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Natkaniec-Nowak L, Drzewicz P, Stach P, Mroczkowska-Szerszeń M, Żukowska G. The overview of analytical methods for studying of fossil natural resins. Crit Rev Anal Chem 2023:1-23. [PMID: 37083454 DOI: 10.1080/10408347.2023.2200855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The review presents methods that are used frequently for multi-analytical study of fossil resins. The preliminary characterization relies on physical methods such as microhardness, density and fluorescence in UV light measurements. The spectroscopic methods: infrared spectroscopy, Raman spectroscopy, fluorescence spectroscopy are also presented in the paper. Besides that, the review also contains examples of the application of chromatographic methods: gas chromatography, thin layer chromatography, high-performance liquid chromatography, two-dimensional gas chromatography coupled to time-of-flight mass spectrometry as well as sample preparation methods for chromatographic studies such as pyrolysis. Additionally, thermal methods such as thermogravimetric analysis and differential scanning calorimetry also are covered by the review. Beside the examples of application, a detailed description with development history and perspective for further improvement are presented for each method. Moreover, fit-for-purpose assessment of each method is illustrated based on many examples from literature. The paper also contains examples of the application of multivariate statistical analysis and chemometric methods for comparing multiple properties of different fossil resin specimens for differentiation and classification purposes.
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Affiliation(s)
- Lucyna Natkaniec-Nowak
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Krakow, Poland
| | | | - Pawel Stach
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Krakow, Poland
| | | | - Grażyna Żukowska
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
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Scarsbrook L, Verry AJF, Walton K, Hitchmough RA, Rawlence NJ. Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: phylogeography of the New Zealand gecko genus
Hoplodactylus. Mol Ecol 2022; 32:2964-2984. [DOI: 10.1111/mec.16434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/04/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Lachie Scarsbrook
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | - Alexander J. F. Verry
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | - Kerry Walton
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | | | - Nicolas J. Rawlence
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
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An unusual elateroid lineage from mid-Cretaceous Burmese amber (Coleoptera: Elateroidea). Sci Rep 2021; 11:21985. [PMID: 34753998 PMCID: PMC8578672 DOI: 10.1038/s41598-021-01398-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/25/2021] [Indexed: 11/24/2022] Open
Abstract
We here report a new elateroid, Anoeuma lawrencei Li, Kundrata and Cai gen. et sp. nov., from mid-Cretaceous Burmese amber. Though superficially similar to some soft-bodied archostematans, Anoeuma could be firmly placed in the polyphagan superfamily Elateroidea based on the hind wing venation. Detailed morphological comparisons between extant elateroids and the Cretaceous fossils suggest that the unique character combination does not fit with confidence into any existing soft-bodied elateroid group, although some characters indicate possible relationships between Anoeuma and Omalisinae. Our discovery of this new lineage further demonstrates the past diversity and morphological disparity of soft-bodied elateroids.
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Successful extraction of insect DNA from recent copal inclusions: limits and perspectives. Sci Rep 2021; 11:6851. [PMID: 33767248 PMCID: PMC7994385 DOI: 10.1038/s41598-021-86058-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 03/01/2021] [Indexed: 01/31/2023] Open
Abstract
Insects entombed in copal, the sub-fossilized resin precursor of amber, represent a potential source of genetic data for extinct and extant, but endangered or elusive, species. Despite several studies demonstrated that it is not possible to recover endogenous DNA from insect inclusions, the preservation of biomolecules in fossilized resins samples is still under debate. In this study, we tested the possibility of obtaining endogenous ancient DNA (aDNA) molecules from insects preserved in copal, applying experimental protocols specifically designed for aDNA recovery. We were able to extract endogenous DNA molecules from one of the two samples analyzed, and to identify the taxonomic status of the specimen. Even if the sample was found well protected from external contaminants, the recovered DNA was low concentrated and extremely degraded, compared to the sample age. We conclude that it is possible to obtain genomic data from resin-entombed organisms, although we discourage aDNA analysis because of the destructive method of extraction protocols and the non-reproducibility of the results.
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Solórzano-Kraemer MM, Delclòs X, Engel MS, Peñalver E. A revised definition for copal and its significance for palaeontological and Anthropocene biodiversity-loss studies. Sci Rep 2020; 10:19904. [PMID: 33199762 PMCID: PMC7669904 DOI: 10.1038/s41598-020-76808-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/02/2020] [Indexed: 11/09/2022] Open
Abstract
The early fossilization steps of natural resins and associated terminology are a subject of constant debate. Copal and resin are archives of palaeontological and historical information, and their study is critical to the discovery of new and/or recently extinct species and to trace changes in forests during the Holocene. For such studies, a clear, suitable definition for copal is vital and is herein established. We propose an age range for copal (2.58 Ma—1760 AD), including Pleistocene and Holocene copals, and the novel term "Defaunation resin", defined as resin produced after the commencement of the Industrial Revolution. Defaunation resin is differentiated from Holocene copal as it was produced during a period of intense human transformative activities. Additionally, the “Latest Amber Bioinclusions Gap” (LABG) since the late Miocene to the end of the Pleistocene is hereby newly defined, and is characterized by its virtual absence of bioinclusions and the consequent lack of palaeontological information, which in part explains the historical differentiation between amber and copal. Crucial time intervals in the study of resin production, and of the biodiversity that could be contained, are now clarified, providing a framework for and focusing future research on bioinclusions preserved in copal and resin.
