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Slater TS, Ito S, Wakamatsu K, Zhang F, Sjövall P, Jarenmark M, Lindgren J, McNamara ME. Taphonomic experiments reveal authentic molecular signals for fossil melanins and verify preservation of phaeomelanin in fossils. Nat Commun 2023; 14:5651. [PMID: 37803012 PMCID: PMC10558522 DOI: 10.1038/s41467-023-40570-w] [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: 06/09/2021] [Accepted: 08/01/2023] [Indexed: 10/08/2023] Open
Abstract
Melanin pigments play a critical role in physiological processes and shaping animal behaviour. Fossil melanin is a unique resource for understanding the functional evolution of melanin but the impact of fossilisation on molecular signatures for eumelanin and, especially, phaeomelanin is not fully understood. Here we present a model for the chemical taphonomy of fossil eumelanin and phaeomelanin based on thermal maturation experiments using feathers from extant birds. Our results reveal which molecular signatures are authentic signals for thermally matured eumelanin and phaeomelanin, which signatures are artefacts derived from the maturation of non-melanin molecules, and how these chemical data are impacted by sample preparation. Our model correctly predicts the molecular composition of eumelanins in diverse vertebrate fossils from the Miocene and Cretaceous and, critically, identifies direct molecular evidence for phaeomelanin in these fossils. This taphonomic framework adds to the geochemical toolbox that underpins reconstructions of melanin evolution and of melanin-based coloration in fossil vertebrates.
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Affiliation(s)
- Tiffany S Slater
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.
- Environmental Research Institute, University College Cork, Cork, Ireland.
| | - Shosuke Ito
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Aichi, Japan
| | - Kazumasa Wakamatsu
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Aichi, Japan
| | - Fucheng Zhang
- Institute of Geology and Paleontology, Linyi University, Linyi City, Shandong, China
| | - Peter Sjövall
- RISE Research Institutes of Sweden, Materials and Production, 501 15, Borås, Sweden
| | | | - Johan Lindgren
- Department of Geology, Lund University, 223 62, Lund, Sweden
| | - Maria E McNamara
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.
- Environmental Research Institute, University College Cork, Cork, Ireland.
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Roy A, Pittman M, Kaye TG, Saitta ET, Xu X. Correction statement for Recent advances in amniote palaeocolour reconstruction and a framework for future research (volume 95, issue 1, pp. 22-50). Biol Rev Camb Philos Soc 2023; 98:386-389. [PMID: 36320106 PMCID: PMC10117546 DOI: 10.1111/brv.12901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 01/11/2023]
Affiliation(s)
- Arindam Roy
- Department of Earth Sciences, The University of Hong Kong, Pokfulam, Hong Kong, SAR, China.,School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol, BS8 1RJ, UK
| | - Michael Pittman
- School of Life Sciences, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, SAR, China.,Foundation for Scientific Advancement, 7023 Alhambra Drive, Sierra Vista, AZ, 85650, USA
| | - Thomas G Kaye
- Foundation for Scientific Advancement, 7023 Alhambra Drive, Sierra Vista, AZ, 85650, USA
| | - Evan T Saitta
- Department of Organismal Biology & Anatomy, University of Chicago, 1027 E 57th St, Chicago, IL, 60637, USA
| | - Xing Xu
- Chinese Academy of Sciences - Institute of Vertebrate Paleontology and Paleoanthropology, Beijing, China
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3
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Ospina-Rozo L, Roberts A, Stuart-Fox D. A generalized approach to characterize optical properties of natural objects. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
To understand the diversity of ways in which natural materials interact with light, it is important to consider how their reflectance changes with the angle of illumination or viewing and to consider wavelengths beyond the visible. Efforts to characterize these optical properties, however, have been hampered by heterogeneity in measurement techniques, parameters and terminology. Here, we propose a standardized set of measurements, parameters and terminology to describe the optical properties of natural objects based on spectrometry, including angle-dependent effects, such as iridescence and specularity. We select a set of existing measurements and parameters that are generalizable to any wavelength range and spectral shape, and we highlight which subsets of measures are relevant to different biological questions. As a case study, we have applied these measures to 30 species of Christmas beetles, in which we observed previously unrealized diversity in visible and near-infrared reflectance. As expected, reflection of short wavelengths was associated with high spectral purity and angle dependence. In contrast to simple, artificial structures, iridescence and specularity were not strongly correlated, highlighting the complexity and modularity of natural materials. Species did not cluster according to spectral parameters or genus, suggesting high lability of optical properties. The proposed standardization of measures and parameters will improve our understanding of biological adaptations for manipulating light by facilitating the systematic comparison of complex optical properties, such as glossy or metallic appearances and visible or near-infrared iridescence.
