Archaic admixture in the human genome

Current Opinion in Genetics and Development

Volumn 16, Issue 6, 2006, Pages 606-610

  Wall, Jeffrey D ^a   Hammer, Michael F ^b  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS DNA; MITOCHONDRIAL DNA;

AFRICA; ARCHEOLOGY; DEMOGRAPHY; DNA SEQUENCE; EVOLUTION; FOSSIL; GENE POOL; GENETIC POLYMORPHISM; HUMAN GENOME; POPULATION GENETICS; PRIORITY JOURNAL; REVIEW;

ANIMALS; ANTHROPOLOGY, PHYSICAL; EVOLUTION, MOLECULAR; GENOME, HUMAN; HOMINIDAE; HUMANS;

EID: 33750951625     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2006.09.006     Document Type: Review

References (47)

1. Kaessmann H., Wiebe V., Weiss G., and Paabo S. Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nat Genet 27 (2001) 155-156
2. Fischer A., Pollack J., Thalmann O., Nickel B., and Paabo S. Demographic history and genetic differentiation in apes. Curr Biol 16 (2006) 1133-1138
3. Yu N., Jensen-Seaman M.I., Chemnick L., Ryder O., and Li W.H. Nucleotide diversity in gorillas. Genetics 166 (2004) 1375-1383
4. Gagneux P. The genus Pan: population genetics of an endangered outgroup. Trends Genet 18 (2002) 327-330
5. Aiello L.C., and Collard M. Palaeoanthropology our newest oldest ancestor?. Nature 410 (2001) 526-527
6. Haile-Selassie Y. Late Miocene hominids from the Middle Awash, Ethiopia. Nature 412 (2001) 178-181
7. Leakey M.G., Spoor F., Brown F.H., Gathogo P.N., Kiarie C., Leakey L.N., and McDougall I. New hominin genus from eastern Africa shows diverse middle Pliocene lineages. Nature 410 (2001) 433-440
8. Brunet M., Guy F., Pilbeam D., Mackaye H.T., Likius A., Ahounta D., Beauvilain A., Blondel C., Bocherens H., Boisserie J.R., et al. A new hominid from the Upper Miocene of Chad, central Africa. Nature 418 (2002) 145-151
9. Carroll S.B. Genetics and the making of Homo sapiens. Nature 422 (2003) 849-857
10. Holliday T.W. Species concepts, reticulation, and human evolution. Curr Anthropol 44 (2003) 653-673
11. McDougall I., Brown F.H., and Fleagle J.G. Stratigraphic placement and age of modern humans from Kibish, Ethiopia. Nature 433 (2005) 733-736. The authors use potassium-argon dating to infer the ages of two hominin skulls from comparable stratigraphic levels in Omo, Kibish (Ethiopia). They find that earlier efforts to date these skulls in 1967 underestimated their ages by ∼30 thousand years. Their inferred age of ∼195 ± 5 thousand years makes one of these two skulls, Omo I, the earliest well-dated anatomically modern human described to date. Interestingly, the other skull, Omo II, is distinguished from Omo I by several morphological features that make it appear more primitive, suggesting that more than one taxa of hominins coexisted in this region.
12. Coppa A., Grun R., Stringer C., Eggins S., and Vargiu R. Newly recognized Pleistocene human teeth from Tabun Cave, Israel. J Hum Evol 49 (2005) 301-315
13. Grun R., Stringer C., McDermott F., Nathan R., Porat N., Robertson S., Taylor L., Mortimer G., Eggins S., and McCulloch M. U-series and ESR analyses of bones and teeth relating to the human burials from Skhul. J Hum Evol 49 (2005) 316-334
14. Grun R., Maroto J., Eggins S., Stringer C., Robertson S., Taylor L., Mortimer G., and McCulloch M. ESR and U-series analyses of enamel and dentine fragments of the Banyoles mandible. J Hum Evol 50 (2006) 347-358
15. Stringer C., Pälike H., Andel T., Huntley B., Valdes P., and Allen J. Climatic stress and the extinction of the Neanderthals. In: van Andel T., and Davies W. (Eds). Neanderthals and Modern Humans in the European Landscape during the Last Glaciation (2003), McDonald Institute 233-240
16. Swisher III C.C., Rink W.J., Anton S.C., Schwarcz H.P., Curtis G.H., and Suprijo A. Widiasmoro: Latest Homo erectus of Java: potential contemporaneity with Homo sapiens in southeast Asia. Science 274 (1996) 1870-1874
