examine the role of soil preference in speciation. D-statistics analyses strongly support a scenario whereby ancestral Howea hybridized frequently with its mainland relatives, but this only occurred prior to speciation. Expression analysis, population genetic and phylogenetic tests of selection, identified several flowering time genes with evidence of adaptive divergence between the Howea species. We found expression plasticity in flowering time genes in response to soil chemistry as well as adaptive expression and sequence divergence in genes pleiotropically linked to soil adaptation and flowering time. Ancestral hybridization may have provided the genetic diversity that promoted their subsequent adaptive divergence and speciation, a process that may be common for rapid ecological speciation.
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32
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Barrett CF, McKain MR, Sinn BT, Ge XJ, Zhang Y, Antonelli A, Bacon CD. Ancient Polyploidy and Genome Evolution in Palms. Genome Biol Evol 2019; 11:1501-1511. [PMID: 31028709 PMCID: PMC6535811 DOI: 10.1093/gbe/evz092] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2019] [Indexed: 12/23/2022] Open
Abstract
Mechanisms of genome evolution are fundamental to our understanding of adaptation and the generation and maintenance of biodiversity, yet genome dynamics are still poorly characterized in many clades. Strong correlations between variation in genomic attributes and species diversity across the plant tree of life suggest that polyploidy or other mechanisms of genome size change confer selective advantages due to the introduction of genomic novelty. Palms (order Arecales, family Arecaceae) are diverse, widespread, and dominant in tropical ecosystems, yet little is known about genome evolution in this ecologically and economically important clade. Here, we take a phylogenetic comparative approach to investigate palm genome dynamics using genomic and transcriptomic data in combination with a recent, densely sampled, phylogenetic tree. We find conclusive evidence of a paleopolyploid event shared by the ancestor of palms but not with the sister clade, Dasypogonales. We find evidence of incremental chromosome number change in the palms as opposed to one of recurrent polyploidy. We find strong phylogenetic signal in chromosome number, but no signal in genome size, and further no correlation between the two when correcting for phylogenetic relationships. Palms thus add to a growing number of diverse, ecologically successful clades with evidence of whole-genome duplication, sister to a species-poor clade with no evidence of such an event. Disentangling the causes of genome size variation in palms moves us closer to understanding the genomic conditions facilitating adaptive radiation and ecological dominance in an evolutionarily successful, emblematic tropical clade.
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Affiliation(s)
| | | | | | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Yuqu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Royal Botanical Gardens Kew, Richmond, United Kingdom
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
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33
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Onstein RE, Baker WJ, Couvreur TLP, Faurby S, Herrera-Alsina L, Svenning JC, Kissling WD. To adapt or go extinct? The fate of megafaunal palm fruits under past global change. Proc Biol Sci 2019; 285:rspb.2018.0882. [PMID: 29899077 PMCID: PMC6015859 DOI: 10.1098/rspb.2018.0882] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 05/17/2018] [Indexed: 01/03/2023] Open
Abstract
Past global change may have forced animal-dispersed plants with megafaunal fruits to adapt or go extinct, but these processes have remained unexplored at broad spatio-temporal scales. Here, we combine phylogenetic, distributional and fruit size data for more than 2500 palm (Arecaceae) species in a time-slice diversification analysis to quantify how extinction and adaptation have changed over deep time. Our results indicate that extinction rates of palms with megafaunal fruits have increased in the New World since the onset of the Quaternary (2.6 million years ago). In contrast, Old World palms show a Quaternary increase in transition rates towards evolving small fruits from megafaunal fruits. We suggest that Quaternary climate oscillations and concurrent habitat fragmentation and defaunation of megafaunal frugivores in the New World have reduced seed dispersal distances and geographical ranges of palms with megafaunal fruits, resulting in their extinction. The increasing adaptation to smaller fruits in the Old World could reflect selection for seed dispersal by ocean-crossing frugivores (e.g. medium-sized birds and bats) to colonize Indo-Pacific islands against a background of Quaternary sea-level fluctuations. Our macro-evolutionary results suggest that megafaunal fruits are increasingly being lost from tropical ecosystems, either due to extinctions or by adapting to smaller fruit sizes.
