A 400,000-year-old mitochondrial genome questions phylogenetic relationships amongst archaic hominins: Using the latest advances in ancient genomics, the mitochondrial genome sequence of a 400,000-year-old hominin has been deciphered Prospects & Overviews L. Orlando

BioEssays

Volumn 36, Issue 6, 2014, Pages 598-605

  Orlando, Ludovic ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Admixture; Ancient DNA; Genomics; Human evolution; Mitochondrial DNA; Next generation sequencing

Indexed keywords

DNA FRAGMENT; MITOCHONDRIAL DNA;

ANTHROPOLOGY; ARCHAIC HOMININ; ARTICLE; DENISOVAN; DNA DAMAGE; DNA SEQUENCE; FOSSIL HOMININ; GENETIC ANALYSIS; HAPLOTYPE; HOMO NEANDERTHALENSIS; HUMAN; HUMAN GENOME; MIDDLE PLEISTOCENE; MITOCHONDRIAL GENOME; PHYLOGENETIC TREE; PHYLOGENY; SEQUENCE ANALYSIS; ANIMAL; GENETICS; GENOMICS; HOMINID; NUCLEOTIDE SEQUENCE; PROCEDURES; TIME;

ANIMALS; BASE SEQUENCE; DNA DAMAGE; GENOME, MITOCHONDRIAL; GENOMICS; HOMINIDAE; PHYLOGENY; TIME FACTORS;

EID: 84900009860     PISSN: 02659247     EISSN: 15211878     Source Type: Journal    
DOI: 10.1002/bies.201400018     Document Type: Article

References (79)

