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Shimwell C, Atkinson L, Graham MR, Murdoch B. A first molecular characterization of the scorpion telson microbiota of Hadrurus arizonensis and Smeringurus mesaensis. PLoS One 2023; 18:e0277303. [PMID: 36649362 PMCID: PMC9844838 DOI: 10.1371/journal.pone.0277303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/24/2022] [Indexed: 01/18/2023] Open
Abstract
Scorpions represent an ancient lineage of arachnids that have radiated across the globe and are incredibly resilient-since some thrive in harsh environments and can exist on minimal and intermittent feedings. Given the emerging importance of microbiomes to an organism's health, it is intriguing to suggest that the long-term success of the scorpion bauplan may be linked to the microbiome. Little is known about scorpion microbiomes, and what is known, concentrates on the gut. The microbiome is not limited to the gut, rather it can be found within tissues, fluids and on external surfaces. We tested whether the scorpion telson, the venom-producing organ, of two species, Smeringurus mesaensis and Hadrurus arizonensis, contain bacteria. We isolated telson DNA from each species, amplified bacterial 16S rRNA genes, and identified the collection of bacteria present within each scorpion species. Our results show for the first time that telsons of non-buthid scorpion species do indeed contain bacteria. Interestingly, each scorpion species has a phylogenetically unique telson microbiome including Mollicutes symbionts. This study may change how we view scorpion biology and their venoms.
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Affiliation(s)
- Christopher Shimwell
- Department of Biology, Eastern Connecticut State University, Willimantic, CT, United States of America
| | - Lauren Atkinson
- Department of Biology, Eastern Connecticut State University, Willimantic, CT, United States of America
| | - Matthew R. Graham
- Department of Biology, Eastern Connecticut State University, Willimantic, CT, United States of America
| | - Barbara Murdoch
- Department of Biology, Eastern Connecticut State University, Willimantic, CT, United States of America
- * E-mail:
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Buckman S, Morris RH, Bourman RP. Fire-induced rock spalling as a mechanism of weathering responsible for flared slope and inselberg development. Nat Commun 2021; 12:2150. [PMID: 33846314 PMCID: PMC8041894 DOI: 10.1038/s41467-021-22451-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 03/16/2021] [Indexed: 11/24/2022] Open
Abstract
Inselbergs, such as Uluru in central Australia, are iconic landscape features of semi-arid and deeply denuded continental interiors. These islands of rock are commonly skirted by steep, overhanging cliffs (flared slopes) at ground level. The weathering processes responsible for formation of flared slopes and steep-sided inselbergs in flat, planated landscapes are enigmatic. One model emphasizes sub-surface weathering followed by denudation and excavation of saprolite to expose the unweathered bedrock while other models advocate slope development under subaerial conditions at ground level. We present a new hypothesis that identifies wildfire as a primary agent of flared slope development via fire-induced rock spalling around the periphery of inselbergs. Widespread fire-spalling following the 2019-2020 Australian fires illustrates that this is a common form of physical weathering in fire-prone environments but its effects are particularly evident in semi-arid regions where lateral fire-spalling dominates over fluvial and chemical weathering to create flared slopes and steep-sided inselbergs.
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Affiliation(s)
- Solomon Buckman
- GeoQuest Research Centre, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, Australia.
| | - Rowena H Morris
- GeoQuest Research Centre, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, Australia
| | - Robert P Bourman
- GeoQuest Research Centre, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, Australia
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3
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Wright JL, Wasef S, Heupink TH, Westaway MC, Rasmussen S, Pardoe C, Fourmile GG, Young M, Johnson T, Slade J, Kennedy R, Winch P, Pappin M, Wales T, Bates W“B, Hamilton S, Whyman N, van Holst Pellekaan S, McAllister PJ, Taçon PS, Curnoe D, Li R, Millar C, Subramanian S, Willerslev E, Malaspinas AS, Sikora M, Lambert DM. Ancient nuclear genomes enable repatriation of Indigenous human remains. SCIENCE ADVANCES 2018; 4:eaau5064. [PMID: 30585290 PMCID: PMC6300400 DOI: 10.1126/sciadv.aau5064] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 11/20/2018] [Indexed: 05/21/2023]
Abstract
After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many decades, Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return. However, many of these remains have no recorded provenance, making their repatriation very difficult or impossible. To determine whether DNA-based methods could resolve this important problem, we sequenced 10 nuclear genomes and 27 mitogenomes from ancient pre-European Aboriginal Australians (up to 1540 years before the present) of known provenance and compared them to 100 high-coverage contemporary Aboriginal Australian genomes, also of known provenance. We report substantial ancient population structure showing strong genetic affinities between ancient and contemporary Aboriginal Australian individuals from the same geographic location. Our findings demonstrate the feasibility of successfully identifying the origins of unprovenanced ancestral remains using genomic methods.
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Affiliation(s)
- Joanne L. Wright
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Sally Wasef
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Tim H. Heupink
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
- Global Health Institute, Epidemiology and Social Medicine, University of Antwerp, Belgium
| | - Michael C. Westaway
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Simon Rasmussen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Colin Pardoe
- Department of Archaeology and Natural History, Australian National University, Canberra, ACT, Australia
| | | | - Michael Young
- Barkandji/Paakantyi Elder, Red Cliffs, VIC, Australia
| | - Trish Johnson
- Barkandji/Paakantyi Elder, Pooncarie, NSW, Australia
| | - Joan Slade
- Ngiyampaa Elder, Ivanhoe, NSW, Australia
| | | | - Patsy Winch
- Mutthi Mutthi Elder, Balranald, NSW, Australia
| | - Mary Pappin
- Mutthi Mutthi Elder, Broken Hill, NSW, Australia
| | - Tapij Wales
- Thanynakwith Elder, Napranum, QLD, Australia
| | | | | | | | - Sheila van Holst Pellekaan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
| | | | - Paul S.C. Taçon
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Darren Curnoe
- ARC Centre of Excellence for Australian Biodiversity and Heritage and Paleontology, Geobiology and Earth Archives Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Craig Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Sankar Subramanian
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Corresponding author. (M.S.); (D.M.L.)
| | - David M. Lambert
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
- Corresponding author. (M.S.); (D.M.L.)
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4
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The evolutionary history and human settlement of Australia and the Pacific. Curr Opin Genet Dev 2018; 53:53-59. [PMID: 30029008 DOI: 10.1016/j.gde.2018.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/09/2018] [Accepted: 06/26/2018] [Indexed: 11/21/2022]
Abstract
Understanding the timing and processes involved in the human settlement of Australia and the Pacific has significance for addressing some key debates relating to human origins and population expansions worldwide. Despite this, for many years, Pacific populations were seriously under-represented in genetic studies of human origins. The last 15 years, however, have seen some major genetic studies involving Australian and Pacific populations which have shed light on their origins and interactions, and the last five years have seen some major developments that are challenging long-held concepts of Pacific settlement.
