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Wagner ND, Marinček P, Pittet L, Hörandl E. Insights into the Taxonomically Challenging Hexaploid Alpine Shrub Willows of Salix Sections Phylicifoliae and Nigricantes (Salicaceae). PLANTS (BASEL, SWITZERLAND) 2023; 12:1144. [PMID: 36904002 PMCID: PMC10005704 DOI: 10.3390/plants12051144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
The complex genomic composition of allopolyploid plants leads to morphologically diverse species. The traditional taxonomical treatment of the medium-sized, hexaploid shrub willows distributed in the Alps is difficult based on their variable morphological characters. In this study, RAD sequencing data, infrared-spectroscopy, and morphometric data are used to analyze the phylogenetic relationships of the hexaploid species of the sections Nigricantes and Phylicifoliae in a phylogenetic framework of 45 Eurasian Salix species. Both sections comprise local endemics as well as widespread species. Based on the molecular data, the described morphological species appeared as monophyletic lineages (except for S. phylicifolia s.str. and S. bicolor, which are intermingled). Both sections Phylicifoliae and Nigricantes are polyphyletic. Infrared-spectroscopy mostly confirmed the differentiation of hexaploid alpine species. The morphometric data confirmed the molecular results and supported the inclusion of S. bicolor into S. phylicifolia s.l., whereas the alpine endemic S. hegetschweileri is distinct and closely related to species of the section Nigricantes. The genomic structure and co-ancestry analyses of the hexaploid species revealed a geographical pattern for widespread S. myrsinifolia, separating the Scandinavian from the alpine populations. The newly described S. kaptarae is tetraploid and is grouped within S. cinerea. Our data reveal that both sections Phylicifoliae and Nigricantes need to be redefined.
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Buono D, Albach DC. Infrared spectroscopy for ploidy estimation: An example in two species of Veronica using fresh and herbarium specimens. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11516. [PMID: 37051581 PMCID: PMC10083463 DOI: 10.1002/aps3.11516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 12/20/2022] [Indexed: 06/19/2023]
Abstract
PREMISE Polyploidy has become a central factor in plant evolutionary biological research in recent decades. Methods such as flow cytometry have revealed the widespread occurrence of polyploidy; however, its inference relies on expensive lab equipment and is largely restricted to fresh or recently dried material. METHODS Here, we assess the applicability of infrared spectroscopy to infer ploidy in two related species of Veronica (Plantaginaceae). Infrared spectroscopy relies on differences in the absorbance of tissues, which could be affected by primary and secondary metabolites related to polyploidy. We sampled 33 living plants from the greenhouse and 74 herbarium specimens with ploidy known through flow cytometrical measurements and analyzed the resulting spectra using discriminant analysis of principal components (DAPC) and neural network (NNET) classifiers. RESULTS Living material of both species combined was classified with 70% (DAPC) to 75% (NNET) accuracy, whereas herbarium material was classified with 84% (DAPC) to 85% (NNET) accuracy. Analyzing both species separately resulted in less clear results. DISCUSSION Infrared spectroscopy is quite reliable but is not a certain method for assessing intraspecific ploidy level differences in two species of Veronica. More accurate inferences rely on large training data sets and herbarium material. This study demonstrates an important way to expand the field of polyploid research to herbaria.
