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Houldcroft CJ, Underdown S. Infectious disease in the Pleistocene: Old friends or old foes? AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:513-531. [PMID: 38006200 DOI: 10.1002/ajpa.24737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 11/26/2023]
Abstract
The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.
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Affiliation(s)
| | - Simon Underdown
- Human Origins and Palaeoenvironmental Research Group, School of Social Sciences, Oxford Brookes University, Oxford, UK
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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2
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Luis JV, Andréeacute;s VD, Levano KS, Pedro NB, Marco MR, Ruth GDLG, Rony CC, Diana PL, Sharma AK, Samuel D, Pedro o FV, Raul J C, A G, Ruth SS, Heinner G. Analysis of microbiome diversity in coprolites from Caral, Peru. Bioinformation 2022; 18:1159-1165. [PMID: 37701514 PMCID: PMC10492910 DOI: 10.6026/973206300181159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/20/2022] [Accepted: 12/31/2022] [Indexed: 09/14/2023] Open
Abstract
We analyzed human coprolites from the Sacred City of Caral, the oldest civilization in America (3000- and 1800-years BC). Our objective was to know the microbial diversity of the Caral Civilization through the use of a mobile ancient laboratory. DNA extraction conducted in a mobile laboratory placed near the collection site to reduce exposure of samples to contaminants and favor a rapid molecular processing. Using 16S rRNA and ITS 1 amplicon sequencing, we have elaborated the first list of the microbiomes of Caral, based on the bacterial and fungal community fingerprints detected in the coprolites recovered in six sectors of that ancient urban center. Among the most abundant sequences were those associated with Firmicutes for bacteria, Ascomycota and Basidiomycota for fungi. Bacillus was the most abundant bacterial genera in all samples analyzed, compromising up to 24.81% of the total bacterial abundance; while Aspergillus (11.43%) was the most abundant genera among fungal communities.
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Affiliation(s)
- Jaramillo-Valverde Luis
- ALBIOTEC, Lima, Perú
- INBIOMEDIC Research and Technological Center, Lima, Perú
- Universidad de Huánuco, Huánuco, Perú
| | - Váaacute;squez-Domínguez Andréeacute;s
- ALBIOTEC, Lima, Perú
- INBIOMEDIC Research and Technological Center, Lima, Perú
- Facultad de Ciencias Biolóoacute;gicas, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Kelly S Levano
- ALBIOTEC, Lima, Perú
- INBIOMEDIC Research and Technological Center, Lima, Perú
| | - Novoa-Bellota Pedro
- Zona Arqueológica Caral, Unidad Ejecutora 003, Ministerio de Cultura., Lima, Perú
- Escuela Profesional de ArqueologÍa, Facultad de Ciencias Sociales, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | | | - Garcia-de-la-Guarda Ruth
- Laboratorio de MicrobiologÍa Molecular y BiotecnologÍa, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | | | | | - Ashok K Sharma
- Department of Animal Science, University of Minnesota, St. Paul, MN
| | - Davison Samuel
- Department of Animal Science, University of Minnesota, St. Paul, MN
| | | | - Cano Raul J
- Centro de Investigación en Biodiversidad para la Salud, Universidad Privada Norbert Wiener, Lima, Perú; +These authors contributed equally to the article
| | - Gomez A
- Department of Animal Science, University of Minnesota, St. Paul, MN
| | - Shady-Solis Ruth
- Zona Arqueológica Caral, Unidad Ejecutora 003, Ministerio de Cultura., Lima, Perú
- Escuela Profesional de ArqueologÍa, Facultad de Ciencias Sociales, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Guio Heinner
- ALBIOTEC, Lima, Perú
- INBIOMEDIC Research and Technological Center, Lima, Perú
- Centro de Investigación en Biodiversidad para la Salud, Universidad Privada Norbert Wiener, Lima, Perú; +These authors contributed equally to the article
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Malmstrom CM, Martin MD, Gagnevin L. Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:187-209. [PMID: 35483672 DOI: 10.1146/annurev-phyto-021021-041830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.
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Affiliation(s)
- Carolyn M Malmstrom
- Department of Plant Biology and Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Michael D Martin
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lionel Gagnevin
- Plant Health Institute of Montpellier, CIRAD, Montpellier, France;
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Yang L, Zhang X, Zhao X, Xiang H. The Technological Advance and Application of Coprolite Analysis. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.797370] [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] Open
Abstract
Coprolites (mummified or fossilized feces), belonging to the group of ichnofossils, are fossilized remains of feces produced by animals. Various types of data from coprolites provide detailed evidence of the producer’s condition, like diet, intestinal microbiome, virus infection and parasites diseases. In addition, the palaeoenvironment information relevant to producers’ ecological niche can be drawn from taphonomy details the coprolites mirrored. At present, the phylogenetic clues of the producer’s population can be determined by advanced molecular biotechnologies. With the integration of multiple methods and techniques, coprolite has been widely accepted as an ideal material to study the diet, evolution, and palaeoenvironment of producers. In this paper, we reviewed the history of coprolite research, enumerated and interpreted the data recovered from coprolites, and explained their research value to palaeocoprology and evolutionary biology. Finally, we summarized the current directions of coprolite research and looked into its future prospects.
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Maixner F, Sarhan MS, Huang KD, Tett A, Schoenafinger A, Zingale S, Blanco-Míguez A, Manghi P, Cemper-Kiesslich J, Rosendahl W, Kusebauch U, Morrone SR, Hoopmann MR, Rota-Stabelli O, Rattei T, Moritz RL, Oeggl K, Segata N, Zink A, Reschreiter H, Kowarik K. Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period. Curr Biol 2021; 31:5149-5162.e6. [PMID: 34648730 PMCID: PMC8660109 DOI: 10.1016/j.cub.2021.09.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/16/2021] [Accepted: 09/14/2021] [Indexed: 02/06/2023]
Abstract
We subjected human paleofeces dating from the Bronze Age to the Baroque period (18th century AD) to in-depth microscopic, metagenomic, and proteomic analyses. The paleofeces were preserved in the underground salt mines of the UNESCO World Heritage site of Hallstatt in Austria. This allowed us to reconstruct the diet of the former population and gain insights into their ancient gut microbiome composition. Our dietary survey identified bran and glumes of different cereals as some of the most prevalent plant fragments. This highly fibrous, carbohydrate-rich diet was supplemented with proteins from broad beans and occasionally with fruits, nuts, or animal food products. Due to these traditional dietary habits, all ancient miners up to the Baroque period have gut microbiome structures akin to modern non-Westernized individuals whose diets are also mainly composed of unprocessed foods and fresh fruits and vegetables. This may indicate a shift in the gut community composition of modern Westernized populations due to quite recent dietary and lifestyle changes. When we extended our microbial survey to fungi present in the paleofeces, in one of the Iron Age samples, we observed a high abundance of Penicillium roqueforti and Saccharomyces cerevisiae DNA. Genome-wide analysis indicates that both fungi were involved in food fermentation and provides the first molecular evidence for blue cheese and beer consumption in Iron Age Europe. Gut microbiome and diet of European salt miners determined using paleofeces Until the Baroque, the microbiome resembled that of modern non-Westernized people Food-fermenting fungi in Iron Age feces indicates blue cheese and beer consumption
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Affiliation(s)
- Frank Maixner
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy.
| | - Mohamed S Sarhan
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Kun D Huang
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy; Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, Via Edmund Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Adrian Tett
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy; CUBE (Division of Computational Systems Biology), Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Alexander Schoenafinger
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy; Institute of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Stefania Zingale
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Aitor Blanco-Míguez
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Paolo Manghi
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Jan Cemper-Kiesslich
- Interfaculty Department of Legal Medicine & Department of Classics, University of Salzburg, Ignaz-Harrer-Straße 79, 5020 Salzburg, Austria
| | - Wilfried Rosendahl
- Reiss-Engelhorn-Museen, Zeughaus C5, 68159 Mannheim, Germany; Curt-Egelhorn-Zentrum Archäomtrie, D6,3, 61859 Mannheim, Germany
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Seamus R Morrone
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Michael R Hoopmann
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Omar Rota-Stabelli
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all'Adige (TN), Italy
| | - Thomas Rattei
- CUBE (Division of Computational Systems Biology), Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Klaus Oeggl
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Nicola Segata
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Albert Zink
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Hans Reschreiter
- Prehistoric Department, Museum of Natural History Vienna, Burgring 7, 1010 Vienna, Austria
| | - Kerstin Kowarik
- Prehistoric Department, Museum of Natural History Vienna, Burgring 7, 1010 Vienna, Austria.