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Lindberg MR, Schmedes SE, Hewitt FC, Haas JL, Ternus KL, Kadavy DR, Budowle B. A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes. PLoS One 2016; 11:e0167600. [PMID: 27936026 PMCID: PMC5147911 DOI: 10.1371/journal.pone.0167600] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/16/2016] [Indexed: 12/17/2022] Open
Abstract
Single source and multiple donor (mixed) samples of human mitochondrial DNA were analyzed and compared using the MinION and the MiSeq platforms. A generalized variant detection strategy was employed to provide a cursory framework for evaluating the reliability and accuracy of mitochondrial sequences produced by the MinION. The feasibility of long-read phasing was investigated to establish its efficacy in quantitatively distinguishing and deconvolving individuals in a mixture. Finally, a proof-of-concept was demonstrated by integrating both platforms in a hybrid assembly that leverages solely mixture data to accurately reconstruct full mitochondrial genomes.
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Affiliation(s)
| | - Sarah E. Schmedes
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | | | - Jamie L. Haas
- Signature Science, LLC, Austin, Texas, United States of America
| | | | - Dana R. Kadavy
- Signature Science, LLC, Austin, Texas, United States of America
| | - Bruce Budowle
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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6
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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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7
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Heupink TH, Subramanian S, Wright JL, Endicott P, Westaway MC, Huynen L, Parson W, Millar CD, Willerslev E, Lambert DM. Ancient mtDNA sequences from the First Australians revisited. Proc Natl Acad Sci U S A 2016; 113:6892-7. [PMID: 27274055 PMCID: PMC4922152 DOI: 10.1073/pnas.1521066113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537-542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the "Out of Africa" model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains ∼1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains.
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Affiliation(s)
- Tim H Heupink
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Sankar Subramanian
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Joanne L Wright
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Phillip Endicott
- Department of Zoology, Oxford University, Oxford OX1 2JD, United Kingdom
| | | | - Leon Huynen
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, 6020 Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA 16801
| | - Craig D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Eske Willerslev
- Centre for GeoGenetics, University of Copenhagen, 1017 Copenhagen, Denmark
| | - David M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia;
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Zhao J, Liu FE, Lin S, Liu ZZ, Sun ZY, Wu XM, Zhang HQ. Investigation on maternal lineage of a Neolithic group from northern Shaanxi based on ancient DNA. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:732-739. [PMID: 27246811 DOI: 10.1080/24701394.2016.1177039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A magnetic bead purification method was successfully used to extract ancient DNA from the skeletal remains of 10 specimens excavated from Wuzhuangguoliang (Wzhgl) site, which was located in northern Shaanxi. The multidimensional scaling (MDS) and analysis of molecular variance approach (AMOVA) revealed that ancient Wzhgl people bored a very high similarity to southern Han Chinese. By constructing the MJ-network of various modern people including Han Chinese and Japanese, the phylogenetic analysis indicated that the Wzhgl population had close maternal distance with ancient Shandong and Xinjiang people. These findings indicated that Wzhgl contributed to the gene pool of Han Chinese and modern Japanese. In addition, population migration and interflow between Wzhgl people and ancient Shandong or Xinjiang probably occurred in Neolithic period.
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Affiliation(s)
- Jing Zhao
- a The Key Laboratory of Biomedical Information Engineering of Ministry of Education , Department of Biological Science and Engineering, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an , PR China
| | - Fang-E Liu
- b The Center of Basic Medicine Teaching Experiments , School of Basic Medicine, Fourth Military Medicine University (FMMU) , Xi'an , PR China
| | - Song Lin
- a The Key Laboratory of Biomedical Information Engineering of Ministry of Education , Department of Biological Science and Engineering, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an , PR China
| | - Zhi-Zhen Liu
- a The Key Laboratory of Biomedical Information Engineering of Ministry of Education , Department of Biological Science and Engineering, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an , PR China
| | - Zhou-Yong Sun
- c Shaanxi Provincial Institute of Archaeology , Xi'an , Shaanxi Province , PR China
| | - Xiao-Ming Wu
- a The Key Laboratory of Biomedical Information Engineering of Ministry of Education , Department of Biological Science and Engineering, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an , PR China
| | - Hu-Qin Zhang
- a The Key Laboratory of Biomedical Information Engineering of Ministry of Education , Department of Biological Science and Engineering, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an , PR China
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9
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Bašić Ž, Fox AR, Anterić I, Jerković I, Polašek O, Anđelinović Š, Holland MM, Primorac D. Cultural inter-population differences do not reflect biological distances: an example of interdisciplinary analysis of populations from Eastern Adriatic coast. Croat Med J 2016; 56:230-8. [PMID: 26088847 PMCID: PMC4500963 DOI: 10.3325/cmj.2015.56.230] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
AIM To compare the population group from the Šopot graveyard with population groups from traditional Croatian medieval graveyards by using anthropological, craniometrics, and mitochondrial (mtDNA) analysis and to examine if the cultural differences between population groups reflect biological differences. METHODS We determined sex, age at death, pathological, and traumatic changes of skeletal remains from the Šopot graveyard and compared them with a cumulative medieval sample from the same region. We also performed principal component analysis to compare skeletal remains from Šopot with those from Ostrovica and other Central European samples according to 8 cranial measurements. Finally, we compared 46 skeletons from Šopot with medieval (Ostrovica) and contemporary populations using mDNA haplogroup profiling. RESULTS The remains from Šopot were similar to the cumulative sample in lifestyle and quality of life markers. Principal component analysis showed that they were closely related to Eastern Adriatic coast sites (including Ostrovica and Šopot) in terms of cranial morphology, indicating similar biological makeup. According to mDNA testing, Šopot population showed no significant differences in the haplogroup prevalence from either medieval or contemporary populations. CONCLUSION This study shows that the Šopot population does not significantly differ from other medieval populations from this area. Besides similar quality of life markers, these populations also had similar biological markers. Substantial archeological differences can therefore be attributed to apparent cultural influences, which in this case do not reflect biological differences.
