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Morin E, Oldfield EM, Baković M, Bordes JG, Castel JC, Crevecoeur I, Rougier H, Monnier G, Tostevin G, Buckley M. A double-blind comparison of morphological and collagen fingerprinting (ZooMS) methods of skeletal identifications from Paleolithic contexts. Sci Rep 2023; 13:18825. [PMID: 37914773 PMCID: PMC10620384 DOI: 10.1038/s41598-023-45843-4] [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: 06/19/2023] [Accepted: 10/24/2023] [Indexed: 11/03/2023] Open
Abstract
Modeling the subsistence strategies of prehistoric groups depends on the accuracy of the faunal identifications that provide the basis for these models. However, our knowledge remains limited about the reproducibility of published taxonomic identifications and how they accurately reflect the range of species deposited in the archaeological record. This study compares taxonomic identifications at three Paleolithic sites (Saint-Césaire and Le Piage in France, Crvena Stijena in Montenegro) characterized by high levels of fragmentation. Identifications at these sites were derived using two methods: morphological identification and collagen fingerprinting, the latter a peptide-based approach known as ZooMS. Using a double-blind experimental design, we show that the two methods give taxonomic profiles that are statistically indistinguishable at all three sites. However, rare species and parts difficult to identify such as ribs seem more frequently associated with errors of identification. Comparisons with the indeterminate fraction indicate that large game is over-represented in the ZooMS sample at two of the three sites. These differences possibly signal differential fragmentation of elements from large species. Collagen fingerprinting can produce critical insights on the range distribution of animal prey in the past while also contributing to improved models of taphonomic processes and subsistence behavior.
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Affiliation(s)
- Eugène Morin
- Department of Anthropology, Trent University, DNA Bldg Block C, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada.
- Université de Bordeaux, PACEA, Allée Geoffroy St-Hilaire CS 50023, 33615, Pessac Cedex, France.
| | - Ellie-May Oldfield
- School of Natural Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Mile Baković
- Center for Conservation and Archaeology of Montenegro, UI. Njegoseva bb., Cetinje, Montenegro
| | - Jean-Guillaume Bordes
- Université de Bordeaux, PACEA, Allée Geoffroy St-Hilaire CS 50023, 33615, Pessac Cedex, France
| | - Jean-Christophe Castel
- Département d'Archéozoologie, Muséum d'histoire naturelle, Route de Malagnou 1, 1208, Geneva, Switzerland
| | - Isabelle Crevecoeur
- Université de Bordeaux, PACEA, Allée Geoffroy St-Hilaire CS 50023, 33615, Pessac Cedex, France
| | - Hélène Rougier
- Department of Anthropology, California State University, Northridge, 18111 Nordhoff St., Northridge, CA, 91330-8244, USA
| | - Gilliane Monnier
- Department of Anthropology, University of Minnesota, 395 H.H. Humphrey Center, 301 19th Ave. S, Minneapolis, MN, 55455, USA
| | - Gilbert Tostevin
- Department of Anthropology, University of Minnesota, 395 H.H. Humphrey Center, 301 19th Ave. S, Minneapolis, MN, 55455, USA
| | - Michael Buckley
- School of Natural Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
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2
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Gautney JR. A new approach to exploratory data analysis in hominin phylogenetic reconstruction. J Hum Evol 2023; 182:103412. [PMID: 37499423 DOI: 10.1016/j.jhevol.2023.103412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/29/2023]
Abstract
The phylogenetic relationships between fossil hominin taxa have been a contentious topic for decades. Recent discoveries of new taxa, rather than resolving the issue, have only further confused it. Compounding this problem are the limitations of some of the tools frequently used by paleoanthropologists to analyze these relationships. Most commonly, phylogenetic questions are investigated using analytical methods such as maximum parsimony and Bayesian analysis. While these are useful analytical tools, these tree-building methods can have limitations when investigating taxa that may have complex evolutionary histories. Exploratory data analysis can provide information about patterns in a dataset that are obscured by tree-based methods. These patterns include phylogenetic signal conflict, which is not depicted in tree-based methods. Signal conflict can have a number of sources, including methodological issues with character choice, taxonomic issues, homoplasy, and gene flow between taxa. In this study, an exploratory data analysis of fossil hominin morphological data is conducted using the tree-based analytical method neighbor-joining and the network-based analytical method neighbor-net with the goal of visualizing phylogenetic signal conflict within a hominin morphological data set. The data set is divided into cranial regions, and each cranial region is analyzed individually to investigate which regions of the skull contain the highest levels of signal conflict. Results of this analysis show that conflicting phylogenetic signals are present in the hominin fossil record during the relatively speciose period between 3 and 1 Ma, and they also indicate that levels of signal conflict vary by cranial region. Possible sources of these conflicting signals are then explored. Exploratory data analyses such as this can be a useful tool in generating phylogenetic hypotheses and in refining character choice. This study also highlights the value network-based approaches can bring to the hominin phylogenetic analysis toolkit.
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Affiliation(s)
- Joanna R Gautney
- Department of Sociology and Anthropology, Weber State University, 1299 Edvalson St., Ogden, UT, USA.
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3
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Génin F, Mazza PP, Pellen R, Rabineau M, Aslanian D, Masters JC. Co-evolution assists geographic dispersal: the case of Madagascar. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Interspecific associations may limit the dispersal of individual species, but may also facilitate it when entire co-evolved systems expand their geographic ranges. We tested the recent proposal that episodic land bridges linked Africa and Madagascar at three stages during the Cenozoic by comparing divergence estimates of Madagascar’s angiosperm taxa with their dispersal mechanisms. Plants that rely on gravity for seed dispersal indicate at least two episodes of land connection between Africa and Madagascar, in the Early Palaeocene and Early Oligocene. Seed dispersal by strepsirrhine primates possibly evolved in the Palaeocene, with the divergence of at least one endemic Malagasy angiosperm genus, Burasaia (Menispermaceae). This genus may have facilitated the lemur colonization of Madagascar. Frugivory, nectarivory and gummivory probably generalized in the Oligocene, with the co-evolution of modern lemurs and at least 10 new Malagasy angiosperm families. In the Late Miocene, more angiosperms were probably brought from Africa by birds via a discontinuous land connection, and radiated on Madagascar in diffuse association with birds (asities) and dwarf nocturnal lemurs (cheirogaleids). During the same connective episode, Madagascar was probably colonized by hippopotamuses, which both followed and re-seeded a variety of plants, forming the grassy Uapaca ‘tapia’ forest and ericoid ‘savoka’ thicket.
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Affiliation(s)
- Fabien Génin
- African Primate Initiative for Ecology and Speciation (APIES) and Africa Earth Observatory Network (AEON), Earth Stewardship Science Research Institute, Nelson Mandela University , Gqeberha (Port Elizabeth) , South Africa
| | - Paul Pa Mazza
- Department of Earth Sciences, University of Florence , via La Pira, Florence , Italy
| | - Romain Pellen
- African Primate Initiative for Ecology and Speciation (APIES) and Africa Earth Observatory Network (AEON), Earth Stewardship Science Research Institute, Nelson Mandela University , Gqeberha (Port Elizabeth) , South Africa
| | - Marina Rabineau
- CNRS, Institut Français de Recherche pour l’Exploration de la Mer (IFREMER ), UMR 6538 Geo-Ocean, IUEM, Univ Brest, Plouzané , France
| | - Daniel Aslanian
- CNRS, Institut Français de Recherche pour l’Exploration de la Mer (IFREMER ), UMR 6538 Geo-Ocean, IUEM, Univ Brest, Plouzané , France
| | - Judith C Masters
- African Primate Initiative for Ecology and Speciation (APIES) and Africa Earth Observatory Network (AEON), Earth Stewardship Science Research Institute, Nelson Mandela University , Gqeberha (Port Elizabeth) , South Africa
- Department of Botany & Zoology, Stellenbosch University , Stellenbosch , South Africa
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4
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Abstract
The goal of paleoproteomics is to characterize proteins from specimens that have been subjected to the degrading and obscuring effects of time, thus obtaining biological information about tissues or organisms both unobservable in the present and unobtainable through morphological study. Although the description of sequences from Tyrannosaurus rex and Brachylophosaurus canadensis suggested that proteins may persist over tens of millions of years, the majority of paleoproteomic analyses have focused on historical, archeological, or relatively young paleontological samples that rarely exceed 1 million years in age. However, recent advances in methodology and analyses of diverse tissues types (e.g., fossil eggshell, dental enamel) have begun closing the large window of time that remains unexplored in the fossil history of the Cenozoic. In this perspective, we discuss the history and current state of deep time paleoproteomics (DTPp), here defined as paleoproteomic study of samples ∼1 million years (1 Ma) or more in age. We then discuss the future of DTPp research, including what we see as critical ways the field can expand, advancements in technology that can be utilized, and the types of questions DTPp can address if such a future is realized.