17. Morwood M.J., Soejono R.P., Roberts R.G., Sutikna T., Turney C.S., Westaway K.E., Rink W.J., Zhao J.X., van den Bergh G.D., Due R.A., et al. Archaeology and age of a new hominin from Flores in eastern Indonesia. Nature 431 (2004) 1087-1091. The authors describe excavations from a cave known as Liang Bua on Flores Island in eastern Indonesia. They find evidence for a population of tiny hominins, with sufficiently distinctive anatomical features to be designated as a new species, Homo floresiensis. Dating by a series of methods indicates that H. floresiensis existed from >38 kya until at least 18 kya. This makes this species a contemporary of H. sapiens in East Asia. The morphological traits of H. floresiensis are consistent with its decent from H. erectus. Stone artefacts and other fossils found at the same level in the cave suggest that H. floresiensis survived by hunting a fellow dwarf endemic mammalian species, Stegodon.
18. Stringer C.B., and Andrews P. Genetic and fossil evidence for the origin of modern humans. Science 158 (1988) 1263-1268
19. Wolpoff M.H. Paleoanthropology (1999), McGraw-Hill, Boston
20. Brauer G. The evolution of modern humans: A comparison of the African and non-African evidence. In: Mellars P., and Stringer C. (Eds). The Human Revolution: Behavioural and Biological Perspectives on the Origins of Modern Humans (1989), Edinburgh University Press 123-154
21. Smith F. The role of continuity in modern human origins. In: Bräuer G., and Smith F. (Eds). Continuity or replacement? Controversies in Homo sapiens evolution (1992), Balkema 145-156
22. Eswaran V. A diffusion wave out of Africa. Curr Anthropol 43 (2002) 749-774
23. Templeton A. Out of Africa again and again. Nature 416 (2002) 45-51
24. Hublin J.J., Spoor F., Braun M., Zonneveld F., and Condemi S. A late Neanderthal associated with Upper Palaeolithic artefacts. Nature 381 (1996) 224-226
25. Stringer C. Human evolution: Out of Ethiopia. Nature 423 (2003) 692-693
26. Duarte C., Mauricio J., Pettitt P.B., Souto P., Trinkaus E., van der Plicht H., and Zilhao J. The early Upper Paleolithic human skeleton from the Abrigo do Lagar Velho (Portugal) and modern human emergence in Iberia. Proc Natl Acad Sci USA 96 (1999) 7604-7609
27. Krings M., Stone A., Schmitz R.W., Krainitzki H., Stoneking M., and Paabo S. Neandertal DNA sequences and the origin of modern humans. Cell 90 (1997) 19-30
28. Krings M., Capelli C., Tschentscher F., Geisert H., Meyer S., von Haeseler A., Grossschmidt K., Possnert G., Paunovic M., and Paabo S. A view of Neandertal genetic diversity. Nat Genet 26 (2000) 144-146
29. Ovchinnikov I.V., Gotherstrom A., Romanova G.P., Kharitonov V.M., Liden K., and Goodwin W. Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404 (2000) 490-493
30. Serre D., Langaney A., Chech M., Teschler-Nicola M., Paunovic M., Mennecier P., Hofreiter M., Possnert G., and Paabo S. No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biol 2 (2004) E57. This study examines mtDNA sequences from a wide range of Neanderthal and modern human fossils. The authors definitively find that there was no genetic contribution of Neanderthals to the current mtDNA pool, and they rule out the possibility of a large Neanderthal contribution to the current nuclear DNA pool.
31. Orlando L., Darlu P., Toussaint M., Bonjean D., Otte M., and Hanni C. Revisiting Neandertal diversity with a 100, 000 year old mtDNA sequence. Curr Biol 16 (2006) R400-R402
32. Caramelli D., Lalueza-Fox C., Vernesi C., Lari M., Casoli A., Mallegni F., Chiarelli B., Dupanloup I., Bertranpetit J., Barbujani G., et al. Evidence for a genetic discontinuity between Neandertals and 24, 000-year-old anatomically modern Europeans. Proc Natl Acad Sci USA 100 (2003) 6593-6597
33. Adcock G.J., Dennis E.S., Easteal S., Huttley G.A., Jermiin L.S., Peacock W.J., and Thorne A. Mitochondrial DNA sequences in ancient Australians: implications for modern human origins. Proc Natl Acad Sci USA 98 (2001) 537-542
34. Currat M., and Excoffier L. Modern humans did not admix with Neanderthals during their range expansion into Europe. PLoS Biol 2 (2004) e421