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Núñez Coronado C, González Rosas H, Fernandez-Pavia YL. Micropropagación de Calibanus hookeri (lem.) trel (1911). Una especie amenazada. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2021. [DOI: 10.15446/rev.colomb.biote.v23n1.80873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
La especie Calibanus hookerii perteneciente a la familia Asparagaceae, está registrada en la NOM-059-SEMARNAT-2010 catalogada como planta amenazada. Sus poblaciones naturales se han visto reducidas de manera importante debido a una explotación excesiva y destrucción de su hábitat, por lo que se requiere de métodos de propagación eficaz que aseguren su conservación. La propagación in vitro es una alternativa viable para especies vegetales amenazadas. En la presente investigación se reporta el protocolo para la micropropagación de Calibanus hookerii mediante la germinación de semilla sin testa inoculada en medio MS complementado con 2.5, 5.0 y 7.0 mg L-1 de 6 benciladenina (BA), cinetina (K), 2-isopentil-adenina (2iP) y tidiazuron (TDZ). Las variables a medir fueron porcentaje de germinación, número y longitud de brotes producidos por semilla.
El tratamiento más eficiente fue de 5.0 mg L-1 de BA produciéndose un promedio de 26 brotes por semilla; el tratamiento menos eficaz fue con 2.5 mg L-1 K en el cual solamente se obtuvieron dos brotes por semilla. De las tres concentraciones de 2iP solamente en la concentración de 7 mg. L-1 mostró resultados produciendo 6 brotes por semilla. En lo que respecta a la longitud del brote ningún tratamiento superó al testigo (8.07cm). La eficiencia la germinación in vitro fue de 56-97%.
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Witt KE, Yarlagadda K, Allen JM, Bader AC, Simon ML, Kuehn SR, Swanson KS, Cross TWL, Hedman KM, Ambrose SH, Malhi RS. Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet. Sci Rep 2021; 11:3113. [PMID: 33542301 PMCID: PMC7862676 DOI: 10.1038/s41598-021-82362-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
Paleofeces or coprolites are often used to reconstruct diet at archaeological sites, usually using macroscopic analyses or targeted DNA amplification and sequencing. Here we present an integrative analysis of dog coprolites, combining macroscopic analyses, stable isotope measurements, and DNA shotgun sequencing to examine diet and health status. Dog coprolites used in this study were recovered from the Janey B. Goode and East Saint Louis archaeological sites, both of which are located in the American Bottom, an extensive Mississippi River floodplain in Southwestern Illinois. Based on the context of recovery, coprolites are assigned to the Late Woodland and Terminal Late Woodland periods (ca. 600-1050 AD). Given the scarcity of human remains from this time period, these dog coprolites can be useful as a proxy for understanding human diet during the Late Woodland period. We find that the Late Woodland dogs consumed a variety of fish as well as bird and plant taxa, possibly including maize, and also harbored intestinal parasites and pathogenic bacteria. By sequencing the fecal microbiome of the coprolites, we find some similarities to modern dog microbiomes, as well as specific taxa that can be used to discriminate between modern and ancient microbiomes, excluding soil contaminants. As dogs are often used as a surrogate to assess human diet, humans living with these dogs likely had a similar diet and were affected by similar parasites. These analyses, when integrated, show a more comprehensive view of ancient dog and human diet and health in the region during the initial expansion of maize agriculture than any individual method could alone.
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Affiliation(s)
- Kelsey E Witt
- Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA.
- Ecology and Evolutionary Biology and Center for Computational and Molecular Biology, Brown University, Providence, RI, USA.
| | - Karthik Yarlagadda
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA
| | - Julie M Allen
- Biology Department, University of Nevada Reno, Reno, NV, USA
| | - Alyssa C Bader
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA
- Sealaska Heritage Institute, Juneau, AK, USA
| | - Mary L Simon
- Illinois State Archaeological Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Steven R Kuehn
- Illinois State Archaeological Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kelly S Swanson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tzu-Wen L Cross
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kristin M Hedman
- Illinois State Archaeological Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Stanley H Ambrose
- Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ripan S Malhi
- Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Jacobson DK, Honap TP, Monroe C, Lund J, Houk BA, Novotny AC, Robin C, Marini E, Lewis CM. Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190586. [PMID: 33012230 PMCID: PMC7702801 DOI: 10.1098/rstb.2019.0586] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human microbiome studies are increasingly incorporating macroecological approaches, such as community assembly, network analysis and functional redundancy to more fully characterize the microbiome. Such analyses have not been applied to ancient human microbiomes, preventing insights into human microbiome evolution. We address this issue by analysing published ancient microbiome datasets: coprolites from Rio Zape (n = 7; 700 CE Mexico) and historic dental calculus (n = 44; 1770–1855 CE, UK), as well as two novel dental calculus datasets: Maya (n = 7; 170 BCE-885 CE, Belize) and Nuragic Sardinians (n = 11; 1400–850 BCE, Italy). Periodontitis-associated bacteria (Treponema denticola, Fusobacterium nucleatum and Eubacterium saphenum) were identified as keystone taxa in the dental calculus datasets. Coprolite keystone taxa included known short-chain fatty acid producers (Eubacterium biforme, Phascolarctobacterium succinatutens) and potentially disease-associated bacteria (Escherichia, Brachyspira). Overlap in ecological profiles between ancient and modern microbiomes was indicated by similarity in functional response diversity profiles between contemporary hunter–gatherers and ancient coprolites, as well as parallels between ancient Maya, historic UK, and modern Spanish dental calculus; however, the ancient Nuragic dental calculus shows a distinct ecological structure. We detected key ecological signatures from ancient microbiome data, paving the way to expand understanding of human microbiome evolution. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
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Affiliation(s)
- David K Jacobson
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Tanvi P Honap
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Cara Monroe
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Justin Lund
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Brett A Houk
- Department of Sociology, Anthropology, and Social Work, Texas Tech University, Lubbock, TX, USA
| | - Anna C Novotny
- Department of Sociology, Anthropology, and Social Work, Texas Tech University, Lubbock, TX, USA
| | - Cynthia Robin
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Elisabetta Marini
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Sardinia, Italy
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
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The Effect of Cladode Drying Techniques on the Prebiotic Potential and Molecular Characteristics of the Mucilage Extracted from Opuntia ficus-indica and Opuntia joconostle. Sci Pharm 2020. [DOI: 10.3390/scipharm88040043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The dry, powdered cladodes of Opuntia ficus-indica are often-used in over-the-counter (OTC) pharmaceutical formulations. Gentle drying techniques, such as lyophilization and vacuum drying are compared with convection drying for the cladodes and also compared with another species of economic importance, Opuntia joconostle. The heteropolysaccharide purified from the mucilage extracted from the dried powders were investigated in their monosaccharide composition (HPAEC-PAD, TLC), mineral and protein content, molecular dimensions (SEC) and fermentability by probiotic bacteria (Bioscreen technique) for evaluation of the prebiotic potential of the mucilage. The heteropolysaccharide is composed of galactose, arabinose, xylose, galacturonic acid and rhamnose. O. ficus-indica includes an additional 13% of glucose coming from an α-glucan. The content of Ca (0.3%) and Mg (0.4%) is relatively low in both species; the content of protein adds up to 1.5% in O. ficus-indica but is significantly lower in O. joconostle with 0.8%. The average molecular mass Mw of the extracted mucilage ranges from 3.7 to 4.7 × 105 g∙mol−1 for both species; only the mucilage from long-time convection drying (C2) delivers a lower average Mw of 2.6 × 105 g∙mol−1, due to partial breakdown of the mucilage matrix. All tested probiotic strains utilized the mucilage to some extent; C2 being the most active, and thus confirms the prebiotic potential of cladode’s powder and its derived products. In general, the molecular dimensions and prebiotic potential are not extremely sensitive to the drying treatment, yet temperature and drying time can modify the cladode’s powder to a profile with better prebiotic characteristics.
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Mudge C, Dallwitz R, Llamas B, Austin JJ. Using Ancient DNA Analysis and Radiocarbon Dating to Determine the Provenance of an Unusual Whaling Artifact. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.505233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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11
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Wagner JK, Colwell C, Claw KG, Stone AC, Bolnick DA, Hawks J, Brothers KB, Garrison NA. Fostering Responsible Research on Ancient DNA. Am J Hum Genet 2020; 107:183-195. [PMID: 32763189 PMCID: PMC7413888 DOI: 10.1016/j.ajhg.2020.06.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Anticipating and addressing the social implications of scientific work is a fundamental responsibility of all scientists. However, expectations for ethically sound practices can evolve over time as the implications of science come to be better understood. Contemporary researchers who work with ancient human remains, including those who conduct ancient DNA research, face precisely this challenge as it becomes clear that practices such as community engagement are needed to address the important social implications of this work. To foster and promote ethical engagement between researchers and communities, we offer five practical recommendations for ancient DNA researchers: (1) formally consult with communities; (2) address cultural and ethical considerations; (3) engage communities and support capacity building; (4) develop plans to report results and manage data; and (5) develop plans for long-term responsibility and stewardship. Ultimately, every member of a research team has an important role in fostering ethical research on ancient DNA.