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Affiliation(s)
- Laura Ospina-Rozo
- School of Biosciences, University of Melbourne , VIC 3010 , Australia
| | - Ann Roberts
- ARC Centre of Excellence for Transformative Meta-Optical Systems, School of Physics, University of Melbourne , VIC 3010 , Australia
| | - Devi Stuart-Fox
- School of Biosciences, University of Melbourne , VIC 3010 , Australia
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Ng CS, Lai CK, Ke HM, Lee HH, Chen CF, Tang PC, Cheng HC, Lu MJ, Li WH, Tsai IJ. Genome Assembly and Evolutionary Analysis of the Mandarin Duck Aix galericulata Reveal Strong Genome Conservation among Ducks. Genome Biol Evol 2022; 14:evac083. [PMID: 35640266 PMCID: PMC9189614 DOI: 10.1093/gbe/evac083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
The mandarin duck, Aix galericulata, is popular in East Asian cultures and displays exaggerated sexual dimorphism, especially in feather traits during breeding seasons. We generated and annotated the first mandarin duck de novo assembly, which was 1.08 Gb in size and encoded 16,615 proteins. Using a phylogenomic approach calibrated with fossils and molecular divergences, we inferred that the last common ancestor of ducks occurred 13.3-26.7 Ma. The majority of the mandarin duck genome repetitive sequences belonged to the chicken repeat 1 (CR1) retroposon CR1-J2_Pass, which underwent a duck lineage-specific burst. Synteny analyses among ducks revealed infrequent chromosomal rearrangements in which breaks were enriched in LINE retrotransposons and DNA transposons. The calculation of the dN/dS ratio revealed that the majority of duck genes were under strong purifying selection. The expanded gene families in the mandarin duck are primarily involved in olfactory perception as well as the development and morphogenesis of feather and branching structures. This new reference genome will improve our understanding of the morphological and physiological characteristics of ducks and provide a valuable resource for functional genomics studies to investigate the feather traits of the mandarin duck.
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Affiliation(s)
- Chen Siang Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
- Bioresource Conservation Research Center, National Tsing Hua University, Hsinchu, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Cheng-Kuo Lai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Feng Chen
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Pin-Chi Tang
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Hsu-Chen Cheng
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Life Science, National Chung Hsing University, Taichung, Taiwan
| | - Meiyeh J. Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Hsiung Li
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Ecology and Evolution, University of Chicago, Illinois, USA
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Cincotta A, Nicolaï M, Campos HBN, McNamara M, D'Alba L, Shawkey MD, Kischlat EE, Yans J, Carleer R, Escuillié F, Godefroit P. Pterosaur melanosomes support signalling functions for early feathers. Nature 2022; 604:684-688. [PMID: 35444275 PMCID: PMC9046085 DOI: 10.1038/s41586-022-04622-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/07/2022] [Indexed: 01/10/2023]
Abstract
Remarkably well-preserved soft tissues in Mesozoic fossils have yielded substantial insights into the evolution of feathers1. New evidence of branched feathers in pterosaurs suggests that feathers originated in the avemetatarsalian ancestor of pterosaurs and dinosaurs in the Early Triassic2, but the homology of these pterosaur structures with feathers is controversial3,4. Reports of pterosaur feathers with homogeneous ovoid melanosome geometries2,5 suggest that they exhibited limited variation in colour, supporting hypotheses that early feathers functioned primarily in thermoregulation6. Here we report the presence of diverse melanosome geometries in the skin and simple and branched feathers of a tapejarid pterosaur from the Early Cretaceous found in Brazil. The melanosomes form distinct populations in different feather types and the skin, a feature previously known only in theropod dinosaurs, including birds. These tissue-specific melanosome geometries in pterosaurs indicate that manipulation of feather colour-and thus functions of feathers in visual communication-has deep evolutionary origins. These features show that genetic regulation of melanosome chemistry and shape7-9 was active early in feather evolution.
