Human evolution

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Human evolution

  1. 1. Human evolution
  2. 2. Human evolution
  3. 3. Human evolutionAncestors, relatives & major transitions
  4. 4. Human evolutionAncestors, relatives & major transitions Recent insights from genomics
  5. 5. Human evolutionAncestors, relatives & major transitions Recent insights from genomics What about today?
  6. 6. Benton (2005) Fig 10.47
  7. 7. Relatives and recent ancestorsPLATYRRHINI CATARRHINI CERCOPITHECOIDS HOMINOIDS HYLOBATIDS HOMINIDSSPIDER MONKEY MACAQUE SIAMANG GIBBON ORANGUTAN GORILLA HUMAN CHIMPANZEE Potential 6 MYA common PROCONSUL SIVAPITHECUS OURANOPITHECUS DRYOPITHECUS 14 MYA 9 MYA ancestors 19 MYA 16 MYA (Miocene) FAMILY TREE of hominoids encompasses the lesser apes (siamangs and 25 MYA gibbons), great apes (orangutans, gorillas and chimpanzees), and humans. Most Miocene apes were evolutionary dead ends. But researchers have identified a handful of them as candidate ancestors of living apes and humans. Proconsul, a primitive Miocene ape, is thought to have been the last common ancestor of the living hominoids; Sivapithecus, an early great ape, is widely regarded as an orangutan forebear; and either 40 MILLION YEARS AGO Dryopithecus or Ouranopithecus may have given rise to African apes and humans. simple chewing surfaces — a feeding ap- suspensory locomotion, especially in east Asia. Most phylogenetic analyses paratus well suited to a diet of soft, ripe the elbow joint, which was fully extend- concur that it is from Sivapithecus that © Scientific American
  8. 8. Relatives and recent ancestorsPLATYRRHINI CATARRHINI CERCOPITHECOIDS HOMINOIDS HYLOBATIDS HOMINIDSSPIDER MONKEY MACAQUE SIAMANG GIBBON ORANGUTAN GORILLA HUMAN CHIMPANZEE Potential 6 MYA common PROCONSUL SIVAPITHECUS OURANOPITHECUS DRYOPITHECUS 14 MYA 9 MYA ancestors 19 MYA 16 MYA (Miocene) FAMILY TREE of hominoids encompasses the lesser apes (siamangs and 25 MYA gibbons), great apes (orangutans, gorillas and chimpanzees), and humans. Most Miocene apes were evolutionary dead ends. But researchers have identified a handful of them as candidate ancestors of living apes and humans. Proconsul, a primitive Miocene ape, is thought to have been the last common ancestor of the living hominoids; Sivapithecus, an early great ape, is widely regarded as an orangutan forebear; and either 40 MILLION YEARS AGO Dryopithecus or Ouranopithecus may have given rise to African apes and humans. simple chewing surfaces — a feeding ap- suspensory locomotion, especially in east Asia. Most phylogenetic analyses paratus well suited to a diet of soft, ripe the elbow joint, which was fully extend- concur that it is from Sivapithecus that © Scientific American
  9. 9. Proconsul
  10. 10. Rift valley
  11. 11. Relatives and recent ancestorsPLATYRRHINI CATARRHINI CERCOPITHECOIDS HOMINOIDS HYLOBATIDS HOMINIDSSPIDER MONKEY MACAQUE SIAMANG GIBBON ORANGUTAN GORILLA HUMAN CHIMPANZEE Potential 6 MYA common PROCONSUL SIVAPITHECUS OURANOPITHECUS DRYOPITHECUS 14 MYA 9 MYA ancestors 19 MYA 16 MYA (Miocene) FAMILY TREE of hominoids encompasses the lesser apes (siamangs and 25 MYA gibbons), great apes (orangutans, gorillas and chimpanzees), and humans. Most Miocene apes were evolutionary dead ends. But researchers have identified a handful of them as candidate ancestors of living apes and humans. Proconsul, a primitive Miocene ape, is thought to have been the last common ancestor of the living hominoids; Sivapithecus, an early great ape, is widely regarded as an orangutan forebear; and either 40 MILLION YEARS AGO Dryopithecus or Ouranopithecus may have given rise to African apes and humans. simple chewing surfaces — a feeding ap- suspensory locomotion, especially in east Asia. Most phylogenetic analyses paratus well suited to a diet of soft, ripe the elbow joint, which was fully extend- concur that it is from Sivapithecus that © Scientific American
  12. 12. Relatives and recent ancestorsPLATYRRHINI CATARRHINI CERCOPITHECOIDS HOMINOIDS HYLOBATIDS HOMINIDSSPIDER MONKEY MACAQUE SIAMANG GIBBON ORANGUTAN GORILLA HUMAN CHIMPANZEE Potential 6 MYA common PROCONSUL SIVAPITHECUS OURANOPITHECUS DRYOPITHECUS 14 MYA 9 MYA ancestors 19 MYA 16 MYA (Miocene) FAMILY TREE of hominoids encompasses the lesser apes (siamangs and 25 MYA gibbons), great apes (orangutans, gorillas and chimpanzees), and humans. Most Miocene apes were evolutionary dead ends. But researchers have identified a handful of them as candidate ancestors of living apes and humans. Proconsul, a primitive Miocene ape, is thought to have been the last common ancestor of the living hominoids; Sivapithecus, an early great ape, is widely regarded as an orangutan forebear; and either 40 MILLION YEARS AGO Dryopithecus or Ouranopithecus may have given rise to African apes and humans. simple chewing surfaces — a feeding ap- suspensory locomotion, especially in east Asia. Most phylogenetic analyses paratus well suited to a diet of soft, ripe the elbow joint, which was fully extend- concur that it is from Sivapithecus that © Scientific American
  13. 13. Major transitions in human evolution
  14. 14. Major transitions in human evolution In which order?