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Affiliation(s)
- Jennifer K Wagner
- Professional Practice and Social Implications Committee (formerly the Social Issues Committee), American Society of Human Genetics, Bethesda, MD 20814, USA; Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Center for Translational Bioethics and Health Care Policy, Geisinger, Danville, PA 17822, USA.
| | - Chip Colwell
- Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Anthropology, Denver Museum of Nature and Science, Denver, CO 80205, USA
| | - Katrina G Claw
- Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Anne C Stone
- Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA
| | - Deborah A Bolnick
- Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - John Hawks
- Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Anthropology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kyle B Brothers
- Professional Practice and Social Implications Committee (formerly the Social Issues Committee), American Society of Human Genetics, Bethesda, MD 20814, USA; Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
| | - Nanibaa' A Garrison
- Professional Practice and Social Implications Committee (formerly the Social Issues Committee), American Society of Human Genetics, Bethesda, MD 20814, USA; Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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12
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Borry M, Cordova B, Perri A, Wibowo M, Prasad Honap T, Ko J, Yu J, Britton K, Girdland-Flink L, Power RC, Stuijts I, Salazar-García DC, Hofman C, Hagan R, Samdapawindé Kagoné T, Meda N, Carabin H, Jacobson D, Reinhard K, Lewis C, Kostic A, Jeong C, Herbig A, Hübner A, Warinner C. CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ 2020; 8:e9001. [PMID: 32337106 PMCID: PMC7169968 DOI: 10.7717/peerj.9001] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/26/2020] [Indexed: 12/11/2022] Open
Abstract
Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts.
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Affiliation(s)
- Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Bryan Cordova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Angela Perri
- Department of Archaeology, Durham University, Durham, UK
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marsha Wibowo
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Tanvi Prasad Honap
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Jada Ko
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Jie Yu
- Department of History, Wuhan University, Wuhan, China
| | - Kate Britton
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Archaeology, University of Aberdeen, Aberdeen, Scotland, UK
| | - Linus Girdland-Flink
- Department of Archaeology, University of Aberdeen, Aberdeen, Scotland, UK
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Robert C. Power
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, München, Germany
| | | | - Domingo C. Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU), IKERBASQUE-Basque Foundation for Science, Vitoria-Gasteiz, Spain
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
| | - Courtney Hofman
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Richard Hagan
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | | | | | - Helene Carabin
- Département de pathologie et de microbiologie, Faculté de Médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - David Jacobson
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Karl Reinhard
- School of Natural Resources, University of Nebraska, Lincoln, NE, USA
| | - Cecil Lewis
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Aleksandar Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Choongwon Jeong
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, USA
- Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany
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13
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Di Donato A, Filippone E, Ercolano MR, Frusciante L. Genome Sequencing of Ancient Plant Remains: Findings, Uses and Potential Applications for the Study and Improvement of Modern Crops. FRONTIERS IN PLANT SCIENCE 2018; 9:441. [PMID: 29719544 PMCID: PMC5914272 DOI: 10.3389/fpls.2018.00441] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/21/2018] [Indexed: 05/08/2023]
Abstract
The advent of new sequencing technologies is revolutionizing the studies of ancient DNA (aDNA). In the last 30 years, DNA extracted from the ancient remains of several plant species has been explored in small-scale studies, contributing to understand the adaptation, and migration patterns of important crops. More recently, NGS technologies applied on aDNA have opened up new avenues of research, allowing investigation of the domestication process on the whole-genome scale. Genomic approaches based on genome-wide and targeted sequencing have been shown to provide important information on crop evolution and on the history of agriculture. Huge amounts of next-generation sequencing (NGS) data offer various solutions to overcome problems related to the origin of the material, such as degradation, fragmentation of polynucleotides, and external contamination. Recent advances made in several crop domestication studies have boosted interest in this research area. Remains of any nature are potential candidates for aDNA recovery and almost all the analyses that can be made on fresh DNA can also be performed on aDNA. The analysis performed on aDNA can shed light on many phylogenetic questions concerning evolution, domestication, and improvement of plant species. It is a powerful instrument to reconstruct patterns of crop adaptation and migration. Information gathered can also be used in many fields of modern agriculture such as classical breeding, genome editing, pest management, and product promotion. Whilst unlocking the hidden genome of ancient crops offers great potential, the onus is now on the research community to use such information to gain new insight into agriculture.
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14
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Green EJ, Speller CF. Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles. Genes (Basel) 2017; 8:E180. [PMID: 28703741 PMCID: PMC5541313 DOI: 10.3390/genes8070180] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022] Open
Abstract
Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.
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Affiliation(s)
- Eleanor Joan Green
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
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15
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Bolnick DA, Raff JA, Springs LC, Reynolds AW, Miró-Herrans AT. Native American Genomics and Population Histories. ANNUAL REVIEW OF ANTHROPOLOGY 2016. [DOI: 10.1146/annurev-anthro-102215-100036] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Studies of Native American genetic diversity and population history have been transformed over the last decade by important developments in anthropological genetics. During this time, researchers have adopted new DNA technologies and computational approaches for analyzing genomic data, and they have become increasingly sensitive to the views of research participants and communities. As new methods are applied to long-standing questions, and as more research is conducted in collaboration with indigenous communities, we are gaining new insights into the history and diversity of indigenous populations. This review discusses the recent methodological advances and genetic studies that have improved our understanding of Native American genomics and population histories. We synthesize current knowledge about Native American genomic variation and build a model of population history in the Americas. We also discuss the broader implications of this research for anthropology and related disciplines, and we highlight challenges and other considerations for future research.
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Affiliation(s)
- Deborah A. Bolnick
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
- Population Research Center, University of Texas at Austin, Austin, Texas 78712
| | - Jennifer A. Raff
- Department of Anthropology, University of Kansas, Lawrence, Kansas 66045-7556
| | - Lauren C. Springs
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
| | - Austin W. Reynolds
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
| | - Aida T. Miró-Herrans
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
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16
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Abstract
The paleomicrobiology of coprolites, which are fossilized fecal materials, has already yielded data about various organisms, including micro-eukaryotes, bacteria, and archaea, thus expanding our comprehension of ancient human dietary habits, gut microbiota, and intestinal and systemic infections. This mini-review briefly describes previous works and summarizes the main techniques used in handling coprolites and the findings obtained about ancient gut microbiota. Past intestinal and systemic infections are outlined.
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17
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Ozga AT, Nieves‐Colón MA, Honap TP, Sankaranarayanan K, Hofman CA, Milner GR, Lewis CM, Stone AC, Warinner C. Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:220-8. [PMID: 26989998 PMCID: PMC4866892 DOI: 10.1002/ajpa.22960] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 01/05/2016] [Accepted: 01/25/2016] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. MATERIALS AND METHODS Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. RESULTS Full mitogenomes (7-34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92-100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. DISCUSSION Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220-228, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Andrew T. Ozga
- Department of AnthropologyUniversity of OklahomaNormanOK73019
| | | | - Tanvi P. Honap
- School of Life SciencesArizona State UniversityTempeAZ85287
| | | | | | - George R. Milner
- Department of AnthropologyPennsylvania State University, University ParkPA16802
| | - Cecil M. Lewis
- Department of AnthropologyUniversity of OklahomaNormanOK73019
| | - Anne C. Stone
- School of Human Evolution and Social ChangeArizona State UniversityTempeAZ85287
- Center for Bioarchaeological Research, Arizona State UniversityTempeAZ85287
- Institute of Human Origins, Arizona State UniversityTempeAZ85287
| | - Christina Warinner
- Department of AnthropologyUniversity of OklahomaNormanOK73019
- Institute of Evolutionary Medicine, University of Zurich8057 ZurichSwitzerland
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18
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Ford MJ, Hempelmann J, Hanson MB, Ayres KL, Baird RW, Emmons CK, Lundin JI, Schorr GS, Wasser SK, Park LK. Estimation of a Killer Whale (Orcinus orca) Population's Diet Using Sequencing Analysis of DNA from Feces. PLoS One 2016; 11:e0144956. [PMID: 26735849 PMCID: PMC4703337 DOI: 10.1371/journal.pone.0144956] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/28/2015] [Indexed: 11/29/2022] Open
Abstract
Estimating diet composition is important for understanding interactions between predators and prey and thus illuminating ecosystem function. The diet of many species, however, is difficult to observe directly. Genetic analysis of fecal material collected in the field is therefore a useful tool for gaining insight into wild animal diets. In this study, we used high-throughput DNA sequencing to quantitatively estimate the diet composition of an endangered population of wild killer whales (Orcinus orca) in their summer range in the Salish Sea. We combined 175 fecal samples collected between May and September from five years between 2006 and 2011 into 13 sample groups. Two known DNA composition control groups were also created. Each group was sequenced at a ~330bp segment of the 16s gene in the mitochondrial genome using an Illumina MiSeq sequencing system. After several quality controls steps, 4,987,107 individual sequences were aligned to a custom sequence database containing 19 potential fish prey species and the most likely species of each fecal-derived sequence was determined. Based on these alignments, salmonids made up >98.6% of the total sequences and thus of the inferred diet. Of the six salmonid species, Chinook salmon made up 79.5% of the sequences, followed by coho salmon (15%). Over all years, a clear pattern emerged with Chinook salmon dominating the estimated diet early in the summer, and coho salmon contributing an average of >40% of the diet in late summer. Sockeye salmon appeared to be occasionally important, at >18% in some sample groups. Non-salmonids were rarely observed. Our results are consistent with earlier results based on surface prey remains, and confirm the importance of Chinook salmon in this population’s summer diet.