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Affiliation(s)
- Renske E Onstein
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94248, 1090 GE Amsterdam, The Netherlands
| | | | | | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden
| | - Leonel Herrera-Alsina
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Jens-Christian Svenning
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Bioscience, Aarhus University, Aarhus, Denmark.,Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - W Daniel Kissling
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94248, 1090 GE Amsterdam, The Netherlands
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34
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Muscarella R, Bacon CD, Faurby S, Antonelli A, Kristiansen SM, Svenning JC, Balslev H. Soil fertility and flood regime are correlated with phylogenetic structure of Amazonian palm communities. ANNALS OF BOTANY 2019; 123:641-655. [PMID: 30395146 PMCID: PMC6417467 DOI: 10.1093/aob/mcy196] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/05/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Identifying the processes that generate and maintain biodiversity requires understanding of how evolutionary processes interact with abiotic conditions to structure communities. Edaphic gradients are strongly associated with floristic patterns but, compared with climatic gradients, have received relatively little attention. We asked (1) How does the phylogenetic composition of palm communities vary along edaphic gradients within major habitat types? and (2) To what extent are phylogenetic patterns determined by (a) habitat specialists, (b) small versus large palms, and (c) hyperdiverse genera? METHODS We paired data on palm community composition from 501 transects of 0.25 ha located in two main habitat types (non-inundated uplands and seasonally inundated floodplains) in western Amazonian rain forests with information on soil chemistry, climate, phylogeny and metrics of plant size. We focused on exchangeable base concentration (cmol+ kg-1) as a metric of soil fertility and a floristic index of inundation intensity. We used a null model approach to quantify the standard effect size of mean phylogenetic distance for each transect (a metric of phylogenetic community composition) and related this value to edaphic variables using generalized linear mixed models, including a term for spatial autocorrelation. KEY RESULTS Overall, we recorded 112 008 individuals belonging to 110 species. Palm communities in non-inundated upland transects (but not floodplain transects) were more phylogenetically clustered in areas of low soil fertility, measured as exchangeable base concentration. In contrast, floodplain transects with more severe flood regimes (as inferred from floristic structure) tended to be phylogenetically clustered. Nearly half of the species recorded (44 %) were upland specialists while 18 % were floodplain specialists. In both habitat types, phylogenetic clustering was largely due to the co-occurrence of small-sized habitat specialists belonging to two hyperdiverse genera (Bactris and Geonoma). CONCLUSIONS Edaphic conditions are associated with the phylogenetic community structure of palms across western Amazonia, and different factors (specifically, soil fertility and inundation intensity) appear to underlie diversity patterns in non-inundated upland versus floodplain habitats. By linking edaphic gradients with palm community phylogenetic structure, our study reinforces the need to integrate edaphic conditions in eco-evolutionary studies in order to better understand the processes that generate and maintain tropical forest diversity. Our results suggest a role for edaphic niche conservatism in the evolution and distribution of Amazonian palms, a finding with potential relevance for other clades.
