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Forrister DL, Endara MJ, Soule AJ, Younkin GC, Mills AG, Lokvam J, Dexter KG, Pennington RT, Kidner CA, Nicholls JA, Loiseau O, Kursar TA, Coley PD. Diversity and divergence: evolution of secondary metabolism in the tropical tree genus Inga. THE NEW PHYTOLOGIST 2023; 237:631-642. [PMID: 36263711 DOI: 10.1111/nph.18554] [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: 08/17/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Plants are widely recognized as chemical factories, with each species producing dozens to hundreds of unique secondary metabolites. These compounds shape the interactions between plants and their natural enemies. We explore the evolutionary patterns and processes by which plants generate chemical diversity, from evolving novel compounds to unique chemical profiles. We characterized the chemical profile of one-third of the species of tropical rainforest trees in the genus Inga (c. 100, Fabaceae) using ultraperformance liquid chromatography-mass spectrometry-based metabolomics and applied phylogenetic comparative methods to understand the mode of chemical evolution. We show: each Inga species contain structurally unrelated compounds and high levels of phytochemical diversity; closely related species have divergent chemical profiles, with individual compounds, compound classes, and chemical profiles showing little-to-no phylogenetic signal; at the evolutionary time scale, a species' chemical profile shows a signature of divergent adaptation. At the ecological time scale, sympatric species were the most divergent, implying it is also advantageous to maintain a unique chemical profile from community members; finally, we integrate these patterns with a model for how chemical diversity evolves. Taken together, these results show that phytochemical diversity and divergence are fundamental to the ecology and evolution of plants.
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Affiliation(s)
- Dale L Forrister
- School of Biological Sciences, University of Utah, Aline W. Skaggs Biology Building, 257 S 1400 E, Salt Lake City, UT, 84112-0840, USA
| | - María-José Endara
- School of Biological Sciences, University of Utah, Aline W. Skaggs Biology Building, 257 S 1400 E, Salt Lake City, UT, 84112-0840, USA
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud-BIOMAS - Universidad de las Américas, 170513, Quito, Ecuador
| | - Abrianna J Soule
- School of Biological Sciences, University of Utah, Aline W. Skaggs Biology Building, 257 S 1400 E, Salt Lake City, UT, 84112-0840, USA
| | - Gordon C Younkin
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Anthony G Mills
- School of Biological Sciences, University of Utah, Aline W. Skaggs Biology Building, 257 S 1400 E, Salt Lake City, UT, 84112-0840, USA
| | - John Lokvam
- School of Biological Sciences, University of Utah, Aline W. Skaggs Biology Building, 257 S 1400 E, Salt Lake City, UT, 84112-0840, USA
| | - Kyle G Dexter
- School of Geosciences, University of Edinburgh, Old College, South Bridge, Edinburgh, EH8 9YL, UK
| | - R Toby Pennington
- Department of Geography, University of Exeter, Laver Building, North Park Road, Exeter, EX4 4QE, UK
| | - Catherine A Kidner
- School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3JW, UK
- Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR, UK
| | - James A Nicholls
- The Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian National Insect Collection (ANIC), Building 101, Clunies Ross Street, Black Mountain, ACT, 2601, Australia
| | - Oriane Loiseau
- School of Geosciences, University of Edinburgh, Old College, South Bridge, Edinburgh, EH8 9YL, UK
| | - Thomas A Kursar
- School of Biological Sciences, University of Utah, Aline W. Skaggs Biology Building, 257 S 1400 E, Salt Lake City, UT, 84112-0840, USA
| | - Phyllis D Coley
- School of Biological Sciences, University of Utah, Aline W. Skaggs Biology Building, 257 S 1400 E, Salt Lake City, UT, 84112-0840, USA
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Guevara Andino JE, Hernández C, Valencia R, Forrister D, Endara MJ. Accelerating the discovery of rare tree species in Amazonian forests: integrating long monitoring tree plot data with metabolomics and phylogenetics for the description of a new species in the hyperdiverse genus Inga Mill. PeerJ 2022; 10:e13767. [PMID: 36061752 PMCID: PMC9435521 DOI: 10.7717/peerj.13767] [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: 03/24/2022] [Accepted: 06/30/2022] [Indexed: 01/17/2023] Open
Abstract
In species-rich regions and highly speciose genera, the need for species identification and taxonomic recognition has led to the development of emergent technologies. Here, we combine long-term plot data with untargated metabolomics, and morphological and phylogenetic data to describe a new rare species in the hyperdiverse genus of trees Inga Mill. Our combined data show that Inga coleyana is a new lineage splitting from their closest relatives I. coruscans and I. cylindrica. Moreover, analyses of the chemical defensive profile demonstrate that I. coleyana has a very distinctive chemistry from their closest relatives, with I. coleyana having a chemistry based on saponins and I. cylindrica and I. coruscans producing a series of dihydroflavonols in addition to saponins. Finally, data from our network of plots suggest that I. coleyana is a rare and probably endemic taxon in the hyper-diverse genus Inga. Thus, the synergy produced by different approaches, such as long-term plot data and metabolomics, could accelerate taxonomic recognition in challenging tropical biomes.