35. Nordborg M. On the probability of Neanderthal ancestry. Am J Hum Genet 63 (1998) 1237-1240
36. Barreiro L.B., Patin E., Neyrolles O., Cann H.M., Gicquel B., and Quintana-Murci L. The heritage of pathogen pressures and ancient demography in the human innate-immunity CD209/CD209L region. Am J Hum Genet 77 (2005) 869-886
37. Garrigan D., Mobasher Z., Severson T., Wilder J.A., and Hammer M.F. Evidence for archaic Asian ancestry on the human X chromosome. Mol Biol Evol 22 (2005) 189-192
38. Hayakawa T., Aki I., Varki A., Satta Y., and Takahata N. Fixation of the human-specific CMP-N-acetylneuraminic acid hydroxylase pseudogene and implications of haplotype diversity for human evolution. Genetics 172 (2006) 1139-1146
39. Harris E.E., and Hey J. X chromosome evidence for ancient human histories. Proc Natl Acad Sci USA 96 (1999) 3320-3324
40. Wall J.D. Detecting ancient admixture in humans using sequence polymorphism data. Genetics 154 (2000) 1271-1279
41. Garrigan D., Mobasher Z., Kingan S.B., Wilder J.A., and Hammer M.F. Deep haplotype divergence and long-range linkage disequilibrium at Xp21.1 provide evidence that humans descend from a structured ancestral population. Genetics 170 (2005) 1849-1856. This study describes a global re-sequencing survey of an X-linked non-coding locus. The Xp21.1 genealogy is characterized by two lineages that are estimated to have diverged from one another nearly two million years ago. All the nucleotide mutations that separate the two lineages are in perfect LD, whereas mutations within one lineage of haplotypes show extensive evidence for historical recombination. It is shown that this high level of nucleotide divergence and LD statistically rejects the hypothesis that humans descend from a single, randomly mating ancestral population.
42. Schaffner S.F., Foo C., Gabriel S., Reich D., Daly M.J., and Altshuler D. Calibrating a coalescent simulation of human genome sequence variation. Genome Res 15 (2005) 1576-1583
43. Voight B.F., Adams A.M., Frisse L.A., Qian Y., Hudson R.R., and Di Rienzo A. Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc Natl Acad Sci USA 102 (2005) 18508-18513. This study introduces new methods for analyzing models of human demography and applies them to estimate recent changes in population size in different human populations.
44. Plagnol V., and Wall J.D. Possible ancestral structure in human populations. PLoS Genet 2 (2006) e105. The authors develop new methodologies for estimating modern human demographic parameters and for testing whether there has been ancient admixture. They find that archaic human groups such as Neanderthals probably contributed to at least 5% of the modern European gene pool.
45. Noonan J.P., Hofreiter M., Smith D., Priest J.R., Rohland N., Rabeder G., Krause J., Detter J.C., Paabo S., and Rubin E.M. Genomic sequencing of Pleistocene cave bears. Science 309 (2005) 597-599
46. Poinar H.N., Schwarz C., Qi J., Shapiro B., Macphee R.D., Buigues B., Tikhonov A., Huson D.H., Tomsho L.P., Auch A., et al. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311 (2006) 392-394. This study describes the first large-scale sequencing study of nuclear DNA obtained from the fossil remains of an extinct species. The authors were able to recover 13 million base pairs of mammoth DNA from a single sample, with a low rate of environmental contaminants.
47. Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, Alessi J, Chen F, Platt D, Paabo S et al.: Sequencing and analysis of Neanderthal genomic DNA. Science 2006, in press. For the first time, the authors sequence ∼66 kb of Neanderthal autosomal DNA from a metagenomic library. They identify a total of 34 human-specific substitutions in 37 636 human-, Neanderthal- and chimpanzee-aligned positions. The Neanderthal and human reference sequence is inferred to have diverged ∼770 kya, with an estimated human-Neanderthal ancestral population split of ∼400 kya.