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Marinček P, Wagner ND, Tomasello S. Ancient DNA extraction methods for herbarium specimens: When is it worth the effort? APPLICATIONS IN PLANT SCIENCES 2022; 10:e11477. [PMID: 35774991 PMCID: PMC9215277 DOI: 10.1002/aps3.11477] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/03/2022] [Accepted: 03/20/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Herbaria harbor a tremendous number of plant specimens that are rarely used for molecular systematic studies, largely due to the difficulty in extracting sufficient amounts of high-quality DNA from the preserved plant material. METHODS We compared the standard Qiagen DNeasy Plant Mini Kit and a specific protocol for extracting ancient DNA (aDNA) (the N-phenacylthiazolium bromide and dithiothreitol [PTB-DTT] extraction method) from two different plant genera (Xanthium and Salix). The included herbarium materials covered about two centuries of plant collections. To analyze the success of DNA extraction using each method, a subset of samples was subjected to a standard library preparation as well as target-enrichment approaches. RESULTS The PTB-DTT method produced a higher DNA yield of better quality than the Qiagen kit; however, extracts from the Qiagen kit over a certain DNA yield and quality threshold produced comparable sequencing results. The sequencing resulted in high proportions of endogenous reads. We were able to successfully sequence 200-year-old samples. DISCUSSION This method comparison revealed that, for younger specimens, DNA extraction using a standard kit might be sufficient. For old and precious herbarium specimens, aDNA extraction methods are better suited to meet the requirements for next-generation sequencing.
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Affiliation(s)
- Pia Marinček
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of Göttingen, Untere Karspüle 237073GöttingenGermany
| | - Natascha D. Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of Göttingen, Untere Karspüle 237073GöttingenGermany
| | - Salvatore Tomasello
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of Göttingen, Untere Karspüle 237073GöttingenGermany
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Ewart KM, Johnson RN, Ogden R, Joseph L, Frankham GJ, Lo N. Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species. Mol Ecol Resour 2019; 19:1578-1592. [PMID: 31484222 DOI: 10.1111/1755-0998.13082] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022]
Abstract
Natural history museums harbour a plethora of biological specimens which are of potential use in population and conservation genetic studies. Although technical advancements in museum genomics have enabled genome-wide markers to be generated from aged museum specimens, the suitability of these data for robust biological inference is not well characterized. The aim of this study was to test the utility of museum specimens in population and conservation genomics by assessing the biological and technical validity of single nucleotide polymorphism (SNP) data derived from such samples. To achieve this, we generated thousands of SNPs from 47 red-tailed black cockatoo (Calyptorhychus banksii) traditional museum samples (i.e. samples that were not collected with the primary intent of DNA analysis) and 113 fresh tissue samples (cryopreserved liver/muscle) using a restriction site-associated DNA marker approach (DArTseq™ ). Thousands of SNPs were successfully generated from most of the traditional museum samples (with a mean age of 44 years, ranging from 5 to 123 years), although 38% did not provide useful data. These SNPs exhibited higher error rates and contained significantly more missing data compared with SNPs from fresh tissue samples, likely due to considerable DNA fragmentation. However, based on simulation results, the level of genotyping error had a negligible effect on inference of population structure in this species. We did identify a bias towards low diversity SNPs in older samples that appears to compromise temporal inferences of genetic diversity. This study demonstrates the utility of a RADseq-based method to produce reliable genome-wide SNP data from traditional museum specimens.
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Affiliation(s)
- Kyle M Ewart
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.,Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Rebecca N Johnson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.,Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO, Canberra, Australia
| | - Greta J Frankham
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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Matsvay AD, Alborova IE, Pimkina EV, Markelov ML, Khafizov K, Mustafin KK. Experimental approaches for ancient DNA extraction and sample preparation for next generation sequencing in ultra-clean conditions. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-018-1016-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Affiliation(s)
- Elaine Y. Y. Cheung
- National Centre for Forensic Studies, Faculty of Science and Technology, University of Canberra, Bruce, Australia
| | - Michelle Elizabeth Gahan
- National Centre for Forensic Studies, Faculty of Science and Technology, University of Canberra, Bruce, Australia
| | - Dennis McNevin
- National Centre for Forensic Studies, Faculty of Science and Technology, University of Canberra, Bruce, Australia
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Rivera-Perez JI, Santiago-Rodriguez TM, Toranzos GA. Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology. Microbiol Spectr 2016; 4:10.1128/microbiolspec.EMF-0006-2015. [PMID: 27726770 PMCID: PMC5287379 DOI: 10.1128/microbiolspec.emf-0006-2015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Indexed: 01/14/2023] Open
Abstract
Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses.
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Morozova I, Flegontov P, Mikheyev AS, Bruskin S, Asgharian H, Ponomarenko P, Klyuchnikov V, ArunKumar G, Prokhortchouk E, Gankin Y, Rogaev E, Nikolsky Y, Baranova A, Elhaik E, Tatarinova TV. Toward high-resolution population genomics using archaeological samples. DNA Res 2016; 23:295-310. [PMID: 27436340 PMCID: PMC4991838 DOI: 10.1093/dnares/dsw029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 05/22/2016] [Indexed: 12/30/2022] Open
Abstract
The term ‘ancient DNA’ (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of ‘molecular paleontology’. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.
