1
|
Seeber PA, Batke L, Dvornikov Y, Schmidt A, Wang Y, Stoof-Leichsenring K, Moon K, Vohr SH, Shapiro B, Epp LS. Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes. eLife 2024; 12:RP89992. [PMID: 38488477 PMCID: PMC10942779 DOI: 10.7554/elife.89992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Abstract
Ancient environmental DNA (aeDNA) from lake sediments has yielded remarkable insights for the reconstruction of past ecosystems, including suggestions of late survival of extinct species. However, translocation and lateral inflow of DNA in sediments can potentially distort the stratigraphic signal of the DNA. Using three different approaches on two short lake sediment cores of the Yamal peninsula, West Siberia, with ages spanning only the past hundreds of years, we detect DNA and identified mitochondrial genomes of multiple mammoth and woolly rhinoceros individuals-both species that have been extinct for thousands of years on the mainland. The occurrence of clearly identifiable aeDNA of extinct Pleistocene megafauna (e.g. >400 K reads in one core) throughout these two short subsurface cores, along with specificities of sedimentology and dating, confirm that processes acting on regional scales, such as extensive permafrost thawing, can influence the aeDNA record and should be accounted for in aeDNA paleoecology.
Collapse
Affiliation(s)
| | - Laura Batke
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Yury Dvornikov
- Agroengineering Department/Department of Landscape Design and Sustainable Ecosystems, Agrarian and Technological Institute, RUDN University, Moscow, Russian Federation
- Laboratory of Carbon Monitoring in Terrestrial Ecosystems, Institute of Physicochemical and Biological Problems of Soil Science of the Russian Academy of Sciences, Pushchino, Russian Federation
| | | | - Yi Wang
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Kathleen Stoof-Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Potsdam, Germany
| | - Katie Moon
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, United States
| | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, United States
| | - Laura S Epp
- Department of Biology, University of Konstanz, Konstanz, Germany
| |
Collapse
|
2
|
DeSantis LRG, Feranec RS, Antón M, Lundelius EL. Dietary ecology of the scimitar-toothed cat Homotherium serum. Curr Biol 2021; 31:2674-2681.e3. [PMID: 33862006 DOI: 10.1016/j.cub.2021.03.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/19/2021] [Accepted: 03/17/2021] [Indexed: 10/21/2022]
Abstract
The scimitar-toothed cat Homotherium was one of the most cosmopolitan cats of the Pleistocene, present throughout Eurasia, Africa, and the Americas until at least ~28 thousand years ago.1-3 Friesenhahn Cave (Bexar County, Texas) contains some of the best-preserved specimens of Homotherium serum alongside an abundance of juvenile mammoths, leading some to argue that H. serum preferentially hunted juvenile mammoths.1,4 Dietary data of Homotherium are rare, with their ecology inferred from morphological, taphonomic, and genetic data.1,3-10 Here, we use a multi-proxy approach to clarify the dietary ecology of H. serum as compared to extinct and extant cats and their relatives. Dental microwear texture analysis (DMTA) reveals that H. serum consumed soft and tough foods, similar to the extant cheetah, which actively avoids bone,11,12 but in stark contrast to extant lions and hyenas, which are observed to engage in durophagy (i.e., bone processing).11-14 DMTA data are consistent with taphonomic evidence of bone defleshing and the absence of bone-crunching behavior in H. serum. Stable carbon isotope values of H. serum indicate a clear preference for C4 grazers including juvenile mammoths, in agreement with taphonomic evidence suggestive of a "Homotherium den"1,4 and morphological data indicative of a relatively cursorial lifestyle.6-8 Notably, the inferred diet of H. serum contrasts with the extinct dirk-tooth sabertooth cat Smilodon fatalis, which preferred forest/woodland prey and engaged in bone processing.15-19Homotherium serum exhibited a novel combination of morphological adaptations for acquiring open-country prey, consuming their soft and tough flesh-including the tough flesh of juvenile mammoths. VIDEO ABSTRACT.