  15. 15. Major transitions in human evolution• Bipedalism (down from the trees) In which order?
  16. 16. Major transitions in human evolution• Bipedalism (down from the trees)• Increased brain size In which order?
  17. 17. Major transitions in human evolution• Bipedalism (down from the trees)• Increased brain size In which order?• Use of simple stone tools
  18. 18. Major transitions in human evolution• Bipedalism (down from the trees)• Increased brain size In which order?• Use of simple stone tools• Fire
  19. 19. Major transitions in human evolution• Bipedalism (down from the trees)• Increased brain size In which order?• Use of simple stone tools• Fire• Sophisticated tools (stone, bone...)
  20. 20. Major transitions in human evolution• Bipedalism (down from the trees)• Increased brain size In which order?• Use of simple stone tools• Fire• Sophisticated tools (stone, bone...)• Language, culture, agriculture...
  21. 21. Million! years! Glacial cycles! Homo! P. robustus! Arctic icecap! Australopithecus africanus/! A. afarensis! Ardipithecus ramidus! Antarctic icecap! Orrorin tugenensis! Cold! Warm! Climate!WP! Mid Miocene! Late Miocene! Climate! cooling! Habitat! fragmentation!
  22. 22. Why bipedalism? Mid Miocene! Late Miocene! Climate! cooling! Habitat! fragmentation! Million! years! Glacial cycles! Homo! P. robustus! Arctic icecap! Australopithecus africanus/! A. afarensis! Ardipithecus ramidus! Antarctic icecap! Orrorin tugenensis! Cold! Warm! Climate!
  23. 23. Why bipedalism? Mid Miocene! Late Miocene!• Energy efficient locomotion Climate! cooling! (for distant food sources) Habitat! fragmentation! Million! years! Glacial cycles! Homo! P. robustus! Arctic icecap! Australopithecus africanus/! A. afarensis! Ardipithecus ramidus! Antarctic icecap! Orrorin tugenensis! Cold! Warm! Climate!
  24. 24. Why bipedalism? Mid Miocene! Late Miocene!• Energy efficient locomotion Climate! cooling! (for distant food sources) Habitat!• Less exposure to sun? fragmentation! Million! years! Glacial cycles! Homo! P. robustus! Arctic icecap! Australopithecus africanus/! A. afarensis! Ardipithecus ramidus! Antarctic icecap! Orrorin tugenensis! Cold! Warm! Climate!
  25. 25. Why bipedalism? Mid Miocene! Late Miocene!• Energy efficient locomotion Climate! cooling! (for distant food sources) Habitat!• Less exposure to sun? fragmentation!• Free the hands? Million! years! Glacial cycles! Homo! P. robustus! Arctic icecap! Australopithecus africanus/! A. afarensis! Ardipithecus ramidus! Antarctic icecap! Orrorin tugenensis! Cold! Warm! Climate!
  26. 26. Why bipedalism? Mid Miocene! Late Miocene!• Energy efficient locomotion Climate! cooling! (for distant food sources) Habitat!• Less exposure to sun? fragmentation!• Free the hands? Million! years! Glacial cycles! Homo!• Seeingfarther: Finding food & avoiding predators? P. robustus! Arctic icecap! Australopithecus africanus/! A. afarensis! Ardipithecus ramidus! Antarctic icecap! Orrorin tugenensis! Cold! Warm! Climate!
  27. 27. Why bipedalism? Mid Miocene! Late Miocene!• Energy efficient locomotion Climate! cooling! (for distant food sources) Habitat!• Less exposure to sun? fragmentation!• Free the hands? Million! years! Glacial cycles! Homo!• Seeingfarther: Finding food & avoiding predators? P. robustus! Arctic icecap! Australopithecus africanus/! A. afarensis!• Sexual or anti-predator Ardipithecus ramidus! Antarctic icecap! displays? Orrorin tugenensis! Cold! Warm! Climate!
  28. 28. Running
  29. 29. Running• sweating for thermoregulation.
  30. 30. Running• sweating for thermoregulation.• arched foot + achilles tendon
  31. 31. Running• sweating for thermoregulation.• arched foot + achilles tendon• head stabilization
  32. 32. Running• sweating for thermoregulation.• arched foot + achilles tendon• head stabilization• early Homo?
  33. 33. Running• sweating for thermoregulation.• arched foot + achilles tendon• head stabilization• early Homo?• first: improved scavenging.