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Affiliation(s)
- Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, Maryland 20746, United States
| | - Mary H Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States.,North Carolina Museum of Natural Sciences, Raleigh, North Carolina 27605, United States.,Department of Geology, Lund University, Lund SE-221 00, Sweden
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5
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Trends in deamidation across archaeological bones, ceramics and dental calculus. Methods 2021; 200:67-79. [PMID: 34450289 DOI: 10.1016/j.ymeth.2021.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/04/2021] [Accepted: 08/14/2021] [Indexed: 11/23/2022] Open
Abstract
The accumulation of post-translational modifications (PTMs) in proteins throughout the lifecycle has been studied for decades, particularly more so with the advent of soft-ionization mass spectrometry-based proteomic techniques. However, particular PTMs, such as the deamidations of asparagine and glutamine residues, continue to accumulate in proteins that remain into the forensic, archaeological, and palaeontological records. The accurate measurement of these ancient 'molecular timers' has been proposed as a method to not only differentiate between exogenous and endogenous proteins within complex mixtures (i.e., contamination), but also as a method of providing relative age estimations into geological time. In this study we explored the extent to which deamidation varies with chronological age across different proteins in bones, as well as investigated differences between proteins across dental calculus and archaeological ceramics. We also analysed the relationships between the observed extent of deamidation and the protein primary structure. We found that collagen obtained from archaeological bones showed a chronological dependence on the extent of deamidation observed, but only when they were from similar environments, supporting prior suggestions about 'thermal age' being a major influence on the deamidation observed. Our study on non-collagenous proteins (NCPs) in archaeological bones showed that while biglycan, and to a lesser extent chondroadherin, showed positive correlations between geological age and the extent of deamidation, others including fetuin-A and serum albumin did not. However, despite the well-known dependence of deamidation on the three-dimensional structure of the peptides, we were unable to find any clear correlation between the structural motifs of the peptides in archaeological bones and the extent of deamidation observed. Our analysis of a set of food proteins obtained from Neolithic archaeological ceramics in Çatalhöyük also showed similar deamidation levels irrespective of the protein structure. Overall, our results suggest that deamidation in archaeological samples could be useful for obtaining additional information beyond identification of species and tissue type, be that as a measure of protein endogeneity and potential contamination, or a measure of protein degradation, or as an indicator of thermal age and for relative dating; however, further research needs to be undertaken to understand why particular proteins are better for this than others, going beyond simple consideration of their secondary structure.
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6
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Harvey VL, Keating JN, Buckley M. Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201955. [PMID: 34430038 PMCID: PMC8355665 DOI: 10.1098/rsos.201955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 07/20/2021] [Indexed: 05/12/2023]
Abstract
Ray-finned fishes (Actinopterygii) are the largest and most diverse group of vertebrates, comprising over half of all living vertebrate species. Phylogenetic relationships between ray-finned fishes have historically pivoted on the study of morphology, which has notoriously failed to resolve higher order relationships, such as within the percomorphs. More recently, comprehensive genomic analyses have provided further resolution of actinopterygian phylogeny, including higher order relationships. Such analyses are rightfully regarded as the 'gold standard' for phylogenetics. However, DNA retrieval requires modern or well-preserved tissue and is less likely to be preserved in archaeological or fossil specimens. By contrast, some proteins, such as collagen, are phylogenetically informative and can survive into deep time. Here, we test the utility of collagen type I amino acid sequences for phylogenetic estimation of ray-finned fishes. We estimate topology using Bayesian approaches and compare the congruence of our estimated trees with published genomic phylogenies. Furthermore, we apply a Bayesian molecular clock approach and compare estimated divergence dates with previously published genomic clock analyses. Our collagen-derived trees exhibit 77% of node positions as congruent with recent genomic-derived trees, with the majority of discrepancies occurring in higher order node positions, almost exclusively within the Percomorpha. Our molecular clock trees present divergence times that are fairly comparable with genomic-based phylogenetic analyses. We estimate the mean node age of Actinopteri at ∼293 million years (Ma), the base of Teleostei at ∼211 Ma and the radiation of percomorphs beginning at ∼141 Ma (∼350 Ma, ∼250-283 Ma and ∼120-133 Ma in genomic trees, respectively). Finally, we show that the average rate of collagen (I) sequence evolution is 0.9 amino acid substitutions for every million years of divergence, with the α3 (I) sequence evolving the fastest, followed by the α2 (I) chain. This is the quickest rate known for any vertebrate group. We demonstrate that phylogenetic analyses using collagen type I amino acid sequences generate tangible signals for actinopterygians that are highly congruent with recent genomic-level studies. However, there is limited congruence within percomorphs, perhaps due to clade-specific functional constraints acting upon collagen sequences. Our results provide important insights for future phylogenetic analyses incorporating extinct actinopterygian species via collagen (I) sequencing.
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Affiliation(s)
- Virginia L. Harvey
- Department of Earth and Environmental Sciences, School of Natural Sciences, University of Manchester, Manchester M13 9PL, UK
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Joseph N. Keating
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Michael Buckley
- Department of Earth and Environmental Sciences, School of Natural Sciences, University of Manchester, Manchester M13 9PL, UK
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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7
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Mickleburgh HL, Schwalbe EC, Bonicelli A, Mizukami H, Sellitto F, Starace S, Wescott DJ, Carter DO, Procopio N. Human Bone Proteomes before and after Decomposition: Investigating the Effects of Biological Variation and Taphonomic Alteration on Bone Protein Profiles and the Implications for Forensic Proteomics. J Proteome Res 2021; 20:2533-2546. [PMID: 33683123 PMCID: PMC8155572 DOI: 10.1021/acs.jproteome.0c00992] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
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Bone proteomic studies
using animal proxies and skeletonized human
remains have delivered encouraging results in the search for potential
biomarkers for precise and accurate post-mortem interval (PMI) and
the age-at-death (AAD) estimation in medico-legal investigations.
The development of forensic proteomics for PMI and AAD estimation
is in critical need of research on human remains throughout decomposition,
as currently the effects of both inter-individual biological differences
and taphonomic alteration on the survival of human bone protein profiles
are unclear. This study investigated the human bone proteome in four
human body donors studied throughout decomposition outdoors. The effects
of ageing phenomena (in vivo and post-mortem) and
intrinsic and extrinsic variables on the variety and abundancy of
the bone proteome were assessed. Results indicate that taphonomic
and biological variables play a significant role in the survival of
proteins in bone. Our findings suggest that inter-individual and inter-skeletal
differences in bone mineral density (BMD) are important variables
affecting the survival of proteins. Specific proteins survive better
within the mineral matrix due to their mineral-binding properties.
The mineral matrix likely also protects these proteins by restricting
the movement of decomposer microbes. New potential biomarkers for
PMI estimation and AAD estimation were identified. Future development
of forensic bone proteomics should include standard measurement of
BMD and target a combination of different biomarkers.