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Affiliation(s)
- Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Sergey Bruskin
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Hosseinali Asgharian
- Department of Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Petr Ponomarenko
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
| | | | | | - Egor Prokhortchouk
- Research Center of Biotechnology RAS, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Russia
| | | | - Evgeny Rogaev
- Vavilov Institute of General Genetics RAS, Moscow, Russia University of Massachusetts Medical School, Worcester, MA, USA
| | - Yuri Nikolsky
- Vavilov Institute of General Genetics RAS, Moscow, Russia F1 Genomics, San Diego, CA, USA School of Systems Biology, George Mason University, VA, USA
| | - Ancha Baranova
- School of Systems Biology, George Mason University, VA, USA Research Centre for Medical Genetics, Moscow, Russia Atlas Biomed Group, Moscow, Russia
| | - Eran Elhaik
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, UK
| | - Tatiana V Tatarinova
- Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
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Bribiescas RG, Ellison PT, Gray PB. Male Life History, Reproductive Effort, and the Evolution of the Genus Homo. CURRENT ANTHROPOLOGY 2012. [DOI: 10.1086/667538] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Willerslev E, Hansen AJ, Poinar HN. Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends Ecol Evol 2012; 19:141-7. [PMID: 16701245 DOI: 10.1016/j.tree.2003.11.010] [Citation(s) in RCA: 199] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Owing to their constant low temperatures, glacial ice and permafrost might contain the oldest nucleic acids and microbial cells on Earth, which could prove key to reconstructing past ecosystems and for the planning of missions to other planets. However, recent claims concerning viable cells and microbial nucleic acids obtained from ice- and permafrost cores from hundreds of thousands to millions of years old are not properly authenticated and the findings could be the result of contamination. Here, we discuss the processes that restrict the long-term survival of DNA and/or RNA molecules in ice and permafrost, and highlight sources of contamination that could result in false claims. Additionally, we present a set of precautions, controls and criteria to help ensure that future cultures and sequences are authentic.
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Affiliation(s)
- Eske Willerslev
- Department of Evolutionary Biology, Zoological Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
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Abstract
Museum and archival collections of parasites are available throughout the world but, although they represent a huge diversity of species and forms, they tend to be used solely for reference to morphology, if at all. As biochemical techniques begin to overcome the problems associated with ancient, degraded and formalin-fixed tissues, the value of such collections increases. Molecular data are now available for rare, elusive and extinct species, as well as those densely sampled for epidemiological, biogeographical or clinical collections. Here, Elisabeth Herniou, Auriol Pearce and Tim Littlewood describe some of the advances and pitfalls associated with retrieving DNA from formalin-fixed helminth material and suggest just some of the new ways that parasitologists can tap into these resources.
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Affiliation(s)
- E A Herniou
- The Natural History Museum, Department of Zoology, Cromwell Road, London, UK SW7 5BD
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Vartapetiance Salmasi A, Gillam L. DNA dataveillance: protecting the innocent? JOURNAL OF INFORMATION COMMUNICATION & ETHICS IN SOCIETY 2010. [DOI: 10.1108/14779961011071079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PurposeThe purpose of this paper is to discuss the UK National DNA Database (NDNAD) and some of the controversies surrounding it with reference to legal and ethical issues, focusing particularly on privacy and human rights. Governance of this database involves specific exemptions from the Data Protection Act (DPA), and this gives a rise to concerns regarding both the extent of surveillance on the UK population and the possibility for harm to all citizens. This is of wider importance since every current citizen, and everybody who visits the UK, could become a record in the DNA database. Principally, the paper seeks to explore whether these exemptions would also imply exemptions for software developers from codes of practice and ethics of their professional societies as relate to constructing or maintaining such data and the database.Design/methodology/approachThe paper makes a comparison between the principles of the DPA, as would need to be followed by all other organizations handling personal data, professional responsibilities‐based codes of ethics of professional societies, and the current reality as reported in relation to the NDNAD and the exemptions offered through the DPA.FindingsPrimarily, if NDNAD was not exempted from certain provisions in the DPA, the potential for the kinds of data leakages and other mishandlings could largely be avoided without the need for further considerations over so‐called “data minimization”. It can be seen how the lack of afforded protection allows for a wide range of issues as relate at least to privacy.Originality/valueThe paper provides the first evaluation of the combination of law, codes of ethics, and activities in the real world as related to NDNAD, with concomitant considerations for privacy, liberty, and human rights. Originality is demonstrated through consideration of the implications of certain exemptions in the DPA in relation to crime and taxation and national security and in relating the expected protections for personal data to widely reported evidence that such protections may be variously lacking. In addition, the paper provides a broad overview of controversies over certain newer kinds of DNA analysis, and other relatively recent findings, that seem generally absent from the vast majority of debates over this kind of analysis.
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Ragan MA, Beiko RG. Lateral genetic transfer: open issues. Philos Trans R Soc Lond B Biol Sci 2009; 364:2241-51. [PMID: 19571244 DOI: 10.1098/rstb.2009.0031] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Lateral genetic transfer (LGT) is an important adaptive force in evolution, contributing to metabolic, physiological and ecological innovation in most prokaryotes and some eukaryotes. Genomic sequences and other data have begun to illuminate the processes, mechanisms, quantitative extent and impact of LGT in diverse organisms, populations, taxa and environments; deep questions are being posed, and the provisional answers sometimes challenge existing paradigms. At the same time, there is an enhanced appreciation of the imperfections, biases and blind spots in the data and in analytical approaches. Here we identify and consider significant open questions concerning the role of LGT in genome evolution.
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Affiliation(s)
- Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
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Dittmar K. Old Parasites for a New World: The Future of Paleoparasitological Research. A Review. J Parasitol 2009; 95:365-71. [DOI: 10.1645/ge-1676.1] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Accepted: 08/08/2008] [Indexed: 11/10/2022] Open
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Nielsen KM, Johnsen PJ, Bensasson D, Daffonchio D. Release and persistence of extracellular DNA in the environment. ACTA ACUST UNITED AC 2007; 6:37-53. [DOI: 10.1051/ebr:2007031] [Citation(s) in RCA: 366] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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LIVEZEY BRADLEYC, ZUSI RICHARDL. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zool J Linn Soc 2007; 149:1-95. [PMID: 18784798 PMCID: PMC2517308 DOI: 10.1111/j.1096-3642.2006.00293.x] [Citation(s) in RCA: 281] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.