Collapse
Affiliation(s)
- Larisa R G DeSantis
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235-1634, USA; Department of Earth and Environmental Sciences, Vanderbilt University, Nashville, TN 37235-1805, USA; Department of Rancho La Brea, La Brea Tar Pits and Museum, Los Angeles, CA 90036, USA.
| | - Robert S Feranec
- Research and Collections, New York State Museum, Albany, NY 12230, USA
| | - Mauricio Antón
- Department of Paleobiology, Museo Nacional de Ciencias Naturales, CSIC, C. Jose Gutiérrez Abascal 2, Madrid 28006, Spain
| | - Ernest L Lundelius
- Vertebrate Paleontology Laboratory, Jackson Museum of Earth History, University of Texas, Austin, TX 78712, USA
| |
Collapse
|
3
|
Fry E, Kim SK, Chigurapti S, Mika KM, Ratan A, Dammermann A, Mitchell BJ, Miller W, Lynch VJ. Functional Architecture of Deleterious Genetic Variants in the Genome of a Wrangel Island Mammoth. Genome Biol Evol 2021; 12:48-58. [PMID: 32031213 PMCID: PMC7094797 DOI: 10.1093/gbe/evz279] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2019] [Indexed: 12/21/2022] Open
Abstract
Woolly mammoths were among the most abundant cold-adapted species during the Pleistocene. Their once-large populations went extinct in two waves, an end-Pleistocene extinction of continental populations followed by the mid-Holocene extinction of relict populations on St. Paul Island ∼5,600 years ago and Wrangel Island ∼4,000 years ago. Wrangel Island mammoths experienced an episode of rapid demographic decline coincident with their isolation, leading to a small population, reduced genetic diversity, and the fixation of putatively deleterious alleles, but the functional consequences of these processes are unclear. Here, we show that a Wrangel Island mammoth genome had many putative deleterious mutations that are predicted to cause diverse behavioral and developmental defects. Resurrection and functional characterization of several genes from the Wrangel Island mammoth carrying putatively deleterious substitutions identified both loss and gain of function mutations in genes associated with developmental defects (HYLS1), oligozoospermia and reduced male fertility (NKD1), diabetes (NEUROG3), and the ability to detect floral scents (OR5A1). These data suggest that at least one Wrangel Island mammoth may have suffered adverse consequences from reduced population size and isolation.
Collapse
Affiliation(s)
- Erin Fry
- Department of Human Genetics, The University of Chicago
| | - Sun K Kim
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University
| | | | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia
| | | | - Brian J Mitchell
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University
| | - Webb Miller
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University
| | - Vincent J Lynch
- Department of Biological Sciences, University at Buffalo, SUNY
| |
Collapse
|
4
|
Petrova PG, Egorova EE, Egorova VE, Grigor'ev SE, Turkebaeva LR. The results of the microscopic and hematological studies of liquid body malolyakhovsky mammoth. Wiad Lek 2019; 72:1961-1965. [PMID: 31982023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
INTRODUCTION Mammoth trunk excavation of on the island Malyi Lyakhov in the Laptev Sea became a historical discovery for the Republic Sakha (Yakutia) in 2013. According to paleontologists, the age of this find is 43 thousand years. The main features of the Malolyakhovsky mammoth are preservation of the soft tissues and a detection of the dark-brown liquid substance, which was found along the bottom of the mammoth’s trunk. THE AIM Firstly, to reveal and study preservation of cell elements of biomaterial received at excavation of 2013. Secondly, to find out and study preservation of cell elements taken from a blood vessel of a front extremity, during preparation of the Malolyakhovsky mammoth trunk which was carried out in March, 2014. MATERIAL AND METHODS 1. A dark-brown liquid substance, which flowed out at excavation; 2. biomaterials from a blood vessel taken during preparation of the mammoth’s trunk became the materials of this researches. In order to study morphological properties of gained biomaterials, we used the following methods: microscopic smear research, hematological analyses with use of technology of peroxidase cytochemical reaction, a technique of two-dimensional laser light, and cyanide-free hemoglobin estimation. RESULTS Under microscopic examination, the cell elements similar to elements of blood of mammals, were found: the monocytes, neutrophils, lymphocytes containing nuclear inclusions. The comparative analysis showed that the cells found in a dark-brown liquid substance received at excavation and in smear of the biomaterial taken from a blood vessel, have the identical morphological structure of cell elements. Studying of primary biomaterial on the hematological analyzer confirmed the maintenance of the same cells (lymphocytes, monocytes and granulocytes), and availability of hemoglobin which value was 22 g/l. CONCLUSIONS The unique preservation of the soft tissues, which were found in permafrost, allowed to find and describe morphological properties of cell elements of a fossil animal for the first time.