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Affiliation(s)
- Hayley L Mickleburgh
- Department of Cultural Sciences, Linnaeus University, Kalmar 352 52, Sweden.,Forensic Anthropology Center, Texas State University, San Marcos 78666, Texas, United States
| | - Edward C Schwalbe
- Forensic Science Research Group, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Northumbria University Newcastle, Newcastle Upon Tyne NE1 8ST, U. K
| | - Andrea Bonicelli
- Forensic Science Research Group, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Northumbria University Newcastle, Newcastle Upon Tyne NE1 8ST, U. K
| | - Haruka Mizukami
- Forensic Science Research Group, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Northumbria University Newcastle, Newcastle Upon Tyne NE1 8ST, U. K
| | - Federica Sellitto
- Forensic Science Research Group, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Northumbria University Newcastle, Newcastle Upon Tyne NE1 8ST, U. K
| | - Sefora Starace
- Dipartimento di Chimica, University of Turin, Via P. Giuria 7, 10125 Turin, Italy
| | - Daniel J Wescott
- Forensic Anthropology Center, Texas State University, San Marcos 78666, Texas, United States
| | - David O Carter
- Forensic Sciences Unit, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu 96816, Hawaii, United States
| | - Noemi Procopio
- Forensic Science Research Group, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Northumbria University Newcastle, Newcastle Upon Tyne NE1 8ST, U. K
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8
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Lugli F, Sciutto G, Oliveri P, Malegori C, Prati S, Gatti L, Silvestrini S, Romandini M, Catelli E, Casale M, Talamo S, Iacumin P, Benazzi S, Mazzeo R. Near-infrared hyperspectral imaging (NIR-HSI) and normalized difference image (NDI) data processing: An advanced method to map collagen in archaeological bones. Talanta 2021; 226:122126. [PMID: 33676680 DOI: 10.1016/j.talanta.2021.122126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 12/28/2022]
Abstract
In the present study, an innovative and highly efficient near-infrared hyperspectral imaging (NIR-HSI) method is proposed to provide spectral maps able to reveal collagen distribution in large-size bones, also offering semi-quantitative estimations. A recently introduced method for the construction of chemical maps, based on Normalized Difference Images (NDI), is declined in an innovative approach, through the exploitation of the NDI values computed for each pixel of the hyperspectral image to localize collagen and to extract information on its content by a direct comparison with known reference samples. The developed approach addresses an urgent issue of the analytical chemistry applied to bioarcheology researches, which rely on well-preserved collagen in bones to obtain key information on chronology, paleoecology and taxonomy. Indeed, the high demand for large-sample datasets and the consequent application of a wide variety of destructive analytical methods led to the considerable destruction of precious bone samples. NIR-HSI pre-screening allows researchers to properly select the sampling points for subsequent specific analyses, to minimize costs and time and to preserve integrity of archaeological bones (which are available in a very limited amount), providing further opportunities to understand our past.
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Affiliation(s)
- F Lugli
- University of Bologna, Department of Cultural Heritage, Ravenna Campus, Via Degli Ariani, 1, 48121, Ravenna, Italy
| | - G Sciutto
- University of Bologna, Department of Chemistry "G. Ciamician", Ravenna Campus, Via Guaccimanni, 42, 48121, Ravenna, Italy.
| | - P Oliveri
- University of Genova, Department of Pharmacy, Viale Cembrano 4, I-16148, Genova, Italy.
| | - C Malegori
- University of Genova, Department of Pharmacy, Viale Cembrano 4, I-16148, Genova, Italy
| | - S Prati
- University of Bologna, Department of Chemistry "G. Ciamician", Ravenna Campus, Via Guaccimanni, 42, 48121, Ravenna, Italy
| | - L Gatti
- University of Bologna, Department of Chemistry "G. Ciamician", Ravenna Campus, Via Guaccimanni, 42, 48121, Ravenna, Italy
| | - S Silvestrini
- University of Bologna, Department of Cultural Heritage, Ravenna Campus, Via Degli Ariani, 1, 48121, Ravenna, Italy
| | - M Romandini
- University of Bologna, Department of Cultural Heritage, Ravenna Campus, Via Degli Ariani, 1, 48121, Ravenna, Italy
| | - E Catelli
- University of Bologna, Department of Chemistry "G. Ciamician", Ravenna Campus, Via Guaccimanni, 42, 48121, Ravenna, Italy
| | - M Casale
- University of Genova, Department of Pharmacy, Viale Cembrano 4, I-16148, Genova, Italy
| | - S Talamo
- University of Bologna, Department of Chemistry "G. Ciamician", Via Selmi, 2, 40126, Bologna, Italy; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - P Iacumin
- University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area Delle Scienze, 11/a, Parma, Italy
| | - S Benazzi
- University of Bologna, Department of Cultural Heritage, Ravenna Campus, Via Degli Ariani, 1, 48121, Ravenna, Italy; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - R Mazzeo
- University of Bologna, Department of Chemistry "G. Ciamician", Ravenna Campus, Via Guaccimanni, 42, 48121, Ravenna, Italy
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9
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Hendy J. Ancient protein analysis in archaeology. SCIENCE ADVANCES 2021; 7:7/3/eabb9314. [PMID: 33523896 PMCID: PMC7810370 DOI: 10.1126/sciadv.abb9314] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/20/2020] [Indexed: 05/10/2023]
Abstract
The analysis of ancient proteins from paleontological, archeological, and historic materials is revealing insights into past subsistence practices, patterns of health and disease, evolution and phylogeny, and past environments. This review tracks the development of this field, discusses some of the major methodological strategies used, and synthesizes recent developments in archeological applications of ancient protein analysis. Moreover, this review highlights some of the challenges faced by the field and potential future directions, arguing that the development of minimally invasive or nondestructive techniques, strategies for protein authentication, and the integration of ancient protein analysis with other biomolecular techniques are important research strategies as this field grows.
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Affiliation(s)
- Jessica Hendy
- BioArCh, Department of Archaeology, University of York, York, UK
- Max Planck Institute for the Science of Human History, Jena, Germany.
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10
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Palaeoproteomic analysis of Pleistocene cave hyenas from east Asia. Sci Rep 2020; 10:16674. [PMID: 33028848 PMCID: PMC7541484 DOI: 10.1038/s41598-020-73542-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/14/2020] [Indexed: 12/19/2022] Open
Abstract
The spotted hyena (Crocuta crocuta) is the only extant species of the genus Crocuta, which once occupied a much wider range during the Pliocene and Pleistocene. However, its origin and evolutionary history is somewhat contentious due to discordances between morphological, nuclear, and mitochondrial data. Due to the limited molecular data from east Asian Crocuta, also known as cave hyena, and the difficulty of extracting ancient DNA from this area, here we present proteomic analysis of cave hyenas from three locations in northern China. This marks the first proteomic data generated from cave hyenas, adding new molecular data to the east Asian populations. Phylogenetic analysis based on these protein sequences reveals two different groups of cave hyenas in east Asia, one of which could not be distinguished from modern spotted hyenas from northern Africa, tentatively the result of previously suggested gene flow between these lineages. With developments of instrumentation and analytical methods, proteomics holds promising potential for molecular phylogenetic reconstructions of ancient fauna previously thought to be unreachable using ancient DNA.
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11
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Buckley M, Harvey VL, Orihuela J, Mychajliw AM, Keating JN, Milan JNA, Lawless C, Chamberlain AT, Egerton VM, Manning PL. Collagen Sequence Analysis Reveals Evolutionary History of Extinct West Indies Nesophontes (Island-Shrews). Mol Biol Evol 2020; 37:2931-2943. [PMID: 32497204 PMCID: PMC7530613 DOI: 10.1093/molbev/msaa137] [Citation(s) in RCA: 6] [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] [Indexed: 12/04/2022] Open
Abstract
Ancient biomolecule analyses are proving increasingly useful in the study of evolutionary patterns, including extinct organisms. Proteomic sequencing techniques complement genomic approaches, having the potential to examine lineages further back in time than achievable using ancient DNA, given the less stringent preservation requirements. In this study, we demonstrate the ability to use collagen sequence analyses via proteomics to assist species delimitation as a foundation for informing evolutionary patterns. We uncover biogeographic information of an enigmatic and recently extinct lineage of Nesophontes across their range on the Caribbean islands. First, evolutionary relationships reconstructed from collagen sequences reaffirm the affinity of Nesophontes and Solenodon as sister taxa within Solenodonota. This relationship helps lay the foundation for testing geographical isolation hypotheses across islands within the Greater Antilles, including movement from Cuba toward Hispaniola. Second, our results are consistent with Cuba having just two species of Nesophontes (N. micrus and N. major) that exhibit intrapopulation morphological variation. Finally, analysis of the recently described species from the Cayman Islands (N. hemicingulus) indicates that it is a closer relative to N. major rather than N. micrus as previously speculated. This proteomic sequencing improves our understanding of the origin, evolution, and distribution of this extinct mammal lineage, particularly with respect to the approximate timing of speciation. Such knowledge is vital for this biodiversity hotspot, where the magnitude of recent extinctions may obscure true estimates of species richness in the past.
