Genomic Data Reveal a Complex Making of Humans
In the last few years, two paradigms underlying human evolution have crumbled. Modern humans have not totally replaced previous hominins without any admixture, and the expected signatures of adaptations to new environments are surprisingly lacking at the genomic level. Here we review current evidence about archaic admixture and lack of strong selective sweeps in humans. We underline the need to properly model differential admixture in various populations to correctly reconstruct past demography. We also stress the importance of taking into account the spatial dimension of human evolution, which proceeded by a series of range expansions that could have promoted both the introgression of archaic genes and background selection.
Vyšlo v časopise:
Genomic Data Reveal a Complex Making of Humans. PLoS Genet 8(7): e32767. doi:10.1371/journal.pgen.1002837
Kategorie:
Review
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1002837
Souhrn
In the last few years, two paradigms underlying human evolution have crumbled. Modern humans have not totally replaced previous hominins without any admixture, and the expected signatures of adaptations to new environments are surprisingly lacking at the genomic level. Here we review current evidence about archaic admixture and lack of strong selective sweeps in humans. We underline the need to properly model differential admixture in various populations to correctly reconstruct past demography. We also stress the importance of taking into account the spatial dimension of human evolution, which proceeded by a series of range expansions that could have promoted both the introgression of archaic genes and background selection.
Zdroje
1. PickrellJKCoopGNovembreJKudaravalliSLiJZ 2009 Signals of recent positive selection in a worldwide sample of human populations. Genome Res 19 826 837
2. HernandezRDKelleyJLElyashivEMeltonSCAutonA 2011 Classic selective sweeps were rare in recent human evolution. Science 331 920 924
3. CoopGPickrellJKNovembreJKudaravalliSLiJ 2009 The role of geography in human adaptation. PLoS Genet 5 e1000500 doi:10.1371/journal.pgen.1000500
4. KayserMBrauerSStonekingM 2003 A genome scan to detect candidate regions influenced by local natural selection in human populations. Mol Biol Evol 20 893 900
5. StorzJFPayseurBANachmanMW 2004 Genome scans of DNA variability in humans reveal evidence for selective sweeps outside of Africa. Mol Biol Evol 21 1800 1811
6. VoightBFKudaravalliSWenXPritchardJK 2006 A map of recent positive selection in the human genome. PLoS Biol 4 e72 doi:10.1371/journal.pbio.0040072
7. WilliamsonSHHubiszMJClarkAGPayseurBABustamanteCD 2007 Localizing recent adaptive evolution in the human genome. PLoS Genet 3 e90 doi:10.1371/journal.pgen.0030090
8. LohmuellerKEAlbrechtsenALiYKimSYKorneliussenT 2011 Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genet 7 e1002326 doi:10.1371/journal.pgen.1002326
9. PritchardJKPickrellJKCoopG 2010 The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation. Curr Biol 20 R208 R215
10. EswaranVHarpendingHRogersAR 2005 Genomics refutes an exclusively African origin of humans. J Hum Evol 49 1 18
11. WallJDLohmuellerKEPlagnolV 2009 Detecting ancient admixture and estimating demographic parameters in multiple human populations. Mol Biol Evol 26 1823 1827
12. LabudaDZietkiewiczEYotovaV 2000 Archaic lineages in the history of modern humans. Genetics 156 799 808
13. GreenREKrauseJBriggsAWMaricicTStenzelU 2010 A draft sequence of the Neandertal genome. Science 328 710 722
14. DurandEYPattersonNReichDSlatkinM 2011 Testing for ancient admixture between closely related populations. Mol Biol Evol 28 2239 2252
15. ReichDGreenREKircherMKrauseJPattersonN 2010 Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468 1053 1060
16. ReichDPattersonNKircherMDelfinFNandineniMR 2011 Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am J Hum Genet
