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Umamaheswaran R, Dutta S. Preservation of proteins in the geosphere. Nat Ecol Evol 2024; 8:858-865. [PMID: 38472431 DOI: 10.1038/s41559-024-02366-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 02/13/2024] [Indexed: 03/14/2024]
Abstract
Deep-time protein preservation has attracted increasing interest and rapid research activity within the palaeobiological community in recent years, but there are several different viewpoints without a cohesive framework for the interpretation of these proteins. Therefore, despite this activity, crucial gaps exist in the understanding of how proteins are preserved in the geological record and we believe it is vital to arrive at a synthesis of the various taphonomic pathways in order to proceed forward with their elucidation. Here we take a critical look at the state of knowledge regarding deep-time protein preservation and argue for the necessity of a more nuanced approach to understanding the molecular taphonomy of proteins through the lens of diagenetic pathways. We also propound an initial framework with which to comprehend the chemical changes undergone by proteins via the concept of 'proteagen'.
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Affiliation(s)
- Raman Umamaheswaran
- Department of Earth Sciences, Indian Institute of Technology Bombay, Mumbai, India.
- Department of Earth and Planetary Sciences, Hokkaido University, Sapporo, Japan.
| | - Suryendu Dutta
- Department of Earth Sciences, Indian Institute of Technology Bombay, Mumbai, India.
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2
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Environmental Factors Affecting Feather Taphonomy. BIOLOGY 2022; 11:biology11050703. [PMID: 35625431 PMCID: PMC9138376 DOI: 10.3390/biology11050703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022]
Abstract
The exceptional preservation of feathers in the fossil record has led to a better understanding of both phylogeny and evolution. Here we address factors that may have contributed to the preservation of feathers in ancient organisms using experimental taphonomy. We show that the atmospheres of the Mesozoic, known to be elevated in both CO2 and with temperatures above present levels, may have contributed to the preservation of these soft tissues by facilitating rapid precipitation of hydroxy- or carbonate hydroxyapatite, thus outpacing natural degradative processes. Data also support that that microbial degradation was enhanced in elevated CO2, but mineral deposition was also enhanced, contributing to preservation by stabilizing the organic components of feathers.
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3
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Technical steps towards enhanced localization of proteins in cultural heritage samples by immunofluorescence microscopy and micro-reflectance imaging spectroscopy. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Gatti L, Lugli F, Sciutto G, Zangheri M, Prati S, Mirasoli M, Silvestrini S, Benazzi S, Tütken T, Douka K, Collina C, Boschin F, Romandini M, Iacumin P, Guardigli M, Roda A, Mazzeo R. Combining elemental and immunochemical analyses to characterize diagenetic alteration patterns in ancient skeletal remains. Sci Rep 2022; 12:5112. [PMID: 35332214 PMCID: PMC8948219 DOI: 10.1038/s41598-022-08979-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/18/2022] [Indexed: 11/22/2022] Open
Abstract
Bones and teeth are biological archives, but their structure and composition are subjected to alteration overtime due to biological and chemical degradation postmortem, influenced by burial environment and conditions. Nevertheless, organic fraction preservation is mandatory for several archeometric analyses and applications. The mutual protection between biomineral and organic fractions in bones and teeth may lead to a limited diagenetic alteration, promoting a better conservation of the organic fraction. However, the correlation between elemental variations and the presence of organic materials (e.g., collagen) in the same specimen is still unclear. To fill this gap, chemiluminescent (CL) immunochemical imaging analysis has been applied for the first time for collagen localization. Then, Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS) and CL imaging were combined to investigate the correlation between elemental (i.e., REE, U, Sr, Ba) and collagen distribution. Teeth and bones from various archeological contexts, chronological periods, and characterized by different collagen content were analyzed. Immunochemical analysis revealed a heterogeneous distribution of collagen, especially in highly degraded samples. Subsequently, LA-ICP-MS showed a correlation between the presence of uranium and rare earth elements and areas with low amount of collagen. The innovative integration between the two methods permitted to clarify the mutual relation between elemental variation and collagen preservation overtime, thus contributing to unravel the effects of diagenetic alteration in bones and teeth.
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Affiliation(s)
- L Gatti
- Department of Chemistry, University of Bologna-Ravenna Campus, Via Guaccimanni, 42, 48121, Ravenna, Italy
| | - Federico Lugli
- Department of Cultural Heritage, University of Bologna-Ravenna Campus, Via degli Ariani 1, 48121, Ravenna, Italy.