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Affiliation(s)
- Michael Buckley
- Interdisciplinary Centre for Ancient Life, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Virginia L Harvey
- Interdisciplinary Centre for Ancient Life, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Johanset Orihuela
- Department of Earth and Environment, Florida International University, Miami, FL
| | - Alexis M Mychajliw
- La Brea Tar Pits & Museum, Natural History Museum of Los Angeles County, Los Angeles, CA
| | - Joseph N Keating
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
| | - Juan N Almonte Milan
- Museo Nacional de Historia Natural “Prof. Eugenio de Jesús Marcano”, Santo Domingo, Dominican Republic
| | - Craig Lawless
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Andrew T Chamberlain
- Interdisciplinary Centre for Ancient Life, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
| | - Victoria M Egerton
- Interdisciplinary Centre for Ancient Life, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
- The Children’s Museum of Indianapolis, Natural Sciences, Indianapolis, IN
| | - Phillip L Manning
- Interdisciplinary Centre for Ancient Life, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
- The Children’s Museum of Indianapolis, Natural Sciences, Indianapolis, IN
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Harvey VL, LeFebvre MJ, deFrance SD, Toftgaard C, Drosou K, Kitchener AC, Buckley M. Preserved collagen reveals species identity in archaeological marine turtle bones from Caribbean and Florida sites. ROYAL SOCIETY OPEN SCIENCE 2019; 6:191137. [PMID: 31824722 PMCID: PMC6837194 DOI: 10.1098/rsos.191137] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/04/2019] [Indexed: 05/03/2023]
Abstract
Advancements in molecular science are continually improving our knowledge of marine turtle biology and evolution. However, there are still considerable gaps in our understanding, such as past marine turtle distributions, which can benefit from advanced zooarchaeological analyses. Here, we apply collagen fingerprinting to 130 archaeological marine turtle bone samples up to approximately 2500 years old from the Caribbean and Florida's Gulf Coast for faunal identification, finding the vast majority of samples (88%) to contain preserved collagen despite deposition in the tropics. All samples can be identified to species-level with the exception of the Kemp's ridley (Lepidochelys kempii) and olive ridley (L. olivacea) turtles, which can be separated to genus level, having diverged from one another only approximately 5 Ma. Additionally, we identify a single homologous peptide that allows the separation of archaeological green turtle samples, Chelonia spp., into two distinct groups, which potentially signifies a difference in genetic stock. The majority of the archaeological samples are identified as green turtle (Chelonia spp.; 63%), with hawksbill (Eretmochelys imbricata; 17%) and ridley turtles (Lepidochelys spp.; 3%) making up smaller proportions of the assemblage. There were no molecular identifications of the loggerhead turtle (Caretta caretta) in the assemblage despite 9% of the samples being morphologically identified as such, highlighting the difficulties in relying on morphological identifications alone in archaeological remains. Finally, we present the first marine turtle molecular phylogeny using collagen (I) amino acid sequences and find our analyses match recent phylogenies based on nuclear and mitochondrial DNA. Our results highlight the advantage of using collagen fingerprinting to supplement morphological analyses of turtle bones and support the usefulness of this technique for assessing their past distributions across the Caribbean and Florida's Gulf Coast, especially in these tropical environments where DNA preservation may be poor.
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Affiliation(s)
- Virginia L. Harvey
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Michelle J. LeFebvre
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Susan D. deFrance
- Department of Anthropology, University of Florida, Gainesville, FL 32611, USA
| | - Casper Toftgaard
- The SAXO Institute, University of Copenhagen, Karen Blixens Plads 8, 2300 København S, Denmark
- National Museum of Denmark, Nationalmuseet, Ny Vestergade 10, Prinsens Palæ, DK-1471, København K, Denmark
| | - Konstantina Drosou
- KNH Centre for Biomedical Egyptology, School of Biological Sciences, 99 Oxford Road, Manchester, M13 9PG, UK
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- The University of Edinburgh, Institute of Geography, School of Geosciences, Drummond Street, Edinburgh, EH8 9XP, UK
| | - Michael Buckley
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Buckley M, Lawless C, Rybczynski N. Collagen sequence analysis of fossil camels, Camelops and c.f. Paracamelus, from the Arctic and sub-Arctic of Plio-Pleistocene North America. J Proteomics 2019; 194:218-225. [DOI: 10.1016/j.jprot.2018.11.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/02/2018] [Accepted: 11/19/2018] [Indexed: 11/27/2022]
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Gu M, Buckley M. Semi-supervised machine learning for automated species identification by collagen peptide mass fingerprinting. BMC Bioinformatics 2018; 19:241. [PMID: 29940843 PMCID: PMC6019507 DOI: 10.1186/s12859-018-2221-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 05/28/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biomolecular methods for species identification are increasingly being utilised in the study of changing environments, both at the microscopic and macroscopic levels. High-throughput peptide mass fingerprinting has been largely applied to bacterial identification, but increasingly used to identify archaeological and palaeontological skeletal material to yield information on past environments and human-animal interaction. However, as applications move away from predominantly domesticate and the more abundant wild fauna to a much wider range of less common taxa that do not yet have genetically-derived sequence information, robust methods of species identification and biomarker selection need to be determined. RESULTS Here we developed a supervised machine learning algorithm for classifying the species of ancient remains based on collagen fingerprinting. The aim was to minimise requirements on prior knowledge of known species while yielding satisfactory sensitivity and specificity. The algorithm uses iterations of a modified random forest classifier with a similarity scoring system to expand its identified samples. We tested it on a set of 6805 spectra and found that a high level of accuracy can be achieved with a training set of five identified specimens per taxon. CONCLUSIONS This method consistently achieves higher accuracy than two-dimensional principal component analysis and similar accuracy with hierarchical clustering using optimised parameters, which greatly reduces requirements for human input. Within the vertebrata, we demonstrate that this method was able to achieve the taxonomic resolution of family or sub-family level whereas the genus- or species-level identification may require manual interpretation or further experiments. In addition, it also identifies additional species biomarkers than those previously published.
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Affiliation(s)
- Muxin Gu
- Michael Smith Building, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Michael Buckley
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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Cappellini E, Prohaska A, Racimo F, Welker F, Pedersen MW, Allentoft ME, de Barros Damgaard P, Gutenbrunner P, Dunne J, Hammann S, Roffet-Salque M, Ilardo M, Moreno-Mayar JV, Wang Y, Sikora M, Vinner L, Cox J, Evershed RP, Willerslev E. Ancient Biomolecules and Evolutionary Inference. Annu Rev Biochem 2018; 87:1029-1060. [PMID: 29709200 DOI: 10.1146/annurev-biochem-062917-012002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past three decades, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field.
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Affiliation(s)
- Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Ana Prohaska
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Fernando Racimo
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Frido Welker
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | | | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Peter de Barros Damgaard
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Petra Gutenbrunner
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Julie Dunne
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Simon Hammann
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom; .,Department of Anthropology and Archaeology, University of Bristol, Bristol BS8 1UU, United Kingdom
| | - Mélanie Roffet-Salque
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Melissa Ilardo
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Yucheng Wang
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Jürgen Cox
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Richard P Evershed
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; , .,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
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Cleland TP, Schroeter ER, Feranec RS, Vashishth D. Peptide sequences from the first Castoroides ohioensis skull and the utility of old museum collections for palaeoproteomics. Proc Biol Sci 2017; 283:rspb.2016.0593. [PMID: 27306052 DOI: 10.1098/rspb.2016.0593] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/19/2016] [Indexed: 11/12/2022] Open
Abstract
Vertebrate fossils have been collected for hundreds of years and are stored in museum collections around the world. These remains provide a readily available resource to search for preserved proteins; however, the vast majority of palaeoproteomic studies have focused on relatively recently collected bones with a well-known handling history. Here, we characterize proteins from the nasal turbinates of the first Castoroides ohioensis skull ever discovered. Collected in 1845, this is the oldest museum-curated specimen characterized using palaeoproteomic tools. Our mass spectrometry analysis detected many collagen I peptides, a peptide from haemoglobin beta, and in vivo and diagenetic post-translational modifications. Additionally, the identified collagen I sequences provide enough resolution to place C. ohioensis within Rodentia. This study illustrates the utility of archived museum specimens for both the recovery of preserved proteins and phylogenetic analyses.