17. SkoglundPJakobssonM 2011 Archaic human ancestry in East Asia. Proc Natl Acad Sci U S A 108 18301 18306
18. HammerMFWoernerAEMendezFLWatkinsJCWallJD 2011 Genetic evidence for archaic admixture in Africa. Proc Natl Acad Sci U S A 108 15123 15128
19. Destro-BisolGDonatiFCoiaVBoschiIVerginelliF 2004 Variation of female and male lineages in sub-Saharan populations: the importance of sociocultural factors. Mol Biol Evol 21 1673 1682
20. BatiniCFerriGDestro-BisolGBrisighelliFLuiselliD 2011 Signatures of the preagricultural peopling processes in sub-Saharan Africa as revealed by the phylogeography of early Y chromosome lineages. Mol Biol Evol 28 2603 2613
21. PatinELavalGBarreiroLBSalasASeminoO 2009 Inferring the demographic history of African farmers and pygmy hunter-gatherers using a multilocus resequencing data set. PLoS Genet 5 e1000448 doi:10.1371/journal.pgen.1000448
22. WhiteTDAsfawBDeGustaDGilbertHRichardsGD 2003 Pleistocene Homo sapiens from Middle Awash, Ethiopia. Nature 423 742 747
23. McDougallIBrownFHFleagleJG 2005 Stratigraphic placement and age of modern humans from Kibish, Ethiopia. Nature 433 733 736
24. RasmussenMGuoXWangYLohmuellerKERasmussenS 2011 An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334 94 98
25. CurratMExcoffierL 2011 Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression. Proc Natl Acad Sci U S A 108 15129 15134
26. LiangMNielsenR 2011 Q&A: who is H. sapiens really, and how do we know? BMC Biol 9 20
27. MendezFLWatkinsJCHammerMF 2012 Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations. Mol Biol Evol 29 1513 1520
28. Abi-RachedLJobinMJKulkarniSMcWhinnieADalvaK 2011 The shaping of modern human immune systems by multiregional admixture with archaic humans. Science 334 89 94
29. YotovaVLefebvreJFMoreauCGbehaEHovhannesyanK 2011 An X-linked haplotype of Neandertal origin is present among all non-African populations. Mol Biol Evol 28 1957 1962
30. HawksJCochranGHarpendingHCLahnBT 2008 A genetic legacy from archaic Homo. Trends Genet 24 19 23
31. HobolthADutheilJYHawksJSchierupMHMailundT 2011 Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Res 21 349 356
32. TakahataNNeiM 1990 Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci. Genetics 124 967 978
33. GutenkunstRNHernandezRDWilliamsonSHBustamanteCD 2009 Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet 5 e1000695 doi:10.1371/journal.pgen.1000695
34. BlumMGJakobssonM 2011 Deep divergences of human gene trees and models of human origins. Mol Biol Evol 28 889 898
35. BlumMGHeyerEFrancoisOAusterlitzF 2006 Matrilineal fertility inheritance detected in hunter-gatherer populations using the imbalance of gene genealogies. PLoS Genet 2 e122 doi:10.1371/journal.pgen.0020122
36. BiswasSAkeyJM 2006 Genomic insights into positive selection. Trends Genet 22 437 446
37. BarreiroLBLavalGQuachHPatinEQuintana-MurciL 2008 Natural selection has driven population differentiation in modern humans. Nat Genet 40 340 345
38. DurbinRMAbecasisGRAltshulerDLAutonABrooksLD 2010 A map of human genome variation from population-scale sequencing. Nature 467 1061 1073
39. KeinanAReichD 2010 Human population differentiation is strongly correlated with local recombination rate. PLoS Genet 6 e1000886 doi:10.1371/journal.pgen.1000886
40. CaiJJMacphersonJMSellaGPetrovDA 2009 Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet 5 e1000336 doi:10.1371/journal.pgen.1000336
41. McVickerGGordonDDavisCGreenP 2009 Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet 5 e1000471 doi:10.1371/journal.pgen.1000471
42. CharlesworthB 2012 The effects of deleterious mutations on evolution at linked sites. Genetics 190 5 22
43. StephanW 2010 Genetic hitchhiking versus background selection: the controversy and its implications. Philos Trans R Soc Lond B Biol Sci 365 1245 1253
