Evolutionary anthropology and genes: Investigating the genetics of human evolution from excavated skeletal remains

Gene

Volumn 528, Issue 1, 2013, Pages 27-32

  Anastasiou, Evilena ^a   Mitchell, Piers D ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Ancient DNA; Human evolution; Human remains; Paleogenetics

Indexed keywords

DNA;

DNA DETERMINATION; DNA SEQUENCE; EVOLUTION; GENETIC VARIABILITY; HUMAN; HUMAN GENETICS; HUMAN GENOME; MOLECULAR GENETICS; PHYLOGENY; PHYSICAL ANTHROPOLOGY; POPULATION GENETICS; PRIORITY JOURNAL; REVIEW; SKELETON;

ADNA; ANCIENT DNA; ASP; ASPARTIC ACID; BASE PAIR; BP; HUMAN EVOLUTION; HUMAN REMAINS; HVR; HYPERVARIABLE REGION; NEXT GENERATION SEQUENCING; NGS; PALEOGENETICS; PCR; POLYMERASE CHAIN REACTION; RESTRICTION LENGTH FRAGMENT POLYMORPHISM; RFLP;

ANIMALS; ANTHROPOLOGY; CELL NUCLEUS; DNA; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; FOSSILS; GENETICS, POPULATION; HOMINIDAE; HUMANS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 84882641250     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2013.06.011     Document Type: Review

References (86)

