Evolution - Week 4: Human evolution

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SBC174/SBS110 Evolution lectures from October 14th.

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Evolution - Week 4: Human evolution

  1. 1. Monday, 14 October 13
  2. 2. Human evolution Ancestors, relatives & major transitions Recent insights from genomics What about today? Monday, 14 October 13
  3. 3. Benton (2005) Fig 10.47 Monday, 14 October 13
  4. 4. Relatives and recent ancestors New world monkeys “Higher primates” = Old world monkeys + Apes PLATYRRHINI CATARRHINI Apes CERCOPITHECOIDS Old world monkeys SPIDER MONKEY MACAQUE HOMINOIDS Great Apes HYLOBATIDS HOMINIDS Lesser apes SIAMANG GIBBON ORANGUTAN OURANOPITHECUS PROCONSUL GORILLA DRYOPITHECUS 14 MYA SIVAPITHECUS 16 MYA HUMAN 9 MYA CHIMPANZEE Potential common 6 MYA ancestors (Miocene) 19 MYA 25 MYA 40 MILLION YEARS AGO simple chewing surfaces — a feeding apMonday, 14 October 13 FAMILY TREE of hominoids encompasses the lesser apes (siamangs and 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 Dryopithecus or Ouranopithecus may have given rise to African apes and humans. © Scientific American suspensory locomotion, especially in east Asia. Most phylogenetic analyses
  5. 5. Proconsul Some ape-like features Some monkey-like features Monday, 14 October 13
  6. 6. East African Rift Valley Monday, 14 October 13
  7. 7. Relatives and recent ancestors PLATYRRHINI CATARRHINI CERCOPITHECOIDS HOMINOIDS HYLOBATIDS SPIDER MONKEY MACAQUE SIAMANG HOMINIDS GIBBON ORANGUTAN GORILLA HUMAN CHIMPANZEE 6 MYA OURANOPITHECUS PROCONSUL DRYOPITHECUS 9 MYA 14 MYA SIVAPITHECUS 16 MYA 19 MYA 25 MYA 40 MILLION YEARS AGO simple chewing surfaces — a feeding apparatus well suited to a diet of soft, ripe fruits. They 13 Monday, 14 Octoberalso possessed shortened Potential common ancestors (Miocene) FAMILY TREE of hominoids encompasses the lesser apes (siamangs and 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 Dryopithecus or Ouranopithecus may have given rise to African apes and humans. suspensory locomotion, especially in the elbow joint, which was fully extendable and stable throughout the full range east Asia. Most phylogenetic analyses concur that it is from Sivapithecus that the living orangutan, Pongo pygmaeus, © Scientific American
  8. 8. Major transitions in human evolution • Bipedalism • Increased • Use (down from the trees) brain size of simple stone tools • Fire, spears & other sophisticated tools (stone, bone...) • Language, complex • Agriculture... Monday, 14 October 13 In which order? culture
  9. 9. Million! years! Glacial cycles! Homo! P. robustus! Arctic icecap! Australopithecus africanus/! A. afarensis! Ardipithecus ramidus! Antarctic icecap! Orrorin tugenensis! Cold! Warm! Climate! WP! • Life in trees. • Occassionally • New Monday, 14 October 13 go down context required going down more often?
  10. 10. Why bipedalism? Mid Miocene! efficient locomotion (for distant food sources) Late Miocene! Climate! cooling! • Energy • Less Habitat! fragmentation! exposure to sun? the hands? (for gathering/ hunting?) Million! years! • Free farther: Finding food & avoiding predators? Glacial cycles! Homo! • Seeing P. robustus! Australopithecus africanus/! A. afarensis! Ardipithecus ramidus! • Sexual or anti-predator displays? Arctic icecap! Antarctic icecap! Orrorin tugenensis! Cold! Warm! Climate! Monday, 14 October 13
  11. 11. Running • sweating • arched for thermoregulation. foot + achilles tendon • head stabilization • early Homo? • first: improved • then scavenging. persistence hunting Monday, 14 October 13
  12. 12. Monday, 14 October 13
