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Hyperspectral data as a biodiversity screening tool can differentiate among diverse Neotropical fishes. Sci Rep 2021; 11:16157. [PMID: 34373560 PMCID: PMC8352966 DOI: 10.1038/s41598-021-95713-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 07/13/2021] [Indexed: 11/08/2022] Open
Abstract
Hyperspectral data encode information from electromagnetic radiation (i.e., color) of any object in the form of a spectral signature; these data can then be used to distinguish among materials or even map whole landscapes. Although hyperspectral data have been mostly used to study landscape ecology, floral diversity and many other applications in the natural sciences, we propose that spectral signatures can be used for rapid assessment of faunal biodiversity, akin to DNA barcoding and metabarcoding. We demonstrate that spectral signatures of individual, live fish specimens can accurately capture species and clade-level differences in fish coloration, specifically among piranhas and pacus (Family Serrasalmidae), fishes with a long history of taxonomic confusion. We analyzed 47 serrasalmid species and could distinguish spectra among different species and clades, with the method sensitive enough to document changes in fish coloration over ontogeny. Herbivorous pacu spectra were more like one another than they were to piranhas; however, our method also documented interspecific variation in pacus that corresponds to cryptic lineages. While spectra do not serve as an alternative to the collection of curated specimens, hyperspectral data of fishes in the field should help clarify which specimens might be unique or undescribed, complementing existing molecular and morphological techniques.
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Brenes-Soto A, Dierenfeld ES, Janssens GPJ. Colouration in amphibians as a reflection of nutritional status: The case of tree frogs in Costa Rica. PLoS One 2017; 12:e0182020. [PMID: 28837604 PMCID: PMC5570269 DOI: 10.1371/journal.pone.0182020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 07/11/2017] [Indexed: 12/31/2022] Open
Abstract
Colouration has been considered a cue for mating success in many species; ornaments in males often are related to carotenoid mobilization towards feathers and/or skin and can signal general health and nutrition status. However, there are several factors that can also link with status, such as physiological blood parameters and body condition, but there is not substantial evidence which supports the existence of these relationships and interactions in anurans. This study evaluated how body score and blood values interact with colouration in free-range Agalychnis callidryas and Agalychnis annae males. We found significant associations between body condition and plasmatic proteins and haematocrit, as well as between body condition and colour values from the chromaticity diagram. We also demonstrated that there is a significant relation between the glucose and plasmatic protein values that were reflected in the ventral colours of the animals, and haematocrit inversely affected most of those colour values. Significant differences were found between species as well as between populations of A. callidryas, suggesting that despite colour variation, there are also biochemical differences within animals from the same species located in different regions. These data provide information on underlying factors for colouration of male tree frogs in nature, provide insights about the dynamics of several nutrients in the amphibian model and how this could affect the reproductive output of the animals.
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Affiliation(s)
- Andrea Brenes-Soto
- Laboratory of Animal Nutrition, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
- Animal Science Department, University of Costa Rica, San José, Costa Rica
| | | | - Geert P. J. Janssens
- Laboratory of Animal Nutrition, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Li X, Xu H, Feng L, Fu X, Zhang Y, Nansen C. Using proximal remote sensing in non-invasive phenotyping of invertebrates. PLoS One 2017; 12:e0176392. [PMID: 28472152 PMCID: PMC5417510 DOI: 10.1371/journal.pone.0176392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/10/2017] [Indexed: 11/19/2022] Open
Abstract
Proximal imaging remote sensing technologies are used to phenotype and to characterize organisms based on specific external body reflectance features. These imaging technologies are gaining interest and becoming more widely used and applied in ecological, systematic, evolutionary, and physiological studies of plants and also of animals. However, important factors may impact the quality and consistency of body reflectance features and therefore the ability to use these technologies as part of non-invasive phenotyping and characterization of organisms. We acquired hyperspectral body reflectance profiles from three insect species, and we examined how preparation procedures and preservation time affected the ability to detect reflectance responses to gender, origin, and age. Different portions of the radiometric spectrum varied markedly in their sensitivity to preparation procedures and preservation time. Based on studies of three insect species, we successfully identified specific radiometric regions, in which phenotypic traits become significantly more pronounced based on either: 1) gentle cleaning of museum specimens with distilled water, or 2) killing and preserving insect specimens in 70% ethanol. Standardization of killing and preservation procedures will greatly increase the ability to use proximal imaging remote sensing technologies as part of phenotyping and also when used in ecological and evolutionary studies of invertebrates.