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Affiliation(s)
- Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Deepak Vashishth
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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17
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Welker F, Smith GM, Hutson JM, Kindler L, Garcia-Moreno A, Villaluenga A, Turner E, Gaudzinski-Windheuser S. Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae. PeerJ 2017; 5:e3033. [PMID: 28316883 PMCID: PMC5354071 DOI: 10.7717/peerj.3033] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/26/2017] [Indexed: 11/20/2022] Open
Abstract
Background Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, including Stephanorhinus and Dicerorhinus. Methods ZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genus Stephanorhinus, subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle Pleistocene Stephanorhinus specimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera (Equus, Tapirus), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods. Results Various ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae. Stephanorhinus is shown to be most closely related to the genera Coelodonta and Dicerorhinus. The protein sequence data further places the Sumatran rhino in a clade together with the genus Rhinoceros, opposed to forming a clade with the black and white rhinoceros species. Discussion The first biomolecular dataset available for Stephanorhinus places this genus together with the extinct genus Coelodonta and the extant genus Dicerorhinus. This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genus Dicerorhinus in a clade together with extant Rhinoceros species. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies.
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Affiliation(s)
- Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; BioArCh, Department of Archaeology, University of York, York, UK
| | - Geoff M Smith
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Department of Anthropology, University of California Davis, Davis, CA, USA
| | - Jarod M Hutson
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Current affiliation: Department of Paleobiology, Smithsonian Institution, Washington, D.C., USA
| | - Lutz Kindler
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Department of Pre- and Protohistoric Archaeology, Institute of Ancient Studies, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Alejandro Garcia-Moreno
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM , Neuwied , Germany
| | - Aritza Villaluenga
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM , Neuwied , Germany
| | - Elaine Turner
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM , Neuwied , Germany
| | - Sabine Gaudzinski-Windheuser
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Department of Pre- and Protohistoric Archaeology, Institute of Ancient Studies, Johannes-Gutenberg Universität Mainz, Mainz, Germany
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18
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Wadsworth C, Procopio N, Anderung C, Carretero JM, Iriarte E, Valdiosera C, Elburg R, Penkman K, Buckley M. Comparing ancient DNA survival and proteome content in 69 archaeological cattle tooth and bone samples from multiple European sites. J Proteomics 2017; 158:1-8. [DOI: 10.1016/j.jprot.2017.01.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/21/2016] [Accepted: 01/06/2017] [Indexed: 12/23/2022]
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19
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Schroeter ER, DeHart CJ, Cleland TP, Zheng W, Thomas PM, Kelleher NL, Bern M, Schweitzer MH. Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein. J Proteome Res 2017; 16:920-932. [PMID: 28111950 PMCID: PMC5401637 DOI: 10.1021/acs.jproteome.6b00873] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Sequence data from biomolecules such as DNA and proteins, which provide critical information for evolutionary studies, have been assumed to be forever outside the reach of dinosaur paleontology. Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these results remain controversial. For proteomic data derived from extinct Mesozoic organisms to reach their greatest potential for investigating questions of phylogeny and paleobiology, it must be shown that peptide sequences can be reliably and reproducibly obtained from fossils and that fragmentary sequences for ancient proteins can be increasingly expanded. To test the hypothesis that peptides can be repeatedly detected and validated from fossil tissues many millions of years old, we applied updated extraction methodology, high-resolution mass spectrometry, and bioinformatics analyses on a Brachylophosaurus canadensis specimen (MOR 2598) from which collagen I peptides were recovered in 2009. We recovered eight peptide sequences of collagen I: two identical to peptides recovered in 2009 and six new peptides. Phylogenetic analyses place the recovered sequences within basal archosauria. When only the new sequences are considered, B. canadensis is grouped more closely to crocodylians, but when all sequences (current and those reported in 2009) are analyzed, B. canadensis is placed more closely to basal birds. The data robustly support the hypothesis of an endogenous origin for these peptides, confirm the idea that peptides can survive in specimens tens of millions of years old, and bolster the validity of the 2009 study. Furthermore, the new data expand the coverage of B. canadensis collagen I (a 33.6% increase in collagen I alpha 1 and 116.7% in alpha 2). Finally, this study demonstrates the importance of reexamining previously studied specimens with updated methods and instrumentation, as we obtained roughly the same amount of sequence data as the previous study with substantially less sample material. Data are available via ProteomeXchange with identifier PXD005087.
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Affiliation(s)
- Elena R. Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Caroline J. DeHart
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Timothy P. Cleland
- Department of Chemistry, University of Texas-Austin, Austin, Texas 78712, United States
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Paul M. Thomas
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Marshall Bern
- Protein Metrics, San Carlos, California 94070, United States
| | - Mary H. Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina 27601, United States
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20
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Affiliation(s)
- Noemi Procopio
- Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K
| | - Michael Buckley
- Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K
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21
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Schroeter ER, DeHart CJ, Schweitzer MH, Thomas PM, Kelleher NL. Bone protein "extractomics": comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics. PeerJ 2016; 4:e2603. [PMID: 27812413 PMCID: PMC5088622 DOI: 10.7717/peerj.2603] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/20/2016] [Indexed: 11/22/2022] Open
Abstract
Proteomic studies of bone require specialized extraction protocols to demineralize and solubilize proteins from within the bone matrix. Although various protocols exist for bone protein recovery, little is known about how discrete steps in each protocol affect the subset of the bone proteome recovered by mass spectrometry (MS) analyses. Characterizing these different “extractomes” will provide critical data for development of novel and more efficient protein extraction methodologies for fossils. Here, we analyze 22 unique sub-extractions of chicken bone and directly compare individual extraction components for their total protein yield and diversity and coverage of bone proteins identified by MS. We extracted proteins using different combinations and ratios of demineralizing reagents, protein-solubilizing reagents, and post-extraction buffer removal methods, then evaluated tryptic digests from 20 µg aliquots of each fraction by tandem MS/MS on a 12T FT-ICR mass spectrometer. We compared total numbers of peptide spectral matches, peptides, and proteins identified from each fraction, the redundancy of protein identifications between discrete steps of extraction methods, and the sequence coverage obtained for select, abundant proteins. Although both alpha chains of collagen I (the most abundant protein in bone) were found in all fractions, other collagenous and non-collagenous proteins (e.g., apolipoprotein, osteonectin, hemoglobin) were differentially identified. We found that when a standardized amount of extracted proteins was analyzed, extraction steps that yielded the most protein (by weight) from bone were often not the ones that produced the greatest diversity of bone proteins, or the highest degree of protein coverage. Generally, the highest degrees of diversity and coverage were obtained from demineralization fractions, and the proteins found in the subsequent solubilization fractions were highly redundant with those in the previous fraction. Based on these data, we identify future directions and parameters to consider (e.g., proteins targeted, amount of sample required) when applying discrete parts of these protocols to fossils.
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Affiliation(s)
- Elena R Schroeter
- Department of Biological Sciences, North Carolina State University , Raleigh , NC , United States
| | - Caroline J DeHart
- Proteomics Center of Excellence and Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston , IL , United States
| | - Mary H Schweitzer
- Department of Biological Sciences, North Carolina State University , Raleigh , NC , United States
| | - Paul M Thomas
- Proteomics Center of Excellence and Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston , IL , United States
| | - Neil L Kelleher
- Proteomics Center of Excellence and Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston , IL , United States
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Vinciguerra R, De Chiaro A, Pucci P, Marino G, Birolo L. Proteomic strategies for cultural heritage: From bones to paintings. Microchem J 2016. [DOI: 10.1016/j.microc.2015.12.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Brocklehurst RJ, Crumpton N, Button E, Asher RJ. Jaw anatomy of Potamogale velox (Tenrecidae, Afrotheria) with a focus on cranial arteries and the coronoid canal in mammals. PeerJ 2016; 4:e1906. [PMID: 27114870 PMCID: PMC4841219 DOI: 10.7717/peerj.1906] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 03/16/2016] [Indexed: 11/20/2022] Open
Abstract
Afrotheria is a strongly supported clade within placental mammals, but morphological synapomorphies for the entire group have only recently come to light. Soft tissue characters represent an underutilized source of data for phylogenetic analysis, but nonetheless provide features shared by some or all members of Afrotheria. Here, we investigate the developmental anatomy of Potamogale velox (Tenrecidae) with histological and computerized tomographic data at different ontogenetic ages, combined with osteological data from other mammals, to investigate patterns of cranial arterial supply and the distribution of the coronoid canal. Potamogale is atypical among placental mammals in exhibiting a small superior stapedial artery, a primary supply of the posterior auricular by the posterior stapedial artery, and the development of vascular plexuses (possibly with relevance for heat exchange) in the posterior and dorsal regions of its neck. In addition, the posterior aspect of Meckel's cartilage increases its medial deflection in larger embryonic specimens as the mandibular condyle extends mediolaterally during embryogenesis. We also map the distribution of the coronoid canal across mammals, and discuss potential confusion of this feature with alveoli of the posterior teeth. The widespread distribution of the coronoid canal among living and fossil proboscideans, sirenians, and hyracoids supports previous interpretations that a patent coronoid canal is a synapomorphy of paenungulates, but not afrotherians as a whole.