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Affiliation(s)
- Aude Cincotta
- Directorate Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium. .,Institute of Life, Earth and Environment, University of Namur, Namur, Belgium. .,School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland. .,Environmental Research Institute, University College Cork, Cork, Ireland.
| | - Michaël Nicolaï
- Evolution and Optics of Nanostructures Group, Biology Department, Ghent University, Ghent, Belgium
| | | | - Maria McNamara
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland. .,Environmental Research Institute, University College Cork, Cork, Ireland.
| | - Liliana D'Alba
- Evolution and Optics of Nanostructures Group, Biology Department, Ghent University, Ghent, Belgium.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Matthew D Shawkey
- Evolution and Optics of Nanostructures Group, Biology Department, Ghent University, Ghent, Belgium
| | - Edio-Ernst Kischlat
- Divisão de Bacias Sedimentares, Geological Survey of Brazil, Porto Alegre, Brazil
| | - Johan Yans
- Institute of Life, Earth and Environment, University of Namur, Namur, Belgium
| | - Robert Carleer
- Research Group of Analytical and Circular Chemistry, Institute for Material Research, Hasselt University, Diepenbeek, Belgium
| | | | - Pascal Godefroit
- Directorate Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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Wang M, O'Connor JK, Zhao T, Pan Y, Zheng X, Wang X, Zhou Z. An Early Cretaceous enantiornithine bird with a pintail. Curr Biol 2021; 31:4845-4852.e2. [PMID: 34534442 DOI: 10.1016/j.cub.2021.08.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/18/2021] [Accepted: 08/16/2021] [Indexed: 11/18/2022]
Abstract
Enantiornithes are the most successful group of Mesozoic birds, arguably representing the first global avian radiation,1-4 and commonly resolved as the sister to the Ornithuromorpha, the clade within which all living birds are nested.1,3 The wealth of fossils makes it feasible to comparatively test evolutionary hypotheses about the pattern and mode of eco-morphological diversity of these sister clades that co-existed for approximately 65 Ma. Here, we report a new Early Cretaceous enantiornithine, Yuanchuavis kompsosoura gen. et. sp. nov., with a rectricial fan combined with an elongate central pair of fully pennaceous rachis-dominated plumes, constituting a new tail plumage previously unknown among nonavialan dinosaurs and Mesozoic birds but which strongly resembles the pintail in many neornithines. The extravagant but aerodynamically costly long central plumes, as an honest signal of quality, likely evolved in enantiornithines through the handicap process of sexual selection. The contrasting tail morphotypes observed between enantiornithines and early ornithuromorphs reflect the complex interplay between sexual and natural selections and indicate that each lineage experienced unique pressures reflecting ecological differences. As in neornithines, early avialans repeatedly evolved extravagant structures highlighting the importance of sexual selection in shaping the plumage of feathered dinosaurs, even early in their evolutionary history.
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Affiliation(s)
- Min Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China.
| | | | - Tao Zhao
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Yanhong Pan
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Xiaoting Zheng
- Institute of Geology and Paleontology, Linyi University, Linyi, 276000 Shandong, China; Shandong Tianyu Museum of Nature, Pingyi, 273300 Shandong, China
| | - Xiaoli Wang
- Institute of Geology and Paleontology, Linyi University, Linyi, 276000 Shandong, China; Shandong Tianyu Museum of Nature, Pingyi, 273300 Shandong, China
| | - Zhonghe Zhou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
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7
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Decoding the Evolution of Melanin in Vertebrates. Trends Ecol Evol 2021; 36:430-443. [DOI: 10.1016/j.tree.2020.12.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 02/08/2023]
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8
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Chatragadda R, Dufossé L. Ecological and Biotechnological Aspects of Pigmented Microbes: A Way Forward in Development of Food and Pharmaceutical Grade Pigments. Microorganisms 2021; 9:637. [PMID: 33803896 PMCID: PMC8003166 DOI: 10.3390/microorganisms9030637] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/04/2021] [Accepted: 03/15/2021] [Indexed: 12/17/2022] Open
Abstract
Microbial pigments play multiple roles in the ecosystem construction, survival, and fitness of all kinds of organisms. Considerably, microbial (bacteria, fungi, yeast, and microalgae) pigments offer a wide array of food, drug, colorants, dyes, and imaging applications. In contrast to the natural pigments from microbes, synthetic colorants are widely used due to high production, high intensity, and low cost. Nevertheless, natural pigments are gaining more demand over synthetic pigments as synthetic pigments have demonstrated side effects on human health. Therefore, research on microbial pigments needs to be extended, explored, and exploited to find potential industrial applications. In this review, the evolutionary aspects, the spatial significance of important pigments, biomedical applications, research gaps, and future perspectives are detailed briefly. The pathogenic nature of some pigmented bacteria is also detailed for awareness and safe handling. In addition, pigments from macro-organisms are also discussed in some sections for comparison with microbes.