  34. 34. Running• sweating for thermoregulation.• arched foot + achilles tendon• head stabilization• early Homo?• first: improved scavenging.• then persistence hunting
  35. 35. Relatives and recent ancestorsPLATYRRHINI CATARRHINI CERCOPITHECOIDS HOMINOIDS HYLOBATIDS HOMINIDSSPIDER MONKEY MACAQUE SIAMANG GIBBON ORANGUTAN GORILLA HUMAN CHIMPANZEE Potential 6 MYA common PROCONSUL SIVAPITHECUS OURANOPITHECUS DRYOPITHECUS 14 MYA 9 MYA ancestors 19 MYA 16 MYA (Miocene) FAMILY TREE of hominoids encompasses the lesser apes (siamangs and 25 MYA gibbons), great apes (orangutans, gorillas and chimpanzees), and humans. Most Miocene apes were evolutionary dead ends. But researchers have identified a handful of them as candidate ancestors of living apes and humans. Proconsul, a primitive Miocene ape, is thought to have been the last common ancestor of the living hominoids; Sivapithecus, an early great ape, is widely regarded as an orangutan forebear; and either 40 MILLION YEARS AGO Dryopithecus or Ouranopithecus may have given rise to African apes and humans. simple chewing surfaces — a feeding ap- suspensory locomotion, especially in east Asia. Most phylogenetic analyses paratus well suited to a diet of soft, ripe the elbow joint, which was fully extend- concur that it is from Sivapithecus that © Scientific American
  36. 36. Most lineageswent extinct
  37. 37. Proconsulidae Most lineages went extinct
  38. 38. Proconsulidae Most lineages went extinct
  39. 39. AustralopithecinesProconsulidae Most lineages went extinct
  40. 40. H. erectus AustralopithecinesProconsulidae Most lineages went extinct
  41. 41. H. sapiens H. erectus AustralopithecinesProconsulidae Most lineages went extinct
  42. 42. H. neanderthalensis H. sapiens H. erectus AustralopithecinesProconsulidae Most lineages went extinct
  43. 43. AustralopithecinesWikipedia
  44. 44. Taung child1924 Australopithecus afarensis 2.5 mya
  45. 45. Lucy - Australopithecus afarensis 1978 3.2 mya
  46. 46. Australopithecines 30° 20° 10° 0° 10° 20° 30° 40° 50° 60°30° 30° Brain size: 35% of modern human20° 20° A. Bahrelghazali10° A. Afarensis 10° A. Gahri P. Aethiopicus P. Boisei A. Anamensis0° 0°10° 10°20° P. Robustus (Crassidens) A. Africanus30° 0 (km) 3 000 30°Wikipedia 0 (mi) Projection de Lambert azimutale équivalente 2 000 30° 20° 10° 0° 10° 20° 30° 40° 50° 60°
  47. 47. Evidence for bipedalism in Australopithecines
  48. 48. Evidence for bipedalism in Australopithecines
  49. 49. Evidence for bipedalism in Australopithecines
  50. 50. Evidence for bipedalism in Australopithecines• Pelvis short & broad (like humans), not long & narrow (like gorilla)
  51. 51. Evidence for bipedalism in Australopithecines• Pelvis short & broad (like humans), not long & narrow (like gorilla)• Hip & walking muscles arranged like in a bipedal organism
  52. 52. Evidence for bipedalism in Australopithecines• Pelvis short & broad (like humans), not long & narrow (like gorilla)• Hip & walking muscles arranged like in a bipedal organism• Femur angled as in humans, not straight as in chimps
  53. 53. Evidence for bipedalism in Australopithecines• Pelvis short & broad (like humans), not long & narrow (like gorilla)• Hip & walking muscles arranged like in a bipedal organism• Femur angled as in humans, not straight as in chimps• Feet
  54. 54. Fossilized tracks atLaetoli (Tanzania) Footprints preserved in volcanic ash from: 3 hominids (Australopithecus afarensis) Numerous other mammals
  55. 55. Fossilized tracks atLaetoli (Tanzania) Footprints preserved in volcanic ash from: 3 hominids (Australopithecus afarensis) Numerous other mammals
  56. 56. Tool use?
  57. 57. Tool use?• generally: only simple tools (similarly to current non-human great apes).
  58. 58. Tool use?• generally: only simple tools (similarly to current non-human great apes).• butAustralopithecus garhi (2.5 mya) may have made stone tools.
  59. 59. Summary: Australopithecines• Major group of early bipedal hominids (4mya to 1 mya)• Small brains• Only in Africa• Many forms/species
  60. 60. H. neanderthalensis H. sapiens H. erectus AustralopithecinesProconsulidae Most lineages went extinct
  61. 61. Homo
  62. 62. Homo habilis
  63. 63. Tool useChimps and other animalsmay use objects as tools. H. sapiens! H. habilis! Australopithecine!
  64. 64. Tool use H. habilis made toolsChimps and other animalsmay use objects as tools. H. sapiens! H. habilis! Australopithecine!
  65. 65. Tool use H. habilis made toolsChimps and other animalsmay use objects as tools. Cutting H. sapiens! H. habilis! Australopithecine!
  66. 66. Tool use H. habilis made toolsChimps and other animalsmay use objects as tools. Cutting Scraping H. sapiens! H. habilis! Australopithecine!
  67. 67. Stages of humanevolution are defined bythe style andsophistication of stonetools….e.g.:•Oldowan (2.5-1.5 mya)•Achuelian (1.5-0.2 mya)
  68. 68. Oldowan toolsHammerstone Choppers Scraper Flakes
  69. 69. Brain sizes increase
  70. 70. Out of Africa - H. erectus
  71. 71. Homo erectus (Java, 1893)
  72. 72. Acheulian toolsHandaxes! Cleaver! Handaxe Pick! Scraper! Trimming flakes!
  73. 73. Nariokotome/Turkana boy H. erectus Found 1984 in Kenya. From1.5mya
  74. 74. H. erectus lifestyle• …language?
  75. 75. H. erectus lifestyle• Stone tools (Acheulian) • …language?
  76. 76. H. erectus lifestyle• Stone tools (Acheulian)• Fire • …language?
  77. 77. H. erectus lifestyle• Stone tools (Acheulian)• Fire• Sociality • …language?
  78. 78. H. erectus lifestyle• Stone tools (Acheulian)• Fire• Sociality• Hunting • …language?
  79. 79. Homo floresiensis “The Hobbit”
  80. 80. Homo floresiensis “The Hobbit” H. florensis vs. H. sapiens skull
  81. 81. Homo floresiensis “The Hobbit” H. florensis vs. H. sapiens skull
  82. 82. Nature (2004) vol. 431, 1043-1044
  83. 83. H. neanderthalensis H. sapiens H. erectus AustralopithecinesProconsulidae Most lineages went extinct
  84. 84.