- Department of Chemical and Geological Science, University of Modena and Reggio Emilia, 41125, Modena, Italy.
| | - Giorgia Sciutto
- Department of Chemistry, University of Bologna-Ravenna Campus, Via Guaccimanni, 42, 48121, Ravenna, Italy.
| | - M Zangheri
- Department of Chemistry, "Giacomo Ciamician" Alma Mater Studiorum-University of Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - S Prati
- Department of Chemistry, University of Bologna-Ravenna Campus, Via Guaccimanni, 42, 48121, Ravenna, Italy
| | - M Mirasoli
- Department of Chemistry, "Giacomo Ciamician" Alma Mater Studiorum-University of Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - S Silvestrini
- Department of Cultural Heritage, University of Bologna-Ravenna Campus, Via degli Ariani 1, 48121, Ravenna, Italy
| | - S Benazzi
- Department of Cultural Heritage, University of Bologna-Ravenna Campus, Via degli Ariani 1, 48121, Ravenna, Italy
| | - T Tütken
- Applied and Analytical Paleontology, Institute of Geosciences, Johannes Gutenberg University, 55128, Mainz, Germany
| | - K Douka
- Department of Archaeology, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK
| | - C Collina
- Museo Civico Archeologico Biagio Greco, Mondragone, Caserta, Italy
| | - F Boschin
- Department of Physical Science, Earth and Environment, U.R. Preistoria e Antropologia, University of Siena, Siena, Italy
| | - M Romandini
- Department of Cultural Heritage, University of Bologna-Ravenna Campus, Via degli Ariani 1, 48121, Ravenna, Italy
| | - P Iacumin
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - M Guardigli
- Department of Chemistry, "Giacomo Ciamician" Alma Mater Studiorum-University of Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - A Roda
- INBB, National Institute of Biostructures and Biosystems, Rome, Italy
| | - R Mazzeo
- Department of Cultural Heritage, University of Bologna-Ravenna Campus, Via degli Ariani 1, 48121, Ravenna, Italy
- Department of Chemistry, "Giacomo Ciamician" Alma Mater Studiorum-University of Bologna, Via Selmi 2, 40126, Bologna, Italy
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5
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Miller CV, Pittman M. The diet of early birds based on modern and fossil evidence and a new framework for its reconstruction. Biol Rev Camb Philos Soc 2021; 96:2058-2112. [PMID: 34240530 PMCID: PMC8519158 DOI: 10.1111/brv.12743] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 12/14/2022]
Abstract
Birds are some of the most diverse organisms on Earth, with species inhabiting a wide variety of niches across every major biome. As such, birds are vital to our understanding of modern ecosystems. Unfortunately, our understanding of the evolutionary history of modern ecosystems is hampered by knowledge gaps in the origin of modern bird diversity and ecosystem ecology. A crucial part of addressing these shortcomings is improving our understanding of the earliest birds, the non-avian avialans (i.e. non-crown birds), particularly of their diet. The diet of non-avian avialans has been a matter of debate, in large part because of the ambiguous qualitative approaches that have been used to reconstruct it. Here we review methods for determining diet in modern and fossil avians (i.e. crown birds) as well as non-avian theropods, and comment on their usefulness when applied to non-avian avialans. We use this to propose a set of comparable, quantitative approaches to ascertain fossil bird diet and on this basis provide a consensus of what we currently know about fossil bird diet. While no single approach can precisely predict diet in birds, each can exclude some diets and narrow the dietary possibilities. We recommend combining (i) dental microwear, (ii) landmark-based muscular reconstruction, (iii) stable isotope geochemistry, (iv) body mass estimations, (v) traditional and/or geometric morphometric analysis, (vi) lever modelling, and (vii) finite element analysis to reconstruct fossil bird diet accurately. Our review provides specific methodologies to implement each approach and discusses complications future researchers should keep in mind. We note that current forms of assessment of dental mesowear, skull traditional morphometrics, geometric morphometrics, and certain stable isotope systems have yet to be proven effective at discerning fossil bird diet. On this basis we report the current state of knowledge of non-avian avialan diet which remains very incomplete. The ancestral dietary condition in non-avian avialans remains unclear due to scarce data and contradictory evidence in Archaeopteryx. Among early non-avian pygostylians, Confuciusornis has finite element analysis and mechanical advantage evidence pointing to herbivory, whilst Sapeornis only has mechanical advantage evidence indicating granivory, agreeing with fossilised ingested material known for this taxon. The enantiornithine ornithothoracine Shenqiornis has mechanical advantage and pedal morphometric evidence pointing to carnivory. In the hongshanornithid ornithuromorph Hongshanornis only mechanical advantage evidence indicates granivory, but this agrees with evidence of gastrolith ingestion in this taxon. Mechanical advantage and ingested fish support carnivory in the songlingornithid ornithuromorph Yanornis. Due to the sparsity of robust dietary assignments, no clear trends in non-avian avialan dietary evolution have yet emerged. Dietary diversity seems to increase through time, but this is a preservational bias associated with a predominance of data from the Early Cretaceous Jehol Lagerstätte. With this new framework and our synthesis of the current knowledge of non-avian avialan diet, we expect dietary knowledge and evolutionary trends to become much clearer in the coming years, especially as fossils from other locations and climates are found. This will allow for a deeper and more robust understanding of the role birds played in Mesozoic ecosystems and how this developed into their pivotal role in modern ecosystems.