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Affiliation(s)
- Mónica M Solórzano-Kraemer
- Palaeontology and Historical Geology, Senckenberg Research Institute, 60325, Frankfurt am Main, Germany.
| | - Xavier Delclòs
- Departament de Dinàmica de la Terra i de l'Oceà and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Ciències de la Terra, Universitat de Barcelona, 08028, Barcelona, Spain
| | - Michael S Engel
- Division of Entomology, Natural History Museum, and Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Enrique Peñalver
- Instituto Geológico y Minero de España (Museo Geominero), 46004, Valencia, Spain
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Peris D, Janssen K, Barthel HJ, Bierbaum G, Delclòs X, Peñalver E, Solórzano-Kraemer MM, Jordal BH, Rust J. DNA from resin-embedded organisms: Past, present and future. PLoS One 2020; 15:e0239521. [PMID: 32986737 PMCID: PMC7521698 DOI: 10.1371/journal.pone.0239521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/09/2020] [Indexed: 11/19/2022] Open
Abstract
Past claims have been made for fossil DNA recovery from various organisms (bacteria, plants, insects and mammals, including humans) dating back in time from thousands to several million years BP. However, many of these recoveries, especially those described from million-year-old amber (fossil resin), have faced criticism as being the result of modern environmental contamination and for lack of reproducibility. Using modern genomic techniques, DNA can be obtained with confidence from a variety of substrates (e.g. bones, teeth, gum, museum specimens and fossil insects) of different ages, albeit always less than one million years BP, and results can also be obtained from much older materials using palaeoproteomics. Nevertheless, new attempts to determine if ancient DNA (aDNA) is present in insects preserved in 40 000-year old sub-fossilised resin, the precursor of amber, have been unsuccessful or not well documented. Resin-embedded specimens are therefore regarded as unsuitable for genetic studies. However, we demonstrate here, for the first time, that although a labile molecule, DNA is still present in platypodine beetles (Coleoptera: Curculionidae) embedded in six-year-old and two-year-old resin pieces from Hymenaea verrucosa (Angiospermae: Fabaceae) collected in Madagascar. We describe an optimised method which meets all the requirements and precautions for aDNA experiments for our purpose: to explore the DNA preservation limits in resin. Our objective is far from starting an uncontrolled search for aDNA in amber as it was in the past, but to start resolving basic aspects from the DNA preservation in resin and search from the most modern samples to the ancient ones, step by step. We conclude that it is therefore possible to study genomics from resin-embedded organisms, although the time limits remain to be determined.
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Affiliation(s)
- David Peris
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Kathrin Janssen
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | - H. Jonas Barthel
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Xavier Delclòs
- Department of Earth and Ocean Dynamics and Biodiversity Research Institute (IRBio), Faculty of Earth Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Enrique Peñalver
- Geological and Mining Institute of Spain (Geominero Museum), Valencia, Spain
| | - Mónica M. Solórzano-Kraemer
- Department of Palaeontology and Historical Geology, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Bjarte H. Jordal
- Museum of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Jes Rust
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
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Georgiou R, Gueriau P, Sahle CJ, Bernard S, Mirone A, Garrouste R, Bergmann U, Rueff JP, Bertrand L. Carbon speciation in organic fossils using 2D to 3D x-ray Raman multispectral imaging. SCIENCE ADVANCES 2019; 5:eaaw5019. [PMID: 31497643 PMCID: PMC6716953 DOI: 10.1126/sciadv.aaw5019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 07/25/2019] [Indexed: 05/30/2023]
Abstract
The in situ two-dimensional (2D) and 3D imaging of the chemical speciation of organic fossils is an unsolved problem in paleontology and cultural heritage. Here, we use x-ray Raman scattering (XRS)-based imaging at the carbon K-edge to form 2D and 3D images of the carbon chemistry in two exceptionally preserved specimens, a fossil plant dating back from the Carboniferous and an ancient insect entrapped in 53-million-year-old amber. The 2D XRS imaging of the plant fossil reveals a homogeneous chemical composition with micrometric "pockets" of preservation, likely inherited from its geological history. The 3D XRS imaging of the insect cuticle displays an exceptionally well preserved remaining chemical signature typical of polysaccharides such as chitin around a largely hollowed-out inclusion. Our results open up new perspectives for in situ chemical speciation imaging of fossilized organic materials, with the potential to enhance our understanding of organic specimens and their paleobiology.