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Affiliation(s)
- Michael J Ford
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd E, Seattle, Washington, 98112, United States of America
| | - Jennifer Hempelmann
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd E, Seattle, Washington, 98112, United States of America
| | - M Bradley Hanson
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd E, Seattle, Washington, 98112, United States of America
| | - Katherine L Ayres
- Center for Conservation Biology, Department of Biology, University of Washington, Seattle, Washington, 98195, United States of America
| | - Robin W Baird
- Cascadia Research Collective, Olympia, Washington, 98501, United States of America
| | - Candice K Emmons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd E, Seattle, Washington, 98112, United States of America
| | - Jessica I Lundin
- Center for Conservation Biology, Department of Biology, University of Washington, Seattle, Washington, 98195, United States of America
| | - Gregory S Schorr
- Cascadia Research Collective, Olympia, Washington, 98501, United States of America
| | - Samuel K Wasser
- Center for Conservation Biology, Department of Biology, University of Washington, Seattle, Washington, 98195, United States of America
| | - Linda K Park
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd E, Seattle, Washington, 98112, United States of America
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Rivera-Perez JI, Cano RJ, Narganes-Storde Y, Chanlatte-Baik L, Toranzos GA. Retroviral DNA Sequences as a Means for Determining Ancient Diets. PLoS One 2015; 10:e0144951. [PMID: 26660678 PMCID: PMC4682816 DOI: 10.1371/journal.pone.0144951] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 11/25/2015] [Indexed: 12/22/2022] Open
Abstract
For ages, specialists from varying fields have studied the diets of the primeval inhabitants of our planet, detecting diet remains in archaeological specimens using a range of morphological and biochemical methods. As of recent, metagenomic ancient DNA studies have allowed for the comparison of the fecal and gut microbiomes associated to archaeological specimens from various regions of the world; however the complex dynamics represented in those microbial communities still remain unclear. Theoretically, similar to eukaryote DNA the presence of genes from key microbes or enzymes, as well as the presence of DNA from viruses specific to key organisms, may suggest the ingestion of specific diet components. In this study we demonstrate that ancient virus DNA obtained from coprolites also provides information reconstructing the host’s diet, as inferred from sequences obtained from pre-Columbian coprolites. This depicts a novel and reliable approach to determine new components as well as validate the previously suggested diets of extinct cultures and animals. Furthermore, to our knowledge this represents the first description of the eukaryotic viral diversity found in paleofaeces belonging to pre-Columbian cultures.
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Affiliation(s)
- Jessica I. Rivera-Perez
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico
- * E-mail:
| | - Raul J. Cano
- Center for Applications in Biotechnology, Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California, United States of America
| | - Yvonne Narganes-Storde
- Center for Archaeological Research, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico
| | - Luis Chanlatte-Baik
- Center for Archaeological Research, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico
| | - Gary A. Toranzos
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico
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20
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Warinner C, Speller C, Collins MJ, Lewis CM. Ancient human microbiomes. J Hum Evol 2015; 79:125-36. [PMID: 25559298 PMCID: PMC4312737 DOI: 10.1016/j.jhevol.2014.10.016] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 07/06/2014] [Accepted: 10/29/2014] [Indexed: 12/20/2022]
Abstract
Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.
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Affiliation(s)
- Christina Warinner
- Department of Anthropology, University of Oklahoma, 101 David L. Boren Blvd., Norman, OK 73019, USA
| | - Camilla Speller
- Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Matthew J Collins
- Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, 101 David L. Boren Blvd., Norman, OK 73019, USA.
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21
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Gouba N, Raoult D, Drancourt M. Plant and fungal diversity in gut microbiota as revealed by molecular and culture investigations. PLoS One 2013; 8:e59474. [PMID: 23555039 PMCID: PMC3598745 DOI: 10.1371/journal.pone.0059474] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 02/18/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Few studies describing eukaryotic communities in the human gut microbiota have been published. The objective of this study was to investigate comprehensively the repertoire of plant and fungal species in the gut microbiota of an obese patient. METHODOLOGY/PRINCIPAL FINDINGS A stool specimen was collected from a 27-year-old Caucasian woman with a body mass index of 48.9 who was living in Marseille, France. Plant and fungal species were identified using a PCR-based method incorporating 25 primer pairs specific for each eukaryotic phylum and universal eukaryotic primers targeting 18S rRNA, internal transcribed spacer (ITS) and a chloroplast gene. The PCR products amplified using these primers were cloned and sequenced. Three different culture media were used to isolate fungi, and these cultured fungi were further identified by ITS sequencing. A total of 37 eukaryotic species were identified, including a Diatoms (Blastocystis sp.) species, 18 plant species from the Streptophyta phylum and 18 fungal species from the Ascomycota, Basidiomycota and Chytridiocomycota phyla. Cultures yielded 16 fungal species, while PCR-sequencing identified 7 fungal species. Of these 7 species of fungi, 5 were also identified by culture. Twenty-one eukaryotic species were discovered for the first time in human gut microbiota, including 8 fungi (Aspergillus flavipes, Beauveria bassiana, Isaria farinosa, Penicillium brevicompactum, Penicillium dipodomyicola, Penicillium camemberti, Climacocystis sp. and Malassezia restricta). Many fungal species apparently originated from food, as did 11 plant species. However, four plant species (Atractylodes japonica, Fibraurea tinctoria, Angelica anomala, Mitella nuda) are used as medicinal plants. CONCLUSIONS/SIGNIFICANCE Investigating the eukaryotic components of gut microbiota may help us to understand their role in human health.
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Affiliation(s)
- Nina Gouba
- Aix Marseille Université, URMITE, UMR63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France
| | - Didier Raoult
- Aix Marseille Université, URMITE, UMR63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France
- * E-mail:
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22
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Tito RY, Knights D, Metcalf J, Obregon-Tito AJ, Cleeland L, Najar F, Roe B, Reinhard K, Sobolik K, Belknap S, Foster M, Spicer P, Knight R, Lewis CM. Insights from characterizing extinct human gut microbiomes. PLoS One 2012; 7:e51146. [PMID: 23251439 PMCID: PMC3521025 DOI: 10.1371/journal.pone.0051146] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 11/01/2012] [Indexed: 01/31/2023] Open
Abstract
In an effort to better understand the ancestral state of the human distal gut microbiome, we examine feces retrieved from archaeological contexts (coprolites). To accomplish this, we pyrosequenced the 16S rDNA V3 region from duplicate coprolite samples recovered from three archaeological sites, each representing a different depositional environment: Hinds Cave (∼8000 years B.P.) in the southern United States, Caserones (1600 years B.P.) in northern Chile, and Rio Zape in northern Mexico (1400 years B.P.). Clustering algorithms grouped samples from the same site. Phyletic representation was more similar within sites than between them. A Bayesian approach to source-tracking was used to compare the coprolite data to published data from known sources that include, soil, compost, human gut from rural African children, human gut, oral and skin from US cosmopolitan adults and non-human primate gut. The data from the Hinds Cave samples largely represented unknown sources. The Caserones samples, retrieved directly from natural mummies, matched compost in high proportion. A substantial and robust proportion of Rio Zape data was predicted to match the gut microbiome found in traditional rural communities, with more minor matches to other sources. One of the Rio Zape samples had taxonomic representation consistent with a child. To provide an idealized scenario for sample preservation, we also applied source tracking to previously published data for Ötzi the Iceman and a soldier frozen for 93 years on a glacier. Overall these studies reveal that human microbiome data has been preserved in some coprolites, and these preserved human microbiomes match more closely to those from the rural communities than to those from cosmopolitan communities. These results suggest that the modern cosmopolitan lifestyle resulted in a dramatic change to the human gut microbiome.