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Affiliation(s)
- Robert J Brocklehurst
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom; Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Nick Crumpton
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom; Research Department of Cell & Developmental Biology, University College London, United Kingdom
| | - Evie Button
- Department of Zoology, University of Cambridge , Cambridge , United Kingdom
| | - Robert J Asher
- Department of Zoology, University of Cambridge , Cambridge , United Kingdom
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Cleland TP, Schroeter ER, Schweitzer MH. Biologically and diagenetically derived peptide modifications in moa collagens. Proc Biol Sci 2016; 282:20150015. [PMID: 25972464 DOI: 10.1098/rspb.2015.0015] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The modifications that occur on proteins in natural environments over time are not well studied, yet characterizing them is vital to correctly interpret sequence data recovered from fossils. The recently extinct moa (Dinornithidae) is an excellent candidate for investigating the preservation of proteins, their post-translational modifications (PTMs) and diagenetic alterations during degradation. Moa protein extracts were analysed using mass spectrometry, and peptides from collagen I, collagen II and collagen V were identified. We also identified biologically derived PTMs (i.e. methylation, di-methylation, alkylation, hydroxylation, fucosylation) on amino acids at locations consistent with extant proteins. In addition to these in vivo modifications, we detected novel modifications that are probably diagenetically derived. These include loss of hydroxylation/glutamic semialdehyde, carboxymethyllysine and peptide backbone cleavage, as well as previously noted deamidation. Moa collagen sequences and modifications provide a baseline by which to evaluate proteomic studies of other fossils, and a framework for defining the molecular relationship of moa to other closely related taxa.
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Affiliation(s)
- Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12182, USA
| | - Elena R Schroeter
- 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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25
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Buckley M, Gu M, Shameer S, Patel S, Chamberlain AT. High-throughput collagen fingerprinting of intact microfaunal remains; a low-cost method for distinguishing between murine rodent bones. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:805-12. [PMID: 27408951 PMCID: PMC4831026 DOI: 10.1002/rcm.7483] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/07/2015] [Accepted: 12/13/2015] [Indexed: 05/19/2023]
Abstract
RATIONALE Microfaunal skeletal remains can be sensitive indicators of the contemporary ecosystem in which they are sampled and are often recovered in owl pellets in large numbers. Species identification of these remains can be obtained using a range of morphological criteria established for particular skeletal elements, but typically dominated by a reliance on cranial characters. However, this can induce biases under different environmental and taphonomic conditions. The aim of this research was to develop a high-throughput method of objectively identifying rodent remains from archaeological deposits using collagen fingerprinting, most notably the identification of rats from other myomorph rodents as a means to identify disturbances in the archaeofauna through the presence of invasive taxa not contemporary with the archaeological deposits. METHODS Collagen was extracted from complete microfaunal skeletal remains in such a manner as to leave the bones morphologically intact (i.e., weaker concentration of acid than previously used over shorter length of time). Acid-soluble collagen was then ultrafiltered into ammonium bicarbonate and digested with trypsin prior to dilution in the MALDI matrix and acquisition of peptide mass fingerprints using a matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometer. RESULTS Collagen fingerprinting was able to distinguish between Rattus, Mus, Apodemus and Micromys at the genus level; at the species level, R. rattus and R. norvegicus could be separated whereas A. flavicollis and A. sylvaticus could not. A total of 12,317 archaeological microvertebrate samples were screened for myomorph signatures but none were found to be invasive rats (Rattus) or mice (Mus). Of the contemporary murine fauna, no harvest mice (Micromys) were identified and only 24 field mouse (Apodemus) discovered. CONCLUSIONS As a result, no evidence of recent bioturbation could be inferred from the faunal remains of these archaeological deposits. More importantly this work presents a method for high-throughput screening of specific taxa and is the first application of collagen fingerprinting to microfaunal remains of archaeological specimens.
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Buckley M. Ancient collagen reveals evolutionary history of the endemic South American 'ungulates'. Proc Biol Sci 2016; 282:20142671. [PMID: 25833851 PMCID: PMC4426609 DOI: 10.1098/rspb.2014.2671] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Since the late eighteenth century, fossils of bizarre extinct creatures have been described from the Americas, revealing a previously unimagined chapter in the history of mammals. The most bizarre of these are the ‘native’ South American ungulates thought to represent a group of mammals that evolved in relative isolation on South America, but with an uncertain affinity to any particular placental lineage. Many authors have considered them descended from Laurasian ‘condylarths’, which also includes the probable ancestors of perissodactyls and artiodactyls, whereas others have placed them either closer to the uniquely South American xenarthrans (anteaters, armadillos and sloths) or the basal afrotherians (e.g. elephants and hyraxes). These hypotheses have been debated owing to conflicting morphological characteristics and the hitherto inability to retrieve molecular information. Of the ‘native’ South American mammals, only the toxodonts and litopterns persisted until the Late Pleistocene–Early Holocene. Owing to known difficulties in retrieving ancient DNA (aDNA) from specimens from warm climates, this research presents a molecular phylogeny for both Macrauchenia patachonica (Litopterna) and Toxodon platensis (Notoungulata) recovered using proteomics-based (liquid chromatography–tandem mass spectrometry) sequencing analyses of bone collagen. The results place both taxa in a clade that is monophyletic with the perissodactyls, which today are represented by horses, rhinoceroses and tapirs.
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Affiliation(s)
- Michael Buckley
- Faculty of Life Sciences, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
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27
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Cleland TP, Schroeter ER, Zamdborg L, Zheng W, Lee JE, Tran JC, Bern M, Duncan MB, Lebleu VS, Ahlf DR, Thomas PM, Kalluri R, Kelleher NL, Schweitzer MH. Mass Spectrometry and Antibody-Based Characterization of Blood Vessels from Brachylophosaurus canadensis. J Proteome Res 2015; 14:5252-62. [PMID: 26595531 DOI: 10.1021/acs.jproteome.5b00675] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structures similar to blood vessels in location, morphology, flexibility, and transparency have been recovered after demineralization of multiple dinosaur cortical bone fragments from multiple specimens, some of which are as old as 80 Ma. These structures were hypothesized to be either endogenous to the bone (i.e., of vascular origin) or the result of biofilm colonizing the empty osteonal network after degradation of original organic components. Here, we test the hypothesis that these structures are endogenous and thus retain proteins in common with extant archosaur blood vessels that can be detected with high-resolution mass spectrometry and confirmed by immunofluorescence. Two lines of evidence support this hypothesis. First, peptide sequencing of Brachylophosaurus canadensis blood vessel extracts is consistent with peptides comprising extant archosaurian blood vessels and is not consistent with a bacterial, cellular slime mold, or fungal origin. Second, proteins identified by mass spectrometry can be localized to the tissues using antibodies specific to these proteins, validating their identity. Data are available via ProteomeXchange with identifier PXD001738.
