Bio380 hum evolgen2011_major_populations

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Third lecture in my series on human evolution, migration, population genetics and genomics

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Bio380 hum evolgen2011_major_populations

  1. 1. Human Evolution Genes and Genomes Major Population Movements: Peopling of the World Professor Mark Pallen
  2. 2. Overview <ul><li>Africa </li></ul><ul><li>Europe </li></ul><ul><li>India </li></ul><ul><li>China </li></ul><ul><li>Americas </li></ul>
  3. 3. African language groups http://en.wikipedia.org/wiki/File:African_language_families_en.svg Mark Dingemanse Creative Commons Attribution 2.5 license
  4. 4. The San <ul><li>Aka “Bushmen” </li></ul><ul><li>Hunter-gatherers from Southern Africa </li></ul><ul><li>Speak click languages </li></ul><ul><li>Probably related to other click-language groups from East Africa </li></ul>
  5. 11. Bushmen represent early branching lineage of AMH <ul><li>In 117Mb of exome, average difference between a pair of Bushmen was 1.2 bp per kilobase, compared to an average of 1.0 per kilobase between a European and Chinese individual </li></ul><ul><ul><li>More variation among Bushmen than among Eurasians! </li></ul></ul><ul><li>vast majority of Bushmen SNPs are changes that accumulated since Bushmen lineage diverged from other human populations </li></ul><ul><li>gene flow between Bushmen and Bantu shown by Tutu’s L0 (Bushman) type mtDNA and the Bantu-specific Y-chromosomal markers in one of the Bushmen, MD8 </li></ul>
  6. 13. Bantu Expansion <ul><li>Geographic expansion of Bantu Niger-Kordofanian-speakers within the past 5000 years, perhaps driven by change to drier climate and adoption of new crops </li></ul><ul><ul><li>First from Nigeria and Cameroon into equatorial rainforests </li></ul></ul><ul><ul><li>Then into eastern and southern Africa </li></ul></ul><ul><li>Evidenced by Bantu Niger-Kordofanian ancestry in many African populations and widespread distribution of Bantu-related languages </li></ul><ul><ul><li>independent waves of migration of western African and East African Bantu-speakers into southern Africa </li></ul></ul>
  7. 15. Settlement History of Europe <ul><li>Five episodes over the past 50,000 years </li></ul><ul><li>Pioneer colonisation in Upper Palaeolithic (50 kya) </li></ul><ul><li>Late Glacial re-colonisation from southern refugia after Last Glacial Maximum (~20kya) </li></ul><ul><li>Postglacial re-colonization of deserted areas after Younger Dryas cold snap (11.5kya) </li></ul><ul><li>Arrival of Near Easterners with Neolithic package (10–4 kya) </li></ul><ul><li>small-scale migrations along continent-wide economic exchange networks from Copper Age </li></ul>
  8. 16. European mtDNA haplogroups (Torroni et al 2006 Trends in Genetics)
  9. 17. European mtDNA haplogroups <ul><li>set of mtDNA haplotypes in Europe is much poorer than in East Asia </li></ul><ul><ul><li>suggesting small founding population as a minor shoot off the main trunk of migration eastwards. </li></ul></ul><ul><ul><li>Modern European mtDNA haplotypes are mainly branches of the N and R haplogroups. </li></ul></ul><ul><li>Age of European mtDNA haplotypes suggests that Europe was probably populated by anatomically modern humans relatively late, compared to South East Asia </li></ul><ul><ul><li>Distribution of certain haplotypes across Europe reveals an important role of Southern European refugia, in particular, Iberian peninsular in repopulating Europe after the Ice Ages. </li></ul></ul>
  10. 19. Y chromosomes in Europe (Semino et al 2000) Western R1b Y-haplotype Middle-Eastern J Y-haplotype Eastern R1a Y-haplotype <ul><li>Western European ( R1b ), </li></ul><ul><li>Eastern European ( R1a ) and </li></ul><ul><li>Central European ( I ) </li></ul>E C I J R1b R1a P/Q Central I Y-haplotype <ul><li>J haplotype is of Middle-Eastern origin and </li></ul><ul><li>E haplotype is of African origin </li></ul>Major proto-European Palaeolithic Y-haplotypes (~30,000 years old): Recently (<10,000 years ago) introgressed haplotypes : African E Y-haplotype
  11. 21. An E/W gradient in Europe? <ul><li>The allele frequencies of many protein markers have a maximum (or a minimum) in the southeastern corner of Europe/Levant, and decrease (or increase) smoothly as one proceeds west and north </li></ul><ul><li>Recent post-Neolithic migrations were in all possible directions, so they should have blurred rather than formed the gradient </li></ul><ul><li>Such an E/W gradient could have formed only under quite specific conditions </li></ul><ul><ul><li>Neolithic demic diffusion model : the postglacial (<10kY) Neolithic farmers have spread westwards and mixed with local hunter-gatherers who had different gene frequencies </li></ul></ul><ul><ul><li>Cultural diffusion model : the farming & other techniques have spread due to cultural contact and have not involved much people movement </li></ul></ul><ul><li>The gradient in multiple genes in Europe supports the DDM </li></ul>