1. Arsuaga JL, Martinez I, Garcia A, Carretero JM, et al. 1997. Sima de los Huesos (Sierra de Atapuerca, Spain). The site. J Hum Evol 33: 109-27.
2. Carbonell E, Bermudez de Castro JM, Pares JM, Perez-Gonzalez A, et al. 2008. The first hominin of Europe. Nature 452: 465-9.
3. Martinon-Torres M, Bermudez de Castro JM, Gomez-Robles A, Prado-Simon L, et al. 2012. Morphological description and comparison of the dental remains from Atapuerca-Sima de los Huesos site (Spain). J Hum Evol 62: 7-58.
4. Bischoff JL, Fitzpatrick JA, Leon L, Arsuaga JL, et al. 1997. Geology and preliminary dating of the hominid-bearing sedimentary fill of the Sima de los Huesos Chamber, Cueva Mayor of the Sierra de Atapuerca, Burgos, Spain. J Hum Evol 33: 129-54.
5. Arsuaga JL, Martinez I, Gracia A, Lorenzo C. 1997. The Sima de los Huesos crania (Sierra de Atapuerca, Spain). A comparative study. J Hum Evol 33: 219-81.
6. Rightmire GP. 2008. Homo in the Middle Pleistocene: hypodigms, variation, and species recognition. Evol Anthropol 17: 8-21.
7. Hublin JJ. 2009. Out of Africa: modern human origins special feature: the origin of Neandertals. Proc Natl Acad Sci USA 106: 16022-7.
8. Stringer C. 2012. The status of Homo heidelbergensis (Schoetensack 1908). Evol Anthropol 21: 101-7.
9. Rightmire GP. 2013. Homo erectus and Middle Pleistocene hominins: brain size, skull form, and species recognition. J Hum Evol 65: 223-52.
10. Meyer M, Fu Q, Aximu-Petri A, Glocke I, et al. 2014. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505: 403-6.
11. Reich D, Green RE, Kircher M, Krause J, et al. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468: 1053-60.
12. Meyer M, Kircher M, Gansauge MT, Li H, et al. 2012. A high-coverage genome sequence from an archaic Denisova individual. Science 338: 222-6.
13. Prufer K, Racimo F, Patterson N, Jay F, et al. 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505: 43-9.
14. Templeton AR. 2002. Out of Africa again and again. Nature 416: 45-51.
15. Templeton AR. 2013. Biological races in humans. Stud Hist Philos Biol Biomed Sci 44: 262-71.
16. Krause J, Fu A, Good JM, Viola B, et al. 2010. The complete mitochondrial DNA genome of an unknown hominin from sourthern Siberia. Nature 464: 894-7.
17. Nakhleh L. 2013. Computational approaches to species phylogeny inference and gene tree reconciliation. Trends Ecol Evol 28: 719-28.
18. Nielsen R, Beaumont M. 2009. Statistical inferences in phylogeography. Mol Ecol 18: 1034-47.
19. Hobolth A, Dutheil JY, Hawks J, Schierup MH, et al. 2011. Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Res 21: 349-56.
20. Lordkipanidze D, Ponce de Leon MS, Margvelashvili A, Rak Y, et al. 2013. A complete skull from Dmanisi, Georgia, and the evolutionary biology of early Homo. Science 342: 326-31.
21. Ackermann RR. 2005. Variation in Neandertals: a response to Harvati 2003. J Hum Evol 48: 643-6.
22. Ackermann RR. 2009. Morphological integration and the interpretation of fossil hominin diversity. Evol Biol 36: 149-56.
23. Orlando L, Ginolhac A, Zhang G, Froese D, et al. 2013. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499: 74-8.
24. Higuchi R, Bowman B, Freiberger M, Ryder OA, et al. 1984. DNA sequences from the quagga, an extinct member of the horse family. Nature 312: 282-4.
25. Paabo S, Higuchi RG, Wilson AC. 1989. Ancient DNA and the polymerase chain reaction. The emerging field of molecular archaeology. J Biol Chem 264: 9709-12.
26. Hagelberg E, Sykes B, Edges R. 1989. Ancient bone DNA amplified. Nature 342: 345.
27. DeSalle R, Gatesy J, Wheeler W, Grimaldi D. 1992. DNA sequences from a fossil termite in Oligo-Miocene amber and their phylogenetic implications. Science 257: 1933-6.
28. Woodward SE, Weyand NJ, Bunnel M. 1994. DNA sequence from Cretaceous period bone fragments. Science 266: 1229-32.
29. Hofreiter M, Serre D, Poinar HN, Kuch M, et al. 2001. Ancient DNA. Nat Rev Genet 2: 353-9.
30. Paabo S, Poinar H, Serre D, Jaenicke-Despres V, et al. 2004. Genetic analyses from ancient DNA. Annu Rev Genet 38: 645-79.
31. Willerslev E, Hansen AJ, Rønn R, Brand TB, et al. 2004. Long-term persistence of bacterial DNA. Curr Biol 14: R9-10.
32. Willerslev E, Cappellini E, Boomsma W, Nielsen R, et al. 2007. Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science 317: 111-4.
33. Hansen AJ, Mitchell DL, Wiuf C, Paniker L, et al. 2006. Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments. Genetics 173: 1175-9.
34. Krings M, Stone A, Schmitz RW, Krainitzki H, et al. 1997. Neandertal DNA sequences and the origin of modern humans. Cell 90: 19-30.
35. Krings M, Geisert H, Schmitz RW, Krainitski H, et al. 1999. DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen. Proc Natl Acad Sci USA 96: 5581-5.
36. Krings M, Capelli C, Tschentscher F, Geisert H, et al. 2000. A view of Neandertal genetic diversity. Nat Genet 26: 144-6.
37. Ovchinnikov IV, Gotherstrom A, Romanova GP, Kharitonov VM, et al. 2000. Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404: 490-3.
38. Serre D, Langaney A, Chech M, Teschler-Nicola M, et al. 2004. No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biol 2: E57.
39. Lalueza-Fox C, Sampietro ML, Caramelli D, Puder Y, et al. 2005. Neandertal evolutionary genetics: mitochondrial DNA data from the Iberian peninsula. Mol Biol Evol 22: 1077-81.
40. Caramelli D, Lalueza-Fox C, Condemi S, Longo L, et al. 2006. A highly divergent mtDNA sequence in a Neandertal individual from Italy. Curr Biol 16: R630-2.
41. Krause J, Orlando L, Serre D, Viola B, et al. 2007. Neandertals in central Asia and Siberia. Nature 449: 902-4.