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Affiliation(s)
- Juan Ernesto Guevara Andino
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud-BIOMAS, Universidad de las Americas, Quito, Ecuador
| | - Consuelo Hernández
- Laboratorio de Ecología de Plantas. Herbario QCA, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Renato Valencia
- Laboratorio de Ecología de Plantas. Herbario QCA, Escuela de Ciencias Biológicas,, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Dale Forrister
- Department of Biology, University of Utah, Salt Lake City, United States of America,Estación de Biodiversidad Tiputini, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito—USFQ, Quito, Ecuador
| | - María-José Endara
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud-BIOMAS, Universidad de las Americas, Quito, Ecuador
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Fine PVA, Salazar D, Martin RE, Metz MR, Misiewicz TM, Asner GP. Exploring the links between secondary metabolites and leaf spectral reflectance in a diverse genus of Amazonian trees. Ecosphere 2021. [DOI: 10.1002/ecs2.3362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Paul V. A. Fine
- Department of Integrative Biology and Jepson and University Herbaria University of California, Berkeley 3040 Valley Life Sciences Building #3140 Berkeley California94720USA
| | - Diego Salazar
- Department of Biological Sciences, Institute of the Environment, and International Center for Tropical Botany Florida International University 11200 S.W. 8th Street Miami Florida33199USA
| | - Roberta E. Martin
- School of Geographical Sciences and Urban Planning Arizona State University P.O. Box 875302 Tempe Arizona85287USA
- Center for Global Discovery and Conservation Science Arizona State University Tempe Arizona85287USA
| | - Margaret R. Metz
- Department of Biology Lewis & Clark College 615 S Palatine Hill Rd Portland Oregon97219USA
| | - Tracy M. Misiewicz
- Department of Integrative Biology and Jepson and University Herbaria University of California, Berkeley 3040 Valley Life Sciences Building #3140 Berkeley California94720USA
| | - Gregory P. Asner
- School of Geographical Sciences and Urban Planning Arizona State University P.O. Box 875302 Tempe Arizona85287USA
- Center for Global Discovery and Conservation Science Arizona State University Tempe Arizona85287USA
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Wang C, Zhang Y, Ding H, Song M, Yin J, Yu H, Li Z, Han L, Zhang Z. Authentication of Zingiber Species Based on Analysis of Metabolite Profiles. FRONTIERS IN PLANT SCIENCE 2021; 12:705446. [PMID: 34880881 PMCID: PMC8647842 DOI: 10.3389/fpls.2021.705446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/11/2021] [Indexed: 05/10/2023]
Abstract
Zingiber corallinum and Zingiber montanum, which belong to the Zingiberaceae family, are traditional Chinese folk medicinal herbs in Guizhou and Yunnan Province of China. They share great similarities in morphology, chemical constituent, and DNA barcoding sequence. The taxonomy of the two Zingiber species is controversial and discrimination of traditional Chinese medicines directly affects the pharmacological and clinical effects. In the present study, we performed a systemic analysis of "super-barcode" and untargeted metabolomics between Z. corallinum and Z. montanum using chloroplast (cp) genome sequencing and gas chromatography-mass spectrometry (GC-MS) analysis. Comparison and phylogenetic analysis of cp genomes of the two Zingiber species showed that the cp genome could not guarantee the accuracy of identification. An untargeted metabolomics strategy combining GC-MS with chemometric methods was proposed to distinguish the Zingiber samples of known variety. A total of 51 volatile compounds extracted from Z. corallinum and Z. montanum were identified, and nine compounds were selected as candidate metabolic markers to reveal the significant difference between Z. corallinum and Z. montanum. The performance of the untargeted metabolomic approach was verified with unknown Zingiber samples. Although the cp genomes could not be used to identify Zingiber species in this study, it will still provide a valuable genomics resource for population studies in the Zingiberaceae family, and the GC-MS based metabolic fingerprint is more promising for species identification and safe application of Z. corallinum and Z. montanum.