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Affiliation(s)
- Case Vincent Miller
- Vertebrate Palaeontology Laboratory, Research Division for Earth and Planetary ScienceThe University of Hong KongPokfulamHong Kong SARChina
| | - Michael Pittman
- Vertebrate Palaeontology Laboratory, Research Division for Earth and Planetary ScienceThe University of Hong KongPokfulamHong Kong SARChina
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6
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An Integrative Bioinformatic Analysis for Keratinase Detection in Marine-Derived Streptomyces. Mar Drugs 2021; 19:md19060286. [PMID: 34063876 PMCID: PMC8224001 DOI: 10.3390/md19060286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/12/2021] [Accepted: 05/18/2021] [Indexed: 01/08/2023] Open
Abstract
Keratinases present promising biotechnological applications, due to their ability to degrade keratin. Streptomyces appears as one of the main sources of these enzymes, but complete genome sequences of keratinolytic bacteria are still limited. This article reports the complete genomes of three marine-derived streptomycetes that show different levels of feather keratin degradation, with high (strain G11C), low (strain CHD11), and no (strain Vc74B-19) keratinolytic activity. A multi-step bioinformatics approach is described to explore genes encoding putative keratinases in these genomes. Despite their differential keratinolytic activity, multiplatform annotation reveals similar quantities of ORFs encoding putative proteases in strains G11C, CHD11, and Vc74B-19. Comparative genomics classified these putative proteases into 140 orthologous groups and 17 unassigned orthogroup peptidases belonging to strain G11C. Similarity network analysis revealed three network communities of putative peptidases related to known keratinases of the peptidase families S01, S08, and M04. When combined with the prediction of cellular localization and phylogenetic reconstruction, seven putative keratinases from the highly keratinolytic strain Streptomyces sp. G11C are identified. To our knowledge, this is the first multi-step bioinformatics analysis that complements comparative genomics with phylogeny and cellular localization prediction, for the prediction of genes encoding putative keratinases in streptomycetes.
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7
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Molecular tests support the viability of rare earth elements as proxies for fossil biomolecule preservation. Sci Rep 2020; 10:15566. [PMID: 32968129 PMCID: PMC7511940 DOI: 10.1038/s41598-020-72648-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 08/13/2020] [Indexed: 11/22/2022] Open
Abstract
The rare earth element (REE) composition of a fossil bone reflects its chemical alteration during diagenesis. Consequently, fossils presenting low REE concentrations and/or REE profiles indicative of simple diffusion, signifying minimal alteration, have been proposed as ideal candidates for paleomolecular investigation. We directly tested this prediction by conducting multiple biomolecular assays on a well-preserved fibula of the dinosaur Edmontosaurus from the Cretaceous Hell Creek Formation previously found to exhibit low REE concentrations and steeply-declining REE profiles. Gel electrophoresis identified the presence of organic material in this specimen, and subsequent immunofluorescence and enzyme-linked immunosorbant assays identified preservation of epitopes of the structural protein collagen I. Our results thereby support the utility of REE profiles as proxies for soft tissue and biomolecular preservation in fossil bones. Based on considerations of trace element taphonomy, we also draw predictions as to the biomolecular recovery potential of additional REE profile types exhibited by fossil bones.