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Affiliation(s)
- Raul Y. Tito
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Dan Knights
- Department of Computer Science, University of Colorado, Boulder, Colorado, United States of America
| | - Jessica Metcalf
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United States of America
| | | | - Lauren Cleeland
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Fares Najar
- Department of Chemistry and Biochemistry, Advanced Center for Genome Technology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Bruce Roe
- Department of Chemistry and Biochemistry, Advanced Center for Genome Technology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Karl Reinhard
- School of Natural Resources, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Kristin Sobolik
- Climate Change Institute and Department of Anthropology, University of Maine, Orono, Maine, United States of America
| | - Samuel Belknap
- Climate Change Institute and Department of Anthropology, University of Maine, Orono, Maine, United States of America
| | - Morris Foster
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Paul Spicer
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United States of America
| | - Cecil M. Lewis
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
- * E-mail:
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23
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Reinhard KJ, Johnson KL, LeRoy-Toren S, Wieseman K, Teixeira-Santos I, Vieira M. Understanding the Pathoecological Relationship between Ancient Diet and Modern Diabetes through Coprolite Analysis. CURRENT ANTHROPOLOGY 2012. [DOI: 10.1086/665923] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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24
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Hünemeier T, Amorim CEG, Azevedo S, Contini V, Acuña-Alonzo V, Rothhammer F, Dugoujon JM, Mazières S, Barrantes R, Villarreal-Molina MT, Paixão-Côrtes VR, Salzano FM, Canizales-Quinteros S, Ruiz-Linares A, Bortolini MC. Evolutionary responses to a constructed niche: ancient Mesoamericans as a model of gene-culture coevolution. PLoS One 2012; 7:e38862. [PMID: 22768049 PMCID: PMC3380856 DOI: 10.1371/journal.pone.0038862] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 05/12/2012] [Indexed: 12/26/2022] Open
Abstract
Culture and genetics rely on two distinct but not isolated transmission systems. Cultural processes may change the human selective environment and thereby affect which individuals survive and reproduce. Here, we evaluated whether the modes of subsistence in Native American populations and the frequencies of the ABCA1*Arg230Cys polymorphism were correlated. Further, we examined whether the evolutionary consequences of the agriculturally constructed niche in Mesoamerica could be considered as a gene-culture coevolution model. For this purpose, we genotyped 229 individuals affiliated with 19 Native American populations and added data for 41 other Native American groups (n = 1905) to the analysis. In combination with the SNP cluster of a neutral region, this dataset was then used to unravel the scenario involved in 230Cys evolutionary history. The estimated age of 230Cys is compatible with its origin occurring in the American continent. The correlation of its frequencies with the archeological data on Zea pollen in Mesoamerica/Central America, the neutral coalescent simulations, and the FST-based natural selection analysis suggest that maize domestication was the driving force in the increase in the frequencies of 230Cys in this region. These results may represent the first example of a gene-culture coevolution involving an autochthonous American allele.
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Affiliation(s)
- Tábita Hünemeier
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Carlos Eduardo Guerra Amorim
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Soledad Azevedo
- Centro Nacional Patagónico, CONICET, U9120ACV, Puerto Madryn, Argentina
| | - Veronica Contini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Víctor Acuña-Alonzo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, Mexico
| | - Francisco Rothhammer
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
| | - Jean-Michel Dugoujon
- Laboratoire d′Anthropologie Moléculaire et d′Imagerie de Synthèse, UMR 5288 CNRS, Université Paul Sabatier (Toulouse3), Toulouse, France
| | - Stephane Mazières
- Anthropologie Bio-culturelle, Droit, Ethique et Santé (ADES), UMR 7268, Aix-Marseille-Université/CNRS/EFS, Marseille, France
| | - Ramiro Barrantes
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | | | - Vanessa Rodrigues Paixão-Côrtes
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Francisco M. Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Samuel Canizales-Quinteros
- Unit of Molecular Biology and Genomic Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Andres Ruiz-Linares
- The Galton Laboratory, Department of Biology, University College London, London, United Kingdom
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
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25
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Huynen L, Millar CD, Lambert DM. Resurrecting ancient animal genomes: the extinct moa and more. Bioessays 2012; 34:661-9. [PMID: 22674514 DOI: 10.1002/bies.201200040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Recently two developments have had a major impact on the field of ancient DNA (aDNA). First, new advances in DNA sequencing, in combination with improved capture/enrichment methods, have resulted in the recovery of orders of magnitude more DNA sequence data from ancient animals. Second, there has been an increase in the range of tissue types employed in aDNA. Hair in particular has proven to be very successful as a source of DNA because of its low levels of contamination and high level of ancient endogenous DNA. These developments have resulted in significant advances in our understanding of recently extinct animals: namely their evolutionary relationships, physiology, and even behaviour. Hair has been used to recover the first complete ancient nuclear genome, that of the extinct woolly mammoth, which then facilitated the expression and functional analysis of haemoglobins. Finally, we speculate on the consequences of these developments for the possibility of recreating extinct animals.
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Affiliation(s)
- Leon Huynen
- Griffith School of Environment and the School of Biomolecular and Physical Sciences, Griffith University, Nathan, Australia
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26
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Case study: ancient sloth DNA recovered from hairs preserved in paleofeces. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 840:51-6. [PMID: 22237521 DOI: 10.1007/978-1-61779-516-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Ancient hair, which has proved to be an excellent source of well-preserved ancient DNA, is often preserved in paleofeces. Here, we separate and wash hair shafts preserved in a paleofecal specimen believed to be from a Darwin's ground sloth, Mylodon darwinii. After extracting DNA from the recovered and cleaned hair using a protocol optimized for DNA extraction from keratinous substrates, we amplify 12S and 16S rDNA sequences from the DNA extract. As expected, the recovered sequences most closely match previously published sequences of M. darwinii. Our results demonstrate that hair preserved in paleofeces, even from temperate cave environments, is an effective source of ancient DNA.
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27
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Abstract
Paleofeces are the nonmineralized remains of dung from extant and extinct fauna. They represent a surprisingly large proportion of fossil remains recovered from cave sites across the world. Paleofeces contain the DNA of the defecator as well as the DNA of ingested plant and animal remains. To successfully extract DNA from paleofeces, a balance must be achieved between the minimization of DNA loss during extraction and the removal of coeluates that would otherwise inhibit the Taq DNA polymerase during downstream applications. Here we present a simplified version of a protocol to extract DNA from paleofecal remains.
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Affiliation(s)
- Melanie Kuch
- McMaster Ancient DNA Centre, McMaster University, Hamilton, ON, Canada
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28
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The blossoming of plant archaeogenetics. Ann Anat 2012; 194:146-56. [DOI: 10.1016/j.aanat.2011.03.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 03/25/2011] [Accepted: 03/25/2011] [Indexed: 11/19/2022]
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29
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Pompanon F, Deagle BE, Symondson WOC, Brown DS, Jarman SN, Taberlet P. Who is eating what: diet assessment using next generation sequencing. Mol Ecol 2011; 21:1931-50. [PMID: 22171763 DOI: 10.1111/j.1365-294x.2011.05403.x] [Citation(s) in RCA: 585] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The analysis of food webs and their dynamics facilitates understanding of the mechanistic processes behind community ecology and ecosystem functions. Having accurate techniques for determining dietary ranges and components is critical for this endeavour. While visual analyses and early molecular approaches are highly labour intensive and often lack resolution, recent DNA-based approaches potentially provide more accurate methods for dietary studies. A suite of approaches have been used based on the identification of consumed species by characterization of DNA present in gut or faecal samples. In one approach, a standardized DNA region (DNA barcode) is PCR amplified, amplicons are sequenced and then compared to a reference database for identification. Initially, this involved sequencing clones from PCR products, and studies were limited in scale because of the costs and effort required. The recent development of next generation sequencing (NGS) has made this approach much more powerful, by allowing the direct characterization of dozens of samples with several thousand sequences per PCR product, and has the potential to reveal many consumed species simultaneously (DNA metabarcoding). Continual improvement of NGS technologies, on-going decreases in costs and current massive expansion of reference databases make this approach promising. Here we review the power and pitfalls of NGS diet methods. We present the critical factors to take into account when choosing or designing a suitable barcode. Then, we consider both technical and analytical aspects of NGS diet studies. Finally, we discuss the validation of data accuracy including the viability of producing quantitative data.