1. Allentoft M.E., et al. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc. Biol. Sci. 2012, 279(1748):4724-4733.
2. Anastasiou E., Mitchell P.D. Paleopathology and genes: Investigating the genetics of infectious diseases in excavated human skeletal remains and mummies from past populations. Gene 2013, 528:33-40.
3. Bramanti B., et al. Genetic discontinuity between local hunter-gatherers and central Europe's first farmers. Science 2009, 326(5949):137-140.
4. Briggs A.W., et al. Patterns of damage in genomic DNA sequences from a Neandertal. PNAS 2007, 104:14616-14621.
5. Brotherton P., et al. Novel high-resolution characterisation of ancient DNA reveals C>U-type base modification events as the sole cause of post mortem miscoding lesions. Nucleic Acids Res. 2007, 35:5717-5728.
6. Brown T.A., Brown K.A. Ancient DNA and the archaeologist. Antiq. 1992, 66:10-23.
7. Burbano H.A., et al. Targeted investigation of the Neandertal genome by array-based sequence capture. Science 2010, 328:723-725.
8. Burger J., Hummel S., Hermann B., Henke W. DNA preservation: a microsatellite-DNA study on ancient skeletal remains. Electrophoresis 1999, 20:1722-1728.
9. Cann R.L., Stoneking M., Wilson A.C. Mitochondrial DNA and human evolution. Nature 1987, 325:31-36.
10. Carlyle S.W., Parr R.L., Hayes M.G., Rourke D.H.O. The context of maternal lineages in the Greater Southwest. Am. J. Phys. Anthropol. 2000, 113:85-101.
11. Chelomina G. Ancient DNA. Russ. J. Gen. Chem. 2006, 42:219-233.
12. Cipollaro M., et al. Ancient DNA in human bone remains from Pompeii archaeological site. Biochem. Biophys. Res. Commun. 1998, 247:901-904.
13. Cipollaro M., Galderisi U., Di Bernardo G. Ancient DNA as a multidisciplinary experience. J. Cell. Physiol. 2005, 202:315-322.
14. Collins M.J., Penkman K.E.H., Rohland N., Shapiro B., Dobberstein R.C., Ritz-Timme S., Hofreiter M. Is amino acid racemization a useful tool for screening ancient DNA in bone?. Proc. Roy. Soc. B: Biol. Sci. 2009, 276:2971-2977.
15. Cooper A., Poinar H. Ancient DNA: do it right or not at all. Science 2000, 289:1139.
16. Crubézy E., Ludes B., Poveda J.-D., Clayton J., Crouau-Roy B., Montagnon D. Identification of Mycobacterium DNA in an Egyptian Pott's disease of 5400years old. C. R. Acad. Sci. III 1998, 321:941-951.
17. Dayton L. Modern human origins meeting. Tracing the road down under. Science 2003, 302:555.
18. Donoghue H.D., et al. Tuberculosis: from prehistory to Robert Koch, as revealed by ancient DNA. Lancet Infect. Dis. 2004, 4:584-592.
19. Donoghue H.D., Lee O.Y.-C., Minnikin D.E., Besra G.S., Taylor J.H., Spigelman M. Tuberculosis in Dr Granville's mummy: a molecular re-examination of the earliest known Egyptian mummy to be scientifically examined and given a medical diagnosis. Proc. Biol. Sci. 2010, 277:51-56.
20. Ermini L., et al. Complete mitochondrial genome sequence of the Tyrolean iceman. Curr. Biol. 2008, 18:1687-1693.
21. Filon D., Faerman M., Smith P., Oppenheim A. Sequence analysis reveals a beta-thalassaemia mutation in the DNA of skeletal remains from the archaeological site of Akhziv, Israel. Nat. Genet. 1995, 9:365-368.
22. Gamba C., Fernández E., López-Parra A.M., Arroyo-Pardo E. Statistical evaluation of pre-laboratory and laboratory factors that influence DNA recovery from archaeological material. Forensic Sci. Int. Genet. Suppl. Ser. 2011, 3:e109-e110.
23. Gilbert M.T.P., Bandelt H.-J., Hofreiter M., Barnes I. Assessing ancient DNA studies. Trends Ecol. Evol. 2005, 20:541-544.
24. Gilbert M.T.P., et al. Long-term survival of ancient DNA in Egypt: response to Zink and Nerlich (2003). Am. J. Phys. Anthropol. 2005, 128:110-114.
25. Gilbert M.T.P., et al. Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland. Science 2008, 320:1787-1789.
26. Ginolhac A., Rasmussen M., Gilbert M.T.P., Willerslev E., Orlando L. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics 2011, 27:2153-2155.
27. Green R.E., et al. Analysis of one million base pairs of Neanderthal DNA. Nature 2006, 444:330-336.
28. Green R.E., et al. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 2008, 134:416-426.
29. Green R.E., et al. A draft sequence of the Neandertal genome. Science 2010, 328:710-722.
30. Hagelberg E., Sykes B., Hedges R. Ancient bone DNA amplified. Nature 1989, 342:485.
31. Hagelberg E., Thomas M.G., Cook C.E., Sher A.V., Baryshnikov G.F., Lister A.M. DNA from ancient mammoth bones. Nature 1994, 370:333-334.
32. Handt O., Hoss M., Kirngs M., Paabo S. Ancient DNA: methodological challenges. Experientia 1994, 15:524-529.
33. Handt O., et al. Molecular genetic analyses of the Tyrolean ice man. Science 1994, 264:1175-1178.
34. Hawass Z., et al. Ancestry and pathology of King Tutankhamen's family. J. Am. Med. Assoc. 2010, 303:638-647.
35. Higuchi R.G., Bowman B., Freiberger M., Ryder O.A., Wilson A.C. DNA sequences from the Quagga, an extinct member of horse family. Nature 1984, 312:282-284.
36. Hofreiter M., Serre D., Poinar H.N., Kuch M., Paabo S. Ancient DNA. Nat. Rev. Genet. 2001, 2:353-359.
37. Hoss M., Paabo S., Vereschagin N.K. Mammoth DNA sequences. Nature 1994, 370:333-334.
38. Hoss M., Jaruga P., Zastawny T.H., Dizdaroglu M., Paabo S. DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res. 1996, 24:1304-1307.
39. Hummel S., Herrmann B. Y-chromosome specific DNA amplified in ancient human bone. Naturwissenschaften 1991, 78:266-267.
40. Kaestle F. Molecular analysis of ancient Native American DNA from Western Nevada. Nev. Hist. Soc. Q 1997, 40:85-96.
41. Keller A., et al. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat. Commun. 2012, 3:698.
42. Knapp M., Hofreiter M. Next Generation Sequencing of Ancient DNA: requirements, strategies and perspectives. Genes 2010, 1:227-243.
43. Krause J., et al. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 2010, 464:894-897.