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Affiliation(s)
- Željana Bašić
- Željana Bašić, University Center for Forensic Sciences, University of Split, Ruđera Boškovića 31/IV, 21000 Split, Croatia,
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10
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Hagelberg E, Hofreiter M, Keyser C. Introduction. Ancient DNA: the first three decades. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130371. [PMID: 25487324 PMCID: PMC4275880 DOI: 10.1098/rstb.2013.0371] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Erika Hagelberg
- Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Christine Keyser
- Institut de Médecine Légale, Laboratoire AMIS, Université de Strasbourg, CNRS UMR 5288, Strasbourg, France
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11
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Aspects of ancient mitochondrial DNA analysis in different populations for understanding human evolution. Balkan J Med Genet 2014; 17:5-14. [PMID: 25741209 PMCID: PMC4347471 DOI: 10.2478/bjmg-2014-0019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The evolution of modern humans is a long and difficult process which started from their first appearance and continues to the present day. The study of the genetic origin of populations can help to determine population kinship and to better understand the gradual changes of the gene pool in space and time. Mitochondrial DNA (mtDNA) is a proper tool for the determination of the origin of populations due to its high evolutionary importance. Ancient mitochondrial DNA retrieved from museum specimens, archaeological finds and fossil remains can provide direct evidence for population origins and migration processes. Despite the problems with contaminations and authenticity of ancient mitochondrial DNA, there is a developed set of criteria and platforms for obtaining authentic ancient DNA. During the last two decades, the application of different methods and techniques for analysis of ancient mitochondrial DNA gave promising results. Still, the literature is relatively poor with information for the origin of human populations. Using comprehensive phylogeographic and population analyses we can observe the development and formation of the contemporary populations. The aim of this study was to shed light on human migratory processes and the formation of populations based on available ancient mtDNA data.
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12
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Blau S, Catelli L, Garrone F, Hartman D, Romanini C, Romero M, Vullo C. The contributions of anthropology and mitochondrial DNA analysis to the identification of the human skeletal remains of the Australian outlaw Edward ‘Ned’ Kelly. Forensic Sci Int 2014; 240:e11-21. [DOI: 10.1016/j.forsciint.2014.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 02/07/2014] [Accepted: 04/02/2014] [Indexed: 11/27/2022]
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13
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Gallagher A. Absolute and relative endocranial size in Neandertals and later Pleistocene Homo. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2014; 65:349-75. [PMID: 24954798 DOI: 10.1016/j.jchb.2014.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 02/12/2014] [Indexed: 10/25/2022]
Abstract
Eurasian Neandertals encompass the entire observed range of recent and fossil Homo sapiens in absolute, but not relative endocranial volume, and Neandertals attest an average EQ significantly lower than their Upper Pleistocene successors. While the cognitive, social, and evolutionary implications of this phenomenon have been emphasised, the statistical basis of a mean inference of EQ in the Neandertal hypodigm has not been appropriately demonstrated. A demonstrable male bias in the available postcranial, not cranial, series has skewed perceptions of Neandertal brain-to-body size scaling towards a rejection of the null hypothesis. A simple resolution to this problem is a concise assessment of paired associated covariates against a suitable recent human comparator series. Permutations of Fisher's z and Student's t statistics are valid metrics in tests of significance in single datum hypotheses. Bootstrapped single observation tests determined significance in body size, absolute and relative endocranial volume in Pleistocene archaic, early modern, and late Pleistocene H. sapiens. With respect to absolute ECV, all current Middle-Upper Pleistocene crania fall within the substantial recent Homo range. Nevertheless, simple indices derived from raw and modified data in normal and logarithmic space reveal that Western European Neandertal males approach the lower extremes of our observed size range in relative ECV, yet none exceed statistical significance. Results confirm that relative ECV/brain size in Neandertals was not significantly depressed relative to recent and fossil H. sapiens and this is consistent with a substantial body of data from living humans dismissing any simple correspondence of relative brain size with intelligence and, by extension, evolutionary success.
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Affiliation(s)
- Andrew Gallagher
- Centre for Anthropological Research (CAfR), University of Johannesburg, Auckland Park 2006, Johannesburg, South Africa.
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14
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Morey M, Fernández-Marmiesse A, Castiñeiras D, Fraga JM, Couce ML, Cocho JA. A glimpse into past, present, and future DNA sequencing. Mol Genet Metab 2013; 110:3-24. [PMID: 23742747 DOI: 10.1016/j.ymgme.2013.04.024] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 04/30/2013] [Accepted: 04/30/2013] [Indexed: 12/21/2022]
Abstract
Current advances in DNA sequencing technologies are dropping down sequencing cost while increasing throughput at a pace never shown before. Past-decade great milestones, as the establishment of a reference human genome (amongst others) and large-scale human genetic variation study in the 1000 Genome project are, in conjunction with the use of these techniques, triggering advances in many areas of basic and applied science. These tools, stored in and combined with the vast amount of information present in biological online databases are, with the use of automated interpretation and analysis tools, allowing the fulfillment of increasingly ambitious studies in many areas and also are democratizing the access to information, interpretation and technologies, being the first opportunity for researchers to assess the influence of genetics in complex events as multifactorial diseases, evolutionary studies, metagenomics, transcriptomics, etc. In this review, we present the current state of the art of these technologies, focusing on second generation sequencing, from sample and library preparation to sequencing chemistries and bioinformatic software available for final data analysis and visualisation, with its possible applications. We also make an overview of first and third generation, due to its historical importance and for being the upcoming future tools for genetic analysis, respectively.
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Affiliation(s)
- Marcos Morey
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas, Hospital Clínico Universitario de Santiago, A Choupana s/n, 15706 Santiago de Compostela, Spain.
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Pilli E, Modi A, Serpico C, Achilli A, Lancioni H, Lippi B, Bertoldi F, Gelichi S, Lari M, Caramelli D. Monitoring DNA contamination in handled vs. directly excavated ancient human skeletal remains. PLoS One 2013; 8:e52524. [PMID: 23372650 PMCID: PMC3556025 DOI: 10.1371/journal.pone.0052524] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 11/15/2012] [Indexed: 11/18/2022] Open
Abstract
Bones, teeth and hair are often the only physical evidence of human or animal presence at an archaeological site; they are also the most widely used sources of samples for ancient DNA (aDNA) analysis. Unfortunately, the DNA extracted from ancient samples, already scarce and highly degraded, is widely susceptible to exogenous contaminations that can affect the reliability of aDNA studies. We evaluated the molecular effects of sample handling on five human skeletons freshly excavated from a cemetery dated between the 11 to the 14(th) century. We collected specimens from several skeletal areas (teeth, ribs, femurs and ulnas) from each individual burial. We then divided the samples into two different sets: one labeled as "virgin samples" (i.e. samples that were taken by archaeologists under contamination-controlled conditions and then immediately sent to the laboratory for genetic analyses), and the second called "lab samples"(i.e. samples that were handled without any particular precautions and subject to normal washing, handling and measuring procedures in the osteological lab). Our results show that genetic profiles from "lab samples" are incomplete or ambiguous in the different skeletal areas while a different outcome is observed in the "virgin samples" set. Generally, all specimens from different skeletal areas in the exception of teeth present incongruent results between "lab" and "virgin" samples. Therefore teeth are less prone to contamination than the other skeletal areas we analyzed and may be considered a material of choice for classical aDNA studies. In addition, we showed that bones can also be a good candidate for human aDNA analysis if they come directly from the excavation site and are accompanied by a clear taphonomic history.