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Wang S, Chang WL, Zhang Q, Ma M, Yang F, Zhuo D, Hans HIC, Yang R, Wu P, Habib M, Juan WT, Chuong CM. Variations of Mesozoic feathers: Insights from the morphogenesis of extant feather rachises. Evolution 2020; 74:2121-2133. [PMID: 32614075 DOI: 10.1111/evo.14051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/21/2020] [Accepted: 06/27/2020] [Indexed: 12/14/2022]
Abstract
The rachises of extant feathers, composed of dense cortex and spongy internal medulla, are flexible and light, yet stiff enough to withstand the load required for flight, among other functions. Incomplete knowledge of early feathers prevents a full understanding of how cylindrical rachises have evolved. Bizarre feathers with unusually wide and flattened rachises, known as "rachis-dominated feathers" (RDFs), have been observed in fossil nonavian and avian theropods. Newly discovered RDFs embedded in early Late Cretaceous Burmese ambers (about 99 million year ago) suggest the unusually wide and flattened rachises mainly consist of a dorsal cortex, lacking a medulla and a ventral cortex. Coupled with findings on extant feather morphogenesis, known fossil RDFs were categorized into three morphotypes based on their rachidial configurations. For each morphotype, potential developmental scenarios were depicted by referring to the rachidial development in chickens, and relative stiffness of each morphotype was estimated through functional simulations. The results suggest rachises of RDFs are developmentally equivalent to a variety of immature stages of cylindrical rachises. Similar rachidial morphotypes documented in extant penguins suggest that the RDFs are not unique to Mesozoic theropods, although they are likely to have evolved independently in extant penguins.
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Affiliation(s)
- Shuo Wang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033
| | - Wei-Ling Chang
- Integrative Stem Cell Center, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Qiyue Zhang
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Menglu Ma
- Laboratory of Vertebrate Evolution, College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Feng Yang
- Beijing Advanced Innovation Center for Imaging Technology, Capital Normal University, Beijing, 100048, China
| | - De Zhuo
- Beijing Xiachong Amber Museum, Beijing, 100083, China
| | - Harn I-Chen Hans
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033
- International Research Center of Wound Repair and Regeneration, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Rui Yang
- Laboratory of Vertebrate Evolution, College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033
| | - Michael Habib
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033
- Los Angeles County Museum of Natural History, Los Angeles, California, 90007
| | - Wen-Tau Juan
- Integrative Stem Cell Center, China Medical University Hospital, Taichung, 40447, Taiwan
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, 40402, Taiwan
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033
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9
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Slater TS, McNamara ME, Orr PJ, Foley TB, Ito S, Wakamatsu K. Taphonomic experiments resolve controls on the preservation of melanosomes and keratinous tissues in feathers. PALAEONTOLOGY 2020; 63:103-115. [PMID: 32025055 PMCID: PMC6988486 DOI: 10.1111/pala.12445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/15/2019] [Indexed: 06/10/2023]
Abstract
Fossils are a key source of data on the evolution of feather structure and function through deep time, but their ability to resolve macroevolutionary questions is compromised by an incomplete understanding of their taphonomy. Critically, the relative preservation potential of two key feather components, melanosomes and keratinous tissue, is not fully resolved. Recent studies suggesting that melanosomes are preferentially preserved conflict with observations that melanosomes preserve in fossil feathers as external moulds in an organic matrix. To date, there is no model to explain the latter mode of melanosome preservation. We addressed these issues by degrading feathers in systematic taphonomic experiments incorporating decay, maturation and oxidation in isolation and combination. Our results reveal that the production of mouldic melanosomes requires interactions with an oxidant and is most likely to occur prior to substantial maturation. This constrains the taphonomic conditions under which melanosomes are likely to be fossilized. Critically, our experiments also confirm that keratinous feather structures have a higher preservation potential than melanosomes under a range of diagenetic conditions, supporting hitherto controversial hypotheses that fossil feathers can retain degraded keratinous structures.