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Affiliation(s)
- Chenxi Wang
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yue Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong, China
| | - Hui Ding
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Meifang Song
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong, China
| | - Jiaxin Yin
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Heshui Yu
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zheng Li
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lifeng Han
- Tianjin State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhonglian Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong, China
- *Correspondence: Zhonglian Zhang,
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Draper FC, Baker TR, Baraloto C, Chave J, Costa F, Martin RE, Pennington RT, Vicentini A, Asner GP. Quantifying Tropical Plant Diversity Requires an Integrated Technological Approach. Trends Ecol Evol 2020; 35:1100-1109. [PMID: 32912632 DOI: 10.1016/j.tree.2020.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/04/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022]
Abstract
Tropical biomes are the most diverse plant communities on Earth, and quantifying this diversity at large spatial scales is vital for many purposes. As macroecological approaches proliferate, the taxonomic uncertainties in species occurrence data are easily neglected and can lead to spurious findings in downstream analyses. Here, we argue that technological approaches offer potential solutions, but there is no single silver bullet to resolve uncertainty in plant biodiversity quantification. Instead, we propose the use of artificial intelligence (AI) approaches to build a data-driven framework that integrates several data sources - including spectroscopy, DNA sequences, image recognition, and morphological data. Such a framework would provide a foundation for improving species identification in macroecological analyses while simultaneously improving the taxonomic process of species delimitation.
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Affiliation(s)
- Frederick C Draper
- Center for Global Discovery and Conservation Science, Arizona State University, Tempe, AZ, USA; School of Geography, University of Leeds, Leeds, UK.
| | | | - Christopher Baraloto
- Institute of Environment, Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Jerome Chave
- Laboratoire Evolution et Diversité Biologique (EDB) CNRS/UPS, Toulouse, France
| | - Flavia Costa
- Instituto Nacional de Pesquisas da Amazônia - INPA, Manaus, Brazil
| | - Roberta E Martin
- Center for Global Discovery and Conservation Science, Arizona State University, Tempe, AZ, USA
| | - R Toby Pennington
- Department of Geography, University of Exeter, Exeter, UK; Royal Botanic Garden, Edinburgh, UK
| | | | - Gregory P Asner
- Center for Global Discovery and Conservation Science, Arizona State University, Tempe, AZ, USA
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Forrister DL, Endara MJ, Younkin GC, Coley PD, Kursar TA. Herbivores as drivers of negative density dependence in tropical forest saplings. Science 2019; 363:1213-1216. [PMID: 30872524 DOI: 10.1126/science.aau9460] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 02/19/2019] [Indexed: 01/25/2023]
Abstract
Ecological theory predicts that the high local diversity observed in tropical forests is maintained by negative density-dependent interactions within and between closely related plant species. By using long-term data on tree growth and survival for coexisting Inga (Fabaceae, Mimosoideae) congeners, we tested two mechanisms thought to underlie negative density dependence (NDD): competition for resources and attack by herbivores. We quantified the similarity of neighbors in terms of key ecological traits that mediate these interactions, as well as the similarity of herbivore communities. We show that phytochemical similarity and shared herbivore communities are associated with decreased growth and survival at the sapling stage, a key bottleneck in the life cycle of tropical trees. None of the traits associated with resource acquisition affect plant performance, indicating that competition between neighbors may not shape local tree diversity. These results suggest that herbivore pressure is the primary mechanism driving NDD at the sapling stage.