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Affiliation(s)
- Elena Pilli
- Dipartimento di Biologia Evoluzionistica Laboratori di Antropologia, Università di Firenze, Firenze, Italy
| | - Alessandra Modi
- Dipartimento di Biologia Evoluzionistica Laboratori di Antropologia, Università di Firenze, Firenze, Italy
| | - Ciro Serpico
- Dipartimento di Biologia Evoluzionistica Laboratori di Antropologia, Università di Firenze, Firenze, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy
| | - Hovirag Lancioni
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy
| | - Barbara Lippi
- Dipartimento di Biologia Evoluzionistica Laboratori di Antropologia, Università di Firenze, Firenze, Italy
| | - Francesca Bertoldi
- Dipartimento di Studi Umanistici, Università Ca' Foscari Venezia, Venezia, Italy
| | - Sauro Gelichi
- Dipartimento di Studi Umanistici, Università Ca' Foscari Venezia, Venezia, Italy
| | - Martina Lari
- Dipartimento di Biologia Evoluzionistica Laboratori di Antropologia, Università di Firenze, Firenze, Italy
- * E-mail:
| | - David Caramelli
- Dipartimento di Biologia Evoluzionistica Laboratori di Antropologia, Università di Firenze, Firenze, Italy
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van Holst Pellekaan SM. Socially responsible genetic research with descendants of the First Australians. INVESTIGATIVE GENETICS 2012; 3:22. [PMID: 23151356 PMCID: PMC3528479 DOI: 10.1186/2041-2223-3-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 10/30/2012] [Indexed: 11/21/2022]
Abstract
Aboriginal Australians, one of the world’s indigenous peoples now outnumbered through colonization, are the most under-represented in genetic research because they feel that the benefits do not outweigh the social cost of involvement. Descendants of the First Australians have survived a period of European occupation during which time they were dispossessed of land, language and cultural identity resulting in inequities in health, education, and employment opportunities. Compared to Maori and Native American peoples, the ability to form organizations that help to control their affairs is very recent. The desire to control is understandably strong yet the ‘gate-keeping’ role of some organizations risks shifting the control away from smaller communities and has become increasingly politicized. In the past, research practices by Western scientists were poorly presented and have resulted in resistance to proposals that are perceived to have no beneficial outcomes for participants. In this age of advanced technological expertise in genetics, benefits to all humanity are clear to those carrying out research projects, yet not always to those being asked to participate, presenting extra challenges. Excellent guidelines for ethical conduct in research are available to assist researchers, prospective participants, and ethics committees or review boards that approve and monitor procedures. The essence of these guidelines are that research should be carried out with a spirit of integrity, respect, reciprocity, parity, recognition of survival and protection of social and cultural values, a need for control and shared responsibility. Specific Aboriginal organizations, with which researchers need to work to negotiate partnerships, vary within and between Australian states and will always expect Aboriginal personnel to be involved. People experienced in the consultation process are necessary as part of a team. By working patiently through lengthy negotiations with Aboriginal Australians, scientists can achieve valuable results, but failure to do so with respect and understanding will not yield hoped for outcomes. My own experience working with communities in the Darling River region of western New South Wales has been an enriching and rewarding one, with a long period of successful research lately delayed by increased expectation of monitoring and involvement at state level.
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Affiliation(s)
- Sheila M van Holst Pellekaan
- School of Biotechnology and Biomolecular Sciences D26, University of New South Wales, Kensington, New South Wales, 2052, Australia.
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17
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Disotell TR. Archaic human genomics. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 149 Suppl 55:24-39. [PMID: 23124308 DOI: 10.1002/ajpa.22159] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 12/18/2022]
Abstract
For much of the 20th century, the predominant view of human evolutionary history was derived from the fossil record. Homo erectus was seen arising in Africa from an earlier member of the genus and then spreading throughout the Old World and into the Oceania. A regional continuity model of anagenetic change from H. erectus via various intermediate archaic species into the modern humans in each of the regions inhabited by H. erectus was labeled the multiregional model of human evolution (MRE). A contrasting model positing a single origin, in Africa, of anatomically modern H. sapiens with some populations later migrating out of Africa and replacing the local archaic populations throughout the world with complete replacement became known as the recent African origin (RAO) model. Proponents of both models used different interpretations of the fossil record to bolster their views for decades. In the 1980s, molecular genetic techniques began providing evidence from modern human variation that allowed not only the different models of modern human origins to be tested but also the exploration demographic history and the types of selection that different regions of the genome and even specific traits had undergone. The majority of researchers interpreted these data as strongly supporting the RAO model, especially analyses of mitochondrial DNA (mtDNA). Extrapolating backward from modern patterns of variation and using various calibration points and substitution rates, a consensus arose that saw modern humans evolving from an African population around 200,000 years ago. Much later, around 50,000 years ago, a subset of this population migrated out of Africa replacing Neanderthals in Europe and western Asia as well as archaics in eastern Asia and Oceania. mtDNA sequences from more than two-dozen Neanderthals and early modern humans re-enforced this consensus. In 2010, however, the complete draft genomes of Neanderthals and of heretofore unknown hominins from Siberia, called Denisovans, demonstrated gene flow between these archaic human species and modern Eurasians but not sub-Saharan Africans. Although the levels of gene flow may be very limited, this unexpected finding does not fit well with either the RAO model or MRE model. More thorough sampling of modern human diversity, additional fossil discoveries, and the sequencing of additional hominin fossils are necessary to throw light onto our origins and our history.
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Affiliation(s)
- Todd R Disotell
- Center for Study of Human Origins, Department of Anthropology, New York University, New York, NY 10003, USA.
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Bulbeck D, O'Connor S. The Watinglo mandible: a second terminal Pleistocene Homo sapiens fossil from tropical Sahul with a test on existing models for the human settlement of the region. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2011; 62:1-29. [PMID: 21216399 DOI: 10.1016/j.jchb.2010.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 10/01/2010] [Indexed: 11/28/2022]
Abstract
This paper analyses a fossil human mandible, dated to circa 10ka, from Watinglo rockshelter on the north coast of Papua New Guinea. The fossil is metrically and morphologically similar to male mandibles of recent Melanesians and Australian Aborigines. It is distinguished from Kow Swamp and Coobool Creek male mandibles (Murray Valley, terminal Pleistocene) by being smaller and having different shape characteristics, as well as smaller teeth and a slower rate of tooth wear. It pairs with the Liang Lemdubu female (Late Glacial Maximum, Aru Islands) in suggesting that the morphology of the terminal Pleistocene inhabitants of tropical Sahul was gracile compared to their contemporaries within the southern Murray drainage. An explanatory scenario for this morphological contrast is developed in the context of the Homo sapiens early fossil record, Australasian mtDNA evidence, terminal Pleistocene climatic variation, and the possibility of multiple entry points into Sahul.