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Affiliation(s)
- Francois Pompanon
- Université Grenoble 1, Laboratoire d'Ecologie Alpine, CNRS, UMR 5553, Grenoble, France.
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30
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Abstract
The increasing sensitivity of PCR has meant that in the last two decades PCR has emerged as a major tool in diet studies, enabling us to refine our understanding of trophic links and to elucidate the diets of predators whose prey is as yet uncharacterized. The achievements and methods of PCR-based diet studies have been reviewed several times, but here we review an important development in the field: the use of PCR enrichment techniques to promote the amplification of prey DNA over that of the predator. We first discuss the success of using group-specific primers either in parallel single reactions or in multiplex reactions. We then concentrate on the more recent use of PCR enrichment techniques such as restriction enzyme digests, peptide nucleic acid clamping, DNA blocking and laser capture microdissection. We also survey the vast literature on enrichment techniques in clinical biology, to ascertain the pitfalls of enrichment techniques and what refinements have yielded some highly sensitive methods. We find that while there are several new approaches to enrichment, peptide nucleic acid clamping and DNA blocking are generally sufficient techniques for the characterization of diets of predators and highlight the most important considerations of the approach.
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Affiliation(s)
- R O'Rorke
- Leigh Marine Laboratory, University of Auckland, Warkworth, Northland 0941, New Zealand.
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31
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Murray DC, Bunce M, Cannell BL, Oliver R, Houston J, White NE, Barrero RA, Bellgard MI, Haile J. DNA-based faecal dietary analysis: a comparison of qPCR and high throughput sequencing approaches. PLoS One 2011; 6:e25776. [PMID: 21998697 PMCID: PMC3188572 DOI: 10.1371/journal.pone.0025776] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 09/09/2011] [Indexed: 11/29/2022] Open
Abstract
The genetic analysis of faecal material represents a relatively non-invasive way to study animal diet and has been widely adopted in ecological research. Due to the heterogeneous nature of faecal material the primary obstacle, common to all genetic approaches, is a means to dissect the constituent DNA sequences. Traditionally, bacterial cloning of PCR amplified products was employed; less common has been the use of species-specific quantitative PCR (qPCR) assays. Currently, with the advent of High-Throughput Sequencing (HTS) technologies and indexed primers it has become possible to conduct genetic audits of faecal material to a much greater depth than previously possible. To date, no studies have systematically compared the estimates obtained by HTS with that of qPCR. What are the relative strengths and weaknesses of each technique and how quantitative are deep-sequencing approaches that employ universal primers? Using the locally threatened Little Penguin (Eudyptula minor) as a model organism, it is shown here that both qPCR and HTS techniques are highly correlated and produce strikingly similar quantitative estimates of fish DNA in faecal material, with no statistical difference. By designing four species-specific fish qPCR assays and comparing the data to the same four fish in the HTS data it was possible to directly compare the strengths and weaknesses of both techniques. To obtain reproducible quantitative data one of the key, and often overlooked, steps common to both approaches is ensuring that efficient DNA isolation methods are employed and that extracts are free of inhibitors. Taken together, the methodology chosen for long-term faecal monitoring programs is largely dependent on the complexity of the prey species present and the level of accuracy that is desired. Importantly, these methods should not be thought of as mutually exclusive, as the use of both HTS and qPCR in tandem will generate datasets with the highest fidelity.
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Affiliation(s)
- Dáithí C. Murray
- Australian Wildlife Forensic Services and Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Murdoch, Western Australia, Australia
| | - Michael Bunce
- Australian Wildlife Forensic Services and Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Murdoch, Western Australia, Australia
- * E-mail:
| | - Belinda L. Cannell
- School of Biological Sciences and Biotechnology, Murdoch University, Murdoch, Western Australia, Australia
| | - Rebecca Oliver
- Australian Wildlife Forensic Services and Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Murdoch, Western Australia, Australia
| | - Jayne Houston
- Australian Wildlife Forensic Services and Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Murdoch, Western Australia, Australia
| | - Nicole E. White
- Australian Wildlife Forensic Services and Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Murdoch, Western Australia, Australia
| | - Roberto A. Barrero
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia, Australia
| | - Matthew I. Bellgard
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia, Australia
| | - James Haile
- Australian Wildlife Forensic Services and Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Murdoch, Western Australia, Australia
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32
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Boere AC, Rijpstra WIC, De Lange GJ, Sinninghe Damsté JS, Coolen MJL. Preservation potential of ancient plankton DNA in Pleistocene marine sediments. GEOBIOLOGY 2011; 9:377-393. [PMID: 21884361 DOI: 10.1111/j.1472-4669.2011.00290.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Recent studies have shown that ancient plankton DNA can be recovered from Holocene lacustrine and marine sediments, including from species that do not leave diagnostic microscopic fossils in the sediment record. Therefore, the analysis of this so-called fossil plankton DNA is a promising approach for refining paleoecological and paleoenvironmental information. However, further studies are needed to reveal whether DNA of past plankton is preserved beyond the Holocene. Here, we identified past eukaryotic plankton members based on 18S rRNA gene profiling in eastern Mediterranean Holocene and Pleistocene sapropels S1 (~9 ka), S3 (~80 ka), S4 (~105 ka), and S5 (~125 ka). The majority of preserved ~400- to 500-bp-long 18S rDNA fragments of microalgae that were studied in detail (i.e. from haptophyte algae and dinoflagellates) were found in the youngest sapropel S1, whereas their specific lipid biomarkers (long-chain alkenones and dinosterol) were also abundant in sediments deposited between 80 and 124 ka BP. The late-Pleistocene sediments mainly contained eukaryotic DNA of marine fungi and from terrestrial plants, which could have been introduced via the river Nile at the time of deposition and preserved in pollen grains. A parallel analysis of Branched and Isoprenoid Tetraethers (i.e. BIT index) showed that most of the organic matter in the eastern Mediterranean sediment record was of marine (e.g. pelagic) origin. Therefore, the predominance of terrestrial plant DNA over plankton DNA in older sapropels suggests a preferential degradation of marine plankton DNA.
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Affiliation(s)
- A C Boere
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
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33
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Winters M, Barta JL, Monroe C, Kemp BM. To clone or not to clone: method analysis for retrieving consensus sequences in ancient DNA samples. PLoS One 2011; 6:e21247. [PMID: 21738625 PMCID: PMC3124491 DOI: 10.1371/journal.pone.0021247] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 05/24/2011] [Indexed: 01/06/2023] Open
Abstract
The challenges associated with the retrieval and authentication of ancient DNA (aDNA) evidence are principally due to post-mortem damage which makes ancient samples particularly prone to contamination from "modern" DNA sources. The necessity for authentication of results has led many aDNA researchers to adopt methods considered to be "gold standards" in the field, including cloning aDNA amplicons as opposed to directly sequencing them. However, no standardized protocol has emerged regarding the necessary number of clones to sequence, how a consensus sequence is most appropriately derived, or how results should be reported in the literature. In addition, there has been no systematic demonstration of the degree to which direct sequences are affected by damage or whether direct sequencing would provide disparate results from a consensus of clones.To address this issue, a comparative study was designed to examine both cloned and direct sequences amplified from ∼3,500 year-old ancient northern fur seal DNA extracts. Majority rules and the Consensus Confidence Program were used to generate consensus sequences for each individual from the cloned sequences, which exhibited damage at 31 of 139 base pairs across all clones. In no instance did the consensus of clones differ from the direct sequence. This study demonstrates that, when appropriate, cloning need not be the default method, but instead, should be used as a measure of authentication on a case-by-case basis, especially when this practice adds time and cost to studies where it may be superfluous.