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Affiliation(s)
- BRADLEY C LIVEZEY
- Section of Birds, Carnegie Museum of Natural History4400 Forbes Avenue, Pittsburgh, PA 15213-4080, USA
| | - RICHARD L ZUSI
- Division of Birds, National Museum of Natural HistoryWashington, DC 20013-7012, USA
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Abstract
Twenty years after the advent of ancient DNA studies, this discipline seems to have reached the maturity formerly lacking to the fulfilment of its objectives. In its early development paleogenetics, as it is now acknowledged, had to cope with very limited data due to the technical limitations of molecular biology. It led to phylogenetic assumptions often limited in their scope and sometimes non-focused or even spurious results that cast the reluctance of the scientific community. This time seems now over and huge amounts of sequences have become available which overcome the former limitations and bridge the gap between paleogenetics, genomics and population biology. The recent studies over the charismatic woolly mammoth (independent sequencing of the whole mitochondrial genome and of millions of base pairs of the nuclear genome) exemplify the growing accuracy of ancient DNA studies thanks to new molecular approaches. From the earliest publications up to now, the number of mammoth nucleotides was multiplied by 100,000. Likewise, populational approaches of ice-age taxa provide new historical scenarios about the diversification and extinction of the Pleistocene megafauna on the one hand, and about the processes of domestication of animal and vegetal species by Man on the other. They also shed light on the differential structure of molecular diversity between short-term populational research (below 2 My) and long-term (over 2 My) phylogenetic approaches. All those results confirm the growing importance of paleogenetics among the evolutionary biology disciplines.
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Affiliation(s)
- Régis Debruyne
- Muséum National d'Histoire Naturelle, Département Histoire de la Terre, UMR 5143 CNRS, Paléobiodiversité, 57, rue Cuvier, 75231 Paris Cedex 05, France
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Liepelt S, Sperisen C, Deguilloux MF, Petit RJ, Kissling R, Spencer M, de Beaulieu JL, Taberlet P, Gielly L, Ziegenhagen B. Authenticated DNA from ancient wood remains. ANNALS OF BOTANY 2006; 98:1107-11. [PMID: 16987920 PMCID: PMC3292245 DOI: 10.1093/aob/mcl188] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
BACKGROUND The reconstruction of biological processes and human activities during the last glacial cycle relies mainly on data from biological remains. Highly abundant tissues, such as wood, are candidates for a genetic analysis of past populations. While well-authenticated DNA has now been recovered from various fossil remains, the final 'proof' is still missing for wood, despite some promising studies. SCOPE The goal of this study was to determine if ancient wood can be analysed routinely in studies of archaeology and palaeogenetics. An experiment was designed which included blind testing, independent replicates, extensive contamination controls and rigorous statistical tests. Ten samples of ancient wood from major European forest tree genera were analysed with plastid DNA markers. CONCLUSIONS Authentic DNA was retrieved from wood samples up to 1,000 years of age. A new tool for real-time vegetation history and archaeology is ready to use.
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Affiliation(s)
- Sascha Liepelt
- Philipps-University Marburg, Faculty of Biology Nature Conservation Division, Karl-von-Frisch-Str 2, Marburg, Germany.
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Conservation genetics and species status of an endangered Australian dragon, Tympanocryptis pinguicolla (Reptilia: Agamidae). CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9161-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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AUSTIN JEREMYJ, MELVILLE JANE. Incorporating historical museum specimens into molecular systematic and conservation genetics research. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01443.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Austin JJ, Arnold EN. Using ancient and recent DNA to explore relationships of extinct and endangered Leiolopisma skinks (Reptilia: Scincidae) in the Mascarene islands. Mol Phylogenet Evol 2006; 39:503-11. [PMID: 16473026 DOI: 10.1016/j.ympev.2005.12.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2005] [Revised: 12/15/2005] [Accepted: 12/15/2005] [Indexed: 10/25/2022]
Abstract
Phylogenetic analysis, using 1455 bp of recent mtDNA (cytochrome b 714 bp, 12S rRNA 376 bp) and nuclear (c-mos 365 bp) sequence from 42 species and 33 genera of Scincidae, confirms Leiolopisma telfairii, now confined to Round island off Mauritius, is a member of the mainly Australasian Eugongylus group of the Lygosominae. Ancient mtDNA (cytochrome b 307 bp, 12S rRNA 376 bp) was also extracted from subfossils of two other Mascarene taxa that are now extinct: the giant L. mauritiana from Mauritius and Leiolopisma sp., known only from fragmentary remains from Réunion. Sequence divergences of 4.2-5.7% show that all three forms were distinct and form a clade. There is restricted evidence that L. mauritiana and L. sp. from Réunion were sister species. Monophyly and relationships suggest Leiolopisma arose from a single transmarine invasion of the oceanic Mascarene islands from Australasia, 5600-7000 km away. This origin is similar to that of Cryptoblepharus skinks and Nactus geckos in the archipelago but contrasts with Phelsuma day geckos, which appear to have arrived from Madagascar where Mascarene Cylindraspis tortoises may also have originated. Diversification of the known species of Leiolopisma occurred from about 2.3-3.4 Mya, probably beginning on Mauritius with later invasion of Réunion. The initial coloniser may have had a relatively large body-size, but L. mauritiana is likely to have become gigantic within the Mascarenes. Other relationships supported by this investigation include the following. Scincines: Pamelaescincus+Janetaescincus, and Androngo (Amphiglossus, Paracontias). Lygosomines: Sphenomorphus group--(Sphenomorphus, Lipinia (Ctenotus, Anomalopus (Eulamprus and Gnypetoscincus))): Egernia group--Egernia (Cyclodomorphus, Tiliqua); Eugongylus group--(Oligosoma, Bassiana. (Lampropholis (Niveoscincus, Carlia))).
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Affiliation(s)
- J J Austin
- Department of Zoology, Natural History Museum, Cromwell Rd., London SW7 5BD, UK
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Abstract
Studies continue to report ancient DNA sequences and viable microbial cells that are many millions of years old. In this paper we evaluate some of the most extravagant claims of geologically ancient DNA. We conclude that although exciting, the reports suffer from inadequate experimental setup and insufficient authentication of results. Consequently, it remains doubtful whether amplifiable DNA sequences and viable bacteria can survive over geological timescales. To enhance the credibility of future studies and assist in discarding false-positive results, we propose a rigorous set of authentication criteria for work with geologically ancient DNA.