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Affiliation(s)
- Robert Muscarella
- Department of Bioscience, Section for Ecoinformatics & Biodiversity, Aarhus University, Aarhus, Denmark
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Gothenburg Botanical Garden, Gothenburg, Sweden
| | | | - Jens-Christian Svenning
- Department of Bioscience, Section for Ecoinformatics & Biodiversity, Aarhus University, Aarhus, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Aarhus University, Aarhus, Denmark
| | - Henrik Balslev
- Department of Bioscience, Section for Ecoinformatics & Biodiversity, Aarhus University, Aarhus, Denmark
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35
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Pichardo-Marcano FJ, Nieto-Blázquez ME, MacDonald AN, Galeano G, Roncal J. Phylogeny, historical biogeography and diversification rates in an economically important group of Neotropical palms: Tribe Euterpeae. Mol Phylogenet Evol 2018; 133:67-81. [PMID: 30594734 DOI: 10.1016/j.ympev.2018.12.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 01/23/2023]
Abstract
Tribe Euterpeae is an economically and ecologically important group of Neotropical palms (Arecaceae). Some species are hyperdominant in the Neotropics, and many constitute a good source of revenue. To reconstruct the biogeographical history and diversification of the Euterpeae, we inferred a robust dated molecular phylogenetic hypothesis including 82% of the species sequenced for five DNA regions (trnD-trnT, CISP4, WRKY6, RPB2, and PHYB). Ancestral range was estimated using all models available in BioGeoBEARS and Binary State Speciation and Extinction analysis was used to evaluate the association of biome and inflorescence type with diversification rates. All intergeneric relationships were resolved providing insight on the taxonomic controversy of Jessenia, Euterpe and Prestoea. Three widely distributed Neotropical species were non-monophyletic, inviting a revision of species circumscriptions. The Euterpeae started its diversification in the mid Eocene (40 Mya), with most species-level divergence events occurring in the last 10 million years. Four colonization events from Central to South America were inferred. Different diversification rates were associated with biomes. Lowland rainforest was inferred as the ancestral biome of Euterpeae, attesting to the importance of lowland adapted lineages on the assembly of the montane flora. The two-fold higher speciation rate for montane taxa (compared with lowland rainforest taxa) was contemporaneous to the Andean orogenic uplift. The specialized beetle pollination of Oenocarpus with its hippuriform (horsetail shape) inflorescence was not associated with diversification rates in Euterpeae.
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Affiliation(s)
- Fritz José Pichardo-Marcano
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL A1B3X9, Canada.
| | - María Esther Nieto-Blázquez
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL A1B3X9, Canada.
| | - Ashley Nicolle MacDonald
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL A1B3X9, Canada.
| | - Gloria Galeano
- Universidad Nacional de Colombia, Instituto de Ciencias Naturales, Apartado 7495, Bogotá, Colombia
| | - Julissa Roncal
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL A1B3X9, Canada.
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36
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de La Harpe M, Hess J, Loiseau O, Salamin N, Lexer C, Paris M. A dedicated target capture approach reveals variable genetic markers across micro‐ and macro‐evolutionary time scales in palms. Mol Ecol Resour 2018; 19:221-234. [DOI: 10.1111/1755-0998.12945] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 08/15/2018] [Accepted: 08/28/2018] [Indexed: 11/29/2022]
Affiliation(s)
| | - Jaqueline Hess
- Department of Botany and Biodiversity Research University of Vienna Vienna Austria
| | - Oriane Loiseau
- Department of Computational Biology, Biophore University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, Biophore University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Christian Lexer
- Department of Botany and Biodiversity Research University of Vienna Vienna Austria
| | - Margot Paris
- Department of Biology, Unit Ecology and Evolution University of Fribourg Fribourg Switzerland
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37
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de Santana Lopes A, Gomes Pacheco T, Nimz T, do Nascimento Vieira L, Guerra MP, Nodari RO, de Souza EM, de Oliveira Pedrosa F, Rogalski M. The complete plastome of macaw palm [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] and extensive molecular analyses of the evolution of plastid genes in Arecaceae. PLANTA 2018; 247:1011-1030. [PMID: 29340796 DOI: 10.1007/s00425-018-2841-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/10/2018] [Indexed: 05/08/2023]
Abstract
The plastome of macaw palm was sequenced allowing analyses of evolution and molecular markers. Additionally, we demonstrated that more than half of plastid protein-coding genes in Arecaceae underwent positive selection. Macaw palm is a native species from tropical and subtropical Americas. It shows high production of oil per hectare reaching up to 70% of oil content in fruits and an interesting plasticity to grow in different ecosystems. Its domestication and breeding are still in the beginning, which makes the development of molecular markers essential to assess natural populations and germplasm collections. Therefore, we sequenced and characterized in detail the plastome of macaw palm. A total of 221 SSR loci were identified in the plastome of macaw palm. Additionally, eight polymorphism hotspots were characterized at level of subfamily and tribe. Moreover, several events of gain and loss of RNA editing sites were found within the subfamily Arecoideae. Aiming to uncover evolutionary events in Arecaceae, we also analyzed extensively the evolution of plastid genes. The analyses show that highly divergent genes seem to evolve in a species-specific manner, suggesting that gene degeneration events may be occurring within Arecaceae at the level of genus or species. Unexpectedly, we found that more than half of plastid protein-coding genes are under positive selection, including genes for photosynthesis, gene expression machinery and other essential plastid functions. Furthermore, we performed a phylogenomic analysis using whole plastomes of 40 taxa, representing all subfamilies of Arecaceae, which placed the macaw palm within the tribe Cocoseae. Finally, the data showed here are important for genetic studies in macaw palm and provide new insights into the evolution of plastid genes and environmental adaptation in Arecaceae.