  13. 13. Relatives and recent ancestors PLATYRRHINI CATARRHINI CERCOPITHECOIDS HOMINOIDS HYLOBATIDS SPIDER MONKEY MACAQUE SIAMANG HOMINIDS GIBBON ORANGUTAN GORILLA HUMAN CHIMPANZEE 6 MYA OURANOPITHECUS PROCONSUL DRYOPITHECUS 9 MYA 14 MYA SIVAPITHECUS 16 MYA 19 MYA 25 MYA 40 MILLION YEARS AGO simple chewing surfaces — a feeding apparatus well suited to a diet of soft, ripe fruits. They 13 Monday, 14 Octoberalso possessed shortened Potential common ancestors (Miocene) FAMILY TREE of hominoids encompasses the lesser apes (siamangs and 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 Dryopithecus or Ouranopithecus may have given rise to African apes and humans. suspensory locomotion, especially in the elbow joint, which was fully extendable and stable throughout the full range east Asia. Most phylogenetic analyses concur that it is from Sivapithecus that the living orangutan, Pongo pygmaeus, © Scientific American
  14. 14. H. neanderthalensis H. sapiens H. erectus Australopithecines Proconsulidae Monday, 14 October 13 Most lineages went extinct
  15. 15. Monday, 14 October 13
  16. 16. Australopithecines Wikipedia Monday, 14 October 13
  17. 17. a Taung child Nature 1925 Monday, 14 October 13 Australopithecus afarensis 2.5 mya
  18. 18. Lucy - Australopithecus afarensis 1978 Monday, 14 October 13 3.2 mya
  19. 19. Australopithecines 30° 20° 10° 0° 10° 20° 30° 40° 50° 60° 30° 30° 20° 20° A. Bahrelghazali A. Afarensis 10° 10° A. Gahri P. Boisei P. Aethiopicus A. Anamensis 0° 0° 10° 10° 20° A. Africanus 30° (km) 0 Wikipedia 0 30° Monday, 14 October 13 10° 30° 3 000 (mi) Projection de Lambert azimutale équivalente 20° P. Robustus (Crassidens) 0° 2 000 10° 20° 30° 40° 50° 60° Brain size: 35% of modern human
  20. 20. Monday, 14 October 13
  21. 21. Evidence for bipedalism in Australopithecines Monday, 14 October 13
  22. 22. Evidence for bipedalism in Australopithecines Monday, 14 October 13
  23. 23. 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 Monday, 14 October 13
  24. 24. Fossilized tracks at Laetoli (Tanzania) 3.6Mya Footprints preserved in volcanic ash from: 3 hominids (Australopithecus afarensis) Numerous other mammals Monday, 14 October 13
  25. 25. Tool use? • generally: only great apes). • but simple tools (similarly to current non-human Australopithecus garhi (2.5 mya) may have made stone tools. Monday, 14 October 13
  26. 26. Summary: Australopithecines • Major group of early bipedal hominids (4mya to 1 mya) • Small brains • Only in Africa • Many forms/species Monday, 14 October 13
  27. 27. Monday, 14 October 13
  28. 28. H. neanderthalensis H. sapiens H. erectus Australopithecines Proconsulidae Monday, 14 October 13 Most lineages went extinct
  29. 29. Homo Monday, 14 October 13
  30. 30. Homo habilis Monday, 14 October 13
  31. 31. Tool use H. habilis made tools Chimps and other animals may use objects as tools. Cutting H. sapiens! Monday, 14 October 13 H. habilis! Australopithecine! Scraping
  32. 32. Stages of human evolution are defined by the style and sophistication of stone tools…. e.g.: •Oldowan (2.5-1.5 mya) •Achuelian (1.5-0.2 mya) Monday, 14 October 13
  33. 33. Oldowan tools Hammerstone Scraper Monday, 14 October 13 Choppers Flakes
  34. 34. Brain sizes increase Monday, 14 October 13
  35. 35. Monday, 14 October 13
  36. 36. Out of Africa - H. erectus Monday, 14 October 13
  37. 37. Acheulian tools Handaxes! Cleaver! Handaxe Pick! Scraper! Monday, 14 October 13 Trimming flakes!
  38. 38. Nariokotome/Turkana boy H. erectus Found 1984 in Kenya. From1.5mya Monday, 14 October 13
  39. 39. H. erectus lifestyle • Stone tools (Acheulian) • Fire • Sociality • Hunting Monday, 14 October 13 • …language?