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Affiliation(s)
- D Bulbeck
- Department of Archaeology and Natural History, Research School of Pacific and Asian Studies, School of Culture, History and Language, The Australian National University, ACT 0200, Australia.
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Shapiro B, Hofreiter M. Analysis of ancient human genomes: using next generation sequencing, 20-fold coverage of the genome of a 4,000-year-old human from Greenland has been obtained. Bioessays 2010; 32:388-91. [PMID: 20414896 DOI: 10.1002/bies.201000026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
High-capacity sequencing technologies have dramatically reduced both the cost and time required to generate complete human genome sequences. Besides expanding our knowledge about existing diversity, the nature of these technologies makes it possible to extend knowledge in yet another dimension: time. Recently, the complete genome sequence of a 4,000-year-old human from the Saqqaq culture of Greenland was determined to 20-fold coverage. These data make it possible to investigate the population affinities of this enigmatic culture and, by identifying several phenotypic traits of this individual, provide a limited glimpse into how these people may have looked. While undoubtedly a milestone in ancient DNA research, the cost to generate an ancient genome, even from such an exceptionally preserved specimen, remains out of reach for most. Nonetheless, recently developed DNA capture methods, already applied to Neanderthal and fossil human mitochondrial DNA, may soon make large-scale genome-wide analysis of ancient human diversity a reality, providing a fresh look at human population history.
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Affiliation(s)
- Beth Shapiro
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
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20
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Endicott P, Ho SY, Metspalu M, Stringer C. Evaluating the mitochondrial timescale of human evolution. Trends Ecol Evol 2009; 24:515-21. [DOI: 10.1016/j.tree.2009.04.006] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 03/27/2009] [Accepted: 04/01/2009] [Indexed: 01/28/2023]
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21
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Gibbon VE, Penny CB, Štrkalj G, Ruff P. Brief communication: Minimally invasive bone sampling method for DNA analysis. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 139:596-9. [DOI: 10.1002/ajpa.21048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Ramakrishnan U, Hadly EA. Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies. Mol Ecol 2009; 18:1310-30. [PMID: 19281471 DOI: 10.1111/j.1365-294x.2009.04092.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India
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23
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Bell LS, Kayser M, Jones C. The mineralized osteocyte: A living fossil. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2008; 137:449-56. [DOI: 10.1002/ajpa.20886] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Stoneking M. Wandering off the trail of human evolution human evolution trails from the past. (2007). By Camilo J. Cela-Conde and Francisco J. Ayala. Oxford University Press. Paperback, 437 pp. ISBN: 9780198567806. Bioessays 2008. [DOI: 10.1002/bies.20817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Affiliation(s)
- Elaine R. Mardis
- Departments of Genetics and Molecular Microbiology and Genome Sequencing Center, Washington University School of Medicine, St. Louis MO 63108;
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Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M. The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS. BMC Genomics 2008; 9:267. [PMID: 18522722 PMCID: PMC2447851 DOI: 10.1186/1471-2164-9-267] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Accepted: 06/03/2008] [Indexed: 11/21/2022] Open
Abstract
Background To a greater or lesser extent, eukaryotic nuclear genomes contain fragments of their mitochondrial genome counterpart, deriving from the random insertion of damaged mtDNA fragments. NumtS (Nuclear mt Sequences) are not equally abundant in all species, and are redundant and polymorphic in terms of copy number. In population and clinical genetics, it is important to have a complete overview of NumtS quantity and location. Searching PubMed for NumtS or Mitochondrial pseudo-genes yields hundreds of papers reporting Human NumtS compilations produced by in silico or wet-lab approaches. A comparison of published compilations clearly shows significant discrepancies among data, due both to unwise application of Bioinformatics methods and to a not yet correctly assembled nuclear genome. To optimize quantification and location of NumtS, we produced a consensus compilation of Human NumtS by applying various bioinformatics approaches. Results Location and quantification of NumtS may be achieved by applying database similarity searching methods: we have applied various methods such as Blastn, MegaBlast and BLAT, changing both parameters and database; the results were compared, further analysed and checked against the already published compilations, thus producing the Reference Human Numt Sequences (RHNumtS) compilation. The resulting NumtS total 190. Conclusion The RHNumtS compilation represents a highly reliable reference basis, which may allow designing a lab protocol to test the actual existence of each NumtS. Here we report preliminary results based on PCR amplification and sequencing on 41 NumtS selected from RHNumtS among those with lower score. In parallel, we are currently designing the RHNumtS database structure for implementation in the HmtDB resource. In the future, the same database will host NumtS compilations from other organisms, but these will be generated only when the nuclear genome of a specific organism has reached a high-quality level of assembly.
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Affiliation(s)
- Daniela Lascaro
- Dipartimento di Biochimica e Biologia Molecolare E, Quagliariello, Università di Bari, Via E, Orabona 4, 70126 Bari, Italy.
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Linderholm A, Malmström H, Lidén K, Holmlund G, Götherström A. Cryptic contamination and phylogenetic nonsense. PLoS One 2008; 3:e2316. [PMID: 18509458 PMCID: PMC2384008 DOI: 10.1371/journal.pone.0002316] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Accepted: 04/22/2008] [Indexed: 11/18/2022] Open
Abstract
Ancient human DNA has been treated cautiously ever since the problems related to this type of material were exposed in the early 1990s, but as sequential genetic data from ancient specimens have been key components in several evolutionary and ecological studies, interest in ancient human DNA is on the increase again. It is especially tempting to approach archaeological and anthropological questions through this type of material, but DNA from ancient human tissue is notoriously complicated to work with due to the risk of contamination with modern human DNA. Various ways of authenticating results based on ancient human DNA have been developed to circumvent the problems. One commonly used method is to predict what the contamination is expected to look like and then test whether the ancient human DNA fulfils this prediction. If it does, the results are rejected as contamination, while if it does not, they are often considered authentic. We show here that human contamination in ancient material may well deviate from local allele frequencies or the distributions to be found among the laboratory workers and archaeologists. We conclude that it is not reliable to authenticate ancient human DNA solely by showing that it is different from what would be expected from people who have handled the material.
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Affiliation(s)
- Anna Linderholm
- Archaeological Research laboratory, Stockholm University, Stockholm, Sweden.