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Affiliation(s)
- Daniele Buono
- AG Plant Biodiversity and EvolutionCarl von Ossietzky UniversityAmmerlaender Heerstrasse 114‐11826129OldenburgGermany
- Institute of BotanyTechnical University of DresdenObergraben 601097DresdenGermany
- Present address:
Systematik, Biodiversität und Evolution der PflanzenLudwig‐Maximilians‐UniversityMenzinger Str. 6780638MunichGermany
| | - Dirk C. Albach
- AG Plant Biodiversity and EvolutionCarl von Ossietzky UniversityAmmerlaender Heerstrasse 114‐11826129OldenburgGermany
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3
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Falcioni R, Moriwaki T, Gibin MS, Vollmann A, Pattaro MC, Giacomelli ME, Sato F, Nanni MR, Antunes WC. Classification and Prediction by Pigment Content in Lettuce ( Lactuca sativa L.) Varieties Using Machine Learning and ATR-FTIR Spectroscopy. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11243413. [PMID: 36559526 PMCID: PMC9783279 DOI: 10.3390/plants11243413] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 05/14/2023]
Abstract
Green or purple lettuce varieties produce many secondary metabolites, such as chlorophylls, carotenoids, anthocyanins, flavonoids, and phenolic compounds, which is an emergent search in the field of biomolecule research. The main objective of this study was to use multivariate and machine learning algorithms on Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR)-based spectra to classify, predict, and categorize chemometric attributes. The cluster heatmap showed the highest efficiency in grouping similar lettuce varieties based on pigment profiles. The relationship among pigments was more significant than the absolute contents. Other results allow classification based on ATR-FTIR fingerprints of inflections associated with structural and chemical components present in lettuce, obtaining high accuracy and precision (>97%) by using principal component analysis and discriminant analysis (PCA-LDA)-associated linear LDA and SVM machine learning algorithms. In addition, PLSR models were capable of predicting Chla, Chlb, Chla+b, Car, AnC, Flv, and Phe contents, with R2P and RPDP values considered very good (0.81−0.88) for Car, Anc, and Flv and excellent (0.91−0.93) for Phe. According to the RPDP metric, the models were considered excellent (>2.10) for all variables estimated. Thus, this research shows the potential of machine learning solutions for ATR-FTIR spectroscopy analysis to classify, estimate, and characterize the biomolecules associated with secondary metabolites in lettuce.
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Affiliation(s)
- Renan Falcioni
- Plant Ecophysiology Laboratory, Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
- Correspondence: ; Tel.: +55-44-3011-8940
| | - Thaise Moriwaki
- Plant Ecophysiology Laboratory, Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Mariana Sversut Gibin
- Optical Spectroscopy and Thermophysical Properties Research Group, Graduate Program in Physics, Department of Physics, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Alessandra Vollmann
- Plant Ecophysiology Laboratory, Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Mariana Carmona Pattaro
- Plant Ecophysiology Laboratory, Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Marina Ellen Giacomelli
- Plant Ecophysiology Laboratory, Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Francielle Sato
- Optical Spectroscopy and Thermophysical Properties Research Group, Graduate Program in Physics, Department of Physics, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Marcos Rafael Nanni
- Plant Ecophysiology Laboratory, Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Werner Camargos Antunes
- Plant Ecophysiology Laboratory, Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
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4
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Kothari S, Beauchamp‐Rioux R, Laliberté E, Cavender‐Bares J. Reflectance spectroscopy allows rapid, accurate and non‐destructive estimates of functional traits from pressed leaves. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shan Kothari
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
- Institut de recherche en biologie végétale, Département de sciences biologiques Université de Montréal Montréal QC Canada
| | - Rosalie Beauchamp‐Rioux
- Institut de recherche en biologie végétale, Département de sciences biologiques Université de Montréal Montréal QC Canada
| | - Etienne Laliberté
- Institut de recherche en biologie végétale, Département de sciences biologiques Université de Montréal Montréal QC Canada
| | - Jeannine Cavender‐Bares
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
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Gaem PH, Lucas E, Andrade A, Vicentini A, Mazine FF. A taxonomic account of Myrcia (Myrtaceae) at the sites of the Biological Dynamics of Forest Fragments Project, Amazonas, Brazil. RODRIGUÉSIA 2022. [DOI: 10.1590/2175-7860202273038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract Myrcia is the sole genus of the Myrciinae, one of the nine subtribes of Myrteae (Myrtaceae). The Amazon forest holds about one-quarter of the Brazilian species of Myrcia, but the genus is still understudied in this whole region. In this context, this study presents a floristic survey of Myrcia in the permanent plots of the Biological Dynamics of Forest Fragments Project (BDFFP), in Amazonas state, Brazil. The genus is represented by 36 species in the study area, comprehending 32% of its total richness in the Brazilian Amazon forest, with 19 of them endemic to this domain. Myrcia neospeciosa is reported as a new occurrence for Amazonas state and M. grandis is recorded for the first time from upland terra firme forests on clayish soils. Myrcia cuspidata, a species with calyptrate flowers, is classified under Myrcia sect. Aulomyrcia, representing the second taxon of the genus with this feature removed from Myrcia sect. Calyptranthes. Finally, morphological aspects of the infra-generic categories of Myrcia are reported more overlapping than previously thought. A map containing the location of the study area, an identification key, descriptions, comments, and figures are provided.