  40. 40. Monday, 14 October 13
  41. 41. Homo floresiensis “The Hobbit” H. florensis vs. H. sapiens skull Monday, 14 October 13
  42. 42. Nature (2004) vol. 431, 1043-1044 Monday, 14 October 13
  43. 43. Monday, 14 October 13
  44. 44. Relatives and recent ancestors New world monkeys “Higher primates” = Old world monkeys + Apes PLATYRRHINI CATARRHINI Apes CERCOPITHECOIDS Old world monkeys SPIDER MONKEY MACAQUE HOMINOIDS Great Apes HYLOBATIDS HOMINIDS Lesser apes SIAMANG GIBBON ORANGUTAN OURANOPITHECUS PROCONSUL GORILLA DRYOPITHECUS 14 MYA SIVAPITHECUS 16 MYA HUMAN 9 MYA CHIMPANZEE Potential common 6 MYA ancestors (Miocene) 19 MYA 25 MYA 40 MILLION YEARS AGO simple chewing surfaces — a feeding apMonday, 14 October 13 FAMILY TREE of hominoids encompasses the lesser apes (siamangs and 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 Dryopithecus or Ouranopithecus may have given rise to African apes and humans. © Scientific American suspensory locomotion, especially in east Asia. Most phylogenetic analyses
  45. 45. Major transitions in human evolution • Bipedalism • Increased • Use (down from the trees) brain size of simple stone tools • Fire, spears & other sophisticated tools (stone, bone...) • Language, complex • Agriculture... Monday, 14 October 13 culture
  46. 46. H. neanderthalensis H. sapiens H. erectus Australopithecines Proconsulidae Monday, 14 October 13 Most lineages went extinct
  47. 47. • Monday, 14 October 13
  48. 48. Neanderthal 600,000-30,000 years ago Monday, 14 October 13
  49. 49. Monday, 14 October 13
  50. 50. Burial ritual? Monday, 14 October 13
  51. 51. Neanderthals - Summary • Neanderthals were morphologically and genetically distinct from early H. sapiens • disappeared after H. sapiens arrived - possibly because they were culturally less advanced. Monday, 14 October 13
  52. 52. H. neanderthalensis H. sapiens H. erectus Australopithecines Proconsulidae Monday, 14 October 13 Most lineages went extinct
  53. 53. H. sapiens out of Africa • 50,000 years ago: fully “modern” with language, music, advanced social intelligence, strategic planning etc. • 70,000 years ago: began migrating out of Africa • Simultaneous decline of other Homo species (erectus, neanderthalensis...): competition? • Superior cooperation & learning due to language? • Agriculture ~ 10,000 years ago Monday, 14 October 13
  54. 54. Monday, 14 October 13
  55. 55. 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 Monday, 14 October 13
  56. 56. Examples of early H. sapiens tools Monday, 14 October 13
  57. 57. Lion man, Ulm - 40,000 years ago Lascaux - 35000 years ago Monday, 14 October 13 Flute - 36,000 years ago
  58. 58. Monday, 14 October 13
  59. 59. Recent insights from genomics Monday, 14 October 13
  60. 60. A Draft Sequence of the Neandertal Genome Richard E. Green,1*†‡ Johannes Krause,1†§ Adrian W. Briggs,1†§ Tomislav Maricic,1†§ Udo Stenzel,1†§ Martin Kircher,1†§ Nick Patterson,2†§ Heng Li,2† Weiwei Zhai,3†|| Markus Hsi-Yang Fritz,4† Nancy F. Hansen,5† Eric Y. Durand,3† Anna-Sapfo Malaspinas,3† Jeffrey D. Jensen,6† Tomas Marques-Bonet,7,13† Can Alkan,7† Kay Prüfer,1† Matthias Meyer,1† Hernán A. Burbano,1† Jeffrey M. Good,1,8† Rigo Schultz,1 Ayinuer Aximu-Petri,1 Anne Butthof,1 Barbara Höber,1 Barbara Höffner,1 Madlen Siegemund,1 Antje Weihmann,1 Chad Nusbaum,2 Eric S. Lander,2 Carsten Russ,2 Nathaniel Novod,2 Jason Affourtit,9 Michael Egholm,9 Christine Verna,21 Pavao Rudan,10 Dejana Brajkovic,11 Željko Kucan,10 Ivan Gušic,10 Vladimir B. Doronichev,12 Liubov V. Golovanova,12 Carles Lalueza-Fox,13 Marco de la Rasilla,14 Javier Fortea,14 ¶ Antonio Rosas,15 Ralf W. Schmitz,16,17 Philip L. F. Johnson,18† Evan E. Eichler,7† Daniel Falush,19† Ewan Birney,4† James C. Mullikin,5† Montgomery Slatkin,3† Rasmus Nielsen,3† Janet Kelso,1† Michael Lachmann,1† David Reich,2,20*† Svante Pääbo1*† Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other. T he morphological features typical of Neandertals first appear in the European fossil record about 400,000 years ago (1–3). Progressively more distinctive Neandertal forms subsequently evolved until Neandertals disappeared from the fossil record about 30,000 years ago (4). During the later part of their history, Neandertals lived in Europe and Western Asia as far east as Southern Siberia (5) and as far south as the Middle East. During that time, Neandertals 14 October 13 Monday,presumably came into contact with ana- sumed ancestors of present-day Europeans. Similarly, analysis of DNA sequence data from present-day humans has been interpreted as evidence both for (12, 13) and against (14) a genetic contribution by Neandertals to present-day humans. The only part of the genome that has been examined from multiple Neandertals, the mitochondrial DNA (mtDNA) genome, consistently falls outside the variation found in present-day humans and thus provides no evidence for interbreeding (15–19). However, this observation changed parts of their genome with the ancestors of these groups. Several features of DNA extracted from Late Pleistocene remains make its study challenging. The DNA is invariably degraded to a small average size of less than 200 base pairs (bp) (21, 22), it is chemically