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Affiliation(s)
- Martin B Hebsgaard
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK OX1 3PS
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Abstract
In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.
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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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Abstract
For bacteria, the primary genetic barrier against the genetic exchange of DNA that is not self-transmissible is dissimilarity in the bacterial DNA sequences concerned. Genetic exchange by homologous recombination is frequent among close bacterial relatives and recent experiments have shown that it can enable the uptake of closely linked nonhomologous foreign DNA. Artificial vectors are mosaics of mobile DNA elements from free-living bacterial isolates and so bear a residual similarity to their ubiquitous natural progenitors. This homology is tightly linked to the multitude of different DNA sequences that are inserted into synthetic vectors. Can homology between vector and bacterial DNA enable the uptake of these foreign DNA inserts? In this review we investigate pUC18 as an example of an artificial vector and consider whether its homology to broad host-range antibiotic resistance transposons and plasmid origins of replication could enable the uptake of insert DNA in the light of studies of homology-facilitated foreign DNA uptake. We also discuss the disposal of recombinant DNA, its persistence in the environment and whether homologies to pUC18 may exist in naturally competent bacteria. Most DNA that is inserted into the cloning site of artificial vectors would be of little use to a bacterium, but perhaps not all.
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Affiliation(s)
- D Bensasson
- Evolutionary Genomics Department, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
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Austin JJ, Arnold EN, Jones CG. Reconstructing an island radiation using ancient and recent DNA: the extinct and living day geckos (Phelsuma) of the Mascarene islands. Mol Phylogenet Evol 2004; 31:109-22. [PMID: 15019612 DOI: 10.1016/j.ympev.2003.07.011] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2003] [Revised: 07/10/2003] [Indexed: 11/26/2022]
Abstract
Mitochondrial (12SrRNA and cyt b, 1086 bp) and nuclear (c-mos, 374 bp) DNA sequences were used to investigate relationships and biogeography of 24 living and extinct taxa of Phelsuma geckos. Monophyly of Phelsuma and sister relationship to the SW African Rhoptropella is corroborated. Phelsuma originated on Madagascar and made multiple long-distance invasions of oceanic islands including the Mascarenes, Aldabra, Comores, Seychelles, Andamans, and perhaps Pemba. The Mascarenes were probably colonised once, about 4.2-5.1Ma, and here Phelsuma rosagularis and Phelsuma inexpectata are newly recognised as species, as are three lineages of Phelsuma cepediana. Mascarene relationships are: Phelsuma edwardnewtoni, Phelsuma gigas (Phelsuma guentheri ((((P. cepediana A (P. cepediana B, C)) P. rosagularis) Phelsuma borbonica) ((Phelsuma ornata, P. inexpectata) Phelsuma guimbeaui))). The two recently extinct species, P. edwardnewtoni and the giant secondarily nocturnal Phelsuma gigas, differentiated on Rodrigues while on Mauritius the large nocturnal P. guentheri separated from a small diurnal form that radiated into six species, a likely result of volcanic activity. Two small-bodied lineages from Mauritius invaded the more recent island of Réunion producing two more species. Outside the Mascarenes, two mainly Madagascan assemblages are substantiated: Phelsuma serraticauda (Phelsuma lineata, Phelsuma laticauda, Phelsuma quadriocellata); (Phelsuma m. kochi (Phelsuma m. grandis, Phelsuma abboti)) (Phelsuma astriata, Phelsuma sundbergi). Their relationships to the Mascarene clade, and to Phelsuma mutabilis, Phelsuma standingi and Phelsuma andamanensis are unresolved.
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Affiliation(s)
- J J Austin
- Department of Zoology, The Natural History Museum, London SW7 5BD, UK
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Reed FA, Kontanis EJ, Kennedy KAR, Aquadro CF. Brief communication: ancient DNA prospects from Sri Lankan highland dry caves support an emerging global pattern. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2003; 121:112-6. [PMID: 12740954 DOI: 10.1002/ajpa.10211] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Recovery of ancient DNA has become an increasingly important tool in elucidating the origins of past populations and their relationships. Unfortunately, many human skeletal remains do not contain original DNA amplifiable by polymerase chain reaction (PCR). Amino-acid racemization has proven to be a useful predictor of ancient DNA results. We analyzed the relative levels of amino-acid preservation and racemization of human samples from two highland dry-cave sites in Sri Lanka, and found that amino-acid enantiomer ratios were inconsistent with successful authentic DNA recovery. A review of the literature reveals that these results are consistent with a global pattern of poor DNA preservation in the tropics.
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Affiliation(s)
- Floyd A Reed
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.
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Austin JJ, Arnold EN, Bour R. Was there a second adaptive radiation of giant tortoises in the Indian Ocean? Using mitochondrial DNA to investigate speciation and biogeography of Aldabrachelys (Reptilia, Testudinidae). Mol Ecol 2003; 12:1415-24. [PMID: 12755871 DOI: 10.1046/j.1365-294x.2003.01842.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A radiation of five species of giant tortoises (Cylindraspis) existed in the southwest Indian Ocean, on the Mascarene islands, and another (of Aldabrachelys) has been postulated on small islands north of Madagascar, from where at least eight nominal species have been named and up to five have been recently recognized. Of 37 specimens of Madagascan and small-island Aldabrachelys investigated by us, 23 yielded significant portions of a 428-base-pair (bp) fragment of mitochondrial (cytochrome b and tRNA-Glu), including type material of seven nominal species (A. arnoldi, A. dussumieri, A. hololissa, A. daudinii, A. sumierei, A. ponderosa and A. gouffei). These and nearly all the remaining specimens, including 15 additional captive individuals sequenced previously, show little variation. Thirty-three exhibit no differences and the remainder diverge by only 1-4 bp (0.23-0.93%). This contrasts with more widely accepted tortoise species which show much greater inter- and intraspecific differences. The non-Madagascan material examined may therefore only represent a single species and all specimens may come from Aldabra where the common haplotype is known to occur. The present study provides no evidence against the Madagascan origin for Aldabra tortoises suggested by a previous molecular phylogenetic analysis, the direction of marine currents and phylogeography of other reptiles in the area. Ancient mitochondrial DNA from the extinct subfossil A. grandidieri of Madagascar differs at 25 sites (5.8%) from all other Aldabrachelys samples examined here.