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Affiliation(s)
| | - Eve Lucas
- Royal Botanic Gardens, United Kingdom
| | - Ana Andrade
- Instituto Nacional de Pesquisas da Amazônia, Brazil
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6
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Identification of Amaranthus Species Using Visible-Near-Infrared (Vis-NIR) Spectroscopy and Machine Learning Methods. REMOTE SENSING 2021. [DOI: 10.3390/rs13204149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The feasibility of rapid and non-destructive classification of six different Amaranthus species was investigated using visible-near-infrared (Vis-NIR) spectra coupled with chemometric approaches. The focus of this research would be to use a handheld spectrometer in the field to classify six Amaranthus sp. in different geographical regions of South Korea. Spectra were obtained from the adaxial side of the leaves at 1.5 nm intervals in the Vis-NIR spectral range between 400 and 1075 nm. The obtained spectra were assessed with four different preprocessing methods in order to detect the optimum preprocessing method with high classification accuracy. Preprocessed spectra of six Amaranthus sp. were used as input for the machine learning-based chemometric analysis. All the classification results were validated using cross-validation to produce robust estimates of classification accuracies. The different combinations of preprocessing and modeling were shown to have a classification accuracy of between 71% and 99.7% after the cross-validation. The combination of Savitzky-Golay preprocessing and Support vector machine showed a maximum mean classification accuracy of 99.7% for the discrimination of Amaranthus sp. Considering the high number of spectra involved in this study, the growth stage of the plants, varying measurement locations, and the scanning position of leaves on the plant are all important. We conclude that Vis-NIR spectroscopy, in combination with appropriate preprocessing and machine learning methods, may be used in the field to effectively classify Amaranthus sp. for the effective management of the weedy species and/or for monitoring their food applications.
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Khan AL, Al-Harrasi A, Numan M, AbdulKareem NM, Mabood F, Al-Rawahi A. Spectroscopic and Molecular Methods to Differentiate Gender in Immature Date Palm ( Phoenix dactylifera L.). PLANTS (BASEL, SWITZERLAND) 2021; 10:536. [PMID: 33809251 PMCID: PMC8001243 DOI: 10.3390/plants10030536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 11/29/2022]
Abstract
Phoenix dactylifera (date palm) is a well-known nutritious and economically important fruit tree found in arid regions of the Middle East and North Africa. Being diploid, it has extremely high divergence in gender, where sex differentiation in immature date palms (Phoenix dactylifera L.) has remained an enigma in recent years. Herein, new robust infrared (near-infrared reflectance spectroscopy (NIRS) and Fourier transform infrared attenuated total reflectance (FTIR/ATR)) and nuclear magnetic resonance (NMR) spectroscopy methods coupled with extensive chemometric analysis were used to identify the sex differentiation in immature date palm leaves. NIRS/FTIR reflectance and 1H-NMR profiling suggested that the signals of monosaccharides (glucose and fructose) and/or disaccharides (maltose and sucrose) play key roles in sex differentiation. The three kinds of spectroscopic data were clearly differentiated among known and unknown male and female leaves via principal component and partial least square discriminant analyses. Furthermore, sex-specific genes and molecular markers obtained from the lower halves of LG12 chromosomes showed enhanced transcript accumulation of mPdIRDP52, mPdIRDP50, and PDK101 in females compared with in males. The phylogeny showed that the mPdIRD033, mPdIRD031, and mPdCIR032 markers formed distinctive clades with more than 70% similarity in gender differentiation. The three robust analyses provide an alternative tool to differentiate sex in date palm trees, which offers a solution to the long-standing challenge of dioecism and could enhance in situ tree propagation programs.
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Affiliation(s)
- Abdul Latif Khan
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (A.L.K.); (N.M.A.); (A.A.-R.)