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Affiliation(s)
- Dale L Forrister
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA.
| | - María-José Endara
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA.,Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos. Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Quito, Ecuador
| | - Gordon C Younkin
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Phyllis D Coley
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA.,Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panamá
| | - Thomas A Kursar
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA.,Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panamá
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7
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Godschalx AL, Rodríguez-Castañeda G, Rasmann S. Contribution of different predator guilds to tritrophic interactions along ecological clines. CURRENT OPINION IN INSECT SCIENCE 2019; 32:104-109. [PMID: 31113621 DOI: 10.1016/j.cois.2019.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/19/2018] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
The strengths of interactions between plants, herbivores, and predators are predicted to relax with elevation. Despite the fundamental role predators play in tritrophic interactions, high-resolution experimental evidence describing predation across habitat gradients is still scarce in the literature and varies by predator. With this opinion paper, we look at how tritrophic strength of systems including different vertebrate and invertebrate predator guilds changes with elevation. Specifically, we focus on how birds, ants, parasitoids, and nematodes exert top-down pressure as predators and propose ways, in which each group could be better understood through elevational gradient studies. We hope to enrich future perspectives for disentangling the different biotic and abiotic factors underlying predator-mediated trophic interactions in a diversity of habitats.
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Affiliation(s)
- Adrienne L Godschalx
- Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | | | - Sergio Rasmann
- Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.
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Vleminckx J, Salazar D, Fortunel C, Mesones I, Dávila N, Lokvam J, Beckley K, Baraloto C, Fine PVA. Divergent Secondary Metabolites and Habitat Filtering Both Contribute to Tree Species Coexistence in the Peruvian Amazon. FRONTIERS IN PLANT SCIENCE 2018; 9:836. [PMID: 29971085 PMCID: PMC6018647 DOI: 10.3389/fpls.2018.00836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
Little is known about the mechanisms promoting or limiting the coexistence of functionally divergent species in hyperdiverse tropical tree genera. Density-dependent enemy attacks have been proposed to be a major driver for the local coexistence of chemically divergent congeneric species. At the same time, we expect local soil conditions to favor the coexistence of species sharing similar functional traits related to resource use strategies, while environmental heterogeneity would promote the diversity of these traits at both local and large spatial scales. To test how these traits mediate species coexistence, we used functional trait data for 29 species from the tree genus Protium (Burseraceae), collected in 19 plots (2 ha each) in the Peruvian Amazon. We characterized the presence-absence of 189 plant secondary metabolites (SM) for 27 of these species, and 14 functional traits associated with resource use strategies (RUT) for 16 species. Based on these data, we found that SM were significantly more dissimilar than null expectations for species co-occurring within plots, whereas RUT were significantly more similar. These results were consistent with the hypothesis that density-dependent enemy attacks contribute to the local coexistence of congeneric species displaying divergent chemical defenses, whereas local habitat conditions filter species with similar RUT. Using measurements of nine soil properties in each plot, we also found a significant turnover of RUT traits with increasing dissimilarity of soil texture and nutrient availabilities, providing support for the hypothesis that soil heterogeneity maintains functional diversity at larger spatial scales (from 500 m up to ca. 200 km) in Protium communities. Our study provides new evidence suggesting that density-dependent enemy attacks and soil heterogeneity both contribute to maintaining high species richness in diverse tropical forests.
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Affiliation(s)
- Jason Vleminckx
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Diego Salazar
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Claire Fortunel
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- AMAP (botAnique et Modélisation de l’Architecture des Plantes et des Végétations), IRD, CIRAD, CNRS, INRA, Université de Montpellier, Montpellier, France
| | - Italo Mesones
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Nállarett Dávila
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - John Lokvam
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Krista Beckley
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Christopher Baraloto
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Paul V. A. Fine
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
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