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Affiliation(s)
- Jeremy J Austin
- Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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29
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Genesis of phenotypic and genotypic diversity in land plants: The present as the key to the past. SYST BIODIVERS 2003. [DOI: 10.1017/s1477200003001051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Kaestle FA, Horsburgh KA. Ancient DNA in anthropology: methods, applications, and ethics. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2003; Suppl 35:92-130. [PMID: 12653310 DOI: 10.1002/ajpa.10179] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Anthropologists were quick to recognize the potential of new techniques in molecular biology to provide additional lines of evidence on questions long investigated in anthropology, as well as those questions that, while always of interest, could not have been addressed by more traditional techniques. The earliest ancient DNA studies, both within anthropology and in other fields, lacked rigorous hypothesis testing. However, more recently the true value of ancient DNA studies is being realized, and methods are being applied to a wide variety of anthropological questions. We review the most common methods and applications to date, and describe promising avenues of future research. We find that ancient DNA analyses have a valuable place in the array of anthropological techniques, but argue that such studies must not be undertaken merely to demonstrate that surviving DNA is present in organic remains, and that no such work should be performed before a careful consideration of the possible ethical ramifications of the research is undertaken.
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Affiliation(s)
- Frederika A Kaestle
- Department of Anthropology, Indiana University, Bloomington, Indiana 47405-7100, USA.
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31
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Miller CR, Waits LP. The history of effective population size and genetic diversity in the Yellowstone grizzly (Ursus arctos): implications for conservation. Proc Natl Acad Sci U S A 2003; 100:4334-9. [PMID: 12655042 PMCID: PMC153093 DOI: 10.1073/pnas.0735531100] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2002] [Indexed: 11/18/2022] Open
Abstract
Protein, mtDNA, and nuclear microsatellite DNA analyses have demonstrated that the Yellowstone grizzly bear has low levels of genetic variability compared with other Ursus arctos populations. Researchers have attributed this difference to inbreeding during a century of anthropogenic isolation and population size reduction. We test this hypothesis and assess the seriousness of genetic threats by generating microsatellite data for 110 museum specimens collected between 1912 and 1981. A loss of variability is detected, but it is much less severe than hypothesized. Variance in allele frequencies over time is used to estimate an effective population size of approximately 80 across the 20th century and >100 currently. The viability of the population is unlikely to be substantially reduced by genetic factors in the next several generations. However, gene flow from outside populations will be beneficial in avoiding inbreeding and the erosion of genetic diversity in the future.
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Affiliation(s)
- Craig R Miller
- Department of Fish and Wildlife, College of Natural Resources, University of Idaho, Moscow, ID 83844-1136, USA.
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Debruyne R, Barriel V, Tassy P. Mitochondrial cytochrome b of the Lyakhov mammoth (Proboscidea, Mammalia): new data and phylogenetic analyses of Elephantidae. Mol Phylogenet Evol 2003; 26:421-34. [PMID: 12644401 DOI: 10.1016/s1055-7903(02)00292-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The phylogenetic relationships between recent Elephantidae (Proboscidea, Mammalia), that is to say extant elephants (Asian and African) and extinct woolly mammoth, have remained unclear to date. The prevailing morphological scheme (mammoth grouped with Asian elephant) is either supported or questioned by the molecular results. Recently, the monophyly of woolly mammoths on mitochondrial grounds has been demonstrated (Thomas, et al., 2000), but it conflicts with previous studies (Barriel et al., 1999; Derenko et al., 1997). Here, we report the partial sequencing of two mitochondrial genes: 128 bp of 12S rDNA and 561 bp of cytochrome b for the Lyakhov mammoth, a 49,000-year-old Siberian individual. We use the most comprehensive sample of mammoth (11 sequences) to determine whether the sequences achieved by former studies were congruent or not. The monophyly of a major subset of mammoths sequences (including ours) is recovered. Such a result is assumed to be a good criterion for ascertaining the origin of ancient DNA. Our sequence is incongruent with that of Yang et al. (1996), though obtained for the same individual. As far as the latter sequence is concerned, a contamination by non-identified exogenous DNA is suspected. The robustness and reliability of the sister group relation between Mammuthus primigenius and Loxodonta africana are examined: down-weighting saturated substitutions has no impact on the topology; analyzing data partitions proves that the support of this clade can be assigned to the most conservative phylogenetic signal; insufficient taxonomic and/or characters sampling contributed to former discordant conclusions. We therefore assume the monophyly of "real mammoth sequences" and the (Mammuthus, Loxodonta) clade.
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Affiliation(s)
- Régis Debruyne
- Laboratoire de Paléontologie, CNRS UMR 8569, Muséum National d'Histoire Naturelle, 8 Rue Buffon, F-75005 Paris, France.