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Affiliation(s)
- Xiaowei Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hongxing Xu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ling Feng
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiao Fu
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi, China
| | - Yalin Zhang
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi, China
| | - Christian Nansen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Department of Entomology and Nematology, University of California Davis, Briggs Hall, Davis, California, United States of America
- * E-mail:
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Pinto F, Damm A, Schickling A, Panigada C, Cogliati S, Müller-Linow M, Balvora A, Rascher U. Sun-induced chlorophyll fluorescence from high-resolution imaging spectroscopy data to quantify spatio-temporal patterns of photosynthetic function in crop canopies. PLANT, CELL & ENVIRONMENT 2016; 39:1500-12. [PMID: 26763162 DOI: 10.1111/pce.12710] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/29/2015] [Accepted: 12/30/2015] [Indexed: 05/04/2023]
Abstract
Passive detection of sun-induced chlorophyll fluorescence (SIF) using spectroscopy has been proposed as a proxy to quantify changes in photochemical efficiency at canopy level under natural light conditions. In this study, we explored the use of imaging spectroscopy to quantify spatio-temporal dynamics of SIF within crop canopies and its sensitivity to track patterns of photosynthetic activity originating from the interaction between vegetation structure and incoming radiation as well as variations in plant function. SIF was retrieved using the Fraunhofer Line Depth (FLD) principle from imaging spectroscopy data acquired at different time scales a few metres above several crop canopies growing under natural illumination. We report the first maps of canopy SIF in high spatial resolution. Changes of SIF were monitored at different time scales ranging from quick variations under induced stress conditions to seasonal dynamics. Natural changes were primarily determined by varying levels and distribution of photosynthetic active radiation (PAR). However, this relationship changed throughout the day demonstrating an additional physiological component modulating spatio-temporal patterns of SIF emission. We successfully used detailed SIF maps to track changes in the canopy's photochemical activity under field conditions, providing a new tool to evaluate complex patterns of photosynthesis within the canopy.
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Affiliation(s)
- Francisco Pinto
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Alexander Damm
- Remote Sensing Laboratories, Department of Geography, University of Zurich, 8057, Zürich, Switzerland
| | - Anke Schickling
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Cinzia Panigada
- Remote Sensing of Environmental Dynamics Laboratory, Department of Earth and Environmental Science (DISAT), University of Milano-Bicocca, 20126, Milan, Italy
| | - Sergio Cogliati
- Remote Sensing of Environmental Dynamics Laboratory, Department of Earth and Environmental Science (DISAT), University of Milano-Bicocca, 20126, Milan, Italy
| | - Mark Müller-Linow
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Agim Balvora
- INRES-Plant Breeding, University of Bonn, 53115, Bonn, Germany
- Experimental Station of University of Bonn in Klein-Altendorf, 53359, Rheinbach, Germany
| | - Uwe Rascher
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
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Koprowski R. Hyperspectral imaging in medicine: image pre-processing problems and solutions in Matlab. JOURNAL OF BIOPHOTONICS 2015; 8:935-943. [PMID: 25676816 DOI: 10.1002/jbio.201400133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 12/06/2014] [Accepted: 12/22/2014] [Indexed: 06/04/2023]
Abstract
The paper presents problems and solutions related to hyperspectral image pre-processing. New methods of preliminary image analysis are proposed. The paper shows problems occurring in Matlab when trying to analyse this type of images. Moreover, new methods are discussed which provide the source code in Matlab that can be used in practice without any licensing restrictions. The proposed application and sample result of hyperspectral image analysis.
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Affiliation(s)
- Robert Koprowski
- Department of Biomedical Computer Systems, University of Silesia, Faculty of Computer Science and Materials Science, Institute of Computer Science, ul. Będzińska 39, Sosnowiec, 41-200, Poland.
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Wang C, Zheng W, Bu Y, Chang S, Zhang S, Xu RX. Multi-scale hyperspectral imaging of cervical neoplasia. Arch Gynecol Obstet 2015; 293:1309-17. [PMID: 26446578 DOI: 10.1007/s00404-015-3906-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 09/25/2015] [Indexed: 01/13/2023]
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Russell BJ, Dierssen HM. Use of Hyperspectral Imagery to Assess Cryptic Color Matching in Sargassum Associated Crabs. PLoS One 2015; 10:e0136260. [PMID: 26352667 PMCID: PMC4564216 DOI: 10.1371/journal.pone.0136260] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 08/03/2015] [Indexed: 01/01/2023] Open
Abstract
Mats of the pelagic macroalgae Sargassum represent a complex environment for the study of marine camouflage at the air-sea interface. Endemic organisms have convergently evolved similar colors and patterns, but quantitative assessments of camouflage strategies are lacking. Here, spectral camouflage of two crab species (Portunus sayi and Planes minutus) was assessed using hyperspectral imagery (HSI). Crabs matched Sargassum reflectance across blue and green wavelengths (400-550 nm) and diverged at longer wavelengths. Maximum discrepancy was observed in the far-red (i.e., 675 nm) where Chlorophyll a absorption occurred in Sargassum and not the crabs. In a quantum catch color model, both crabs showed effective color matching against blue/green sensitive dichromat fish, but were still discernible to tetrachromat bird predators that have visual sensitivity to far red wavelengths. The two species showed opposing trends in background matching with relation to body size. Variation in model parameters revealed that discrimination of crab and background was impacted by distance from the predator, and the ratio of cone cell types for bird predators. This is one of the first studies to detail background color matching in this unique, challenging ecosystem at the air-sea interface.
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Affiliation(s)
- Brandon J. Russell
- Department of Marine Science, University of Connecticut, Groton, CT, 06340, United States of America
| | - Heidi M. Dierssen
- Department of Marine Science, University of Connecticut, Groton, CT, 06340, United States of America
- Department of Geography, University of Connecticut, Storrs, CT, 06268, United States of America
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