  85. 85. Neanderthal 600,000-30,000 years ago
  86. 86. Burial ritual?
  87. 87. Neanderthals - Summary• Neanderthals were morphologically and genetically distinct from early H. sapiens• disappearedafter H. sapiens arrived - possibly because they were culturally less advanced.
  88. 88. H. neanderthalensis H. sapiens H. erectus AustralopithecinesProconsulidae Most lineages went extinct
  89. 89. H. sapiens out of Africa
  90. 90. H. sapiens out of Africa• 50,000 years ago: fully “modern” with language, music etc.
  91. 91. H. sapiens out of Africa• 50,000 years ago: fully “modern” with language, music etc.• Began migrating out of Africa 70,000 years ago
  92. 92. H. sapiens out of Africa• 50,000 years ago: fully “modern” with language, music etc.• Began migrating out of Africa 70,000 years ago• Simultaneous decline of other Homo species (competition or hybridization?)
  93. 93. Burial ritual in early H. sapiens• At Sungir, Russia, around 28,000 years ago• A 60 year old buried with an elaborate collection of beads, necklaces and bracelets
  94. 94. Examples of early H. sapiens tools
  95. 95. Lascaux
  96. 96. Recent insights from genomics
  97. 97. RESEARCH ARTICLE changed parts of their genome with the ances- tors of these groups.A Draft Sequence of the Several features of DNA extracted from Late Pleistocene remains make its study challenging. The DNA is invariably degraded to a small aver-Neandertal Genome age size of less than 200 base pairs (bp) (21, 22), it is chemically modified (21, 23–26), and extractsRichard E. Green,1*†‡ Johannes Krause,1†§ Adrian W. Briggs,1†§ Tomislav Maricic,1†§ almost always contain only small amounts of en-Udo Stenzel,1†§ Martin Kircher,1†§ Nick Patterson,2†§ Heng Li,2† Weiwei Zhai,3†|| dogenous DNA but large amounts of DNA fromMarkus Hsi-Yang Fritz,4† Nancy F. Hansen,5† Eric Y. Durand,3† Anna-Sapfo Malaspinas,3† microbial organisms that colonized the specimensJeffrey D. Jensen,6† Tomas Marques-Bonet,7,13† Can Alkan,7† Kay Prüfer,1† Matthias Meyer,1† after death. Over the past 20 years, methods forHernán A. Burbano,1† Jeffrey M. Good,1,8† Rigo Schultz,1 Ayinuer Aximu-Petri,1 Anne Butthof,1 ancient DNA retrieval have been developed (21, 22),Barbara Höber,1 Barbara Höffner,1 Madlen Siegemund,1 Antje Weihmann,1 Chad Nusbaum,2 largely based on the polymerase chain reactionEric S. Lander,2 Carsten Russ,2 Nathaniel Novod,2 Jason Affourtit,9 Michael Egholm,9 (PCR) (27). In the case of the nuclear genome ofChristine Verna,21 Pavao Rudan,10 Dejana Brajkovic,11 Željko Kucan,10 Ivan Gušic,10 Neandertals, four short gene sequences have beenVladimir B. Doronichev,12 Liubov V. Golovanova,12 Carles Lalueza-Fox,13 Marco de la Rasilla,14 determined by PCR: fragments of the MC1R geneJavier Fortea,14 ¶ Antonio Rosas,15 Ralf W. Schmitz,16,17 Philip L. F. Johnson,18† Evan E. Eichler,7† involved in skin pigmentation (28), a segment ofDaniel Falush,19† Ewan Birney,4† James C. Mullikin,5† Montgomery Slatkin,3† Rasmus Nielsen,3† the FOXP2 gene involved in speech and language loaded from www.sciencemag.org on March 24, 2013Janet Kelso,1† Michael Lachmann,1† David Reich,2,20*† Svante Pääbo1*† (29), parts of the ABO blood group locus (30), and a taste receptor gene (31). However, although PCRNeandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe of ancient DNA can be multiplexed (32), it doesand western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal not allow the retrieval of a large proportion of thegenome composed of more than 4 billion nucleotides from three individuals. Comparisons of the genome of an organism.Neandertal genome to the genomes of five present-day humans from different parts of the world The development of high-throughput DNA se-identify a number of genomic regions that may have been affected by positive selection in ancestral quencing technologies (33, 34) allows large-scale,modern humans, including genes involved in metabolism and in cognitive and skeletal development. genome-wide sequencing of random pieces ofWe show that Neandertals shared more genetic variants with present-day humans in Eurasia than with DNA extracted from ancient specimens (35–37)present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the and has recently made it feasible to sequence ge-ancestors of non-Africans occurred before the divergence of Eurasian groups from each other. 1 Department of Evolutionary Genetics, Max-Planck Institute forT Evolutionary Anthropology, D-04103 Leipzig, Germany. 2Broad he morphological features typical of Nean- sumed ancestors of present-day Europeans. Institute of MIT and Harvard, Cambridge, MA 02142, USA. dertals first appear in the European fossil Similarly, analysis of DNA sequence data from 3 Department of Integrative Biology, University of California, record about 400,000 years ago (1–3). present-day humans has been interpreted as evi- Berkeley, CA 94720, USA. 4European Molecular BiologyProgressively more distinctive Neandertal forms dence both for (12, 13) and against (14) a genetic Laboratory–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.subsequently evolved until Neandertals disap- contribution by Neandertals to present-day hu- 5 Genome Technology Branch, National Human Genome Re-peared from the fossil record about 30,000 years mans. The only part of the genome that has been search Institute, National Institutes of Health, Bethesda, MDago (4). During the later part of their history, examined from multiple Neandertals, the mito- 20892, USA. 6Program in Bioinformatics and Integrative Biology,Neandertals lived in Europe and Western Asia chondrial DNA (mtDNA) genome, consistently University of Massachusetts Medical School, Worcester, MA 01655, USA. 7Howard Hughes Medical Institute, Departmentas far east as Southern Siberia (5) and as far falls outside the variation found in present-day of Genome Sciences, University of Washington, Seattle, WAsouth as the Middle East. During that time, Nean- humans and thus provides no evidence for inter- 98195, USA. 8Division of Biological Sciences, University of