Collapse
Affiliation(s)
- Palmira G Petrova
- North-Eastern Federal University Named After M.K. Ammosov, Medical Institute, Yakutsk, Russia
| | - Eya E Egorova
- North-Eastern Federal University Named After M.K. Ammosov, Medical Institute, Yakutsk, Russia
| | - Victoriya E Egorova
- Educational And Scientific Clinical Diagnostic Laboratory Of Clinic Of Mi Nefu, Yakutsk, Russia
| | - Semen E Grigor'ev
- North-Eastern Federal University Named After M.K. Ammosov, Medical Institute, Yakutsk, Russia
| | - Lena R Turkebaeva
- North-Eastern Federal University Named After M.K. Ammosov, Medical Institute, Yakutsk, Russia
| |
Collapse
|
5
|
Palkopoulou E, Lipson M, Mallick S, Nielsen S, Rohland N, Baleka S, Karpinski E, Ivancevic AM, To TH, Kortschak RD, Raison JM, Qu Z, Chin TJ, Alt KW, Claesson S, Dalén L, MacPhee RDE, Meller H, Roca AL, Ryder OA, Heiman D, Young S, Breen M, Williams C, Aken BL, Ruffier M, Karlsson E, Johnson J, Di Palma F, Alfoldi J, Adelson DL, Mailund T, Munch K, Lindblad-Toh K, Hofreiter M, Poinar H, Reich D. A comprehensive genomic history of extinct and living elephants. Proc Natl Acad Sci U S A 2018; 115:E2566-E2574. [PMID: 29483247 PMCID: PMC5856550 DOI: 10.1073/pnas.1720554115] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Elephantids are the world's most iconic megafaunal family, yet there is no comprehensive genomic assessment of their relationships. We report a total of 14 genomes, including 2 from the American mastodon, which is an extinct elephantid relative, and 12 spanning all three extant and three extinct elephantid species including an ∼120,000-y-old straight-tusked elephant, a Columbian mammoth, and woolly mammoths. Earlier genetic studies modeled elephantid evolution via simple bifurcating trees, but here we show that interspecies hybridization has been a recurrent feature of elephantid evolution. We found that the genetic makeup of the straight-tusked elephant, previously placed as a sister group to African forest elephants based on lower coverage data, in fact comprises three major components. Most of the straight-tusked elephant's ancestry derives from a lineage related to the ancestor of African elephants while its remaining ancestry consists of a large contribution from a lineage related to forest elephants and another related to mammoths. Columbian and woolly mammoths also showed evidence of interbreeding, likely following a latitudinal cline across North America. While hybridization events have shaped elephantid history in profound ways, isolation also appears to have played an important role. Our data reveal nearly complete isolation between the ancestors of the African forest and savanna elephants for ∼500,000 y, providing compelling justification for the conservation of forest and savanna elephants as separate species.