modified (21, 23–26), and extracts almost always contain only small amounts of endogenous DNA but large amounts of DNA from microbial organisms that colonized the specimens after death. Over the past 20 years, methods for ancient DNA retrieval have been developed (21, 22), largely based on the polymerase chain reaction (PCR) (27). In the case of the nuclear genome of Neandertals, four short gene sequences have been determined by PCR: fragments of the MC1R gene involved in skin pigmentation (28), a segment of the FOXP2 gene involved in speech and language (29), parts of the ABO blood group locus (30), and a taste receptor gene (31). However, although PCR of ancient DNA can be multiplexed (32), it does not allow the retrieval of a large proportion of the genome of an organism. The development of high-throughput DNA sequencing technologies (33, 34) allows large-scale, genome-wide sequencing of random pieces of DNA extracted from ancient specimens (35–37) and has recently made it feasible to sequence ge1 Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. 2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. 3 Department of Integrative Biology, University of California, Berkeley, CA 94720, USA. 4European Molecular Biology Laboratory–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK. 5 Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. 6Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA. 7Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. 8Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA. 9454 Life Sciences, 2-4% of eurasian DNA comes from Neanderthals wnloaded from www.sciencemag.org on March 24, 2013 RESEARCH ARTICLE
  61. 61. Strong reproductive isolation between human Strong reproductive isolation between humans and Neanderthals inferred from observed Neanderthals inferred from observed patterns of introgression patterns of introgression Mathias Currata,1 and Laurent Excoffierb,c,1 Mathias Currata,1 and Laurent Excoffierb,c,1 a a Anthropology, Genetics, and Peopling History Laboratory, Anthropology Unit, Department Genetics and Evolution, University of o Anthropology, Genetics, and Peopling History Laboratory, Anthropology Unit, Department of of Genetics and Evolution, University G 1227 Geneva, Switzerland; bComputational and Molecular Population Genetics Laboratory, Institute Ecology and Evolution, Univers 1227 Geneva, Switzerland; bComputational and Molecular Population Genetics Laboratory, Institute of of Ecology and Evolution, Uni 3012 Berne, Switzerland; and cSwiss Institute of Bioinformatics, 1015 Lausanne, Switzerland 3012 Berne, Switzerland; and cSwiss Institute of Bioinformatics, 1015 Lausanne, Switzerland Edited by Svante Pääbo, Max Planck Institute of Evolutionary Anthropology, Leipzig, Germany, and approved August 3, 2011 (rece Edited by Svante Pääbo, Max Planck Institute of Evolutionary Anthropology, Leipzig, Germany, and approved August 3, 2011 (receive May 10, 2011) May 10, 2011) Recent studies have revealed that 2–3% of the genome of nonRecent studies have revealed that 2–3% of the genome of nonAfricans might come from Neanderthals, suggesting a a more complex Africans might come from Neanderthals, suggesting more complex scenario of modern human evolution than previously anticipated. InIn scenario of modern human evolution than previously anticipated. this paper, we use a model of admixture during a a spatial expansion this paper, we use a model of admixture during spatial expansion to study the hybridization of Neanderthals with modern humans to study the hybridization of Neanderthals with modern humans during their spread out of Africa. We find that observed low levels during their spread out of Africa. We find that observed low levels of Neanderthal ancestry in Eurasians are compatible with a a very low of Neanderthal ancestry in Eurasians are compatible with very low rate of interbreeding (<2%), potentially attributable to a a very strong rate of interbreeding (<2%), potentially attributable to very strong avoidance of interspecific matings, aa low fitness of hybrids, or both. avoidance of interspecific matings, low fitness of hybrids, or both. These results suggesting the presence of very effective barriers toto These results suggesting the presence of very effective barriers gene flow between the two species are robust to uncertainties about gene flow between the two species are robust to uncertainties about the exact demography of the Paleolithic populations, and they are the exact demography of the Paleolithic populations, and they are also found to be compatible with the observed lack of mtDNA inalso found to be compatible with the observed lack of mtDNA introgression. Our model additionally suggests that similarly low levels trogression. Our model additionally suggests that similarly low levels of introgression in Europe and Asia may result from distinct admixof introgression in Europe and Asia may result from distinct admixture events having occurred beyond the Middle East, after the split ofof ture events having occurred beyond the Middle East, after the split Europeans and Asians. This hypothesis could be tested because it it Europeans and Asians. This