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Melchior L, Kivisild T, Lynnerup N, Dissing J. Evidence of authentic DNA from Danish Viking Age skeletons untouched by humans for 1,000 years. PLoS One 2008; 3:e2214. [PMID: 18509537 PMCID: PMC2386972 DOI: 10.1371/journal.pone.0002214] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 04/02/2008] [Indexed: 11/18/2022] Open
Abstract
Background Given the relative abundance of modern human DNA and the inherent impossibility for incontestable proof of authenticity, results obtained on ancient human DNA have often been questioned. The widely accepted rules regarding ancient DNA work mainly affect laboratory procedures, however, pre-laboratory contamination occurring during excavation and archaeological-/anthropological handling of human remains as well as rapid degradation of authentic DNA after excavation are major obstacles. Methodology/Principal Findings We avoided some of these obstacles by analyzing DNA from ten Viking Age subjects that at the time of sampling were untouched by humans for 1,000 years. We removed teeth from the subjects prior to handling by archaeologists and anthropologists using protective equipment. An additional tooth was removed after standard archaeological and anthropological handling. All pre-PCR work was carried out in a “clean- laboratory” dedicated solely to ancient DNA work. Mitochondrial DNA was extracted and overlapping fragments spanning the HVR-1 region as well as diagnostic sites in the coding region were PCR amplified, cloned and sequenced. Consistent results were obtained with the “unhandled” teeth and there was no indication of contamination, while the latter was the case with half of the “handled” teeth. The results allowed the unequivocal assignment of a specific haplotype to each of the subjects, all haplotypes being compatible in their character states with a phylogenetic tree drawn from present day European populations. Several of the haplotypes are either infrequent or have not been observed in modern Scandinavians. The observation of haplogroup I in the present study (<2% in modern Scandinavians) supports our previous findings of a pronounced frequency of this haplogroup in Viking and Iron Age Danes. Conclusion The present work provides further evidence that retrieval of ancient human DNA is a possible task provided adequate precautions are taken and well-considered sampling is applied.
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Affiliation(s)
- Linea Melchior
- Research Laboratory, Institute of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Toomas Kivisild
- Leverhulme Center for Human Evolutionary Studies, The Henry Wellcome Building, University of Cambridge, Cambridge, United Kingdom
| | - Niels Lynnerup
- Laboratory of Biological Anthropology, Institute of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jørgen Dissing
- Research Laboratory, Institute of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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Habgood PJ, Franklin NR. The revolution that didn't arrive: A review of Pleistocene Sahul. J Hum Evol 2008; 55:187-222. [PMID: 18485448 DOI: 10.1016/j.jhevol.2007.11.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Revised: 06/12/2007] [Accepted: 11/15/2007] [Indexed: 10/22/2022]
Abstract
There is a "package" of cultural innovations that are claimed to reflect modern human behaviour. The introduction of the "package" has been associated with the Middle-to-Upper Palaeolithic transition and the appearance in Europe of modern humans. It has been proposed that modern humans spread from Africa with the "package" and colonised not only Europe but also southern Asia and Australia (McBrearty and Brooks, 2000; Mellars, 2006a). In order to evaluate this proposal, we explore the late Pleistocene archaeological record of Sahul, the combined landmass of Australia and Papua New Guinea, for indications of these cultural innovations at the earliest sites. It was found that following initial occupation of the continent by anatomically and behaviourally modern humans, the components were gradually assembled over a 30,000-year period. We discount the idea that the "package" was lost en route to Sahul and assess the possibility that the "package" was not integrated within the material culture of the initial colonising groups because they may not have been part of a rapid colonisation process from Africa. As the cultural innovations appear at different times and locations within Sahul, the proposed "package" of archaeologically visible traits cannot be used to establish modern human behaviour. Whilst the potential causal role of increasing population densities/pressure in the appearance of the "package" of modern human behaviour in the archaeological record is acknowledged, it is not seen as the sole explanation because the individual components of the "package" appear at sites that are widely separated in space and time.
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Affiliation(s)
- Phillip J Habgood
- School of Social Science, University of Queensland, Brisbane QLD 4072, Australia
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30
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Human cranial diversity and evidence for an ancient lineage of modern humans. J Hum Evol 2008; 54:814-26. [PMID: 18164370 DOI: 10.1016/j.jhevol.2007.10.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Revised: 10/20/2007] [Accepted: 10/31/2007] [Indexed: 11/22/2022]
Abstract
This study examines the genetic affinities of various modern human groupings using a multivariate analysis of morphometric data. Phylogenetic relationships among these groupings are also explored using neighbor-joining analysis of the metric data. Results indicate that the terminal Pleistocene/early Holocene fossils from Australasia exhibit a close genetic affinity with early modern humans from the Levant. Furthermore, recent human populations and Upper Paleolithic Europeans share a most recent common ancestor not shared with either the early Australasians or the early Levantine humans. This pattern of genetic and phylogenetic relationships suggests that the early modern humans from the Levant either contributed directly to the ancestry of an early lineage of Australasians, or that they share a recent common ancestor with them. The principal findings of the study, therefore, lend support to the notion of an early dispersal from Africa by a more ancient lineage of modern human prior to 50 ka, perhaps as early as OIS 5 times (76-100 ka).
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31
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Weaver TD, Roseman CC. New developments in the genetic evidence for modern human origins. Evol Anthropol 2008. [DOI: 10.1002/evan.20161] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Crevecoeur I. New discovery of an Upper Paleolithic auditory ossicle: The right malleus of Nazlet Khater 2. J Hum Evol 2007; 52:341-5. [PMID: 17239938 DOI: 10.1016/j.jhevol.2006.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 11/13/2006] [Accepted: 11/29/2006] [Indexed: 11/21/2022]
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Fu Y, Zhao H, Cui Y, Zhang Q, Xu X, Zhou H, Zhu H. Molecular genetic analysis of Wanggu remains, Inner Mongolia, China. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2007; 132:285-91. [PMID: 16634045 DOI: 10.1002/ajpa.20450] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Wanggu tribe, which contributed significantly to the foundation of the Yuan Dynasty, was one of the groups living on the Mongolian steppes during the Jin-Yuan period (AD 1127-1368) of Chinese history. However, there has been both archaeological and historical dispute regarding the origin of the ancient tribe. Recently, we discovered human remains of the Wanggu tribe in the Chengbozi cemetery in the Siziwang Banner of Inner Mongolia, China. To investigate the genetic structure of the Wanggu tribe and to trace the origins of the tribe at a molecular level, we analyzed the control-region sequences and coding regions of mitochondrial DNA (mtDNA) from the remains by direct sequencing and restriction-fragment length polymorphism analysis. In combination with mtDNA data of 15 extant Eurasian populations, we performed phylogenetic analysis and multidimensional scaling analysis. Our results show that the genetic structure of the Wanggu tribe in the Jin-Yuan period is a complex matriline, containing admixture from both Asian and European populations. In addition, we reveal that on the basis of mtDNA data, the ancient tribe may share a recent common ancestor with the Turkic-speaking Uzbeks and Uighurs.