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Affiliation(s)
- Misa Winters
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Jodi Lynn Barta
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
| | - Cara Monroe
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, University of California-Santa Barbara, Santa Barbara, California, United States of America
| | - Brian M. Kemp
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
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34
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Mylodon darwinii DNA sequences from ancient fecal hair shafts. Ann Anat 2011; 194:26-30. [PMID: 21640569 DOI: 10.1016/j.aanat.2011.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 05/04/2011] [Accepted: 05/05/2011] [Indexed: 11/20/2022]
Abstract
Preserved hair has been increasingly used as an ancient DNA source in high throughput sequencing endeavors, and it may actually offer several advantages compared to more traditional ancient DNA substrates like bone. However, cold environments have yielded the most informative ancient hair specimens, while its preservation, and thus utility, in temperate regions is not well documented. Coprolites could represent a previously underutilized preservation substrate for hairs, which, if present therein, represent macroscopic packages of specific cells that are relatively simple to separate, clean and process. In this pilot study, we report amplicons 147-152 base pairs in length (w/primers) from hair shafts preserved in a south Chilean coprolite attributed to Darwin's extinct ground sloth, Mylodon darwinii. Our results suggest that hairs preserved in coprolites from temperate cave environments can serve as an effective source of ancient DNA. This bodes well for potential molecular-based population and phylogeographic studies on sloths, several species of which have been understudied despite leaving numerous coprolites in caves across of the Americas.
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35
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Vinton SD, Perry L, Reinhard KJ, Santoro CM, Teixeira-Santos I. Impact of empire expansion on household diet: the Inka in Northern Chile's Atacama Desert. PLoS One 2009; 4:e8069. [PMID: 19956668 PMCID: PMC2777378 DOI: 10.1371/journal.pone.0008069] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2008] [Accepted: 10/06/2009] [Indexed: 11/18/2022] Open
Abstract
The impact of expanding civilization on the health of American indigenous societies has long been studied. Most studies have focused on infections and malnutrition that occurred when less complex societies were incorporated into more complex civilizations. The details of dietary change, however, have rarely been explored. Using the analysis of starch residues recovered from coprolites, here we evaluate the dietary adaptations of indigenous farmers in northern Chile's Atacama Desert during the time that the Inka Empire incorporated these communities into their economic system. This system has been described as "complementarity" because it involves interaction and trade in goods produced at different Andean elevations. We find that as local farming societies adapted to this new asymmetric system, a portion of their labor had to be given up to the Inka elite through a corvée tax system for maize production. In return, the Inka system of complementarity introduced previously rare foods from the Andean highlands into local economies. These changes caused a disruption of traditional communities as they instituted a state-level economic system on local farmers. Combined with previously published infection information for the same populations under Inka rule, the data suggest that there may have been a dual health impact from disruption of nutrition and introduction of crowd disease.
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Affiliation(s)
- Sheila Dorsey Vinton
- Department of Anthropology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Linda Perry
- Archaeobiology Program, Department of Anthropology, Smithsonian National Museum of Natural History, Washington D.C., United States of America
| | - Karl J. Reinhard
- School of Natural Resources, University of Nebraska – Lincoln, Lincoln, Nebraska, United States of America
- * E-mail:
| | - Calogero M. Santoro
- Instituto Alta Investigación, Departamento de Antropología, Universidad de Tarapacá, Arica, Chile
- Centro de Investigaciones del Hombre en el Desierto, Arica, Chile
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36
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Abstract
Having begun graduate work in anthropology and prehistoric archaeology at a time (early 1950s) and place (University of Chicago) where the two were closely linked, I subsequently participated in work devoted to early agricultural economies in Western Asia and Eastern North America; to the relations among archaeology, history, and science; and to the place of anthropological archaeology in the contemporary world. In this article I discuss my personal experiences within each of these areas of endeavor.
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37
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Gilbert MTP, Jenkins DL, Higham TFG, Rasmussen M, Malmström H, Svensson EM, Sanchez JJ, Cummings LS, Yohe RM, Hofreiter M, Götherström A, Willerslev E. Response to Comment by Poinar
et al
. on “DNA from Pre-Clovis Human Coprolites in Oregon, North America”. Science 2009. [DOI: 10.1126/science.1168457] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- M. Thomas P. Gilbert
- Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Dennis L. Jenkins
- Museum of Natural and Cultural History, 1224 University of Oregon, Eugene, OR 97403–1224, USA
| | - Thomas F. G. Higham
- Research Laboratory for Archaeology and the History of Art, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
| | - Morten Rasmussen
- Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Helena Malmström
- Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Emma M. Svensson
- Department of Evolutionary Biology, Uppsala University, Norbyvagten 18D, 74236 Uppsala, Sweden
| | - Juan J. Sanchez
- National Institute of Toxicology and Forensic Science, Canary Islands Delegation, 38320 Tenerife, Spain
| | | | - Robert M. Yohe
- Department of Sociology and Anthropology, California State University, 9001 Stockdale Highway, Bakersfield, CA 93311, USA
| | - Michael Hofreiter
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Anders Götherström
- Department of Evolutionary Biology, Uppsala University, Norbyvagten 18D, 74236 Uppsala, Sweden
| | - Eske Willerslev
- Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
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Poinar H, Fiedel S, King CE, Devault AM, Bos K, Kuch M, Debruyne R. Comment on "DNA from Pre-Clovis Human Coprolites in Oregon, North America". Science 2009; 325:148; author reply 148. [PMID: 19589985 DOI: 10.1126/science.1168182] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Hendrik Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9 Canada.
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39
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Valentini A, Miquel C, Nawaz MA, Bellemain E, Coissac E, Pompanon F, Gielly L, Cruaud C, Nascetti G, Wincker P, Swenson JE, Taberlet P. New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: thetrnL approach. Mol Ecol Resour 2009; 9:51-60. [PMID: 21564566 DOI: 10.1111/j.1755-0998.2008.02352.x] [Citation(s) in RCA: 311] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alice Valentini
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble cedex 9, France
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40
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41
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Shapiro B. Engineered polymerases amplify the potential of ancient DNA. Trends Biotechnol 2008; 26:285-7. [PMID: 18440082 DOI: 10.1016/j.tibtech.2008.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 03/03/2008] [Accepted: 03/17/2008] [Indexed: 11/30/2022]
Abstract
The generation of genomic data from mammoths and Neanderthals has reinvigorated discussion about whether extinct species could be brought back within the foreseeable future. However, post-mortem DNA decay rapidly reduces the number and quality of surviving DNA fragments, consequently increasing rates of sequencing error and forming a significant obstacle to accurate sequence reconstruction. Recent work has shown that it is possible to engineer a polymerase capable of using even highly damaged fragments as template sequences.
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Affiliation(s)
- Beth Shapiro
- Department of Biology, 326 Mueller Laboratory, The Pennsylvania State University, University Park, PA 16801, USA.
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Bradley BJ, Stiller M, Doran-Sheehy DM, Harris T, Chapman CA, Vigilant L, Poinar H. Plant DNA sequences from feces: potential means for assessing diets of wild primates. Am J Primatol 2008; 69:699-705. [PMID: 17216626 DOI: 10.1002/ajp.20384] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Analyses of plant DNA in feces provides a promising, yet largely unexplored, means of documenting the diets of elusive primates. Here we demonstrate the promise and pitfalls of this approach using DNA extracted from fecal samples of wild western gorillas (Gorilla gorilla) and black and white colobus monkeys (Colobus guereza). From these DNA extracts we amplified, cloned, and sequenced small segments of chloroplast DNA (part of the rbcL gene) and plant nuclear DNA (ITS-2). The obtained sequences were compared to sequences generated from known plant samples and to those in GenBank to identify plant taxa in the feces. With further optimization, this method could provide a basic evaluation of minimum primate dietary diversity even when knowledge of local flora is limited. This approach may find application in studies characterizing the diets of poorly-known, unhabituated primate species or assaying consumer-resource relationships in an ecosystem.
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Affiliation(s)
- Brenda J Bradley
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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Deagle BE, Eveson JP, Jarman SN. Quantification of damage in DNA recovered from highly degraded samples--a case study on DNA in faeces. Front Zool 2006; 3:11. [PMID: 16911807 PMCID: PMC1564134 DOI: 10.1186/1742-9994-3-11] [Citation(s) in RCA: 270] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2006] [Accepted: 08/16/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Poorly preserved biological tissues have become an important source of DNA for a wide range of zoological studies. Measuring the quality of DNA obtained from these samples is often desired; however, there are no widely used techniques available for quantifying damage in highly degraded DNA samples. We present a general method that can be used to determine the frequency of polymerase blocking DNA damage in specific gene-regions in such samples. The approach uses quantitative PCR to measure the amount of DNA present at several fragment sizes within a sample. According to a model of random degradation the amount of available template will decline exponentially with increasing fragment size in damaged samples, and the frequency of DNA damage (lambda) can be estimated by determining the rate of decline. RESULTS The method is illustrated through the analysis of DNA extracted from sea lion faecal samples. Faeces contain a complex mixture of DNA from several sources and different components are expected to be differentially degraded. We estimated the frequency of DNA damage in both predator and prey DNA within individual faecal samples. The distribution of fragment lengths for each target fit well with the assumption of a random degradation process and, in keeping with our expectations, the estimated frequency of damage was always less in predator DNA than in prey DNA within the same sample (mean lambda(predator) = 0.0106 per nucleotide; mean lambda(prey) = 0.0176 per nucleotide). This study is the first to explicitly define the amount of template damage in any DNA extracted from faeces and the first to quantify the amount of predator and prey DNA present within individual faecal samples. CONCLUSION We present an approach for characterizing mixed, highly degraded PCR templates such as those often encountered in ecological studies using non-invasive samples as a source of DNA, wildlife forensics investigations and ancient DNA research. This method will allow researchers to measure template quality in order to evaluate alternate sources of DNA, different methods of sample preservation and different DNA extraction protocols. The technique could also be applied to study the process of DNA decay.