  98. 98. RESEARCH ARTICLE changed parts of their genome with the ances- tors of these groups.A Draft Sequence of the Several features of DNA extracted from Late Pleistocene remains make its study challenging. The DNA is invariably degraded to a small aver-Neandertal Genome age size of less than 200 base pairs (bp) (21, 22), it is chemically modified (21, 23–26), and extractsRichard E. Green,1*†‡ Johannes Krause,1†§ Adrian W. Briggs,1†§ Tomislav Maricic,1†§ almost always contain only small amounts of en-Udo Stenzel,1†§ Martin Kircher,1†§ Nick Patterson,2†§ Heng Li,2† Weiwei Zhai,3†|| dogenous DNA but large amounts of DNA fromMarkus Hsi-Yang Fritz,4† Nancy F. Hansen,5† Eric Y. Durand,3† Anna-Sapfo Malaspinas,3† microbial organisms that colonized the specimensJeffrey D. Jensen,6† Tomas Marques-Bonet,7,13† Can Alkan,7† Kay Prüfer,1† Matthias Meyer,1† after death. Over the past 20 years, methods forHernán A. Burbano,1† Jeffrey M. Good,1,8† Rigo Schultz,1 Ayinuer Aximu-Petri,1 Anne Butthof,1 ancient DNA retrieval have been developed (21, 22),Barbara Höber,1 Barbara Höffner,1 Madlen Siegemund,1 Antje Weihmann,1 Chad Nusbaum,2 largely based on the polymerase chain reactionEric S. Lander,2 Carsten Russ,2 Nathaniel Novod,2 Jason Affourtit,9 Michael Egholm,9 (PCR) (27). In the case of the nuclear genome ofChristine Verna,21 Pavao Rudan,10 Dejana Brajkovic,11 Željko Kucan,10 Ivan Gušic,10 Neandertals, four short gene sequences have beenVladimir B. Doronichev,12 Liubov V. Golovanova,12 Carles Lalueza-Fox,13 Marco de la Rasilla,14 determined by PCR: fragments of the MC1R geneJavier Fortea,14 ¶ Antonio Rosas,15 Ralf W. Schmitz,16,17 Philip L. F. Johnson,18† Evan E. Eichler,7† involved in skin pigmentation (28), a segment ofDaniel Falush,19† Ewan Birney,4† James C. Mullikin,5† Montgomery Slatkin,3† Rasmus Nielsen,3† the FOXP2 gene involved in speech and language loaded from www.sciencemag.org on March 24, 2013Janet Kelso,1† Michael Lachmann,1† David Reich,2,20*† Svante Pääbo1*† (29), parts of the ABO blood group locus (30), and a taste receptor gene (31). However, although PCRNeandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe of ancient DNA can be multiplexed (32), it doesand western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal not allow the retrieval of a large proportion of thegenome composed of more than 4 billion nucleotides from three individuals. Comparisons of the genome of an organism.Neandertal genome to the genomes of five present-day humans from different parts of the world The development of high-throughput DNA se-identify a number of genomic regions that may have been affected by positive selection in ancestral quencing technologies (33, 34) allows large-scale,modern humans, including genes involved in metabolism and in cognitive and skeletal development. genome-wide sequencing of random pieces ofWe show that Neandertals shared more genetic variants with present-day humans in Eurasia than with DNA extracted from ancient specimens (35–37)present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the and has recently made it feasible to sequence ge-ancestors of non-Africans occurred before the divergence of Eurasian groups from each other. 1 Department of Evolutionary Genetics, Max-Planck Institute forT Evolutionary Anthropology, D-04103 Leipzig, Germany. 2Broad he morphological features typical of Nean- sumed ancestors of present-day Europeans. Institute of MIT and Harvard, Cambridge, MA 02142, USA. dertals first appear in the European fossil Similarly, analysis of DNA sequence data from 3 Department of Integrative Biology, University of California, record about 400,000 years ago (1–3). present-day humans has been interpreted as evi- Berkeley, CA 94720, USA. 4European Molecular BiologyProgressively more distinctive Neandertal forms dence both for (12, 13) and against (14) a genetic Laboratory–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.subsequently evolved until Neandertals disap- contribution by Neandertals to present-day hu- 5 Genome Technology Branch, National Human Genome Re-peared from the fossil record about 30,000 years mans. The only part of the genome that has been 2-4% of eurasian DNA comes from Neanderthals search Institute, National Institutes of Health, Bethesda, MDago (4). During the later part of their history, examined from multiple Neandertals, the mito- 20892, USA. 6Program in Bioinformatics and Integrative Biology,Neandertals lived in Europe and Western Asia chondrial DNA (mtDNA) genome, consistently University of Massachusetts Medical School, Worcester, MA 01655, USA. 7Howard Hughes Medical Institute, Departmentas far east as Southern Siberia (5) and as far falls outside the variation found in present-day of Genome Sciences, University of Washington, Seattle, WAsouth as the Middle East. During that time, Nean- humans and thus provides no evidence for inter- 98195, USA. 8Division of Biological Sciences, University of