44. Krings M., Ston A., Schmitz R.W., Krainitzki H., Stoneking M., Paabo S. Neandertal DNA sequences and the origins of modern humans. Cell 1997, 90:19-30.
45. Krings M., Geisert H., Schmitz R.W., Krainitzki H., Paabo S. DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen. Proc. Natl. Acad. Sci. U. S. A. 1999, 96:5581-5585.
46. Krings M., et al. A view of Neandertal genetic diversity. Nat. Genet. 2000, 26:144-146.
47. Lindahl T. Instability and decay of the primary structure of DNA. Nature 1993, 362:709-715.
48. Marchant J. Curse of the Pharaoh's DNA. Nature 2011, 472:404-406.
49. Margulies M., et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380.
50. Marota I., Rollo F. Molecular paleontology. Cell. Mol. Life Sci. 2002, 59:97-111.
51. Marota I., Basile C., Ubaldi M., Rollo F. DNA decay rate in papyri and human remains from Egyptian archaeological sites. Am. J. Phys. Anthropol. 2002, 117:310-318.
52. Merriwether D.A., Rothhammer F., Ferrel R.E. Genetic variation in the New World: ancient teeth, bone, and tissue as sources of DNA. Experientia 1994, 50:592-601.
53. Meyer M., et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 2012, 338(6104):222-226.
54. Miller W., et al. Sequencing the nuclear genome of the extinct woolly mammoth. Nature 2008, 456:387-390.
55. Mullis K.B., Faloona F.A. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods in Enzymology 1987, 335-350. Academic Press. W. Ray (Ed.).
56. Nerlich A.G., Haas C.J., Zink A., Szeimies U., Hagedorn H.G. Molecular evidence for tuberculosis in an ancient Egyptian mummy. Lancet 1997, 350:1404.
57. Noonan J.P., et al. Sequencing and analysis of Neanderthal genomic DNA. Science 2006, 314:1113-1118.
58. Oota H., Saitou N., Matsushita T., Ueda S. Molecular genetic analysis of remains of a 2,000year old human population in China and its relevance for the origins of the modern Japanese population. Am. J. Hum. Genet. 1999, 64:250-258.
59. O'Rourke D.H., Hayes M.G., Carlyle S.W. Ancient DNA studies in physical anthropology. Annu. Rev. Anthropol. 2000, 29:217-242.
60. Ovchinnikov I.V., Ovtchinnikova O.I., Druzina E.B., Buzhilova A.P., Makarov N.A. Molecular genetic sex determination of Medieval human remains from North Russia: comparison with archaeological and anthropological criteria. Anthropol. Anz. 1998, 56:7-15.
61. Ovchinnikov I.V., Gotherstrom A., Romanova G.P., Kharitonov V.M., Liden K., Goodwin W. Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 2000, 404:490-493.
62. Pääbo S. Molecular cloning of Ancient Egyptian mummy DNA. Nature 1985, 314:644-645.
63. Pääbo S. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc. Natl. Acad. Sci. U. S. A. 1989, 86:1939-1943.
64. Pääbo S., Wilson A.C. Miocene DNA sequences - a dream come true?. Curr. Biol. 1991, 1:45-46.
65. Pääbo S., Gifford J.A., Wilson A.C. Mitochondrial DNA sequences from a 7000-year old brain. Nucleic Acids Res. 1988, 16:9775-9787.
66. Pääbo S., et al. Genetic analyses from ancient DNA. Annu. Rev. Genet. 2004, 38:645-679.
67. Parr R.L., Carlyle S.W., Rourke D.H.O. Ancient DNA analysis of Fremont Amerindians of the Great Salt Lake Wetlands. Am. J. Phys. Anthropol. 1996, 99:507-518.
68. Pinhasi R., Higham T.F.G., Golovanova L.V., Doronichev V.B. Revised age of late Neanderthal occupation and the end of the Middle Paleolithic in the northern Caucasus. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:8611-8616.
69. Poinar H.N., Hoss M., Bada J.L., Paabo S. Amino acid racemization and the preservation of ancient DNA. Science 1996, 272:864-866.
70. Pusch C.M., Broghammer M., Blin N. Molecular phylogenetics employing modern and ancient DNA. J. Appl. Genet. 2003, 44:269-290.
71. Rasmussen M., et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 2010, 463:757-762.
72. Reich D., et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 2010, 468:1053-1060.
73. Reich D., et al. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am. J. Hum. Genet. 2011, 89:516-528.
74. Saiki R., et al. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 1985, 230:1350-1354.
75. Soares P., et al. The Archaeogenetics of Europe. Curr. Biol. 2010, 20:R174-R183.
76. Stone A.C., Stoneking M. mtDNA analysis of a prehistoric Oneota population: implications for the peopling of the World. Am. J. Hum. Genet. 1998, 62:1153-1170.
77. Stone A.C., Stoneking M. Analysis of ancient DNA from a prehistoric Amerindian cemetery. Philos. Trans. R. Soc. Lond. Ser. B 1999, 354:153-159.
78. Stoneking M., Krause J. Learning about human population history from ancient and modern genomes. Nature 2011, 12:603-614.
79. Stringer C.B., Andrews P. Genetic and fossil evidence for the origin of modern humans. Science 1988, 239:1263-1268.
80. Wallace D.C., Brown M.D., Lott M.T. Mitochondrial DNA variation in human evolution and disease. Gene 1999, 238:211-230.
81. Wang L., Oota H., Saitou N., Jin F., Matsushita T., Ueda S. Genetic structure of a 2,500-year-old human population in China and its spatiotemporal changes. Mol. Biol. Evol. 2000, 17:1396-1400.
82. Zierdt H., Hummel S., Herrmann B. Amplification of human short tandem repeats from Medieval teeth and bone samples. Hum. Biol. 1966, 68:185-199.
83. Zink A., Nerlich A.G. Molecular analyses of the "Pharaos:" Feasibility of molecular studies in ancient Egyptian material. Am. J. Phys. Anthropol. 2003, 121:109-111.
84. Zink A., Hass C.J., Reischl U., Szeimies U., Nerlich A.G. Molecular analysis of skeletal tuberculosis in an ancient Egyptian population. J. Med. Microbiol. 2001, 50:355-366.
85. Zink A., et al. Characterization of Mycobacterium tuberculosis complex DNAs from Egyptian mummies by spoligotyping. J. Clin. Microbiol. 2003, 41:539-567.
86. Zink A., Spigelman M., Schraut B., Greenblatt C.L., Nerlich A.G., Donoghue H.D. Leishmaniasis in ancient Egypt and Upper Nubia. Emerg. Infect. Dis. 2006, 12:1616.