hypothesis could be tested because predicts that different components of Neanderthal ancestry should predicts that different components of Neanderthal ancestry should be present in Europeans and in Asians. be present in Europeans and in Asians. Monday, 14 October 13 To examine these issues and clarify the proce To examine these issues and clarify the pro between Neanderthals and modern humans, we between Neanderthals and modern humans, istic and spatially explicit model of of admixt istic and spatially explicit model admixture between modern humans and Neanderthals (3 between modern humans and Neanderthals simulations, we have estimated the interbree simulations, we have estimated the interb between humans and Neanderthals as as well t between humans and Neanderthals well as a hybridization that is is compatible with the o hybridization that compatible with the obs Neanderthal ancestry in in contemporary huma Neanderthal ancestry contemporary humans, latter migrated out of of Africa into Eurasia 50 latter migrated out Africa into Eurasia 50 ky Results Results Low Rates of of Interbreeding Between Huma Low Rates Interbreeding Between Humans Using spatially explicit simulations, wewe Using spatially explicit simulations, hav expected amount of of Neanderthal ancestry pr expected amount Neanderthal ancestry in in from Europe (France) and Asia (China) forfo from Europe (France) and Asia (China) admixture with Neanderthals and over variou admixture with Neanderthals and over var derthal ranges (Fig. 1).1). Under our model derthal ranges (Fig. Under our model of range expansion, we find that observed low leve range expansion, we find that observed low l introgression into Eurasians imply the existe introgression into Eurasians imply the exi strong barriers to gene flow between the two
  62. 62. ARTICLE Nature 2010 doi:10.1038/nature09710 Genetic history of an archaic hominin group from Denisova Cave in Siberia David Reich1,2*, Richard E. Green3,4*, Martin Kircher3*, Johannes Krause3,5*, Nick Patterson2*, Eric Y. Durand6*, Bence Viola3,7*, Adrian W. Briggs1,3, Udo Stenzel3, Philip L. F. Johnson8, Tomislav Maricic3, Jeffrey M. Good9, Tomas Marques-Bonet10,11, Can Alkan10, Qiaomei Fu3,12, Swapan Mallick1,2, Heng Li2, Matthias Meyer3, Evan E. Eichler10, Mark Stoneking3, Michael Richards7,13, Sahra Talamo7, Michael V. Shunkov14, Anatoli P. Derevianko14, Jean-Jacques Hublin7, Janet Kelso3, ¨¨ Montgomery Slatkin6 & Svante Paabo3 • 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 sequenced the genome. Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans. 0°C). • Common ancestor with Neanderthal: 600,000 years ago • Interbreeding with Homo sapiens: 4-6% of Melanesian Less than 200,000 years ago, anatomically modern humans (that is, mitochondrial (mt)DNA sequences have been determined from genomes are from present-day humans) humans with skeletons similar to those of Denisovan. Neanderthals . This has shown that all Neanderthals studied so 9–17 appeared in Africa. At that time, as well as later when modern humans appeared in Eurasia, other ‘archaic’ hominins were already present in Eurasia. In Europe and western Asia, hominins defined as Neanderthals on the basis of their skeletal morphology lived from at least 230,000 years 14 October 13 Monday, ago before disappearing from the fossil record about 30,000 years far share a common mtDNA ancestor on the order of 100,000 years ago10, and in turn, share a common ancestor with the mtDNAs of present-day humans about 500,000 years ago10,18,19 (as expected, this is older than the Neanderthal–modern human population split time of 270,000–440,000 years ago estimated from the nuclear genome8). One
  63. 63. H. neanderthalensis H. sapiens Denisovan H. erectus Australopithecines Proconsulidae Monday, 14 October 13 Most lineages went extinct
  64. 64. Stoneking & Krause 2011 Nature Reviews Genetics ? No additional admixture detected despite probable overlap ! detected admixture (location uncertain) Stoneking & Krause 2011 Figure 4 | Dispersal of modern humans from Africa. A map illustrating the Monday, 14 October 13 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 correla in a populat ulation from
  65. 65. A WINDING PATH H. sapiens spread from Africa to western Asia and then to Europe and southern Asia, eventually reaching Australasia and the Americas. After early modern humans left Africa around 60,000 years ago (top right), they spread across the globe and interbred with other descendants of Homo heidelbergensis. 0 Homo sapiens Denisovans Homo floresiensis Neanderthals Homo erectus 0.4 Million years ago Homo heidelbergensis 0.8 Homo antecessor 1.2 Homo erectus 1.6 2.0 H. floresiensis originated in an unknown location and reached remote parts of Indonesia. H. heidelbergensis originated from H. erectus in an unknown location and dispersed across Africa, southern Asia and southern Europe. H. erectus spread to western Asia, then east Asia and Indonesia. Its presence in Europe is uncertain, but it gave rise 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% 98% 2.5% 97.5% 2.5% 5% 92.5% Genes* African Unknown archaic African source Neanderthal Denisovan *Figures are approximate, and for Africa, based on Monday, 14 October 13 Stringer 2012 Nature