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Affiliation(s)
- Tiffany S. Slater
- School of Biological, Earth & Environmental SciencesUniversity College CorkCorkIreland
| | - Maria E. McNamara
- School of Biological, Earth & Environmental SciencesUniversity College CorkCorkIreland
| | - Patrick J. Orr
- UCDSchool of Earth SciencesUniversity College DublinDublinIreland
| | - Tara B. Foley
- Department of Anatomy & NeuroscienceUniversity College CorkCorkIreland
| | - Shosuke Ito
- Department of ChemistryFujita Health University School of Health SciencesToyoakeAichiJapan
| | - Kazumasa Wakamatsu
- Department of ChemistryFujita Health University School of Health SciencesToyoakeAichiJapan
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10
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Bailleul AM, O’Connor J, Schweitzer MH. Dinosaur paleohistology: review, trends and new avenues of investigation. PeerJ 2019; 7:e7764. [PMID: 31579624 PMCID: PMC6768056 DOI: 10.7717/peerj.7764] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022] Open
Abstract
In the mid-19th century, the discovery that bone microstructure in fossils could be preserved with fidelity provided a new avenue for understanding the evolution, function, and physiology of long extinct organisms. This resulted in the establishment of paleohistology as a subdiscipline of vertebrate paleontology, which has contributed greatly to our current understanding of dinosaurs as living organisms. Dinosaurs are part of a larger group of reptiles, the Archosauria, of which there are only two surviving lineages, crocodilians and birds. The goal of this review is to document progress in the field of archosaur paleohistology, focusing in particular on the Dinosauria. We briefly review the "growth age" of dinosaur histology, which has encompassed new and varied directions since its emergence in the 1950s, resulting in a shift in the scientific perception of non-avian dinosaurs from "sluggish" reptiles to fast-growing animals with relatively high metabolic rates. However, fundamental changes in growth occurred within the sister clade Aves, and we discuss this major evolutionary transition as elucidated by histology. We then review recent innovations in the field, demonstrating how paleohistology has changed and expanded to address a diversity of non-growth related questions. For example, dinosaur skull histology has elucidated the formation of curious cranial tissues (e.g., "metaplastic" tissues), and helped to clarify the evolution and function of oral adaptations, such as the dental batteries of duck-billed dinosaurs. Lastly, we discuss the development of novel techniques with which to investigate not only the skeletal tissues of dinosaurs, but also less-studied soft-tissues, through molecular paleontology and paleohistochemistry-recently developed branches of paleohistology-and the future potential of these methods to further explore fossilized tissues. We suggest that the combination of histological and molecular methods holds great potential for examining the preserved tissues of dinosaurs, basal birds, and their extant relatives. This review demonstrates the importance of traditional bone paleohistology, but also highlights the need for innovation and new analytical directions to improve and broaden the utility of paleohistology, in the pursuit of more diverse, highly specific, and sensitive methods with which to further investigate important paleontological questions.
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Affiliation(s)
- Alida M. Bailleul
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Beijing, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, China
| | - Jingmai O’Connor
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Beijing, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, China
| | - Mary H. Schweitzer
- Department of Biology, North Carolina State University, Raleigh, NC, USA
- North Carolina Museum of Natural Science, Raleigh, NC, USA
- Department of Geology, Lund University, Lund, Sweden
- Museum of the Rockies, Montana State University, Bozeman, MT, USA
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11
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Schweitzer MH, Schroeter ER, Cleland TP, Zheng W. Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils. Proteomics 2019; 19:e1800251. [PMID: 31172628 DOI: 10.1002/pmic.201800251] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 05/07/2019] [Indexed: 12/20/2022]
Abstract
Molecular studies have contributed greatly to our understanding of evolutionary processes that act upon virtually every aspect of living organisms. However, these studies are limited with regard to extinct organisms, particularly those from the Mesozoic because fossils pose unique challenges to molecular workflows, and because prevailing wisdom suggests no endogenous molecular components can persist into deep time. Here, the power and potential of a molecular approach to Mesozoic fossils is discussed. Molecular methods that have been applied to Mesozoic fossils-including iconic, non-avian dinosaurs- and the challenges inherent in such analyses, are compared and evaluated. Taphonomic processes resulting in the transition of living organisms from the biosphere into the fossil record are reviewed, and the possible effects of taphonomic alteration on downstream analyses that can be problematic for very old material (e.g., molecular modifications, limitations of on comparative databases) are addressed. Molecular studies applied to ancient remains are placed in historical context, and past and current studies are evaluated with respect to producing phylogenetically and/or evolutionarily significant data. Finally, some criteria for assessing the presence of endogenous biomolecules in very ancient fossil remains are suggested as a starting framework for such studies.