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (A.L.K.); (N.M.A.); (A.A.-R.)
| | - Muhammad Numan
- Department of Biology, University of North Carolina, Greensboro, NC 27402-6170, USA;
| | - Noor Mazin AbdulKareem
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (A.L.K.); (N.M.A.); (A.A.-R.)
| | - Fazal Mabood
- Institute of Chemical Sciences, University of Swat, Khyber Pakhtunkhwa 19200, Pakistan
| | - Ahmed Al-Rawahi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (A.L.K.); (N.M.A.); (A.A.-R.)
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8
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Gaem PH, Lucas E, Andrade A, Vicentini A, Mazine FF. A taxonomic account of Myrcia (Myrtaceae) at the sites of the Biological Dynamics of Forest Fragments Project, Amazonas, Brazil. RODRIGUÉSIA 2021. [DOI: 10.1590/2175-7860202172139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract Myrcia is the sole genus of the Myrciinae, one of the nine subtribes of Myrteae (Myrtaceae). The Amazon forest holds about one-quarter of the Brazilian species of Myrcia, but the genus is still understudied in this whole region. In this context, this study presents a floristic survey of Myrcia in the permanent plots of the Biological Dynamics of Forest Fragments Project (BDFFP), in Amazonas state, Brazil. The genus is represented by 36 species in the study area, comprehending 32% of its total richness in the Brazilian Amazon forest, with 19 of them endemic to this domain. Myrcia neospeciosa is reported as a new occurrence for Amazonas state and M. grandis is recorded for the first time from upland terra firme forests on clayish soils. Myrcia cuspidata, a species with calyptrate flowers, is classified under Myrcia sect. Aulomyrcia, representing the second taxon of the genus with this feature removed from Myrcia sect. Calyptranthes. Finally, morphological aspects of the infra-generic categories of Myrcia are reported more overlapping than previously thought. A map containing the location of the study area, an identification key, descriptions, comments, and figures are provided.
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Affiliation(s)
| | - Eve Lucas
- Royal Botanic Gardens, United Kingdom
| | - Ana Andrade
- Instituto Nacional de Pesquisas da Amazônia, Brazil
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9
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Torralvo K, Magnusson WE, Durgante F. Effectiveness of Fourier transform near‐infrared spectroscopy spectra for species identification of anurans fixed in formaldehyde and conserved in alcohol: A new tool for integrative taxonomy. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kelly Torralvo
- Programa de Pós Graduação em Ecologia Instituto Nacional de Pesquisas da Amazônia Manaus Brasil
| | - William E. Magnusson
- Coordenação de Biodiversidade Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - Flávia Durgante
- Programa de Pós Graduação em Botânica Instituto Nacional de Pesquisas da Amazônia Manaus Brasil
- Institute of Geography and Geoecology Department of Wetland Ecology Karlsruhe Institute for Technology (KIT) Rastatt Germany
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10
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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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11
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Khan AL, Mabood F, Akber F, Ali A, Shahzad R, Al-Harrasi A, Al-Rawahi A, Shinwari ZK, Lee IJ. Endogenous phytohormones of frankincense producing Boswellia sacra tree populations. PLoS One 2018; 13:e0207910. [PMID: 30566477 PMCID: PMC6300221 DOI: 10.1371/journal.pone.0207910] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 11/08/2018] [Indexed: 12/17/2022] Open
Abstract
Boswellia sacra, an endemic tree to Oman, is exposed to man-made incisions for commercial level frankincense production, whereas unsustainable harvesting may lead to population decline. In this case, assessment of endogenous phytohormones (gibberellic acid (GA), indole-acetic acid (IAA), salicylic acid (SA) and kinetin) can help to understand population health and growth dynamics. Hence, it was aimed to devise a robust method using Near-Infrared spectroscopy (NIRS) coupled with multivariate methods for phytohormone analysis of thirteen different populations of B. sacra. NIRS data was recorded in absorption mode (10000-4000 cm-1) to build partial least squares regression model (calibration set 70%). Model was externally cross validated (30%) as a test set to check their prediction ability before the application to quantify the unknown amount of phytohormones in thirteen different populations of B. sacra. The results showed that phytohormonal contents varied significantly, showing a trend of SA>GA/IAA>kinetin across different populations. SA and GA contents were significantly higher in Pop13 (Hasik), followed by Pop2 (Dowkah)-an extreme end of B. sacra tree cover in Dhofar region. A similar trend in the concentration of phytohormones was found when the samples from 13 populations were subjected to advance liquid chromatography mass spectrophotometer and gas chromatograph with selected ion monitor analysis. The current analysis provides alternative tool to assess plant health, which could be important to in situ propagation of tree population as well as monitoring tree population growth dynamics.