  66. 66. Monday, 14 October 13
  67. 67. What about today? Does natural selection (still) act on humans? Monday, 14 October 13
  68. 68. But... Triple (?) misunderstandings: 1. Evolution (ie genetic change) is not only through natural selection • Drift • Sexual selection • ... 2. Medicine can reduce effect of deleterious traits. • OK many are ‘‘alive who otherwise would have perished’’ • But many have limited access to medicine. 3. Even with the best medical care • there are differences in reproductive success Monday, 14 October 13
  69. 69. Some examples Monday, 14 October 13
  70. 70. Pathogens/disease • “Spanish” Flu population Monday, 14 October 13 pandemic of 1918 killed 1-3% of the world’s
  71. 71. Monday, 14 October 13
  72. 72. Monday, 14 October 13
  73. 73. Pathogens/disease • “Spanish” Flu population pandemic of 1918 killed 1-3% of the world’s • AIDS • Dengue, Typhus, Malaria... Monday, 14 October 13
  74. 74. Other examples Monday, 14 October 13
  75. 75. tans maintain normal aero- gories). The XP-EHH (light e profound arterial hypoxia blue) and iHS (dark blue) EGLN1 H D REPORTSchanges in selection candidate sets in- C he existence of system. For example, ele- clude genes in the top 1% evels increase vasodilation of the empirical distribuwhich, when combined with tions of XP-EHH and iHS re13), may increase the avail- sults, respectively, excluding ells (4). Collectively, these those with evidence of posi* * that Tibetans have adapted tive selection in neighboring igh-altitude conditions. The 1populations (see SOM). The D. Huff,1 Haixia Yun,2* Ga Qin,2* Tatum S. Simonson, Yingzhong Yang,2* Chad daptation, however, remains intersection of functionalFelipe R. Lorenzo,3 Jinchuan Xing,1 David J. Witherspoon,1 Zhenzhong Bai,2* candidates with selection canLynn B. Jorde,1† Josef T. Prchal,1,3† RiLi Ge2*† didates (outlined in black) is enriched for regions containenetics, University of Utah School Tibetans have lived ating genes that contribute thousands of years, and they have a distinctive very high altitudes for to UT 84112, USA. 2Research Center suite of physiological local adaptation to them to tolerate environmental hypoxia. These phenotypes traits that enable hypoxia in Tibetans. The genes in the intersection of functional e, Qinghai University Medical are Republic the result selection candidates still exhibit genetic their genetic the population. (B to D) C of adaptation to this environment, but variability in basis remains 0001, People’s clearly of China. Department of Pathology (ARUP), genome-wide scans that reveal positive selection selection scans. The that and bo unknown. We report Tibetan and CHB-JPT genomic regions identified in in several regions top Medicine and VAH, Salt Lake City, figure represent chromosome regions in the adaptation. Positively selected contain genes whose products are likely involved in high-altitude Tibetan (number of chromosomes haplotypes of EGLN1 populations (62 randomly drawn chromosomes from 90 individuals), respectively, f and PPARA were significantly associated with the decreased hemoglobin gh-Altitude Medicine initiated the EGLN1, and (D) HMOX2 genes identified in XPEHH, both genes provides phenotype phenotyp- unique to this highland population. Identification of thesescans, and iHS, respectiv that is imarily responsible for support for previouslywith the highest iHS and XP-EHH scores (indicated by and asterisk) were desi hypothesized mechanisms of high-altitude adaptation an illuminates the haplotype pathways in humans. e should complexity of hypoxia-response for each genomic region. All haplotypes were sorted to the horizontal m be addressed. E-mail: based on the length of uninterrupted matches to the reference sequence. See fig. B.J); josef.prchal@hsc.utah.edu the remaining seven regions and details about these regions. .com (R.L.G.) We used two intersecting criteria to identify he Tibetan highlands are one of the most extreme environments inhabited by hu- genes potentially involved in high-altitude adapmans. Many present-day Tibetan popula- tation: First, a priori candidates for adaptation to 2 JULY 2010 VOL 329 SCIENCE www.sciencemag.org tions are thought to be descendants of people high-altitude hypoxia were chosen because of Genetic Evidence for High-Altitude Adaptation in Tibet T Monday, 14 October 13
  76. 76. 59.6 REPORTS 22.1 8.6 4.6 2.3 35613 27061 10175 25619 44408 1069 1815 2438 8784 26255 40846 33.3 14.9 4.2 2.9 1.7 Deep Human Genealogies Reveal a Selective Advantage to Be on an Expanding Wave Front SLSJ 25.4 1.79*** 43.2 1.48*** tracing back the founding events of new localities. 