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Affiliation(s)
- Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Tabea Nimz
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Miguel P Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens O Nodari
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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38
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Antonelli A, Hettling H, Condamine FL, Vos K, Nilsson RH, Sanderson MJ, Sauquet H, Scharn R, Silvestro D, Töpel M, Bacon CD, Oxelman B, Vos RA. Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa. Syst Biol 2018; 66:152-166. [PMID: 27616324 PMCID: PMC5410925 DOI: 10.1093/sysbio/syw066] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 07/19/2016] [Indexed: 01/06/2023] Open
Abstract
Rapidly growing biological data—including molecular sequences and fossils—hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a “Dated Tree of Life” where all node ages are directly comparable.
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Affiliation(s)
- Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.,Gothenburg Botanical Garden, Carl Skottsbergs Gata 22A, SE-41319 Göteborg, Sweden
| | - Hannes Hettling
- Naturalis Biodiversity Center, Darwinweg 4, 2333 CR Leiden, The Netherlands
| | - Fabien L Condamine
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.,CNRS, UMR 5554 Institut des Sciences de l'Evolution (Université de Montpellier), Place Eugéne Bataillon, 34095 Montpellier, France
| | - Karin Vos
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden
| | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell, Tucson, AZ 85721, USA
| | - Hervé Sauquet
- Université Paris-Sud, Laboratoire Écologie, Systématique, Évolution, CNRS UMR 8079, 91405 Orsay, France
| | - Ruud Scharn
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.,Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Mats Töpel
- Swedish Bioinformatics Infrastructure for Life Sciences, Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden.,Department of Marine Sciences, University of Gothenburg, Box 460, SE-405 30 Göteborg, Sweden
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden
| | - Rutger A Vos
- Naturalis Biodiversity Center, Darwinweg 4, 2333 CR Leiden, The Netherlands
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39
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Onstein RE, Baker WJ, Couvreur TLP, Faurby S, Svenning JC, Kissling WD. Frugivory-related traits promote speciation of tropical palms. Nat Ecol Evol 2017; 1:1903-1911. [PMID: 29062122 DOI: 10.1038/s41559-017-0348-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/19/2017] [Indexed: 01/15/2023]
Abstract
Animal-mediated seed dispersal by frugivorous birds and mammals is central to the ecology and functioning of ecosystems, but whether and how frugivory-related traits have affected plant speciation remains little explored. Fruit size is directly linked to plant dispersal capacity and therefore influences gene flow and genetic divergence of plant populations. Using a global species-level phylogeny with comprehensive data on fruit sizes and plant species distributions, we test whether fruit size has affected speciation rates of palms (Arecaceae), a plant family characteristic of tropical rainforests. Globally, the results reveal that palms with small fruit sizes have increased speciation rates compared with those with large (megafaunal) fruits. Speciation of small-fruited palms is particularly high in the understory of tropical rainforests in the New World, and on islands in the Old World. This suggests that frugivory-related traits in combination with geography and the movement behaviour of frugivores can influence the speciation of fleshy-fruited plants.
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Affiliation(s)
- Renske E Onstein
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94248, Amsterdam, 1090 GE, The Netherlands.
| | | | | | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE 405 30, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE 405 30, Göteborg, Sweden
| | - Jens-Christian Svenning
- Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, Aarhus C, DK-8000, Denmark
| | - W Daniel Kissling
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94248, Amsterdam, 1090 GE, The Netherlands.