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Affiliation(s)
- Abdul Latif Khan
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Fazal Mabood
- Department of Biological Sciences & Chemistry, University of Nizwa, Nizwa, Oman
| | - Fazal Akber
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Amjad Ali
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Raheem Shahzad
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Ahmed Al-Rawahi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | | | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
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12
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Costa FRC, Lang C, Almeida DRA, Castilho CV, Poorter L. Near-infrared spectrometry allows fast and extensive predictions of functional traits from dry leaves and branches. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2018; 28:1157-1167. [PMID: 29768699 DOI: 10.1002/eap.1728] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 02/26/2018] [Accepted: 03/15/2018] [Indexed: 06/08/2023]
Abstract
The linking of individual functional traits to ecosystem processes is the basis for making generalizations in ecology, but the measurement of individual values is laborious and time consuming, preventing large-scale trait mapping. Also, in hyper-diverse systems, errors occur because identification is difficult, and species level values ignore intra-specific variation. To allow extensive trait mapping at the individual level, we evaluated the potential of Fourrier-Transformed Near Infra-Red Spectrometry (FT-NIR) to adequately describe 14 traits that are key for plant carbon, water, and nutrient balance. FT-NIR absorption spectra (1,000-2,500 nm) were obtained from dry leaves and branches of 1,324 trees of 432 species from a hyper-diverse Amazonian forest. FT-NIR spectra were related to measured traits for the same plants using partial least squares regressions. A further 80 plants were collected from a different site to evaluate model applicability across sites. Relative prediction error (RMSErel ) was calculated as the percentage of the trait value range represented by the final model RMSE. The key traits used in most functional trait studies; specific leaf area, leaf dry matter content, wood density and wood dry matter content can be well predicted by the model (R2 = 0.69-0.78, RMSErel = 9-11%), while leaf density, xylem proportion, bark density and bark dry matter content can be moderately well predicted (R2 = 0.53-0.61, RMSErel = 14-17%). Community-weighted means of all traits were well estimated with NIR, as did the shape of the frequency distribution of the community values for the above key traits. The model developed at the core site provided good estimations of the key traits of a different site. An evaluation of the sampling effort indicated that 400 or less individuals may be sufficient for establishing a good local model. We conclude that FT-NIR is an easy, fast and cheap method for the large-scale estimation of individual plant traits that was previously impossible. The ability to use dry intact leaves and branches unlocks the potential for using herbarium material to estimate functional traits; thus advancing our knowledge of community and ecosystem functioning from local to global scales.
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Affiliation(s)
- Flávia R C Costa
- Coordenação de Pesquisa em Biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Carla Lang
- Coordenação de Pesquisa em Biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Danilo R A Almeida
- USP/ESALQ, University of São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil
| | | | - Lourens Poorter
- Forest Ecology and Forest Management Group, Wageningen University, P.O. Box 47, 6700 AA, Wageningen, The Netherlands
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13
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Endara MJ, Coley PD, Wiggins NL, Forrister DL, Younkin GC, Nicholls JA, Pennington RT, Dexter KG, Kidner CA, Stone GN, Kursar TA. Chemocoding as an identification tool where morphological- and DNA-based methods fall short: Inga as a case study. THE NEW PHYTOLOGIST 2018; 218:847-858. [PMID: 29436716 DOI: 10.1111/nph.15020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/04/2018] [Indexed: 05/12/2023]
Abstract
The need for species identification and taxonomic discovery has led to the development of innovative technologies for large-scale plant identification. DNA barcoding has been useful, but fails to distinguish among many species in species-rich plant genera, particularly in tropical regions. Here, we show that chemical fingerprinting, or 'chemocoding', has great potential for plant identification in challenging tropical biomes. Using untargeted metabolomics in combination with multivariate analysis, we constructed species-level fingerprints, which we define as chemocoding. We evaluated the utility of chemocoding with species that were defined morphologically and subject to next-generation DNA sequencing in the diverse and recently radiated neotropical genus Inga (Leguminosae), both at single study sites and across broad geographic scales. Our results show that chemocoding is a robust method for distinguishing morphologically similar species at a single site and for identifying widespread species across continental-scale ranges. Given that species are the fundamental unit of analysis for conservation and biodiversity research, the development of accurate identification methods is essential. We suggest that chemocoding will be a valuable additional source of data for a quick identification of plants, especially for groups where other methods fall short.