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Affiliation(s)
- Mary Higby Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, 27695, NC.,North Carolina Museum of Natural Sciences, Raleigh, NC.,Museum of the Rockies, Montana State University, Bozeman, MT.,Department of Geology, Lund University, Sölvegatan 12, SE-223 62, Lund, Sweden
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, 27695, NC
| | - Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, 20746, MD
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, 27695, NC
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12
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Combined microscopy and spectroscopy techniques to characterize a fossilized feather with minimal damage to the specimen. Micron 2019; 120:17-24. [DOI: 10.1016/j.micron.2019.01.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 11/20/2022]
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13
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Abstract
Ancient protein analysis is a rapidly developing field of research. Proteins ranging in age from the Quaternary to Jurassic are being used to answer questions about phylogeny, evolution, and extinction. However, these analyses are sometimes contentious, and focus primarily on large vertebrates in sedimentary fossilisation environments; there are few studies of protein preservation in fossils in amber. Here we show exceptionally slow racemisation rates during thermal degradation experiments of resin enclosed feathers, relative to previous thermal degradation experiments of ostrich eggshell, coral skeleton, and limpet shell. We also recover amino acids from two specimens of fossil feathers in amber. The amino acid compositions are broadly similar to those of degraded feathers, but concentrations are very low, suggesting that much of the original protein has been degraded and lost. High levels of racemisation in more apolar, slowly racemising amino acids suggest that some of the amino acids were ancient and therefore original. Our findings indicate that the unique fossilisation environment inside amber shows potential for the recovery of ancient amino acids and proteins.
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14
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Cullen TM, Longstaffe FJ, Wortmann UG, Goodwin MB, Huang L, Evans DC. Stable isotopic characterization of a coastal floodplain forest community: a case study for isotopic reconstruction of Mesozoic vertebrate assemblages. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181210. [PMID: 30891263 PMCID: PMC6408390 DOI: 10.1098/rsos.181210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 01/04/2019] [Indexed: 06/09/2023]
Abstract
Stable isotopes are powerful tools for elucidating ecological trends in extant vertebrate communities, though their application to Mesozoic ecosystems is complicated by a lack of extant isotope data from comparable environments/ecosystems (e.g. coastal floodplain forest environments, lacking significant C4 plant components). We sampled 20 taxa across a broad phylogenetic, body size, and physiological scope from the Atchafalaya River Basin of Louisiana as an environmental analogue to the Late Cretaceous coastal floodplains of North America. Samples were analysed for stable carbon, oxygen and nitrogen isotope compositions from bioapatite and keratin tissues to test the degree of ecological resolution that can be determined in a system with similar environmental conditions, and using similar constraints, as those in many Mesozoic assemblages. Isotopic results suggest a broad overlap in resource use among taxa and considerable terrestrial-aquatic interchange, highlighting the challenges of ecological interpretation in C3 systems, particularly when lacking observational data for comparison. We also propose a modified oxygen isotope-temperature equation that uses mean endotherm and mean ectotherm isotope data to more precisely predict temperature when compared with measured Atchafalaya River water data. These results provide a critical isotopic baseline for coastal floodplain forests, and act as a framework for future studies of Mesozoic palaeoecology.