Collapse
Affiliation(s)
- Eleftheria Palkopoulou
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Svend Nielsen
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus, Denmark
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Sina Baleka
- Unit of General Zoology-Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Mathematics and Life Sciences, University of Potsdam, 14476 Potsdam, Germany
| | - Emil Karpinski
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Biochemistry, McMaster University, Hamilton, ON L8S 4L8, Canada
- The Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Atma M Ivancevic
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia
| | - Thu-Hien To
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia
| | - R Daniel Kortschak
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia
| | - Joy M Raison
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia
| | - Zhipeng Qu
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia
| | - Tat-Jun Chin
- School of Computer Science, The University of Adelaide, 5005 SA, Australia
| | - Kurt W Alt
- Center of Natural and Cultural Human History, Danube Private University, A-3500 Krems, Austria
- Department of Biomedical Engineering, University Hospital Basel, University of Basel, CH-4123 Basel, Switzerland
- Integrative Prehistory and Archaeological Science, University of Basel, CH-4055 Basel, Switzerland
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405 Stockholm, Sweden
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, New York, NY 10024
| | - Harald Meller
- State Office for Heritage Management and Archaeology, 06114 Halle (Saale), Germany
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo, Escondido, CA 92027
| | - David Heiman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Sarah Young
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607
| | - Christina Williams
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607
| | - Bronwen L Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, CB10 1SD Cambridge, United Kingdom
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, CB10 1SD Cambridge, United Kingdom
| | - Elinor Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | | | | | | | - David L Adelson
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus, Denmark
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus, Denmark
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Michael Hofreiter
- Unit of General Zoology-Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Mathematics and Life Sciences, University of Potsdam, 14476 Potsdam, Germany
| | - Hendrik Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Biochemistry, McMaster University, Hamilton, ON L8S 4L8, Canada
- The Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
| |
Collapse
|
6
|
Graham RW, Belmecheri S, Choy K, Culleton BJ, Davies LJ, Froese D, Heintzman PD, Hritz C, Kapp JD, Newsom LA, Rawcliffe R, Saulnier-Talbot É, Shapiro B, Wang Y, Williams JW, Wooller MJ. Timing and causes of mid-Holocene mammoth extinction on St. Paul Island, Alaska. Proc Natl Acad Sci U S A 2016; 113:9310-4. [PMID: 27482085 DOI: 10.1073/pnas.1604903113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Relict woolly mammoth (Mammuthus primigenius) populations survived on several small Beringian islands for thousands of years after mainland populations went extinct. Here we present multiproxy paleoenvironmental records to investigate the timing, causes, and consequences of mammoth disappearance from St. Paul Island, Alaska. Five independent indicators of extinction show that mammoths survived on St. Paul until 5,600 ± 100 y ago. Vegetation composition remained stable during the extinction window, and there is no evidence of human presence on the island before 1787 CE, suggesting that these factors were not extinction drivers. Instead, the extinction coincided with declining freshwater resources and drier climates between 7,850 and 5,600 y ago, as inferred from sedimentary magnetic susceptibility, oxygen isotopes, and diatom and cladoceran assemblages in a sediment core from a freshwater lake on the island, and stable nitrogen isotopes from mammoth remains. Contrary to other extinction models for the St. Paul mammoth population, this evidence indicates that this mammoth population died out because of the synergistic effects of shrinking island area and freshwater scarcity caused by rising sea levels and regional climate change. Degradation of water quality by intensified mammoth activity around the lake likely exacerbated the situation. The St. Paul mammoth demise is now one of the best-dated prehistoric extinctions, highlighting freshwater limitation as an overlooked extinction driver and underscoring the vulnerability of small island populations to environmental change, even in the absence of human influence.