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The Provenance of Type Specimens of Extinct Mascarene Island Giant Tortoises (Cylindraspis) Revealed by Ancient Mitochondrial DNA Sequences. J HERPETOL 2002. [DOI: 10.1670/0022-1511(2002)036[0280:tpotso]2.0.co;2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Austin JJ, Arnold EN. Ancient mitochondrial DNA and morphology elucidate an extinct island radiation of Indian Ocean giant tortoises (Cylindraspis). Proc Biol Sci 2001; 268:2515-23. [PMID: 11749704 PMCID: PMC1088909 DOI: 10.1098/rspb.2001.1825] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ancient mitochondrial DNA sequences were used for investigating the evolution of an entire clade of extinct vertebrates, the endemic tortoises (Cylindraspis) of the Mascarene Islands in the Indian Ocean. Mitochondrial DNA corroborates morphological evidence that there were five species of tortoise with the following relationships: Cylindraspis triserrata ((Cylindraspis vosmaeri and Cylindraspis peltastes) (Cylindraspis inepta and Cylindraspis indica)). Phylogeny indicates that the ancestor of the group first colonized Mauritius where speciation produced C. triserrata and the ancestor of the other species including a second sympatric Mauritian form, C. inepta. A propagule derived from this lineage colonized Rodrigues 590 km to the east, where a second within-island speciation took place producing the sympatric C. vosmaeri and C. peltastes. A recent colonization of Réunion 150 km to the southwest produced C. indica. In the virtual absence of predators, the defensive features of the shells of Mascarene tortoises were largely dismantled, apparently in two stages. 'Saddlebacked' shells with high fronts evolved independently on all three islands. This and other features, such as a derived jaw structure and small body size, may be associated with niche differentiation in sympatric species and may represent a striking example of parallel differentiation in a large terrestrial vertebrate. The history of Mascarene tortoises contrasts with that of the Galápagos, where only a single species is present and surviving populations are genetically much more similar. However, they too show some reduction in anti-predator mechanisms and multiple development of populations with saddlebacked shells.
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Affiliation(s)
- J J Austin
- Reptile Research Group, Department of Zoology, The Natural History Museum, London, UK
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van Vuuren BJ, Robinson TJ. Retrieval of four adaptive lineages in duiker antelope: evidence from mitochondrial DNA sequences and fluorescence in situ hybridization. Mol Phylogenet Evol 2001; 20:409-25. [PMID: 11527467 DOI: 10.1006/mpev.2001.0962] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Independent molecular markers (mitochondrial DNA sequences from two genes and fluorescence in situ hybridization with satellite DNA sequences as hybridization probes) were employed to investigate phylogenetic relationships among duiker antelope. When analyzed singly or taken together, the molecular and cytogenetic data allowed for the delimitation of four adaptive groups: the conservative dwarfs which are basal, a savanna specialist which groups apart from the forest duikers, the giant duikers, and the red duikers. Within the latter, a further subdivision comprising an east African and a west African red duiker clade is evident. The placement of the endangered zebra duiker and Aders' duiker remains problematic. Several of the nomenclatural divisions in current use are questioned by our results. These include the recognition of Philantomba as genus name for the blue and Maxwell's duiker and that Harvey's duiker be relegated to a subspecies of the Natal red duiker. We place our results in a biogeographic context and argue that duiker speciation has been driven predominantly by habitat fragmentation which probably led to the disruption of gene flow between geographic populations.
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Affiliation(s)
- B J van Vuuren
- Department of Zoology & Entomology, University of Pretoria, Pretoria, South Africa
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Molecular anthropology: Touching the past through ancient DNA retrieval. Methodological aspects. ANTHROPOLOGICAL REVIEW 2001. [DOI: 10.18778/1898-6773.64.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The revolution which introduced new techniques of molecular biology applied to DNA analysis enormously accelerated the progress in most areas of medicine and biology. Techniques such as polymerase chain reaction (PCR), restriction analysis and sequencing are widely used for diagnosis of a number of diseases, for genetic screening, phylogenetic analysis and population studies. Moreover, it became possible to study genetic relationships of extinct to contemporary organisms and even to follow evolutionary events. Variation in DNA sequences, especially that of humans, is fascinating not only for our own sake, but also because of the inferences that can be drawn from it about our recent evolution, demography and movements. Selected problems arising during ancient DNA (aDNA) isolation and analysis are discussed. Environment and time related factors altering the structure of nucleic acids as well as contamination of isolated material are among methodological problems that arise during the procedure of isolation and processing of aDNA. Resolving them is of great importance for the authentication of the identified sequences. Most common informative targets of aDNA are presented and among them mtDNA, and the sequences localized within nuclear DNA. The first, as well as the most important findings in the field are mentioned.
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Abstract
DNA that has been recovered from archaeological and palaeontological remains makes it possible to go back in time and study the genetic relationships of extinct organisms to their contemporary relatives. This provides a new perspective on the evolution of organisms and DNA sequences. However, the field is fraught with technical pitfalls and needs stringent criteria to ensure the reliability of results, particularly when human remains are studied.
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Affiliation(s)
- M Hofreiter
- Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D-04103 Leipzig, Germany
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Loreille O, Orlando L, Patou-Mathis M, Philippe M, Taberlet P, Hänni C. Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages. Curr Biol 2001; 11:200-3. [PMID: 11231157 DOI: 10.1016/s0960-9822(01)00046-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cave bear, Ursus spelaeus, represents one of the most frequently found paleontological remains from the Pleistocene in Europe. The species has always been confined to Europe and was contemporary with the brown bear, Ursus arctos. Relationships between the cave bear and the two lineages of brown bears defined in Europe, as well as the origins of the two species, remain controversial, mainly due to the wide morphological diversity of the fossil remains, which makes interpretation difficult [1, 2]. Sequence analysis of ancient DNA is a useful tool for resolving such problems because it provides an independent source of data [3]. We previously amplified a short DNA fragment of the mitochondrial DNA control region (mt control region) of a 40,000-year-old Ursus spelaeus sample [4]. In this paper, we describe the DNA analysis of two mtDNA regions, the control region and the cytochrome b gene. Control region sequences were obtained from ten samples of cave bears ranging from 130,000 to 20,000 years BP, and one particularly well-conserved sample gave a complete cyt b sequence. Our data demonstrate that cave bears split largely before the lineages of brown bears around 1.2 million years ago. Given its abundance, its wide distribution in space and time, and its large morphological diversity, the cave bear is a promising model for direct observation of the evolution of sequences throughout time, extinction periods, and the differentiation of populations shaped by climatic fluctuations during the Pleistocene.