44. CharlesworthBMorganMTCharlesworthD 1993 The effect of deleterious mutations on neutral molecular variation. Genetics 134 1289 1303
45. ZengKCharlesworthB 2011 The joint effects of background selection and genetic recombination on local gene genealogies. Genetics 189 251 266
46. HuXSHeF 2005 Background selection and population differentiation. J Theor Biol 235 207 219
47. CharlesworthDCharlesworthBMorganMT 1995 The pattern of neutral molecular variation under the background selection model. Genetics 141 1619 1632
48. HudsonRRKaplanNL 1995 The coalescent process and background selection. Philos Trans R Soc Lond B Biol Sci 349 19 23
49. CrisciJLWongAGoodJMJensenJD 2011 On characterizing adaptive events unique to modern humans. Genome Biol Evol 3 791 798
50. PritchardJKDi RienzoA 2010 Adaptation - not by sweeps alone. Nat Rev Genet 11 665 667
51. HoferTFollMExcoffierL 2012 Evolutionary forces shaping genomic islands of population differentiation in humans. BMC Genomics 13 107
52. ExcoffierLFollMPetitRJ 2009 Genetic consequences of range expansions. Annual Review in Ecology, Evolution, and Systematics 40 481 501
53. HermissonJPenningsPS 2005 Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169 2335 2352
54. PenningsPSHermissonJ 2006 Soft sweeps II–molecular population genetics of adaptation from recurrent mutation or migration. Mol Biol Evol 23 1076 1084
55. RalphPCoopG 2010 Parallel adaptation: one or many waves of advance of an advantageous allele? Genetics 186 647 668
56. KlopfsteinSCurratMExcoffierL 2006 The fate of mutations surfing on the wave of a range expansion. Mol Biol Evol 23 482 490
57. FabreVCondemiSDegioanniAHerrscherE 2011 Neanderthals versus modern humans: evidence for resource competition from isotopic modelling. Int J Evol Biol 2011 689315
58. BanksWEd'ErricoFPetersonATKageyamaMSimaA 2008 Neanderthal extinction by competitive exclusion. PLoS ONE 3 e3972 doi:10.1371/journal.pone.0003972
59. MellarsPFrenchJC 2011 Tenfold population increase in Western Europe at the Neandertal-to-modern human transition. Science 333 623 627
60. CurratMRuediMPetitRJExcoffierL 2008 The hidden side of invasions: massive introgression by local genes. Evolution 62 1908 1920
61. CurratMExcoffierL 2004 Modern humans did not admix with Neanderthals during their range expansion into Europe. PLoS Biol 2 e421 doi:10.1371/journal.pbio.0020421
62. CurratMExcoffierL 2005 The effect of the Neolithic expansion on European molecular diversity. Proc Biol Sci 272 679 688
63. PugachIMatveyevRWollsteinAKayserMStonekingM 2011 Dating the age of admixture via wavelet transform analysis of genome-wide data. Genome Biol 12 R19
64. TravisJMMunkemullerTBurtonOJBestADythamC 2007 Deleterious mutations can surf to high densities on the wave front of an expanding population. Mol Biol Evol 24 2334 2343
65. HallatschekONelsonDR 2010 Life at the front of an expanding population. Evolution 64 193 206
66. MoreauCBhererCVezinaHJompheMLabudaD 2011 Deep human genealogies reveal a selective advantage to be on an expanding wave front. Science 334 1148 1150
67. LohmuellerKEIndapARSchmidtSBoykoARHernandezRD 2008 Proportionally more deleterious genetic variation in European than in African populations. Nature 451 994 997
68. AdamsAMHudsonRR 2004 Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms. Genetics 168 1699 1712
69. NielsenRPaulJSAlbrechtsenASongYS 2011 Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12 443 451
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2012 Číslo 7
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- Guidelines for Genome-Wide Association Studies
- The Role of Rice HEI10 in the Formation of Meiotic Crossovers
- Identification of Chromatin-Associated Regulators of MSL Complex Targeting in Dosage Compensation
- GWAS Identifies Novel Susceptibility Loci on 6p21.32 and 21q21.3 for Hepatocellular Carcinoma in Chronic Hepatitis B Virus Carriers