  99. 99. RESEARCH ARTICLE changed parts of their genome with the ances- tors of these groups.A Draft Sequence of the Several features of DNA extracted from Late Pleistocene remains make its study challenging. The DNA is invariably degraded to a small aver-Neandertal Genome age size of less than 200 base pairs (bp) (21, 22), it is chemically modified (21, 23–26), and extractsRichard E. Green,1*†‡ Johannes Krause,1†§ Adrian W. Briggs,1†§ Tomislav Maricic,1†§ almost always contain only small amounts of en-Udo Stenzel,1†§ Martin Kircher,1†§ Nick Patterson,2†§ Heng Li,2† Weiwei Zhai,3†|| dogenous DNA but large amounts of DNA fromMarkus Hsi-Yang Fritz,4† Nancy F. Hansen,5† Eric Y. Durand,3† Anna-Sapfo Malaspinas,3† microbial organisms that colonized the specimensJeffrey D. Jensen,6† Tomas Marques-Bonet,7,13† Can Alkan,7† Kay Prüfer,1† Matthias Meyer,1† after death. Over the past 20 years, methods forHernán A. Burbano,1† Jeffrey M. Good,1,8† Rigo Schultz,1 Ayinuer Aximu-Petri,1 Anne Butthof,1 ancient DNA retrieval have been developed (21, 22),Barbara Höber,1 Barbara Höffner,1 Madlen Siegemund,1 Antje Weihmann,1 Chad Nusbaum,2 largely based on the polymerase chain reactionEric S. Lander,2 Carsten Russ,2 Nathaniel Novod,2 Jason Affourtit,9 Michael Egholm,9 (PCR) (27). In the case of the nuclear genome ofChristine Verna,21 Pavao Rudan,10 Dejana Brajkovic,11 Željko Kucan,10 Ivan Gušic,10 Neandertals, four short gene sequences have beenVladimir B. Doronichev,12 Liubov V. Golovanova,12 Carles Lalueza-Fox,13 Marco de la Rasilla,14 determined by PCR: fragments of the MC1R geneJavier Fortea,14 ¶ Antonio Rosas,15 Ralf W. Schmitz,16,17 Philip L. F. Johnson,18† Evan E. Eichler,7† involved in skin pigmentation (28), a segment ofDaniel Falush,19† Ewan Birney,4† James C. Mullikin,5† Montgomery Slatkin,3† Rasmus Nielsen,3† the FOXP2 gene involved in speech and language loaded from www.sciencemag.org on March 24, 2013Janet Kelso,1† Michael Lachmann,1† David Reich,2,20*† Svante Pääbo1*† (29), parts of the ABO blood group locus (30), and a taste receptor gene (31). However, although PCRNeandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe of ancient DNA can be multiplexed (32), it doesand western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal not allow the retrieval of a large proportion of thegenome composed of more than 4 billion nucleotides from three individuals. Comparisons of the genome of an organism.Neandertal genome to the genomes of five present-day humans from different parts of the world The development of high-throughput DNA se-identify a number of genomic regions that may have been affected by positive selection in ancestral quencing technologies (33, 34) allows large-scale,modern humans, including genes involved in metabolism and in cognitive and skeletal development. genome-wide sequencing of random pieces ofWe show that Neandertals shared more genetic variants with present-day humans in Eurasia than with DNA extracted from ancient specimens (35–37)present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the and has recently made it feasible to sequence ge-ancestors of non-Africans occurred before the divergence of Eurasian groups from each other. 1 Department of Evolutionary Genetics, Max-Planck Institute forT Evolutionary Anthropology, D-04103 Leipzig, Germany. 2Broad he morphological features typical of Nean- sumed ancestors of present-day Europeans. Institute of MIT and Harvard, Cambridge, MA 02142, USA. dertals first appear in the European fossil Similarly, analysis of DNA sequence data from 3 Department of Integrative Biology, University of California, record about 400,000 years ago (1–3). present-day humans has been interpreted as evi- Berkeley, CA 94720, USA. 4European Molecular BiologyProgressively more distinctive Neandertal forms dence both for (12, 13) and against (14) a genetic Laboratory–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.subsequently evolved until Neandertals disap- contribution by Neandertals to present-day hu- 5 Genome Technology Branch, National Human Genome Re-peared from the fossil record about 30,000 years mans. The only part of the genome that has been 2-4% of eurasian DNA comes from Neanderthals search Institute, National Institutes of Health, Bethesda, MDago (4). During the later part of their history, examined from multiple Neandertals, the mito- 20892, USA. 6Program in Bioinformatics and Integrative Biology,Neandertals lived in Europe and Western Asia chondrial DNA (mtDNA) genome, consistently University of Massachusetts Medical School, Worcester, MA 01655, USA. 7Howard Hughes Medical Institute, Departmentas far east as Southern Siberia (5) and as far falls outside the variation found in present-day of Genome Sciences, University of Washington, Seattle, WAsouth as the Middle East. During that time, Nean- humans and thus provides no evidence for inter- 98195, USA. 8Division of Biological Sciences, University of