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Affiliation(s)
- Rafaella Georgiou
- IPANEMA, CNRS, ministère de la culture, Université de Versailles Saint-Quentin-en-Yvelines, Université Paris-Saclay, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
- Synchrotron SOLEIL, l’Orme des Merisiers, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
| | - Pierre Gueriau
- IPANEMA, CNRS, ministère de la culture, Université de Versailles Saint-Quentin-en-Yvelines, Université Paris-Saclay, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
- Institute of Earth Sciences, University of Lausanne, Géopolis, CH-1015 Lausanne, Switzerland
| | - Christoph J. Sahle
- ESRF–The European Synchrotron, 71, avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Sylvain Bernard
- Muséum National d’Histoire Naturelle, Sorbonne Université, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 75005 Paris, France
| | - Alessandro Mirone
- ESRF–The European Synchrotron, 71, avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Romain Garrouste
- Institut de Systématique Evolution Biodiversité (ISYEB), UMR 7205 MNHN/CNRS/Sorbonne Univ./EPHE/Univ. Antilles, Muséum National d’Histoire Naturelle, 57 rue Cuvier, CP 50, F-75005 Paris, France
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Jean-Pascal Rueff
- Synchrotron SOLEIL, l’Orme des Merisiers, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique–Matière et Rayonnement, LCPMR, F-75005 Paris, France
| | - Loïc Bertrand
- IPANEMA, CNRS, ministère de la culture, Université de Versailles Saint-Quentin-en-Yvelines, Université Paris-Saclay, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
- Synchrotron SOLEIL, l’Orme des Merisiers, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
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Seyfullah LJ, Beimforde C, Dal Corso J, Perrichot V, Rikkinen J, Schmidt AR. Production and preservation of resins - past and present. Biol Rev Camb Philos Soc 2018; 93:1684-1714. [DOI: 10.1111/brv.12414] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 03/14/2018] [Accepted: 03/21/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Leyla J. Seyfullah
- Department of Geobiology; University of Göttingen; 37077 Göttingen Germany
| | | | - Jacopo Dal Corso
- Hanse-Wissenschaftskolleg, Institute for Advanced Study; 27753 Delmenhorst Germany
| | - Vincent Perrichot
- Univ Rennes, CNRS, Géosciences Rennes - UMR 6118; 35000 Rennes France
| | - Jouko Rikkinen
- Finnish Museum of Natural History, University of Helsinki; 00014 Helsinki Finland
- Faculty of Biological and Environmental Sciences; University of Helsinki; 00014 Helsinki Finland
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Negro JJ, Finlayson C, Galván I. Melanins in Fossil Animals: Is It Possible to Infer Life History Traits from the Coloration of Extinct Species? Int J Mol Sci 2018; 19:ijms19020230. [PMID: 29360744 PMCID: PMC5855542 DOI: 10.3390/ijms19020230] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/17/2018] [Accepted: 01/22/2018] [Indexed: 01/31/2023] Open
Abstract
Paleo-colour scientists have recently made the transition from describing melanin-based colouration in fossil specimens to inferring life-history traits of the species involved. Two such cases correspond to counter-shaded dinosaurs: dark-coloured due to melanins dorsally, and light-coloured ventrally. We believe that colour reconstruction of fossils based on the shape of preserved microstructures—the majority of paleo-colour studies involve melanin granules—is not without risks. In addition, animals with contrasting dorso-ventral colouration may be under different selection pressures beyond the need for camouflage, including, for instance, visual communication or ultraviolet (UV) protection. Melanin production is costly, and animals may invest less in areas of the integument where pigments are less needed. In addition, melanocytes exposed to UV radiation produce more melanin than unexposed melanocytes. Pigment economization may thus explain the colour pattern of some counter-shaded animals, including extinct species. Even in well-studied extant species, their diversity of hues and patterns is far from being understood; inferring colours and their functions in species only known from one or few specimens from the fossil record should be exerted with special prudence.
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Affiliation(s)
- Juan J Negro
- Department of Evolutionary Ecology, Doñana Biological Station-CSIC, 41092 Sevilla, Spain.
| | - Clive Finlayson
- The Gibraltar Museum, Gibraltar GX11 1AA, UK.
- Department of Anthropology, University of Toronto, Scarborough, ON M1C 1A4, Canada.
| | - Ismael Galván
- Department of Evolutionary Ecology, Doñana Biological Station-CSIC, 41092 Sevilla, Spain.
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Risso VA, Gavira JA, Sanchez-Ruiz JM. Thermostable and promiscuous Precambrian proteins. Environ Microbiol 2014; 16:1485-9. [PMID: 25009840 DOI: 10.1111/1462-2920.12319] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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