Collapse
|
7
|
Boeskorov GG, Potapova OR, Mashchenko EN, Protopopov AV, Kuznetsova TV, Agenbroad L, Tikhonov AN. Preliminary analyses of the frozen mummies of mammoth (Mammuthus primigenius), bison (Bison priscus) and horse (Equus sp.) from the Yana-Indigirka Lowland, Yakutia, Russia. Integr Zool 2015; 9:471-80. [PMID: 24148659 DOI: 10.1111/1749-4877.12079] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The frozen bodies of a young woolly mammoth (Mammuthus primigenius), a wild horse (Equus sp.) and a steppe bison (Bison priscus) were recently found in the northern Yakutia (northeastern Siberia). All specimens have preserved bones, skin and soft tissues. Whereas the woolly mammoth and the Pleistocene horse were represented by partial frozen bodies, the steppe bison body was recovered in an absolutely complete state. All specimens were found frozen in the permafrost, with some of the tissues mummified. The wild horse and steppe bison are of Holocene age, and the mammoth is of Late Pleistocene age.
Collapse
Affiliation(s)
- Gennady G Boeskorov
- Diamond and Precious Metal Geology Institute, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | | | | | | | | | | | | |
Collapse
|
8
|
Kato H, Anzai M, Mitani T, Morita M, Nishiyama Y, Nakao A, Kondo K, Lazarev PA, Ohtani T, Shibata Y, Iritani A. Recovery of cell nuclei from 15,000 years old mammoth tissues and its injection into mouse enucleated matured oocytes. Proc Jpn Acad Ser B Phys Biol Sci 2009; 85:240-247. [PMID: 19644224 PMCID: PMC3561847 DOI: 10.2183/pjab.85.240] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 05/22/2009] [Indexed: 05/28/2023]
Abstract
Here, we report the recovery of cell nuclei from 14,000-15,000 years old mammoth tissues and the injection of those nuclei into mouse enucleated matured oocytes by somatic cell nuclear transfer (SCNT). From both skin and muscle tissues, cell nucleus-like structures were successfully recovered. Those nuclei were then injected into enucleated oocytes and more than half of the oocytes were able to survive. Injected nuclei were not taken apart and remained its nuclear structure. Those oocytes did not show disappearance of nuclear membrane or premature chromosome condensation (PCC) at 1 hour after injection and did not form pronuclear-like structures at 7 hours after injection. As half of the oocytes injected with nuclei derived from frozen-thawed mouse bone marrow cells were able to form pronuclear-like structures, it might be possible to promote the cell cycle of nuclei from ancient animal tissues by suitable pre-treatment in SCNT. This is the first report of SCNT with nuclei derived from mammoth tissues.
Collapse
Affiliation(s)
- Hiromi Kato
- Institute of Advanced Technology, Kinki University, Wakayama, Japan.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Stiller M, Green RE, Ronan M, Simons JF, Du L, He W, Egholm M, Rothberg JM, Keates SG, Keats SG, Ovodov ND, Antipina EE, Baryshnikov GF, Kuzmin YV, Vasilevski AA, Wuenschell GE, Termini J, Hofreiter M, Jaenicke-Després V, Pääbo S. Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. Proc Natl Acad Sci U S A 2006; 103:13578-84. [PMID: 16938852 PMCID: PMC1564221 DOI: 10.1073/pnas.0605327103] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whereas evolutionary inferences derived from present-day DNA sequences are by necessity indirect, ancient DNA sequences provide a direct view of past genetic variants. However, base lesions that accumulate in DNA over time may cause nucleotide misincorporations when ancient DNA sequences are replicated. By repeated amplifications of mitochondrial DNA sequences from a large number of ancient wolf remains, we show that C/G-to-T/A transitions are the predominant type of such misincorporations. Using a massively parallel sequencing method that allows large numbers of single DNA strands to be sequenced, we show that modifications of C, as well as to a lesser extent of G, residues cause such misincorporations. Experiments where oligonucleotides containing modified bases are used as templates in amplification reactions suggest that both of these types of misincorporations can be caused by deamination of the template bases. New DNA sequencing methods in conjunction with knowledge of misincorporation processes have now, in principle, opened the way for the determination of complete genomes from organisms that became extinct during and after the last glaciation.
Collapse
Affiliation(s)
- M Stiller
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|