  100. 100. Strong reproductive isolation between humanStrong reproductive isolation between humansand Neanderthals inferred from observed Neanderthals inferred from observedpatterns of introgressionpatterns of introgressionMathias Currata,1 and Laurent Excoffierb,c,1Mathias Currata,1 and Laurent Excoffierb,c,1aa Anthropology, Anthropology, Genetics, and Peopling History Laboratory, Anthropology Unit, Department of of Genetics and Evolution, University G Genetics, and Peopling History Laboratory, Anthropology Unit, Department Genetics and Evolution, University of o1227 Geneva, Switzerland; bComputational and Molecular Population Genetics Laboratory, Institute Ecology and Evolution, Univers1227 Geneva, Switzerland; bComputational and Molecular Population Genetics Laboratory, Institute of of Ecology and Evolution, Uni3012 Berne, Switzerland; and cSwiss Institute of Bioinformatics, 1015 Lausanne, Switzerland3012 Berne, Switzerland; and cSwiss Institute of Bioinformatics, 1015 Lausanne, SwitzerlandEdited by Svante Pääbo, Max Planck Institute of Evolutionary Anthropology, Leipzig, Germany, and approved August 3, 2011 (receEdited by Svante Pääbo, Max Planck Institute of Evolutionary Anthropology, Leipzig, Germany, and approved August 3, 2011 (receiveMay 10, 2011)May 10, 2011)Recent studies have revealed that 2–3% of the genome of non-Recent studies have revealed that 2–3% of the genome of non- To examine these issues and clarify the proce To examine these issues and clarify the proAfricans might come from Neanderthals, suggesting a a more complexAfricans might come from Neanderthals, suggesting more complex between Neanderthals and modern humans, we between Neanderthals and modern humans,scenario of modern human evolution than previously anticipated. InInscenario of modern human evolution than previously anticipated. istic and spatially explicit model of of admixt istic and spatially explicit model admixturethis paper, we use a model of admixture during a a spatial expansionthis paper, we use a model of admixture during spatial expansion between modern humans and Neanderthals (3 between modern humans and Neanderthalsto study the hybridization of Neanderthals with modern humansto study the hybridization of Neanderthals with modern humans simulations, we have estimated the interbree simulations, we have estimated the interbduring their spread out of Africa. We find that observed low levelsduring their spread out of Africa. We find that observed low levels between humans and Neanderthals as as well t between humans and Neanderthals well as aof Neanderthal ancestry in Eurasians are compatible with a a very lowof Neanderthal ancestry in Eurasians are compatible with very low hybridization that is is compatible with the o hybridization that compatible with the obsrate of interbreeding (<2%), potentially attributable to a a very strongrate of interbreeding (<2%), potentially attributable to very strong Neanderthal ancestry in in contemporary huma Neanderthal ancestry contemporary humans,avoidance of interspecific matings, aa low fitness of hybrids, or both.avoidance of interspecific matings, low fitness of hybrids, or both. latter migrated out of of Africa into Eurasia 50 latter migrated out Africa into Eurasia 50 kyThese results suggesting the presence of very effective barriers totoThese results suggesting the presence of very effective barriersgene flow between the two species are robust to uncertainties aboutgene flow between the two species are robust to uncertainties about Results Resultsthe exact demography of the Paleolithic populations, and they are Low Rates of of Interbreeding Between Humathe exact demography of the Paleolithic populations, and they are Low Rates Interbreeding Between Humansalso found to be compatible with the observed lack of mtDNA in- Using spatially explicit simulations, wewealso found to be compatible with the observed lack of mtDNA in-trogression. Our model additionally suggests that similarly low levels Using spatially explicit simulations, havtrogression. Our model additionally suggests that similarly low levels expected amount of of Neanderthal ancestry pr expected amount Neanderthal ancestry in inof introgression in Europe and Asia may result from distinct admix-of introgression in Europe and Asia may result from distinct admix- from Europe (France) and Asia (China) forfoture events having occurred beyond the Middle East, after the split ofof from Europe (France) and Asia (China)ture events having occurred beyond the Middle East, after the split admixture with Neanderthals and over variou admixture with Neanderthals and over varEuropeans and Asians. This hypothesis could be tested because it it derthal ranges (Fig. 1).1). Under our modelEuropeans and Asians. This hypothesis could be tested becausepredicts that different components of Neanderthal ancestry should derthal ranges (Fig. Under our model ofpredicts that different components of Neanderthal ancestry should range expansion, we find that observed low leve range expansion, we find that observed low lbe present in Europeans and in Asians.be present in Europeans and in Asians. introgression into Eurasians imply the existe
  101. 101. Denisovans
  102. 102. Denisovans• Only known remains(all found since 2010): phalanx (finger bone), three teeth, a toe bone. From 41,000 years ago.
  103. 103. Denisovans• Only known remains(all found since 2010): phalanx (finger bone), three teeth, a toe bone. From 41,000 years ago.• Amazinglywell preserved DNA (Siberia; average temperature 0°C). sequenced the genome.
  104. 104. Denisovans• Only known remains(all found since 2010): phalanx (finger bone), three teeth, a toe bone. From 41,000 years ago.• Amazinglywell preserved DNA (Siberia; average temperature 0°C). sequenced the genome.• Common ancestor with Neanderthal: 600,000 years ago
  105. 105. Denisovans• Only known remains(all found since 2010): phalanx (finger bone), three teeth, a toe bone. From 41,000 years ago.• Amazingly well preserved DNA (Siberia; average temperature 0°C). sequenced the genome.• Common ancestor with Neanderthal: 600,000 years ago• Interbreeding with Homo sapiens: 4-6% of Melanesian genomes are from Denisovan.