42. Dalen L, Orlando L, Shapiro B, Brandstrom-Durling M, et al. 2012. Partial genetic turnover in Neandertals: continuity in the East and population replacement in the West. Mol Biol Evol 29: 1893-7.
43. Orlando L, Darlu P, Toussaint M, Bonjean D, et al. 2006. Revisiting Neandertal diversity with a 100, 000 year old mtDNA sequence. Curr Biol 16: R400-2.
44. Krause J, Lalueza-Fox C, Orlando L, Enard W, et al. 2007. The derived FOXP2 variant of modern humans was shared with Neandertals. Curr Biol 17: 1908-12.
45. Lalueza-Fox C, Rompler H, Caramelli D, Staubert C, et al. 2007. A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science 318: 1453-5.
46. Lalueza-Fox C, Gigli E, de la Rasilla M, Fortea J, et al. 2009. Bitter taste perception in Neanderthals through the analysis of the TAS2R38 gene. Biol Lett 5: 809-11.
47. Lari M, Rizzi E, Milani L, Corti G, et al. 2010. The microcephalin ancestral allele in a Neanderthal individual. PLoS One 5: e10648.
48. Valdiosera C, Garcia N, Dalen L, Smith C, et al. 2006. Typing single polymorphic nucleotides in mitochondrial DNA as a way to access Middle Pleistocene DNA. Biol Lett 2: 601-3.
49. Noonan JP, Coop G, Kudaravalli S, Smith D, et al. 2006. Sequencing and analysis of Neanderthal genomic DNA. Science 314: 1113-8.
50. Poinar HN, Schwarz C, Qi J, Shapiro N, et al. 2006. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311: 392-4.
51. Green RE, Krause J, Ptak SE, Briggs AW, et al. 2006. Analysis of one million base pairs of Neanderthal DNA. Nature 444: 330-6.
52. Green RE, Krause J, Briggs AW, Maricic T, et al. 2010. A draft sequence of the Neanderthal genome. Science 328: 710-22.
53. Miller W, Drautz DI, Ratan A, Pusey B, et al. 2008. Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456: 387-90.
54. Rasmussen M, Li Y, Lindgreen S, Pedersen JS, et al. 2010. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463: 757-62.
55. Rasmussen M, Guo X, Wang Y, Lohmueller KE, et al. 2011. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334: 94-8.
56. Rasmussen M, Anzick SL, Waters MR, Skoglund P, et al. 2014. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506: 225-9.
57. Keller A, Graefen A, Ball M, Matzas M, et al. 2012. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat Commun 3: 698.
58. Raghavan M, Skoglund P, Graf KE, Metspalu M, et al. 2014. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505: 87-91.
59. Olalde I, Allentoft ME, Sanchez-Quinto F, Santpere G, et al. 2014. Derived immune and ancestral pigmentation alleles in a 7, 000-year-old Mesolithic European. Nature, 507: 225-8.
60. Rohland N, Hofreiter M. 2007. Ancient DNA extraction from bones and teeth. Nat Protoc 2: 1756-62.
61. Dabney J, Knapp M, Glock I, Gansauge MT, et al. 2013. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc Natl Acad Sci USA 110: 15578-63.
62. Gansauge MT, Meyer M. 2012. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat Protoc 8: 737-48.
63. Orlando L, Ginolhac A, Raghavan M, Vilstrup J, et al. 2011. True single-molecule DNA sequencing of a Pleistocene horse bone. Genome Res 21: 1705-19.
64. Ginolhac A, Vilstrup J, Stenderup J, Rasmussen M, et al. 2012. Improving the performance of true single molecule sequencing for ancient DNA. BMC Genomics 13: 177.
65. Jonsson H, Ginolhac A, Schubert M, Johnson PL, et al. 2013. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage patterns. Bioinformatics 29: 1682-4.
66. Briggs AW, Stenzel U, Johnson PL, Green RE, et al. 2007. Patterns of damage in genomic DNA sequences from a Neanderthal. Proc Natl Acad Sci USA 104: 14616-21.
67. Shapiro B, Ho SY, Drummond AJ, Suchard MA, et al. 2011. A Bayesian phylogenetic method to estimate unknown sequence ages. Mol Biol Evol 28: 879-87.
68. Fu Q, Meyer M, Gao X, Stenzel U, et al. 2013. DNA analysis of an early modern human from Tianyuan cave, China. Proc Natl Acad Sci USA 110: 2223-7.
69. Burbano HA, Hodges E, Green RE, Briggs AW, et al. 2010. Targeted investigation of the Neandertal genome by array-based sequenced capture. Science 328: 723-5.
70. Gnirke A, Melnikov A, Maguire J, Rogov P, et al. 2010. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27: 182-9.
71. Carpenter ML, Buenrostro JD, Valdiosera C, Schroeder H, et al. 2013. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am J Hum Genet 93: 852-64.
72. Enk J, Devault A, Kuch M, Murgha Y, et al. 2014. Ancient whole genome enrichment using baits built from modern DNA. Mol Biol Evol, in press, doi: 10.1093/molbev/msu074
73. Skoglund P, Northoff BH, Shunkov MV, Derevianko AP, et al. 2014. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc Natl Acad Sci USA 111: 2229-34.
74. Schubert M, Ginolhac A, Lindgreen S, Thompson JF, et al. 2012. Improving ancient DNA read mapping against modern reference genomes. BMC Genomics 13: 178.
75. Millar CD, Lambert DM. 2013. Ancient DNA: towards a million-year-old genome. Nature 499: 34-45.
76. Smith CI, Chamberlain AT, Riley MS, Stringer CB, et al. 2003. The thermal history of human fossils and the likelihood of successful DNA amplification. J Hum Evol 45: 203-17.
77. Morwood MJ, Soejono RP, Roberts RG, Sutikna T, et al. 2004. Archaeology and age of a new hominin from Flores in eastern Indonesia. Nature 431: 1087-91.
78. Arensburg B, Tillier AM, Vandermeersch B, Duday H, et al. 1989. A Middle Palaeolithic human hyoid bone. Nature 338: 758-60.
79. Stringer CB, Grun R, Schwarcz HP, Goldberg P. 1989. ESR dates for the hominid burial site of Es Skhul in Israel. Nature 338: 756-8.