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Affiliation(s)
- Yuqin Fu
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China
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Hebsgaard MB, Wiuf C, Gilbert MTP, Glenner H, Willerslev E. Evaluating Neanderthal genetics and phylogeny. J Mol Evol 2006; 64:50-60. [PMID: 17146600 DOI: 10.1007/s00239-006-0017-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Accepted: 08/29/2006] [Indexed: 11/28/2022]
Abstract
The retrieval of Neanderthal (Homo neanderthalsensis) mitochondrial DNA is thought to be among the most significant ancient DNA contributions to date, allowing conflicting hypotheses on modern human (Homo sapiens) evolution to be tested directly. Recently, however, both the authenticity of the Neanderthal sequences and their phylogenetic position outside contemporary human diversity have been questioned. Using Bayesian inference and the largest dataset to date, we find strong support for a monophyletic Neanderthal clade outside the diversity of contemporary humans, in agreement with the expectations of the Out-of-Africa replacement model of modern human origin. From average pairwise sequence differences, we obtain support for claims that the first published Neanderthal sequence may include errors due to postmortem damage in the template molecules for PCR. In contrast, we find that recent results implying that the Neanderthal sequences are products of PCR artifacts are not well supported, suffering from inadequate experimental design and a presumably high percentage (>68%) of chimeric sequences due to "jumping PCR" events.
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Affiliation(s)
- Martin B Hebsgaard
- Centré for Ancient Genetics, Niels Bohr Institute and Biological Institute, University of Copenhagen, Juliane Maries vej 30, Copenhagen DK-2100, Denmark
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van Holst Pellekaan SM, Ingman M, Roberts-Thomson J, Harding RM. Mitochondrial genomics identifies major haplogroups in Aboriginal Australians. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2006; 131:282-94. [PMID: 16596590 DOI: 10.1002/ajpa.20426] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We classified diversity in eight new complete mitochondrial genome sequences and 41 partial sequences from living Aboriginal Australians into five haplogroups. Haplogroup AuB belongs to global lineage M, and AuA, AuC, AuD, and AuE to N. Within N, we recognize subdivisions, assigning AuA to haplogroup S, AuD to haplogroup O, AuC to P4, and AuE to P8. On available evidence, (S)AuA and (M)AuB are widespread in Australia. (P4)AuC is found in the Riverine region of western New South Wales, and was identified by others in northern Australia. (O)AuD and (P8)AuE were clearly identified only from central Australia. Our eight Australian full mt genome sequences, combined with 20 others (Ingman and Gyllensten 2003 Genome Res. 13:1600-1606) and compared with full mt genome sequences from regions to the north that include Papua New Guinea, Malaya, and Andaman and Nicobar Islands, show that ancestral connections between regions are deep and limited to clustering at the level of the N and M macrohaplogroups. The Australian-specific distribution of the five haplogroups identified indicates genetic isolation over a long period. Ancestral connections within Australia are deeper than those reflected by known linguistic or culturally based affinities. Applying a coalescence analysis to a gene tree for the coding regions of the eight genomic sequences, we made estimates of time depth that support a continuity of presence for the descendants of a founding population already established by 40,000 years ago.
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Affiliation(s)
- Sheila M van Holst Pellekaan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales 2052, Australia.
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Changchun Y, Li X, Xiaolei Z, Hui Z, Hong Z. Genetic analysis on Tuoba Xianbei remains excavated from Qilang Mountain Cemetery in Qahar Right Wing Middle Banner of Inner Mongolia. FEBS Lett 2006; 580:6242-6. [PMID: 17070809 DOI: 10.1016/j.febslet.2006.10.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Revised: 10/05/2006] [Accepted: 10/12/2006] [Indexed: 11/29/2022]
Abstract
Sixteen sequences of the hypervariable segment I (HVS-I, 16039-16398) in mtDNA control region from ancient Tuoba Xianbei remains excavated from Qilang Mountain Cemetery were analyzed. In which, 13 haplotypes were found by 25 polymorphic sites. The haplotype diversity and nucleotide diversity were 0.98 and 0.0189, respectively, and the mean of nucleotide number differences was 6.25. Haplogroup analysis indicates these remains mainly belong to haplogroup C (31.25%) and D (43.75%). According to the published data were considered, we can suggest that the Tuoba Xianbei presented a close genetic affinity to Oroqen, Outer Mongolian and Ewenki populations, especially Oroqen.
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Affiliation(s)
- Yu Changchun
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, P.R. China
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Wall JD, Hammer MF. Archaic admixture in the human genome. Curr Opin Genet Dev 2006; 16:606-10. [PMID: 17027252 DOI: 10.1016/j.gde.2006.09.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Accepted: 09/22/2006] [Indexed: 10/24/2022]
Abstract
One of the enduring questions in the evolution of our species surrounds the fate of 'archaic' forms of Homo. Did Neanderthals go extinct without interbreeding with modern humans 25-40 thousand years ago or are their genes present among modern-day Europeans? Recent work suggests that Neanderthals and an as yet unidentified archaic African population contributed to at least 5% of the modern European and West African gene pools, respectively. Extensive sequencing of Neanderthal and other archaic human nuclear DNA has the potential to answer this question definitively within the next few years.
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Affiliation(s)
- Jeffrey D Wall
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
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Arcadi AC. Species resilience in Pleistocene hominids that traveled far and ate widely: An analogy to the wolf-like canids. J Hum Evol 2006; 51:383-94. [PMID: 16904731 DOI: 10.1016/j.jhevol.2006.04.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 03/22/2006] [Accepted: 04/24/2006] [Indexed: 11/24/2022]
Abstract
Morphological and genetic analyses have yet to resolve the question of whether more than one species of Homo existed contemporaneously in the Pleistocene. In an effort to contribute a process-related perspective to hominid phylogenetic reconstruction, this paper uses an analogy to the northern wolf-like canids (the wolves and coyotes) to ask the question, How many Homo species should there be, given their likely behavioral profile(s)? In contrast to earlier comparisons to social carnivores which sought to illuminate specific aspects of hominid behavioral ecology, this paper explores behavioral constraints on the process of speciation itself. The analogy suggests that because Pleistocene Homo probably exhibited high habitat tolerance, they would not have had the opportunity to speciate, especially in Africa. In contrast to an earlier single-species hypothesis based on competitive exclusion between sympatric hominid species, this paper explores constraints on the process of speciation under conditions of temporary allopatry.