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Affiliation(s)
- María-José Endara
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, 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, EC170103, Ecuador
| | - Phyllis D Coley
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Ancón, Republic of Panamá
| | - Natasha L Wiggins
- School of Biological Sciences, University of Tasmania, Sandy Bay, TAS, 7001, Australia
| | - Dale L Forrister
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
| | - Gordon C Younkin
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
| | - James A Nicholls
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JY, UK
| | | | - Kyle G Dexter
- Royal Botanic Garden Edinburgh, Edinburgh, EH3 5LR, UK
- School of GeoSciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Catherine A Kidner
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JY, UK
- Royal Botanic Garden Edinburgh, Edinburgh, EH3 5LR, UK
| | - Graham N Stone
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JY, UK
| | - Thomas A Kursar
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Ancón, Republic of Panamá
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14
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Wu J, Chavana-Bryant C, Prohaska N, Serbin SP, Guan K, Albert LP, Yang X, van Leeuwen WJD, Garnello AJ, Martins G, Malhi Y, Gerard F, Oliviera RC, Saleska SR. Convergence in relationships between leaf traits, spectra and age across diverse canopy environments and two contrasting tropical forests. THE NEW PHYTOLOGIST 2017; 214:1033-1048. [PMID: 27381054 DOI: 10.1111/nph.14051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 05/03/2016] [Indexed: 06/06/2023]
Abstract
Leaf age structures the phenology and development of plants, as well as the evolution of leaf traits over life histories. However, a general method for efficiently estimating leaf age across forests and canopy environments is lacking. Here, we explored the potential for a statistical model, previously developed for Peruvian sunlit leaves, to consistently predict leaf ages from leaf reflectance spectra across two contrasting forests in Peru and Brazil and across diverse canopy environments. The model performed well for independent Brazilian sunlit and shade canopy leaves (R2 = 0.75-0.78), suggesting that canopy leaves (and their associated spectra) follow constrained developmental trajectories even in contrasting forests. The model did not perform as well for mid-canopy and understory leaves (R2 = 0.27-0.29), because leaves in different environments have distinct traits and trait developmental trajectories. When we accounted for distinct environment-trait linkages - either by explicitly including traits and environments in the model, or, even better, by re-parameterizing the spectra-only model to implicitly capture distinct trait-trajectories in different environments - we achieved a more general model that well-predicted leaf age across forests and environments (R2 = 0.79). Fundamental rules, linked to leaf environments, constrain the development of leaf traits and allow for general prediction of leaf age from spectra across species, sites and canopy environments.