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Affiliation(s)
- T M Cullen
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada M5S 3B2
- Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, Canada M5S 2C6
| | - F J Longstaffe
- Department of Earth Sciences, The University of Western Ontario, 1151 Richmond Street, London, Ontario, Canada N6A 5B7
| | - U G Wortmann
- Department of Earth Sciences, University of Toronto, 22 Russell Street, Toronto, Ontario, Canada M5S 3B1
| | - M B Goodwin
- University of California Museum of Paleontology, 1101 Valley Life Sciences, Berkeley, CA 94720-4780, USA
| | - L Huang
- Department of Earth Sciences, The University of Western Ontario, 1151 Richmond Street, London, Ontario, Canada N6A 5B7
| | - D C Evans
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada M5S 3B2
- Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, Canada M5S 2C6
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15
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Lindgren J, Sjövall P, Thiel V, Zheng W, Ito S, Wakamatsu K, Hauff R, Kear BP, Engdahl A, Alwmark C, Eriksson ME, Jarenmark M, Sachs S, Ahlberg PE, Marone F, Kuriyama T, Gustafsson O, Malmberg P, Thomen A, Rodríguez-Meizoso I, Uvdal P, Ojika M, Schweitzer MH. Soft-tissue evidence for homeothermy and crypsis in a Jurassic ichthyosaur. Nature 2018; 564:359-365. [PMID: 30518862 DOI: 10.1038/s41586-018-0775-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 10/16/2018] [Indexed: 12/20/2022]
Abstract
Ichthyosaurs are extinct marine reptiles that display a notable external similarity to modern toothed whales. Here we show that this resemblance is more than skin deep. We apply a multidisciplinary experimental approach to characterize the cellular and molecular composition of integumental tissues in an exceptionally preserved specimen of the Early Jurassic ichthyosaur Stenopterygius. Our analyses recovered still-flexible remnants of the original scaleless skin, which comprises morphologically distinct epidermal and dermal layers. These are underlain by insulating blubber that would have augmented streamlining, buoyancy and homeothermy. Additionally, we identify endogenous proteinaceous and lipid constituents, together with keratinocytes and branched melanophores that contain eumelanin pigment. Distributional variation of melanophores across the body suggests countershading, possibly enhanced by physiological adjustments of colour to enable photoprotection, concealment and/or thermoregulation. Convergence of ichthyosaurs with extant marine amniotes thus extends to the ultrastructural and molecular levels, reflecting the omnipresent constraints of their shared adaptation to pelagic life.
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Affiliation(s)
| | - Peter Sjövall
- RISE Research Institutes of Sweden, Chemistry and Materials, Borås, Sweden
| | - Volker Thiel
- Geobiology, Geoscience Centre, University of Göttingen, Göttingen, Germany
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Shosuke Ito
- Department of Chemistry, Fujita Health University School of Health Sciences, Toyoake, Japan
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University School of Health Sciences, Toyoake, Japan
| | | | | | | | - Carl Alwmark
- Department of Geology, Lund University, Lund, Sweden
| | | | | | - Sven Sachs
- Naturkunde-Museum Bielefeld, Abteilung Geowissenschaften, Bielefeld, Germany
| | - Per E Ahlberg
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Federica Marone
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Takeo Kuriyama
- Institute of Natural and Environmental Sciences, University of Hyogo, Hyogo, Japan.,Wildlife Management Research Center, Hyogo, Japan
| | | | - Per Malmberg
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Aurélien Thomen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | | | - Per Uvdal
- Chemical Physics, Department of Chemistry, Lund University, Lund, Sweden
| | - Makoto Ojika
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mary H Schweitzer
- Department of Geology, Lund University, Lund, Sweden.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,North Carolina Museum of Natural Sciences, Raleigh, NC, USA
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16
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Schweitzer MH, Zheng W, Moyer AE, Sjövall P, Lindgren J. Preservation potential of keratin in deep time. PLoS One 2018; 13:e0206569. [PMID: 30485294 PMCID: PMC6261410 DOI: 10.1371/journal.pone.0206569] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 10/16/2018] [Indexed: 11/18/2022] Open
Abstract
Multiple fossil discoveries and taphonomic experiments have established the durability of keratin. The utility and specificity of antibodies to identify keratin peptides has also been established, both in extant feathers under varying treatment conditions, and in feathers from extinct organisms. Here, we show localization of feather-keratin antibodies to control and heat-treated feathers, testifying to the repeatability of initial data supporting the preservation potential of keratin. We then show new data at higher resolution that demonstrates the specific response of these antibodies to the feather matrix, we support the presence of protein in heat-treated feathers using ToF-SIMS, and we apply these methods to a fossil feather preserved in the unusual environment of sinter hot springs. We stress the importance of employing realistic conditions such as sediment burial when designing experiments intended as proxies for taphonomic processes occurring in the fossil record. Our data support the hypothesis that keratin, particularly the β-keratin that comprises feathers, has potential to preserve in fossil remains.