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Affiliation(s)
- A Clark Arcadi
- Department of Anthropology, 265 McGraw Hall, Cornell University, Ithaca, New York 14853, USA.
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Webb S, Cupper ML, Robins R. Pleistocene human footprints from the Willandra Lakes, southeastern Australia. J Hum Evol 2006; 50:405-13. [PMID: 16343597 DOI: 10.1016/j.jhevol.2005.10.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2005] [Revised: 10/24/2005] [Accepted: 10/26/2005] [Indexed: 11/26/2022]
Abstract
Human and other hominid fossil footprints provide rare but important insights into anatomy and behavior. Here we report recently discovered fossil trackways of human footprints from the Willandra Lakes region of western New South Wales, Australia. Optically dated to between 19-23 ka and consisting of at least 124 prints, the trackways form the largest collection of Pleistocene human footprints in the world. The prints were made by adults, adolescents, and children traversing the moist surface of an ephemeral soak. This site offers a unique glimpse of humans living in the arid inland of Australia at the height of the last glacial period.
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Affiliation(s)
- Steve Webb
- Faculty of Humanities and Social Sciences, Bond University, Robina, Queensland 4229, Australia
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Excavating the mitochondrial genome identifies major haplogroups in Aboriginal Australians. ACTA ACUST UNITED AC 2006. [DOI: 10.3828/bfarm.2006.1.3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Neanderthals and modern humans: an example of a mammalian syngameon? NEANDERTHALS REVISITED: NEW APPROACHES AND PERSPECTIVES 2006. [DOI: 10.1007/978-1-4020-5121-0_16] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Movsessian AA. Phenetic Analysis in Paleoanthropology: Phenogeography of Peoples of the World. RUSS J GENET+ 2005. [DOI: 10.1007/s11177-005-0198-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Bandelt HJ. Mosaics of ancient mitochondrial DNA: positive indicators of nonauthenticity. Eur J Hum Genet 2005; 13:1106-12. [PMID: 16077732 DOI: 10.1038/sj.ejhg.5201476] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Research into ancient mitochondrial DNA is plagued by contamination, post mortem damage, and other artefacts. The stringent set of controls suggested by Cooper and Poinar a few years ago are, however, rarely followed in practice, and even when applied carefully, these criteria need not be sufficient to guarantee authenticity. The fairly relaxed prerequisites now common for ancient population studies have opened the door for all kinds of contamination and sequencing errors to enter ancient mtDNA data. To reject or question authenticity of particular sequencing results a posteriori, one can follow similar strategies of focused database comparisons that have proven to be effective and successful in the case of flawed modern mtDNA data.
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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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Bower MA, Spencer M, Matsumura S, Nisbet RER, Howe CJ. How many clones need to be sequenced from a single forensic or ancient DNA sample in order to determine a reliable consensus sequence? Nucleic Acids Res 2005; 33:2549-56. [PMID: 15870386 PMCID: PMC1088305 DOI: 10.1093/nar/gki550] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Forensic and ancient DNA (aDNA) extracts are mixtures of endogenous aDNA, existing in more or less damaged state, and contaminant DNA. To obtain the true aDNA sequence, it is not sufficient to generate a single direct sequence of the mixture, even where the authentic aDNA is the most abundant (e.g. 25% or more) in the component mixture. Only bacterial cloning can elucidate the components of this mixture. We calculate the number of clones that need to be sampled (for various mixture ratios) in order to be confident (at various levels of confidence) to have identified the major component. We demonstrate that to be >95% confident of identifying the most abundant sequence present at 70% in the ancient sample, 20 clones must be sampled. We make recommendations and offer a free-access web-based program, which constructs the most reliable consensus sequence from the user's input clone sequences and analyses the confidence limits for each nucleotide position and for the whole consensus sequence. Accepted authentication methods must be employed in order to assess the authenticity and endogeneity of the resulting consensus sequences (e.g. quantification and replication by another laboratory, blind testing, amelogenin sex versus morphological sex, the effective use of controls, etc.) and determine whether they are indeed aDNA.
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Affiliation(s)
- Mim A Bower
- Archaeogenetics Laboratory, McDonald Institute for Archaeological Research, University of Cambridge Downing Street, Cambridge CB2 3ER, UK.
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Abstract
Prior to European settlement indigenous Australians were hunter-gatherers who lived in geographically isolated small clan groups, also separated by elaborate totemic rules. Today they still reside in isolated communities throughout Australia but many have moved to the cities. They share a high incidence of a range of health problems including cardiovascular disease, renal disease and infectious diseases largely attributed to a change to a more sedentary lifestyle. This paper reviews the haematology of indigenous Australians, including blood count, frequency and causes of anaemia, inherited risk factors for thrombophilia, blood groups and the incidence and types of haematological malignancies. There are some significant genetic differences between indigenous and non-indigenous Australians particularly in the frequency of blood groups, factor V Leiden and prothrombin mutations and presence of -alpha3.7 kb thalassaemia. These findings may have practical therapeutic implications (e.g. HPA phenotype for transfusion therapy and pregnancy risk) and in predicting disease risk. Other differences are acquired, related to lifestyle and living conditions (e.g. eosinophilia secondary to parasitic infections; iron and folate deficiencies), and are largely preventable.
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Affiliation(s)
- W N Erber
- Department of Haematology, The Western Australian Centre for Pathology and Medical Research, Perth, W.A., Australia.
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Inagaki F, Okada H, Tsapin AI, Nealson KH. Microbial survival: the paleome: a sedimentary genetic record of past microbial communities. ASTROBIOLOGY 2005; 5:141-153. [PMID: 15815165 DOI: 10.1089/ast.2005.5.141] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Molecular genetic methods were used to analyze the remnants of microbial ecosystems contained within an ancient oceanic microbial habitat that was recovered from a continental drilled core of black shale approximately 100 million years in age. Bacterial ribosomal RNA genes were vertically amplified from the six different depths of a black shale core associated with a phosphate-rich stratum, defined as one of the mid-Cretaceous oceanic anoxic events (OAEs). Although the black shale core was recovered from a terrestrial coring effort, the recovered 16S rRNA gene sequences showed affinity to microbial communities previously seen in deep-sea sedimentary environments (i.e., the microbial assemblage was easily recognizable as a marine community). In particular, a number of 16S rRNA gene clones of oceanic sulfate-reducing bacteria within the delta-Proteobacteria predominated at the OAE layer. The recovered bacterial DNA signatures are consistent with the interpretation that the sequences are derived from the past microbial communities buried in either sea-bottom or subseafloor environments during the sedimentation process and, after ceasing growth, preserved until the present.
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Affiliation(s)
- Fumio Inagaki
- Subground Animalcule Retrieval (SUGAR) Project, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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