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Affiliation(s)
- Jin Wu
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Cecilia Chavana-Bryant
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, OX1 3QY, UK
| | - Neill Prohaska
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Shawn P Serbin
- Biological, Environmental & Climate Sciences Department, Brookhaven National Lab, Upton, New York, NY, 11973, USA
| | - Kaiyu Guan
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana Champaign, Urbana, IL, 61801, USA
| | - Loren P Albert
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Xi Yang
- Department of Earth, Environmental, and Planetary Sciences, Brown University, Providence, RI, 02912, USA
| | - Willem J D van Leeuwen
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, 85721, USA
| | - Anthony John Garnello
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Giordane Martins
- Brazil's National Institute for Amazon Research (INPA), Manaus, AM, 69067-375, Brasil
| | - Yadvinder Malhi
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, OX1 3QY, UK
| | - France Gerard
- Centre for Ecology and Hydrology (CEH), Wallingford, OX10 8BB, UK
| | | | - Scott R Saleska
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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15
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Jin X, Chen X, Xiao L, Shi C, Chen L, Yu B, Yi Z, Yoo JH, Heo K, Yu CY, Yamada T, Sacks EJ, Peng J. Application of visible and near-infrared spectroscopy to classification of Miscanthus species. PLoS One 2017; 12:e0171360. [PMID: 28369059 PMCID: PMC5378329 DOI: 10.1371/journal.pone.0171360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/18/2017] [Indexed: 11/30/2022] Open
Abstract
The feasibility of visible and near infrared (NIR) spectroscopy as tool to classify Miscanthus samples was explored in this study. Three types of Miscanthus plants, namely, M. sinensis, M. sacchariflorus and M. fIoridulus, were analyzed using a NIR spectrophotometer. Several classification models based on the NIR spectra data were developed using line discriminated analysis (LDA), partial least squares (PLS), least squares support vector machine regression (LSSVR), radial basis function (RBF) and neural network (NN). The principal component analysis (PCA) presented rough classification with overlapping samples, while the models of Line_LSSVR, RBF_LSSVR and RBF_NN presented almost same calibration and validation results. Due to the higher speed of Line_LSSVR than RBF_LSSVR and RBF_NN, we selected the line_LSSVR model as a representative. In our study, the model based on line_LSSVR showed higher accuracy than LDA and PLS models. The total correct classification rates of 87.79 and 96.51% were observed based on LDA and PLS model in the testing set, respectively, while the line_LSSVR showed 99.42% of total correct classification rate. Meanwhile, the lin_LSSVR model in the testing set showed correct classification rate of 100, 100 and 96.77% for M. sinensis, M. sacchariflorus and M. fIoridulus, respectively. The lin_LSSVR model assigned 99.42% of samples to the right groups, except one M. fIoridulus sample. The results demonstrated that NIR spectra combined with a preliminary morphological classification could be an effective and reliable procedure for the classification of Miscanthus species.
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Affiliation(s)
- Xiaoli Jin
- Department of Agronomy & The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Xiaoling Chen
- Department of Agronomy & The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Liang Xiao
- Hunan Provincial Key Laboratory for Germplasm Innovation and Utilization of Crop, Hunan Agricultural University, Hunan Changsha, China
| | - Chunhai Shi
- Department of Agronomy & The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Liang Chen
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Bin Yu
- Wuhan Junxiu Horticultural Science and Technology Co., Ltd. Wuhan, Hubei, China
| | - Zili Yi
- Hunan Provincial Key Laboratory for Germplasm Innovation and Utilization of Crop, Hunan Agricultural University, Hunan Changsha, China
| | - Ji Hye Yoo
- Kangwon National University, Chuncheon, Gangwon, South Korea
| | - Kweon Heo
- Kangwon National University, Chuncheon, Gangwon, South Korea
| | - Chang Yeon Yu
- Kangwon National University, Chuncheon, Gangwon, South Korea
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Erik J. Sacks
- Department of Crop Sciences, University of Illinois, Urbana-Champaign, Urbana, Illinois, United States of America
| | - Junhua Peng
- Life Science and Technology Center, China National Seed Group Co., Ltd., Wuhan, Hubei, China
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16
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Baker TR, Pennington RT, Dexter KG, Fine PVA, Fortune-Hopkins H, Honorio EN, Huamantupa-Chuquimaco I, Klitgård BB, Lewis GP, de Lima HC, Ashton P, Baraloto C, Davies S, Donoghue MJ, Kaye M, Kress WJ, Lehmann CER, Monteagudo A, Phillips OL, Vasquez R. Maximising Synergy among Tropical Plant Systematists, Ecologists, and Evolutionary Biologists. Trends Ecol Evol 2017; 32:258-267. [PMID: 28214038 DOI: 10.1016/j.tree.2017.01.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/19/2017] [Accepted: 01/20/2017] [Indexed: 11/26/2022]
Abstract
Closer collaboration among ecologists, systematists, and evolutionary biologists working in tropical forests, centred on studies within long-term permanent plots, would be highly beneficial for their respective fields. With a key unifying theme of the importance of vouchered collection and precise identification of species, especially rare ones, we identify four priority areas where improving links between these communities could achieve significant progress in biodiversity and conservation science: (i) increasing the pace of species discovery; (ii) documenting species turnover across space and time; (iii) improving models of ecosystem change; and (iv) understanding the evolutionary assembly of communities and biomes.