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Affiliation(s)
- Mary Higby Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, United States of America
- Department of Geology, Lund University, Lund, Sweden
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Alison E. Moyer
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Peter Sjövall
- RISE Research Institutes of Sweden, Chemistry and Materials, Borås, Sweden
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17
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Moyer AE, Zheng W, Schweitzer MH. Microscopic and immunohistochemical analyses of the claw of the nesting dinosaur, Citipati osmolskae. Proc Biol Sci 2017; 283:rspb.2016.1997. [PMID: 28120795 DOI: 10.1098/rspb.2016.1997] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 10/19/2016] [Indexed: 02/02/2023] Open
Abstract
One of the most well-recognized Cretaceous fossils is Citipati osmolskae (MPC-D 100/979), an oviraptorid dinosaur discovered in brooding position on a nest of unhatched eggs. The original description refers to a thin lens of white material extending from a manus ungual, which was proposed to represent original keratinous claw sheath that, in life, would have covered it. Here, we test the hypothesis that this exceptional morphological preservation extends to the molecular level. The fossil sheath was compared with that of extant birds, revealing similar morphology and microstructural organization. In living birds, the claw sheath consists primarily of two structural proteins; alpha-keratin, expressed in all vertebrates, and beta-keratin, found only in reptiles and birds (sauropsids). We employed antibodies raised against avian feathers, which comprise almost entirely of beta-keratin, to demonstrate that fossil tissues respond with the same specificity, though less intensity, as those from living birds. Furthermore, we show that calcium chelation greatly increased antibody reactivity, suggesting a role for calcium in the preservation of this fossil material.
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Affiliation(s)
- Alison E Moyer
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA .,Department of Biology, Drexel University, Philadelphia, PA 19104, USA
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Mary H Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA.,North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
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18
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Biochemistry and adaptive colouration of an exceptionally preserved juvenile fossil sea turtle. Sci Rep 2017; 7:13324. [PMID: 29042651 PMCID: PMC5645316 DOI: 10.1038/s41598-017-13187-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/19/2017] [Indexed: 12/27/2022] Open
Abstract
The holotype (MHM-K2) of the Eocene cheloniine Tasbacka danica is arguably one of the best preserved juvenile fossil sea turtles on record. Notwithstanding compactional flattening, the specimen is virtually intact, comprising a fully articulated skeleton exposed in dorsal view. MHM-K2 also preserves, with great fidelity, soft tissue traces visible as a sharply delineated carbon film around the bones and marginal scutes along the edge of the carapace. Here we show that the extraordinary preservation of the type of T. danica goes beyond gross morphology to include ultrastructural details and labile molecular components of the once-living animal. Haemoglobin-derived compounds, eumelanic pigments and proteinaceous materials retaining the immunological characteristics of sauropsid-specific β-keratin and tropomyosin were detected in tissues containing remnant melanosomes and decayed keratin plates. The preserved organics represent condensed remains of the cornified epidermis and, likely also, deeper anatomical features, and provide direct chemical evidence that adaptive melanism – a biological means used by extant sea turtle hatchlings to elevate metabolic and growth rates – had evolved 54 million years ago.
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19
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An Exceptionally Preserved Three-Dimensional Armored Dinosaur Reveals Insights into Coloration and Cretaceous Predator-Prey Dynamics. Curr Biol 2017; 27:2514-2521.e3. [DOI: 10.1016/j.cub.2017.06.071] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/16/2017] [Accepted: 06/27/2017] [Indexed: 02/08/2023]
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20
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Molecular evidence of keratin and melanosomes in feathers of the Early Cretaceous bird Eoconfuciusornis. Proc Natl Acad Sci U S A 2016; 113:E7900-E7907. [PMID: 27872291 DOI: 10.1073/pnas.1617168113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microbodies associated with feathers of both nonavian dinosaurs and early birds were first identified as bacteria but have been reinterpreted as melanosomes. Whereas melanosomes in modern feathers are always surrounded by and embedded in keratin, melanosomes embedded in keratin in fossils has not been demonstrated. Here we provide multiple independent molecular analyses of both microbodies and the associated matrix recovered from feathers of a new specimen of the basal bird Eoconfuciusornis from the Early Cretaceous Jehol Biota of China. Our work represents the oldest ultrastructural and immunological recognition of avian beta-keratin from an Early Cretaceous (∼130-Ma) bird. We apply immunogold to identify protein epitopes at high resolution, by localizing antibody-antigen complexes to specific fossil ultrastructures. Retention of original keratinous proteins in the matrix surrounding electron-opaque microbodies supports their assignment as melanosomes and adds to the criteria employable to distinguish melanosomes from microbial bodies. Our work sheds new light on molecular preservation within normally labile tissues preserved in fossils.
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