72.9 2.07*** As shown in Fig. 1, the inferred colonization pro49.9 1.58*** cess is a mixture of long-distance settlements creating an irregular wave front, followed by fur27.7 1.38*** ther, more progressive, short-range expansions, 40.2 which then filled gaps and created a more reg- ular wave front. On the basis of the computation of a wave 7.4 Claudia Moreau,1 Claude Bhérer,1 Hélène Vézina,2 Michèle Jomphe,2 39 15 2.6 99.6 (WFI) (21), we find that the ancestors 2.8*** front index 1,3 1,4,5 * Laurent of the Saguenay and the Lac-Saint-Jean people 4.6 Damian Labuda, 15444 Excoffier *4420 3.5 62.3 1.3*** lived more often on or close to the wave front 2.4 Since their origin, human populations have colonized the whole planet, but the demographic 35777 19726 1.8 30.9 1.3*** than expected by chance (WFI, P < 0.001 in both regions) (fig. S1). Indeed, the very high WFI of processes governing range expansions are mostly unknown. We analyzed the genealogy of more 24161 45.1 than one million individuals resulting from a range expansion in Quebec between 1686 and 1960 0.75 observed in Lac-Saint-Jean corresponds to a situation in which half of the Lac-Saint-Jean and reconstructed the spatial dynamics of the expansion. We find that a majority of the present ancestors had lived directly on the wave front and Saguenay Lac-Saint-Jean population can be traced back to ancestors having lived directly on or 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 2. Age of from the range core, likely due to a of larger effective fertility of from In in the period 1840 lower in the Table pool than thosereproduction and number 20%children of women women SLSJcontrast, WFI is significantlyto 1900. Charlevoix region (P = 0.003) (fig. S1). These on the wave front. This fitness component is heritable on the wave front and not in the core, Note thatthat this table only includes women with known birth dates, such that age at marriage can be this life-history trait evolves during range expansions. results are consistent with different colonization implying dynamics of SLSJ and Charlevoix. The wave computed. front was always widespread in SLSJ where new ost species go through environmental- Quebec parish registers that document the recent localities were continuously settled, whereas it was Mean no. of ly induced range expansions or range temporal and spatial expansion of the settle- much smaller in Charlevoix where most localities Marriage Mean of ment of the Charlevoix Saguenay Lac-Saint- remained in the range core until the 20th century no. of shifts (1), promoting the evolution Mean age at FS ratio EFS ratio married No. of traits associated with dispersal and reproduction Jean (ChSLSJ) region, northeast of Quebec City, (Fig. 1). New immigrants from outsideratio age ChSLSJ children WF/RC WF/RC women prime example of a marriage recent, fast, and constituted an important minority of the people (2). Humans likely colonized the world by a Canada: a children WF/RC (FS) well-documented range expansion (17) (Fig. 1). getting married, with a greater proportion of imseries of range expansions from Africa (3), pos(EFS) sibly with episodes of interbreeding with now The European colonization of Quebec was ini- migrants settling on the wave front than on the with extinct Waveand hominins (4, 5), clines from entry points tiatedand 16084.9 was well establishedQuebec range core, especially before 1900the range core) front (WF) leading to allele frequen- City, in the colony the foundation of by the the wave front and up to 10% in (up to 20% on 2663 9.1 20.5 cy heterozygosity 1.15*** 1.20*** 0.95*** into several continents [e.g., (6, 7)]. Range7.9 end of the 17th century (18). The peopling of the (table S2). Generally, more male than female imexRange core (RC) 1783 4.1 21.6 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, differencemimicking the effect P < 0.001 a rapid demographic growth and the de- toward males is significantly higher in the core t test of sometimes between means; of and both positive selection in recently colonized habitats velopment of the timber industry promoted further than on the wave front (table S3). Nevertheless, (8, 9), neutral through a process called gene surfing (9). a expansions afterof region (SLSJ) (19,River The of reproduction (frontbeen largely colsurfing or even deleteriousalso to the Lac-Saint-Jean upspatial location the newby people of SLSJ have or core) process but mutations net effect 1838 the Saguenay 20). and onized territories recruited directly on the wave Neutral, favorable, can surf selection frequency (10, 11), (P < 0.001 for of front effects) not that there is range positive and increase inon the front. im- spatial and temporal dynamics of the peopling the twoor next to it, butby people from the no s ll n d at e s n s r r J eMonday, 14 October 13 M
  77. 77. Monday, 14 October 13
  78. 78. Natural selection in a contemporary human population c Stephen C. Stearnsa,1 Sean G. Byarsa, Douglas Ewbankb, Diddahally R. Govindarajuc, and Stephen C. Stearnsa,1 a New Haven, CT 06520-8102; bPopulation Studies Center, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8102; bPopulation Studies Center, U Boston University School of Medicine, Boston, MA 02118-2526 Philadelphia, PA 19104-6299; and cDepartment of Neurology, Boston University School of Medicine, Boston, MA 02118-2526 approved September 16, 2009 (received for review June 2 Edited by Peter T. Ellison, Harvard University, Cambridge, MA, and approved September 16, 2009 (received for review June 2 Our aims were to demonstrate that natural selection is operating on contemporary humans, predict future evolutionary change for specific traits with medical significance, and show that