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Affiliation(s)
- Bruce E Deagle
- School of Zoology, University of Tasmania, Box 252-05, Hobart, Tasmania, Australia
- Australian Antarctic Division, Channel Highway, Kingston, Tasmania, Australia
| | - J Paige Eveson
- CSIRO Marine and Atmospheric Research, Box 1538, Hobart, Tasmania, Australia
| | - Simon N Jarman
- Australian Antarctic Division, Channel Highway, Kingston, Tasmania, Australia
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Parducci L, Suyama Y, Lascoux M, Bennett KD. Ancient DNA from pollen: a genetic record of population history in Scots pine. Mol Ecol 2005; 14:2873-82. [PMID: 16029485 DOI: 10.1111/j.1365-294x.2005.02644.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Assessments of plant population dynamics in space and time have depended on dated records of fossil pollen synthesized on a subcontinental scale. Genetic analyses of extant populations have revealed spatial relationships that are indicative of past spatial dynamics, but lack an explicit timescale. Synthesis of these data requires genetic analyses from abundant dated fossil material, and this has hitherto been lacking. Fossil pollen is the most abundant material with which to fill this data gap. Here we report genetic analyses of fossil pollen retrieved from Holtjärnen postglacial lake sediment in Sweden and show that plastid DNA is recoverable from Scots Pine and Norway spruce pollen grains that are 100 and 10 000 years old. By sequencing clones from two short plastid PCR products and by using multiple controls we show that the ancient sequences were endogenous to the fossil grains. Comparison of ancient sequences and those obtained from an extant population of Scots pine establishes the first genetic link between extant and fossil samples in this species, providing genetic continuity through time. The finding of one common haplotype present in modern, 100-year old and 10 000-year old samples suggests that it may have persisted near Holtjärnen throughout the postglacial period. This retrieval of ancient DNA from pollen has major implications for plant palaeoecology in conifer species by allowing direct estimates of population dynamics in space and time.
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Affiliation(s)
- L Parducci
- Department of Earth Sciences, Palaeobiology Program, Uppsala University, Villavägen 16, SE-752 36 Uppsala, Sweden.
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Abstract
Ancient DNA has received much attention since the mid-1980s, when the first sequence of an extinct animal species was recovered from a museum specimen. Since then, the majority of ancient DNA studies have focused predominantly on animal species, while studies in plant palaeogenetics have been rather limited, with the notable exception of cultivated species found in archaeological sites. Here, we outline the recent developments in the analysis of plant ancient DNA. We emphasize the trend from species identification to population-level investigation and highlight the potential and the difficulties in this field, related to DNA preservation and to risks of contamination. Further efforts towards the analysis of ancient DNA from the abundant store of fossil plant remains should provide new research opportunities in palaeoecology and phylogeography. In particular, intraspecific variation should be considered not only in cultivated plants but also in wild taxa if palaeogenetics is to become a fully emancipated field of plant research.
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Affiliation(s)
- Felix Gugerli
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
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Eggert LS, Maldonado JE, Fleischer RC. Nucleic acid isolation from ecological samples--animal scat and other associated materials. Methods Enzymol 2005; 395:73-87. [PMID: 15865962 DOI: 10.1016/s0076-6879(05)95006-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Noninvasive sampling is very attractive to field biologists and has tremendous potential for studying secretive species and being a cost-effective method of increasing sample sizes in studies of large, dangerous animals. Extracting DNA from noninvasively collected samples can be challenging, and the methods have been developed mainly through modification of previously developed protocols for other sample types. We present the most commonly used methods along with modifications used by some researchers to deal with the problem of coextraction of polymerase chain reaction (PCR) inhibitors. Although it is difficult to generalize about which methods should be used on particular sample types, we discuss the success of the methods in studies to date. We close with general suggestions for dealing with potential problems associated with the analysis of DNA obtained from noninvasively collected samples.
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Affiliation(s)
- Lori S Eggert
- Department of Systematic Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20008-0551, USA
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Jarman SN, Deagle BE, Gales NJ. Group-specific polymerase chain reaction for DNA-based analysis of species diversity and identity in dietary samples. Mol Ecol 2004; 13:1313-22. [PMID: 15078466 DOI: 10.1111/j.1365-294x.2004.02109.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Unique DNA sequences are present in all species and can be used as biomarkers for the detection of cells from that species. These DNA sequences can most easily be detected using the polymerase chain reaction (PCR), which allows very small quantities of target DNA sequence to be amplified even when the target is mixed with large amounts of nontarget DNA. PCR amplification of DNA markers that are present in a wide range of species has proven very useful for studies of species diversity in environmental samples. The taxonomic range of species to be identified from environmental samples may often need to be restricted to simplify downstream analyses and to ensure that less abundant sequences are amplified. Group-specific PCR primer sets are one means of specifying the range of taxa that produce an amplicon in a PCR. We have developed a range of group-specific PCR primers for studying the prey diversity found in predator stomach contents and scats. These primers, their design and their application to studying prey diversity and identity in predator diet are described.
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Affiliation(s)
- S N Jarman
- Australian Antarctic Division, Channel Highway, Kingston, Tasmania 7050, Australia.
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Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M. Genetic Analyses from Ancient DNA. Annu Rev Genet 2004; 38:645-79. [PMID: 15568989 DOI: 10.1146/annurev.genet.37.110801.143214] [Citation(s) in RCA: 654] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
About 20 years ago, DNA sequences were separately described from the quagga (a type of zebra) and an ancient Egyptian individual. What made these DNA sequences exceptional was that they were derived from 140- and 2400-year-old specimens. However, ancient DNA research, defined broadly as the retrieval of DNA sequences from museum specimens, archaeological finds, fossil remains, and other unusual sources of DNA, only really became feasible with the advent of techniques for the enzymatic amplification of specific DNA sequences. Today, reports of analyses of specimens hundreds, thousands, and even millions of years old are almost commonplace. But can all these results be believed? In this paper, we critically assess the state of ancient DNA research. In particular, we discuss the precautions and criteria necessary to ascertain to the greatest extent possible that results represent authentic ancient DNA sequences. We also highlight some significant results and areas of promising future research.
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Affiliation(s)
- Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, D-04013 Leipzig, Germany.
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Thalmann O, Hebler J, Poinar HN, Pääbo S, Vigilant L. Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Mol Ecol 2004; 13:321-35. [PMID: 14717890 DOI: 10.1046/j.1365-294x.2003.02070.x] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Analysis of mitochondrial DNA sequence variation has been used extensively to study the evolutionary relationships of individuals and populations, both within and across species. So ubiquitous and easily acquired are mtDNA data that it has been suggested that such data could serve as a taxonomic 'barcode' for an objective species classification scheme. However, there are technical pitfalls associated with the acquisition of mtDNA data. One problem is the presence of translocated pieces of mtDNA in the nuclear genome of many taxa that may be mistaken for authentic organellar mtDNA. We assessed the extent to which such 'numt' sequences may pose an overlooked problem in analyses of mtDNA from humans and apes. Using long-range polymerase chain reaction (PCR), we generated necessarily authentic mtDNA sequences for comparison with sequences obtained using typical methods for a segment of the mtDNA control region in humans, chimpanzees, bonobos, gorillas and orangutans. Results revealed that gorillas are notable for having such a variety of numt sequences bearing high similarity to authentic mtDNA that any analysis of mtDNA using standard approaches is rendered impossible. Studies on humans, chimpanzees, bonobos or orangutans are apparently less problematic. One implication is that explicit measures need to be taken to authenticate mtDNA sequences in newly studied taxa or when any irregularities arise. Furthermore, some taxa may not be amenable to analysis of mtDNA variation at all.
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Affiliation(s)
- O Thalmann
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany.
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