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Affiliation(s)
| | | | - Leonid Zamdborg
- Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | | | - Ji Eun Lee
- Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States.,Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - John C Tran
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Marshall Bern
- Protein Metrics , San Carlos, California 94070, United States
| | - Michael B Duncan
- Division of Matrix Biology, Beth Israel Deaconess Medical Center , Boston, Massachusetts 02115, United States.,Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Valerie S Lebleu
- Division of Matrix Biology, Beth Israel Deaconess Medical Center , Boston, Massachusetts 02115, United States.,Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States.,Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center , Houston, Texas 77054, United States
| | - Dorothy R Ahlf
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Paul M Thomas
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Raghu Kalluri
- Division of Matrix Biology, Beth Israel Deaconess Medical Center , Boston, Massachusetts 02115, United States.,Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States.,Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center , Houston, Texas 77054, United States.,Department of Biological Chemistry and Molecular Pharmacology and Harvard-MIT Division of Health Sciences and Technology, Harvard University , Cambridge, Massachusetts 02139, United States
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Mary H Schweitzer
- North Carolina Museum of Natural Sciences , Raleigh, North Carolina 27601, United States
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28
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Buckley M, Fariña RA, Lawless C, Tambusso PS, Varela L, Carlini AA, Powell JE, Martinez JG. Collagen Sequence Analysis of the Extinct Giant Ground Sloths Lestodon and Megatherium. PLoS One 2015; 10:e0139611. [PMID: 26540101 PMCID: PMC4634953 DOI: 10.1371/journal.pone.0139611] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 09/14/2015] [Indexed: 11/19/2022] Open
Abstract
For over 200 years, fossils of bizarre extinct creatures have been described from the Americas that have ranged from giant ground sloths to the ‘native’ South American ungulates, groups of mammals that evolved in relative isolation on South America. Ground sloths belong to the South American xenarthrans, a group with modern although morphologically and ecologically very different representatives (anteaters, armadillos and sloths), which has been proposed to be one of the four main eutherian clades. Recently, proteomics analyses of bone collagen have recently been used to yield a molecular phylogeny for a range of mammals including the unusual ‘Malagasy aardvark’ shown to be most closely related to the afrotherian tenrecs, and the south American ungulates supporting their morphological association with condylarths. However, proteomics results generate partial sequence information that could impact upon the phylogenetic placement that has not been appropriately tested. For comparison, this paper examines the phylogenetic potential of proteomics-based sequencing through the analysis of collagen extracted from two extinct giant ground sloths, Lestodon and Megatherium. The ground sloths were placed as sister taxa to extant sloths, but with a closer relationship between Lestodon and the extant sloths than the basal Megatherium. These results highlight that proteomics methods could yield plausible phylogenies that share similarities with other methods, but have the potential to be more useful in fossils beyond the limits of ancient DNA survival.
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Affiliation(s)
- Michael Buckley
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, United Kingdom
- * E-mail:
| | - Richard A. Fariña
- Sección Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, Uruguay
| | - Craig Lawless
- Michael Smith Building, The University of Manchester, Manchester, United Kingdom
| | - P. Sebastián Tambusso
- Sección Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, Uruguay
| | - Luciano Varela
- Sección Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, Uruguay
| | - Alfredo A. Carlini
- Facultad de Ciencias Naturales y Museo, Museo de La Plata, Buenos Aires, Argentina
| | - Jaime E. Powell
- Facultad de Ciencias Naturales, Universidad Nacional de Tucumán, Tucumán Province, Argentina
| | - Jorge G. Martinez
- Instituto Superior de Estudios Sociales-CONICET, Instituto de Arqueología y Museo-UNT, Tucumán Province, Argentina
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29
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Campbell K, Hofreiter M. Resurrecting phenotypes from ancient DNA sequences: promises and perspectives. CAN J ZOOL 2015. [DOI: 10.1139/cjz-2014-0337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Anatomical changes in extinct mammalian lineages over evolutionary time, such as the loss of fingers and teeth and the rapid increase in body size that accompanied the late Miocene dispersal of the progenitors of Steller’s sea cows (Hydrodamalis gigas (Zimmermann, 1780)) into North Pacific waters and the convergent development of a thick pelage and accompanying reductions in ear and tail surface area of woolly mammoths (Mammuthus primigenius (Blumenbach, 1799)) and woolly rhinoceros (Coelodonta antiquitatis (Blumenbach, 1799)), are prime examples of adaptive evolution underlying the exploitation of new habitats. It is likely, however, that biochemical specializations adopted during these evolutionary transitions were of similar or even greater biological importance. As these “living” processes do not fossilize, direct information regarding the physiological attributes of extinct species has largely remained beyond the range of scientific inquiry. However, the ability to retrieve genomic sequences from ancient DNA samples, combined with ectopic expression systems, now permit the evolutionary origins and structural and functional properties of authentic prehistoric proteins to be examined in great detail. Exponential technical advances in ancient DNA retrieval, enrichment, and sequencing will soon permit targeted generation of complete genomes from hundreds of extinct species across the last one million years that, in combination with emerging in vitro expression, genome engineering, and cell differentiation techniques, promises to herald an exciting new trajectory of evolutionary research at the interface of biochemistry, genomics, palaeontology, and cell biology.
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Affiliation(s)
- K.L. Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - M. Hofreiter
- Faculty of Mathematics and Life Sciences, Institute of Biochemistry and Biology, Unit of General Zoology–Evolutionary Adaptive Genomics, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany
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30
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Hill RC, Wither MJ, Nemkov T, Barrett A, D'Alessandro A, Dzieciatkowska M, Hansen KC. Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry; Hydroxylysine Glycosides are a Common Feature of Ancient Collagen. Mol Cell Proteomics 2015; 14:1946-58. [PMID: 25948757 DOI: 10.1074/mcp.m114.047787] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Indexed: 11/06/2022] Open
Abstract
Bone samples from several vertebrates were collected from the Ziegler Reservoir fossil site, in Snowmass Village, Colorado, and processed for proteomics analysis. The specimens come from Pleistocene megafauna Bison latifrons, dating back ∼ 120,000 years. Proteomics analysis using a simplified sample preparation procedure and tandem mass spectrometry (MS/MS) was applied to obtain protein identifications. Several bioinformatics resources were used to obtain peptide identifications based on sequence homology to extant species with annotated genomes. With the exception of soil sample controls, all samples resulted in confident peptide identifications that mapped to type I collagen. In addition, we analyzed a specimen from the extinct B. latifrons that yielded peptide identifications mapping to over 33 bovine proteins. Our analysis resulted in extensive fibrillar collagen sequence coverage, including the identification of posttranslational modifications. Hydroxylysine glucosylgalactosylation, a modification thought to be involved in collagen fiber formation and bone mineralization, was identified for the first time in an ancient protein dataset. Meta-analysis of data from other studies indicates that this modification may be common in well-preserved prehistoric samples. Additional peptide sequences from extracellular matrix (ECM) and non-ECM proteins have also been identified for the first time in ancient tissue samples. These data provide a framework for analyzing ancient protein signatures in well-preserved fossil specimens, while also contributing novel insights into the molecular basis of organic matter preservation. As such, this analysis has unearthed common posttranslational modifications of collagen that may assist in its preservation over time. The data are available via ProteomeXchange with identifier PXD001827.
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Affiliation(s)
- Ryan C Hill
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Matthew J Wither
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Travis Nemkov
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Alexander Barrett
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Angelo D'Alessandro
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Monika Dzieciatkowska
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Kirk C Hansen
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
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31
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Ancient proteins resolve the evolutionary history of Darwin's South American ungulates. Nature 2015; 522:81-4. [PMID: 25799987 DOI: 10.1038/nature14249] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 01/22/2015] [Indexed: 01/23/2023]
Abstract
No large group of recently extinct placental mammals remains as evolutionarily cryptic as the approximately 280 genera grouped as 'South American native ungulates'. To Charles Darwin, who first collected their remains, they included perhaps the 'strangest animal[s] ever discovered'. Today, much like 180 years ago, it is no clearer whether they had one origin or several, arose before or after the Cretaceous/Palaeogene transition 66.2 million years ago, or are more likely to belong with the elephants and sirenians of superorder Afrotheria than with the euungulates (cattle, horses, and allies) of superorder Laurasiatheria. Morphology-based analyses have proved unconvincing because convergences are pervasive among unrelated ungulate-like placentals. Approaches using ancient DNA have also been unsuccessful, probably because of rapid DNA degradation in semitropical and temperate deposits. Here we apply proteomic analysis to screen bone samples of the Late Quaternary South American native ungulate taxa Toxodon (Notoungulata) and Macrauchenia (Litopterna) for phylogenetically informative protein sequences. For each ungulate, we obtain approximately 90% direct sequence coverage of type I collagen α1- and α2-chains, representing approximately 900 of 1,140 amino-acid residues for each subunit. A phylogeny is estimated from an alignment of these fossil sequences with collagen (I) gene transcripts from available mammalian genomes or mass spectrometrically derived sequence data obtained for this study. The resulting consensus tree agrees well with recent higher-level mammalian phylogenies. Toxodon and Macrauchenia form a monophyletic group whose sister taxon is not Afrotheria or any of its constituent clades as recently claimed, but instead crown Perissodactyla (horses, tapirs, and rhinoceroses). These results are consistent with the origin of at least some South American native ungulates from 'condylarths', a paraphyletic assembly of archaic placentals. With ongoing improvements in instrumentation and analytical procedures, proteomics may produce a revolution in systematics such as that achieved by genomics, but with the possibility of reaching much further back in time.