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Affiliation(s)
- O Loreille
- CNRS UMR 5534, Centre de Génétique Moléculaire et Cellulaire, Université Claude Bernard, Lyon 1, Cedex 69622, Villeurbanne, France
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Hansen A, Willerslev E, Wiuf C, Mourier T, Arctander P. Statistical evidence for miscoding lesions in ancient DNA templates. Mol Biol Evol 2001; 18:262-5. [PMID: 11158385 DOI: 10.1093/oxfordjournals.molbev.a003800] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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Weber DS, Stewart BS, Garza JC, Lehman N. An empirical genetic assessment of the severity of the northern elephant seal population bottleneck. Curr Biol 2000; 10:1287-90. [PMID: 11069110 DOI: 10.1016/s0960-9822(00)00759-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A bottleneck in population size of a species is often correlated with a sharp reduction in genetic variation. The northern elephant seal (Mirounga angustirostris) has undergone at least one extreme bottleneck, having rebounded from 20-100 individuals a century ago to over 175,000 individuals today. The relative lack of molecular-genetic variation in contemporary populations has been documented, but the extent of variation before the late 19th century remains unknown. We have determined the nucleotide sequence of a 179 base-pair segment of the mitochondrial DNA (mtDNA) control region from seals that lived before, during and after a bottleneck low in 1892. A 'primerless' PCR was used to improve the recovery of information from older samples. Only two mtDNA genotypes were present in all 150+ seals from the 1892 bottleneck on, but we discovered four genotypes in five pre-bottleneck seals. This suggests a much greater amount of mtDNA genotypic variation before this bottleneck, and that the persistence of two genotypes today is a consequence of random lineage sampling. We cannot correlate the loss of mtDNA genotypes with a lowered mean fitness of individuals in the species today. However, we show that the species historically possessed additional genotypes to those present now, and that sampling of ancient DNA could elucidate the genetic consequences of severe reductions in population size.
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Affiliation(s)
- D S Weber
- Department of Biological Sciences, University at Albany, State University of New York, 12222, USA
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42
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Pusch CM, Bachmann L, Broghammer M, Scholz M. Internal Alu-polymerase chain reaction: a sensitive contamination monitoring protocol for DNA extracted from prehistoric animal bones. Anal Biochem 2000; 284:408-11. [PMID: 10964428 DOI: 10.1006/abio.2000.4666] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- C M Pusch
- Molecular Genetics Laboratory, University Eye Hospital, University of Tübingen, Auf der Morgenstelle 15, Tübingen, D-72076, Germany
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Abstract
Biochemical studies have complemented ultrastructural and, subsequently molecular genetic evidence consistent with the Charophyceae being the closest extant algal relatives of the embryophytes. Among the genes used in such molecular phylogenetic studies is that rbcL) for the large subunit of ribulose bisphosphate carboxylase-oxygenase (RUBISCO). The RUBISCO of the embryophytes is derived, via the Chlorophyta. from that of the cyanobacteria. This clade of the molecular phylogeny of RUBISCO shows a range of kinetic characteristics, especially of CO2 affinities and of CO2/O2 selectivities. The range of these kinetic values within the bryophytes is no greater than in the rest of the embryophytes; this has implications for the evolution of the embryophytes in the high atmospheric CO2 environment of the late Lower Palaeozoic. The differences in biochemistry between charophycean algae and embryophytes can to some extent be related functionally to the structure and physiology of embryophytes. Examples of components of embryophytes, which are qualitatively or quantitatively different from those of charophytes, are the water repellent/water resistant extracellular lipids, the rigid phenolic polymers functional in water-conducting elements and mechanical support in air, and in UV-B absorption, flavonoid phenolics involved in UV-B absorption and in interactions with other organisms, and the greater emphasis on low Mr organic acids. retained in the plant as free acids or salts, or secreted to the rhizosphere. The roles of these components are discussed in relation to the environmental conditions at the time of evolution of the terrestrial embryophytes. A significant point about embryophytes is the predominance of nitrogen-free extracellular structural material (a trait shared by most algae) and UV-B screening components, by contrast with analogous components in many other organisms. An important question, which has thus far been incompletely addressed, is the extent to which the absence from bryophytes of the biochemical pathways which produce components found only in tracheophytes is the result of evolutionary loss of these functions.
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Affiliation(s)
- J A Raven
- Department of Biological Sciences, Univervity of Dundee, UK
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44
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Caterino MS, Cho S, Sperling FA. The current state of insect molecular systematics: a thriving Tower of Babel. ANNUAL REVIEW OF ENTOMOLOGY 2000; 45:1-54. [PMID: 10761569 DOI: 10.1146/annurev.ento.45.1.1] [Citation(s) in RCA: 210] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Insect molecular systematics has undergone remarkable recent growth. Advances in methods of data generation and analysis have led to the accumulation of large amounts of DNA sequence data from most major insect groups. In addition to reviewing theoretical and methodological advances, we have compiled information on the taxa and regions sequenced from all available phylogenetic studies of insects. It is evident that investigators have not usually coordinated their efforts. The genes and regions that have been sequenced differ substantially among studies and the whole of our efforts is thus little greater than the sum of its parts. The cytochrome oxidase I, 16S, 18S, and elongation factor-1 alpha genes have been widely used and are informative across a broad range of divergences in insects. We advocate their use as standards for insect phylogenetics. Insect molecular systematics has complemented and enhanced the value of morphological and ecological data, making substantial contributions to evolutionary biology in the process. A more coordinated approach focused on gathering homologous sequence data will greatly facilitate such efforts.