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40
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Eiserhardt WL, Couvreur TLP, Baker WJ. Plant phylogeny as a window on the evolution of hyperdiversity in the tropical rainforest biome. THE NEW PHYTOLOGIST 2017; 214:1408-1422. [PMID: 28277624 DOI: 10.1111/nph.14516] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 01/29/2017] [Indexed: 06/06/2023]
Abstract
I. II. III. IV. V. VI. VII. VIII. IX. References SUMMARY: Tropical rainforest (TRF) is the most species-rich terrestrial biome on Earth, harbouring just under half of the world's plant species in c. 7% of the land surface. Phylogenetic trees provide important insights into mechanisms underpinning TRF hyperdiversity that are complementary to those obtained from the fossil record. Phylogenetic studies of TRF plant diversity have mainly focused on whether this biome is an evolutionary 'cradle' or 'museum', emphasizing speciation and extinction rates. However, other explanations, such as biome age, immigration and ecological limits, must also be considered. We present a conceptual framework for addressing the drivers of TRF diversity, and review plant studies that have tested them with phylogenetic data. Although surprisingly few in number, these studies point to old age of TRF, low extinction and high speciation rates as credible drivers of TRF hyperdiversity. There is less evidence for immigration and ecological limits, but these cannot be dismissed owing to the limited number of studies. Rapid methodological developments in DNA sequencing, macroevolutionary analysis and the integration of phylogenetics with other disciplines may improve our grasp of TRF hyperdiversity in the future. However, such advances are critically dependent on fundamental systematic research, yielding numerous, additional, well-sampled phylogenies of TRF lineages.
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Affiliation(s)
| | - Thomas L P Couvreur
- Institut de Recherche pour le Développement (IRD), UMR DIADE, F-34394, Montpellier, France
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41
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Cámara-Leret R, Faurby S, Macía MJ, Balslev H, Göldel B, Svenning JC, Kissling WD, Rønsted N, Saslis-Lagoudakis CH. Fundamental species traits explain provisioning services of tropical American palms. NATURE PLANTS 2017; 3:16220. [PMID: 28112717 DOI: 10.1038/nplants.2016.220] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/15/2016] [Indexed: 05/21/2023]
Abstract
The well-being of the global human population rests on provisioning services delivered by 12% of the Earth's ∼400,000 plant species1. Plant utilization by humans is influenced by species traits2-4, but it is not well understood which traits underpin different human needs5. Here, we focus on palms (Arecaceae), one of the most economically important plant groups globally6, and demonstrate that provisioning services related to basic needs, such as food and medicine, show a strong link to fundamental functional and geographic traits. We integrate data from 2,201 interviews on plant utilization from three biomes in South America-spanning 68 communities, 43 ethnic groups and 2,221 plant uses-with a dataset of 4 traits (leaf length, stem volume, fruit volume, geographic range size) and a species-level phylogeny7. For all 208 palm species occurring in our study area, we test for relations between their traits and perceived value. We find that people preferentially use large, widespread species rather than small, narrow-ranged species, and that different traits are linked to different uses. Further, plant size and geographic range size are stronger predictors of ecosystem service realization for palm services related to basic human needs than less-basic needs (for example, ritual). These findings suggest that reliance on plant size and availability may have prevented our optimal realization of wild-plant services, since ecologically rare yet functionally important (for example, chemically) clades may have been overlooked. Beyond expanding our understanding of how local people use biodiversity in mega-diverse regions, our trait- and phylogeny-based approach helps to understand the processes that underpin ecosystem service realization, a necessary step to meet societal needs in a changing world with a growing human population5,8.
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Affiliation(s)
- Rodrigo Cámara-Leret
- Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Søren Faurby
- Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, CSIC, Calle José Gutiérrez Abascal 2, 28006 Madrid, Spain
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE 405 30 Göteborg, Sweden
| | - Manuel J Macía
- Departamento de Biología, Área de Botánica, Universidad Autónoma de Madrid, Calle Darwin 2, 28049 Madrid, Spain
| | - Henrik Balslev
- Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Bastian Göldel
- Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Jens-Christian Svenning
- Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - W Daniel Kissling
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94248, 1090 GE Amsterdam, The Netherlands
| | - Nina Rønsted
- Evolutionary Genomics Section, Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Sølvgade 83S, 1307 Copenhagen K, Denmark
| | - C Haris Saslis-Lagoudakis
- Evolutionary Genomics Section, Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Sølvgade 83S, 1307 Copenhagen K, Denmark
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