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32
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Cleland TP, Vashishth D. Bone protein extraction without demineralization using principles from hydroxyapatite chromatography. Anal Biochem 2014; 472:62-6. [PMID: 25535955 DOI: 10.1016/j.ab.2014.12.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 12/02/2014] [Accepted: 12/10/2014] [Indexed: 01/22/2023]
Abstract
Historically, extraction of bone proteins has relied on the use of demineralization to better retrieve proteins from the extracellular matrix; however, demineralization can be a slow process that restricts subsequent analysis of the samples. Here, we developed a novel protein extraction method that does not use demineralization but instead uses a methodology from hydroxyapatite chromatography where high concentrations of ammonium phosphate and ammonium bicarbonate are used to extract bone proteins. We report that this method has a higher yield than those with previously published small-scale extant bone extractions, with and without demineralization. Furthermore, after digestion with trypsin and subsequent high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analysis, we were able to detect several extracellular matrix and vascular proteins in addition to collagen I and osteocalcin. Our new method has the potential to isolate proteins within a short period (4h) and provide information about bone proteins that may be lost during demineralization or with the use of denaturing agents.
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Affiliation(s)
- Timothy P Cleland
- Department of Biomedical Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12182, USA
| | - Deepak Vashishth
- Department of Biomedical Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12182, USA.
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Brandt LØ, Schmidt AL, Mannering U, Sarret M, Kelstrup CD, Olsen JV, Cappellini E. Species identification of archaeological skin objects from Danish bogs: comparison between mass spectrometry-based peptide sequencing and microscopy-based methods. PLoS One 2014; 9:e106875. [PMID: 25260035 PMCID: PMC4178020 DOI: 10.1371/journal.pone.0106875] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 07/24/2014] [Indexed: 11/18/2022] Open
Abstract
Denmark has an extraordinarily large and well-preserved collection of archaeological skin garments found in peat bogs, dated to approximately 920 BC - AD 775. These objects provide not only the possibility to study prehistoric skin costume and technologies, but also to investigate the animal species used for the production of skin garments. Until recently, species identification of archaeological skin was primarily performed by light and scanning electron microscopy or the analysis of ancient DNA. However, the efficacy of these methods can be limited due to the harsh, mostly acidic environment of peat bogs leading to morphological and molecular degradation within the samples. We compared species assignment results of twelve archaeological skin samples from Danish bogs using Mass Spectrometry (MS)-based peptide sequencing, against results obtained using light and scanning electron microscopy. While it was difficult to obtain reliable results using microscopy, MS enabled the identification of several species-diagnostic peptides, mostly from collagen and keratins, allowing confident species discrimination even among taxonomically close organisms, such as sheep and goat. Unlike previous MS-based methods, mostly relying on peptide fingerprinting, the shotgun sequencing approach we describe aims to identify the complete extracted ancient proteome, without preselected specific targets. As an example, we report the identification, in one of the samples, of two peptides uniquely assigned to bovine foetal haemoglobin, indicating the production of skin from a calf slaughtered within the first months of its life. We conclude that MS-based peptide sequencing is a reliable method for species identification of samples from bogs. The mass spectrometry proteomics data were deposited in the ProteomeXchange Consortium with the dataset identifier PXD001029.
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Affiliation(s)
- Luise Ørsted Brandt
- Centre for Textile Research, University of Copenhagen, Copenhagen, Denmark
- Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (LØB); (EC)
| | - Anne Lisbeth Schmidt
- Department of Environmental Archaeology and Materials Science, The National Museum of Denmark, Copenhagen, Denmark
| | - Ulla Mannering
- Centre for Textile Research, University of Copenhagen, Copenhagen, Denmark
- Department of Ancient Cultures in Denmark and the Mediterranean, The National Museum of Denmark, Copenhagen, Denmark
| | - Mathilde Sarret
- European School of Chemistry, Polymers and Materials Science, University of Strasbourg, Strasbourg, France
| | - Christian D. Kelstrup
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jesper V. Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (LØB); (EC)
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Schweitzer MH, Schroeter ER, Goshe MB. Protein Molecular Data from Ancient (>1 million years old) Fossil Material: Pitfalls, Possibilities and Grand Challenges. Anal Chem 2014; 86:6731-40. [DOI: 10.1021/ac500803w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mary Higby Schweitzer
- North
Carolina Museum of Natural Sciences, Raleigh, North Carolina 27601, United States
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Wadsworth C, Buckley M. Proteome degradation in fossils: investigating the longevity of protein survival in ancient bone. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:605-15. [PMID: 24519823 PMCID: PMC4282581 DOI: 10.1002/rcm.6821] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/23/2013] [Accepted: 12/30/2013] [Indexed: 05/19/2023]
Abstract
RATIONALE We report the use of proteomics techniques to study how the fossil bone proteome changes in complexity over one million years. METHODS We include the attempted use of a previously unreported methodology in proteome research, to remove the dominant bone collagens using bacterial collagenase as well as conventional shotgun proteomics methodology following digestion with the protease trypsin. In this study we expand upon a set of 19 bovine sub-fossil specimens ranging over one and a half million years that had previously been shown to possess collagen, using a total of 46 LTQ-Orbitrap liquid chromatography/tandem mass spectrometry (LC/MS/MS) analyses containing 462,186 precursor ion analyses. RESULTS Although many types of proteins can typically be identified in recent bone, in degraded bone we observe a rapid loss of lower abundance proteins. Abundant serum proteins such as serum albumin and alpha-2-HS-glycoprotein appear to be more easily recovered in ancient bone, both being identified in specimens dating to the Early Pleistocene, the earliest period tested in this study. Proteins belonging to the leucine-rich repeat family such as lumican, biglycan and chondroadherin also survive well, possibly because of their interactions with bone collagen. CONCLUSIONS Of these 'survivor proteins' A2HSG shows a remarkable amount of sequence variation, making it potentially one of the most useful proteins to study for species identification and phylogenetic inference in archaeological and palaeontological bone.
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Affiliation(s)
- Caroline Wadsworth
- Faculty of Life Sciences, Manchester Institute of Biotechnology131 Princess Street, Manchester, M1 7DN, UK
| | - Mike Buckley
- *Correspondence to: M. Buckley, Faculty of Life Sciences, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK., E-mail:
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36
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Baab KL, Perry JMG, Rohlf FJ, Jungers WL. PHYLOGENETIC, ECOLOGICAL, AND ALLOMETRIC CORRELATES OF CRANIAL SHAPE IN MALAGASY LEMURIFORMS. Evolution 2014; 68:1450-68. [DOI: 10.1111/evo.12361] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 01/06/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Karen L. Baab
- Department of Anthropology; Stony Brook University; Social and Behavioral Sciences Building; 5th Floor Stony Brook New York 11794
- Interdepartmental Program in Anthropological Sciences; Stony Brook University; Stony Brook New York 11794
| | - Jonathan M. G. Perry
- Center for Functional Anatomy and Evolution; The Johns Hopkins University School of Medicine; Baltimore Maryland 21205
| | - F. James Rohlf
- Department of Ecology and Evolution; Stony Brook University; Stony Brook New York 11794
| | - William L. Jungers
- Interdepartmental Program in Anthropological Sciences; Stony Brook University; Stony Brook New York 11794
- Department of Anatomical Sciences; Stony Brook University; Stony Brook New York 11794
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37
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Abstract
Ancient biomolecules including DNA, proteins, and lipids are often preserved in archaeological skeletons or artifacts such as potsherds from cooking vessels. Techniques for analyzing these molecules have improved dramatically in recent years, though challenges remain in ensuring that results are authentic and not confused by the presence of contaminating modern biomolecules. Ancient DNA (aDNA) can be used to identify the sex, kinship relationships, and population affinities of human skeletons, and also to detect the presence of disease-causing organisms such as the plague and tuberculosis bacteria. Stable isotope ratios in collagen and other skeletal proteins enable past diets to be studied, and similar work with lipids from potsherds have revealed that dairying in Europe began 2,000 years earlier than previously thought. Biomolecular archaeology has therefore developed into a mature discipline that is making a significant contribution to different aspects of our understanding of the human past.
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Affiliation(s)
- Keri A. Brown
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom;,
| | - Terence A. Brown
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom;,
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