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Affiliation(s)
- Ramesh Chatragadda
- Biological Oceanography Division (BOD), Council of Scientific and Industrial Research-National Institute of Oceanography (CSIR-NIO), Dona Paula 403004, Goa, India
| | - Laurent Dufossé
- Chemistry and Biotechnology of Natural Products (CHEMBIOPRO Lab), Ecole Supérieure d’Ingénieurs Réunion Océan Indien (ESIROI), Département Agroalimentaire, Université de La Réunion, F-97744 Saint-Denis, France
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Roy A, Pittman M, Saitta ET, Kaye TG, Xu X. Recent advances in amniote palaeocolour reconstruction and a framework for future research. Biol Rev Camb Philos Soc 2020; 95:22-50. [PMID: 31538399 PMCID: PMC7004074 DOI: 10.1111/brv.12552] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 08/12/2019] [Accepted: 08/15/2019] [Indexed: 01/24/2023]
Abstract
Preserved melanin pigments have been discovered in fossilised integumentary appendages of several amniote lineages (fishes, frogs, snakes, marine reptiles, non-avialan dinosaurs, birds, and mammals) excavated from lagerstätten across the globe. Melanisation is a leading factor in organic integument preservation in these fossils. Melanin in extant vertebrates is typically stored in rod- to sphere-shaped, lysosome-derived, membrane-bound vesicles called melanosomes. Black, dark brown, and grey colours are produced by eumelanin, and reddish-brown colours are produced by phaeomelanin. Specific morphotypes and nanostructural arrangements of melanosomes and their relation to the keratin matrix in integumentary appendages create the so-called 'structural colours'. Reconstruction of colour patterns in ancient animals has opened an exciting new avenue for studying their life, behaviour and ecology. Modern relationships between the shape, arrangement, and size of avian melanosomes, melanin chemistry, and feather colour have been applied to reconstruct the hues and colour patterns of isolated feathers and plumages of the dinosaurs Anchiornis, Sinosauropteryx, and Microraptor in seminal papers that initiated the field of palaeocolour reconstruction. Since then, further research has identified countershading camouflage patterns, and informed subsequent predictions on the ecology and behaviour of these extinct animals. However, palaeocolour reconstruction remains a nascent field, and current approaches have considerable potential for further refinement, standardisation, and expansion. This includes detailed study of non-melanic pigments that might be preserved in fossilised integuments. A common issue among existing palaeocolour studies is the lack of contextualisation of different lines of evidence and the wide variety of techniques currently employed. To that end, this review focused on fossil amniotes: (i) produces an overarching framework that appropriately reconstructs palaeocolour by accounting for the chemical signatures of various pigments, morphology and local arrangement of pigment-bearing vesicles, pigment concentration, macroscopic colour patterns, and taphonomy; (ii) provides background context for the evolution of colour-producing mechanisms; and (iii) encourages future efforts in palaeocolour reconstructions particularly of less-studied groups such as non-dinosaur archosaurs and non-archosaur amniotes.
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Affiliation(s)
- Arindam Roy
- Vertebrate Palaeontology Laboratory, Department of Earth SciencesThe University of Hong KongPokfulamHong Kong SARChina
| | - Michael Pittman
- Vertebrate Palaeontology Laboratory, Department of Earth SciencesThe University of Hong KongPokfulamHong Kong SARChina
| | - Evan T. Saitta
- Integrative Research Center, Section of Earth SciencesField Museum of Natural History1400 S. Lake Shore Drive, ChicagoIL60605U.S.A.
| | - Thomas G. Kaye
- Foundation for Scientific Advancement7023 Alhambra Drive, Sierra VistaAZ85650U.S.A.
| | - Xing Xu
- Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of Sciences142 Xizhimenwai Street.Beijing100044China
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