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Affiliation(s)
- M S Caterino
- Department of Environmental Science, Policy and Management, University of California, Berkeley 94720-3112, USA
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45
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Abstract
The use of ancient DNA (aDNA) in the reconstruction of population origins and evolution is becoming increasingly common. The resultant increase in number of samples and polymorphic sites assayed and the number of studies published may give the impression that all technological hurdles associated with aDNA technology have been overcome. However, analysis of aDNA is still plagued by two issues that emerged at the advent of aDNA technology, namely the inability to amplify a significant number of samples and the contamination of samples with modern DNA. Herein, we analyze five well-preserved skeletal specimens from the western United States dating from 800-1600 A.D. These specimens yielded DNA samples with levels of contamination ranging from 0-100%, as determined by the presence or absence of New World-specific mitochondrial markers. All samples were analyzed by a variety of protocols intended to assay genetic variability and detect contamination, including amplification of variously sized DNA targets, direct DNA sequence analysis of amplification products and sequence analysis of cloned amplification products, analysis of restriction fragment length polymorphisms, quantitation of target DNA, amino acid racemization, and amino acid quantitation. Only the determination of DNA sequence from a cloned amplification product clearly revealed the presence of both ancient DNA and contaminating DNA in the same extract. Our results demonstrate that the analysis of aDNA is still an excruciatingly slow and meticulous process. All experiments, including stringent quality and contamination controls, must be performed in an environment as free as possible of potential sources of contaminating DNA, including modern DNA extracts. Careful selection of polymorphic markers capable of discriminating between ancient DNA and probable DNA contaminants is critical. Research strategies must be designed with a goal of identifying all DNA contaminants in order to differentiate convincingly between contamination and endogenous DNA.
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Affiliation(s)
- C J Kolman
- Smithsonian Center for Materials Research and Education, Suitland, Maryland 20746-0534, USA.
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46
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Robinson TJ, Matthee CA. Molecular genetic relationships of the extinct ostrich, Struthio camelus syriacus: consequences for ostrich introductions into Saudi Arabia. Anim Conserv 1999. [DOI: 10.1111/j.1469-1795.1999.tb00062.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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47
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Matthee CA, Robinson TJ. Mitochondrial DNA population structure of roan and sable antelope: implications for the translocation and conservation of the species. Mol Ecol 1999; 8:227-38. [PMID: 10065541 DOI: 10.1046/j.1365-294x.1999.00556.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mitochondrial DNA (mtDNA) control region sequences were analysed to determine the geographical genetic structure of Hippotragus niger (sable antelope) and H. equinus (roan antelope). Analyses by AMOVA, minimum evolution networks, parsimony, neighbour joining and maximum likelihood show that the roan antelope populations are geographically partitioned and that their phylogeography corresponds well with subspecific boundaries. In sharp contrast, however, our sequence data group all the sable antelope into two well-delineated maternal clades. One comprising specimens from the strictly east African H.n. roosevelti, and a second geographically diverse group which includes H.n. niger (South Africa, Zimbabwe), H.n. variani (Angola), and H.n. Kirkii (Zambia, Malawi). The differences in the genetic population structure suggest that distinct extrinsic and intrinsic factors have shaped the phylogeography of these two closely related antelope species. In the absence of obvious extrinsic barriers to gene flow, we suggest that behavioural differences may be responsible, at least in part, for the contrasting spatial patterns detected among geographical localities. Although our data reflect only the maternal phylogeny of these important game species, they nonetheless suggest that different management strategies should be applied. We recommend that roan antelope be translocated only within the currently defined subspecies boundaries, while in the case of sable antelope, conservation measures should focus on preserving the genetic integrity of the east African and southern African sable populations. Implicit in this is that translocations of animals between populations comprising these two distinct maternal genetic clades should be actively discouraged.
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Affiliation(s)
- C A Matthee
- Department of Zoology and Entomology, University of Pretoria, South Africa
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48
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MacHugh DE, Troy CS, McCormick F, Olsaker I, Eythórsdóttir E, Bradley DG. Early medieval cattle remains from a Scandinavian settlement in Dublin: genetic analysis and comparison with extant breeds. Philos Trans R Soc Lond B Biol Sci 1999; 354:99-108; discussion 108-9. [PMID: 10091250 PMCID: PMC1692458 DOI: 10.1098/rstb.1999.0363] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A panel of cattle bones excavated from the 1000-year-old Viking Fishamble Street site in Dublin was assessed for the presence of surviving mitochondrial DNA (mtDNA). Eleven of these bones gave amplifiable mtDNA and a portion of the hypervariable control region was determined for each specimen. A comparative analysis was performed with control region sequences from five extant Nordic and Irish cattle breeds. The medieval population displayed similar levels of mtDNA diversity to modern European breeds. However, a number of novel mtDNA haplotypes were also detected in these bone samples. In addition, the presence of a putative ancestral sequence at high frequency in the medieval population supports an early post-domestication expansion of cattle in Europe.
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Affiliation(s)
- D E MacHugh
- Department of Genetics, Trinity College, Dublin 2, Ireland
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49
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Quicke DLJ, Lopez-Vaamonde C, Belshaw R. Preservation of hymenopteran specimens for subsequent molecular and morphological study. ZOOL SCR 1999. [DOI: 10.1046/j.1463-6409.1999.00004.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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50
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Hadly EA, Kohn MH, Leonard JA, Wayne RK. A genetic record of population isolation in pocket gophers during Holocene climatic change. Proc Natl Acad Sci U S A 1998; 95:6893-6. [PMID: 9618509 PMCID: PMC22676 DOI: 10.1073/pnas.95.12.6893] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/1997] [Accepted: 04/06/1998] [Indexed: 02/07/2023] Open
Abstract
A long-standing question in Quaternary paleontology is whether climate-induced, population-level phenotypic change is a result of large-scale migration or evolution in isolation. To directly measure genetic variation through time, ancient DNA and morphologic variation was measured over 2,400 years in a Holocene sequence of pocket gophers (Thomomys talpoides) from Lamar Cave, Yellowstone National Park, Wyoming. Ancient specimens and modern samples collected near Lamar Cave share mitochondrial cytochrome b sequences that are absent from adjacent localities, suggesting that the population was isolated for the entire period. In contrast, diastemal length, a morphologic character correlated with body size and nutritional level, changed predictably in response to climatic change. Our results demonstrate that small mammal populations can experience the long-term isolation assumed by many theoretical models of microevolutionary change.
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Affiliation(s)
- E A Hadly
- Mountain Research Center and Department of Biology, Montana State University, Bozeman, MT 59717, USA.
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