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Affiliation(s)
| | | | - Kyle G Dexter
- Royal Botanic Garden Edinburgh, Edinburgh, UK; School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Paul V A Fine
- Department of Integrative Biology and University and Jepson Herbaria, University of California, Berkeley, CA, USA
| | | | | | - Isau Huamantupa-Chuquimaco
- Programa de Pós-Graduação em Botânica, Escola Nacional de Botânica Tropical, Instituto de Pesquisas Jardim Botânico de Rio de Janeiro (ENBT/JBRJ). Rua Pacheco Leão, 2040. RJ, Brazil
| | - Bente B Klitgård
- Department for Identification and Naming, Royal Botanic Gardens, Kew, UK
| | - Gwilym P Lewis
- Department for Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, UK
| | - Haroldo C de Lima
- Programa de Pós-Graduação em Botânica, Escola Nacional de Botânica Tropical, Instituto de Pesquisas Jardim Botânico de Rio de Janeiro (ENBT/JBRJ). Rua Pacheco Leão, 2040. RJ, Brazil
| | | | - Christopher Baraloto
- International Center for Tropical Botany, Florida International University, Miami, USA
| | - Stuart Davies
- Center for Tropical Forest Science - Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Washington, DC, USA; National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Michael J Donoghue
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Maria Kaye
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - W John Kress
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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17
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ter Steege H, Vaessen RW, Cárdenas-López D, Sabatier D, Antonelli A, de Oliveira SM, Pitman NCA, Jørgensen PM, Salomão RP. The discovery of the Amazonian tree flora with an updated checklist of all known tree taxa. Sci Rep 2016; 6:29549. [PMID: 27406027 PMCID: PMC4942782 DOI: 10.1038/srep29549] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/17/2016] [Indexed: 11/15/2022] Open
Abstract
Amazonia is the most biodiverse rainforest on Earth, and the debate over how many tree species grow there remains contentious. Here we provide a checklist of all tree species collected to date, and describe spatial and temporal trends in data accumulation. We report 530,025 unique collections of trees in Amazonia, dating between 1707 and 2015, for a total of 11,676 species in 1225 genera and 140 families. These figures support recent estimates of 16,000 total Amazonian tree species based on ecological plot data from the Amazonian Tree Diversity Network. Botanical collection in Amazonia is characterized by three major peaks, centred around 1840, 1920, and 1980, which are associated with flora projects and the establishment of inventory plots. Most collections were made in the 20th century. The number of collections has increased exponentially, but shows a slowdown in the last two decades. We find that a species' range size is a better predictor of the number of times it has been collected than the species' estimated basin-wide population size. Finding, describing, and documenting the distribution of the remaining species will require coordinated efforts at under-collected sites.
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Affiliation(s)
- Hans ter Steege
- Naturalis Biodiversity Center, Vondellaan 55, Postbus 9517, 2300 RA Leiden, The Netherlands
- Coordenação de Botânica, Museu Paraense Emílio Goeldi, Av. Magalhães Barata 376, C.P. 399, Belém, PA 66040–170, Brazil
| | - Rens W. Vaessen
- Naturalis Biodiversity Center, Vondellaan 55, Postbus 9517, 2300 RA Leiden, The Netherlands
| | - Dairon Cárdenas-López
- Herbario Amazónico Colombiano, Instituto SINCHI, Calle 20 No 5-44, Bogotá, DF, Colombia
| | - Daniel Sabatier
- Institut de Recherche pour le Développement (IRD, UMR AMAP), TA A-51/PS2, Bd. de la Lironde, 34398 Montpellier cedex 5, France
| | - 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-413 19, Göteborg, Sweden
| | | | - Nigel C. A. Pitman
- Science and Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605–2496, USA
- Nicholas School of the Environment, Duke University, Durham, North Carolina 27705, USA
| | | | - Rafael P. Salomão
- Coordenação de Botânica, Museu Paraense Emílio Goeldi, Av. Magalhães Barata 376, C.P. 399, Belém, PA 66040–170, Brazil
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18
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Phylogenetic Structure of Foliar Spectral Traits in Tropical Forest Canopies. REMOTE SENSING 2016. [DOI: 10.3390/rs8030196] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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