  106. 106. H. neanderthalensis H. sapiens H. erectus AustralopithecinesProconsulidae Most lineages went extinct
  107. 107. H. neanderthalensis H. sapiens Denisovan H. erectus AustralopithecinesProconsulidae Most lineages went extinct
  108. 108. Stoneking & Krause 2011? No admixture detected despite probable overlap! detected admixture (location uncertain) African ori of mtDNA lations have of our spec the deepest sity 14,62–65. G view 7–9, and humans ind within mod from south mately 115 humans fir divergences 35–50 kya13 of a strong our genome close correlaStoneking & Krause 2011 in a populat ulation from
  109. 109. A WINDING PATH H. sapiens spread from Africa toAfter early modern humans left Africa around 60,000 years ago (top western Asia and then to Europe andright), they spread across the globe and interbred with other southern Asia, eventually reachingdescendants of Homo heidelbergensis. Australasia and the Americas. 0 Homo sapiens Homo floresiensis Denisovans Neanderthals Homo erectus 0.4 Homo heidelbergensisMillion years ago 0.8 Homo antecessor H. heidelbergensis originated from 1.2 H. erectus in an unknown location and dispersed across Homo erectus Africa, southern Asia and southern Europe. 1.6 H. floresiensis originated H. erectus spread to western Asia, then in an unknown location east Asia and Indonesia. Its presence and reached remote in Europe is uncertain, but it gave rise 2.0 parts of Indonesia. to H. antecessor, found in Spain. Wavy branch edges suggest presumed fluctuations in population. PATCHWORK PLANET Most people’s genomes contain remnants of archaic DNA from ancient interbreeding3–6. 2% 2.5% 2.5% 5% Genes* African Unknown archaic African source 98% 97.5% 92.5% Neanderthal Denisovan Stringer 2012 *Figures are approximate, and for Africa, based on limited data6. Sub-Saharan Africa Eurasia and Americas Australia and New Guinea
  110. 110. REPORTS Deep Human Genealogies Reveal a tracing back the founding events of new localities. As shown in Fig. 1, the inferred colonization pro- cess is a mixture of long-distance settlements Selective Advantage to Be on an creating an irregular wave front, followed by fur- ther, more progressive, short-range expansions, Expanding Wave Front which then filled gaps and created a more reg- ular wave front. On the basis of the computation of a wave Claudia Moreau,1 Claude Bhérer,1 Hélène Vézina,2 Michèle Jomphe,2 front index (WFI) (21), we find that the ancestors Damian Labuda,1,3* Laurent Excoffier1,4,5* of the Saguenay and the Lac-Saint-Jean people lived more often on or close to the wave front Since their origin, human populations have colonized the whole planet, but the demographic than expected by chance (WFI, P < 0.001 in both processes governing range expansions are mostly unknown. We analyzed the genealogy of more regions) (fig. S1). Indeed, the very high WFI of than one million individuals resulting from a range expansion in Quebec between 1686 and 1960 0.75 observed in Lac-Saint-Jean corresponds to and reconstructed the spatial dynamics of the expansion. We find that a majority of the present a situation in which half of the Lac-Saint-Jean Saguenay Lac-Saint-Jean population can be traced back to ancestors having lived directly on or ancestors had lived directly on the wave front and close to the wave front. Ancestors located on the front contributed significantly more to the current the other half just one generation away from it. gene pool than those from the range core, likely due to a 20% larger effective fertility of women In contrast, WFI is significantly lower in the on the wave front. This fitness component is heritable on the wave front and not in the core, Charlevoix region (P = 0.003) (fig. S1). These Downloaded from www.sciencemag.org on March 24, 2013 implying that this life-history trait evolves during range expansions. results are consistent with different colonization dynamics of SLSJ and Charlevoix. The wave front was always widespread in SLSJ where new M ost species go through environmental- Quebec parish registers that document the recent localities were continuously settled, whereas it was ly induced range expansions or range temporal and spatial expansion of the settle- much smaller in Charlevoix where most localities shifts (1), promoting the evolution of ment of the Charlevoix Saguenay Lac-Saint- remained in the range core until the 20th century traits associated with dispersal and reproduction Jean (ChSLSJ) region, northeast of Quebec City, (Fig. 1). New immigrants from outside ChSLSJ (2). Humans likely colonized the world by a Canada: a prime example of a recent, fast, and constituted an important minority of the people series of range expansions from Africa (3), pos- well-documented range expansion (17) (Fig. 1). getting married, with a greater proportion of im- sibly with episodes of interbreeding with now The European colonization of Quebec was ini- migrants settling on the wave front than on the extinct hominins (4, 5), leading to allele frequen- tiated in 1608 with the foundation of Quebec range core, especially before 1900 (up to 20% on cy and heterozygosity clines from entry points City, and the colony was well established by the the wave front and up to 10% in the range core) into several continents [e.g., (6, 7)]. Range ex- end of the 17th century (18). The peopling of the (table S2). Generally, more male than female im- pansions can also lead to drastic changes in allele Charlevoix region started from Baie-Saint-Paul, migration occurred in all regions, and this bias frequencies, sometimes mimicking the effect of and both a rapid demographic growth and the de- toward males is significantly higher in the core positive selection in recently colonized habitats velopment of the timber industry promoted further than on the wave front (table S3). Nevertheless, (8, 9), through a process called gene surfing (9). expansions after 1838 up the Saguenay River and the new territories of SLSJ have been largely col- Neutral, favorable, or even deleterious mutations the Lac-Saint-Jean region (SLSJ) (19, 20). The onized by people recruited directly on the wave can surf and increase in frequency (10, 11), im- spatial and temporal dynamics of the peopling of front or next to it, not by people from the range plying that wave fronts may harbor mutations the whole ChSLSJ region can be reconstructed by core (table S4). with a wider range of selective coefficients than core populations. The evolutionary consequences of range expansions have been studied in a wide array of species (2, 12), but studies of the dy- namics of range expansions have been generally restricted to species with short generation times Saguenay River (13, 14) or to invasive species (15, 16), because
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