for some traits we can make short-term predictions about our future evolution. To do so, we measured the strength of selection, estimated genetic variation and covariation, and predicted the response to selection for women in the Framingham Heart Study, a project of the National Heart, Lung, and Blood Institute and Boston University that began in 1948. We found that natural selection is acting to cause slow, gradual evolutionary change. The descendants of these women are predicted to be on average slightly shorter and stouter, to have lower total cholesterol levels and systolic blood pressure, to have their first child earlier, and to reach menopause later than they would in the absence of evolution. Selection is tending to lengthen the reproductive period at both ends. To better understand and predict such changes, the design of planned large, long-term, multicohort studies should include input from evolutionary biologists. | | | evolutionary rates heritability Homo sapiens medical traits Monday, 14 October 13 identify factors that contribute sity to identify factors that contribute It is the longest running multigenera longest running multigener history. The people originally enrolled The people originally enrolled dominantly European ancestry (20% dominantly European ancestry (20% Ireland, 10% Italy, 10% Quebec). T 10% Italy, 10% Quebec). T 5,209) has been examined every 2 ye has been examined every 2 y between 1948 and 2008. The offspring 1948 and 2008. The offsprin been examined approximately every 4 y examined approximately every 4 y between 1971 and 2008 (4). There is 1971 and 2008 (4). There i cohort (n = 4,095) that is not included ii = 4,095) that is not included in it have not yet completed reproduct not yet completed reproduct many physical and blood chemistry tr physical and blood chemistry tr questionnaire is administered, yielding questionnaire is administered, yielding are deidentified by the FHS and de deidentified by the FHS and d Institutes of Health dbGaP database of Health dbGaP database loaded them for analysis. In this study them for analysis. In this study individuals who were measured three o individuals who were measured three o 5000 people & their kids; 70 traits measured every 2-4 years since 1948. Measuring Selection in a Multicohort Measuring Selection in a Multicohort Natural selection has been measured selection has been measured populations of animals and plants (5) u populations of animals and plants (5) u
  79. 79. NATURE REVIEWS | GENETICS VOLUME 11 | FEBRUARY 2010 | 137 How culture shaped the human genome: bringing genetics and the human sciences together Kevin N. Laland*, John Odling-Smee‡ and Sean Myles§ || Abstract | Researchers from diverse backgrounds are converging on the view that human evolution has been shaped by gene–culture interactions. Theoretical biologists have used population genetic models to demonstrate that cultural processes can have a profound effect on human evolution, and anthropologists are investigating cultural practices that modify current selection. These findings are supported by recent analyses of human genetic variation, which reveal that hundreds of genes have been subject to recent positive selection, often in response to human activities. Here, we collate these data, highlighting the considerable potential for cross-disciplinary exchange to provide novel insights into how culture has shaped the human genome. Accounts of human evolution frequently assume that Monday, 14 October 13 the selective events that shaped us were changes in the adult lactose tolerance12,13,15,16. Estimates for the number of human genes that have been subject to recent rapid
  80. 80. Genetics of our behavior? Monday, 14 October 13
  81. 81. Evolutionary Psychology • Generosity higher if affects reputation • Pheromones Monday, 14 October 13 help identify our mates
  82. 82. Monday, 14 October 13
  83. 83. Summary • Human • (just Monday, 14 October 13 evolution is complicated but fascinating! like any other species!!)
  84. 84. For more info • http://humanorigins.si.edu/ • PBS (Smithonian Institution) Nova Becoming Human (on youtube) • Stoneking & Krause. Learning about human population history from ancient and modern genomes. Nature Reviews Genetics 2011. Monday, 14 October 13
  85. 85. Any questions About first lectures? Monday, 14 October 13
  86. 86. http://qmplus.qmul.ac.uk/course/view.php?id=3972 Semester A: Evolution Week 1: YW – Introduction, Historical context, Neo Darwinism Week 2: YW – Geological Aspects, Drivers of Evolution, Levels of Evolution Week 3: YW – Fossils, DNA and Molecules Week 4: YW – Human Evolution Week 5: DH – Evolution of Sex, Sexual Selection Week 6: AH – Genetic Basis of Evolution Week 7: Mid semester break, no lectures. Week 8: AH – Founder Effects, Genetic Drift In Jean Smith’s Timetable; + Computer Practical (tues or thurs afternoon) not yet on “SMART” Week 9: AH – Mutation, Selection and Gene Selection Week 10: DH – Systematics, Speciation Week 11: DH – Evolution of Parasites, Antibiotics Week 12: DH – Convergence, Revision Session Final Grade: 20% Workshop Monday, 14 October 13 80% Exam

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