  12. 22. The Proto-Indo-Europeans <ul><li>1786, William Jones in Kolkata noted similarities between Sanskrit and Greek/Latin; later added Gothic, Persian, Celtic </li></ul><ul><li>1813, Thomas Young coined term Indo-European </li></ul><ul><li>1833, Franz Bopp’s Comparative Grammar </li></ul><ul><li>mid 19 th C, August Schleicher’s Stammbaumtheorie; parallels with Darwinian evolution noted by Darwin and Schleicher </li></ul><ul><li>Saussure’s laryngeal theory; confirmed by discovery of Hittite </li></ul><ul><li>Attempts to construct Proto-Indo-European </li></ul><ul><li>But when and where was Proto-Indo-European (PIE) spoken? </li></ul>
  13. 23. <ul><li>Reconstructions of PIE society </li></ul><ul><ul><li>animal husbandry: domesticated cattle, horses, and dogs </li></ul></ul><ul><ul><li>agriculture and cereal cultivation </li></ul></ul><ul><ul><li>climate with winter snow; boats, wheels for carts </li></ul></ul><ul><ul><li>sky god; oral heroic poetry; patrilineal kinship system </li></ul></ul>Nowadays most people speak an Indo-European language Dark green: countries where most speak IE language Light green: countries where IE language has official status
  14. 24. Schleicher’s reconstruction
  15. 28. Rival Hypotheses for PIE origins <ul><li>Anatolian Hypothesis </li></ul><ul><ul><li>Proposed by Colin Renfrew. </li></ul></ul><ul><ul><li>Indo-European languages spread peacefully into Europe from Asia Minor from ~ 7000 BCE with advance of farming (“wave of advance”). </li></ul></ul><ul><li>Armenian hypothesis </li></ul><ul><ul><li>PIE spoken during the 4th millennium BC in Armenian highlands </li></ul></ul><ul><li>Kurgan Hypothesis </li></ul><ul><ul><li>Proposed by Marija Gimbutas </li></ul></ul><ul><ul><li>After kurgans (burial mounds) of the Eurasian steppes </li></ul></ul><ul><ul><li>Indo-Europeans as a nomadic tribe of Pontic-Caspian steppe (Eastern Ukraine/Southern Russia) </li></ul></ul><ul><ul><li>Tamed the horse, expanded in waves of invasion during 3rd millennium BCE. </li></ul></ul>Anatolia
  16. 31. http://www.nature.com/nature/journal/v426/n6965/pdf/426391a.pdf
  17. 34. mtDNA in India Basu et al (2003) studied 44 geographically & socially disparate ethnic populations of India (over 1000 humans) for Y chromosomal & mitochondrial genotype Mitochondrial haplogroups Haplogroup M is the most common (>46%) ancestral type Haplogroup U is common in the North Came later from the North West Ancestral mtDNA haplogroup M is most common in tribal groups that represent “original” Indian population and uncommon in caste societies, especially brahmins, which mainly represent more recent immigrants M U
  18. 35. Y chromosomes in India ( McElreavey & Quintana-Murci 2005 Annals of Human Biology. Basu et al 2003 Genome Research ) K* The K* Y-haplotype is one of the oldest in India and most common in tribes, but not in castes M M-haplotype is of Iranian origin and was probably brought to India by Zoroastrians in the 7 th century AD C C-haplotype is most common in Mongolians. Traces of Mongolian influence?
  19. 37. CASTE The Dravidian speaking groups inhabit southern India, Indo-European speakers inhabit northern India and Tibeto- Burman speakers are confined to northeastern India. TRIBAL Small group of Austro-Asiatic speakers in fragmented geographical areas of eastern and central India. Andamanese
  20. 38. Demic diffusion in Asia (Wen et al 2004 Nature ) Three north-to-south migrations: <ul><li>The first wave involving 0.9 million (~ one-sixth of southern population at that time) during Western Jin Dynasty (AD 265–316) </li></ul><ul><li>The second migration, more extensive than the first, during Tang Dynasty (AD 618–907) </li></ul><ul><li>The third wave, including 5m immigrants, occurred during Southern Song Dynasty (AD 1127–1279), fleeing Mongols? </li></ul><ul><li>The spread of Han Chinese culture and language explained by two alternative models </li></ul><ul><li>demic diffusion model , which involves mass movement of people </li></ul><ul><li>cultural diffusion model , which refers to cultural impact with limited genetic exchange. </li></ul>Han Chinese, the world’s largest tribe, with 1.4 bn members Han migrations AD 265–316 AD 618–907 AD 1127–1279 Proportion of Northern Han genes in Southern Han population Y mtDNA 82% 56% Male-biased migration?
  21. 39. The genetic legacy of Genghis Khan? The age of haplogroup C is about 1,000 years and it seemed to have originated in Mongolia. It is thought haplogroup C represents putative male-line descendants of Genghis Khan (circa 1162–1227) Haplogroup C is widespread in Asia (Jobling and Tyler-Smith 2003)
  22. 40. Peopling of the Americas <ul><li>Asian origin of the earliest Americans amply established by numerous classical marker studies by the mid-twentieth century: </li></ul><ul><ul><li>blood group, serum protein, enzyme polymorphisms </li></ul></ul><ul><li>More recently, mtDNA sequences, Y-chromosome and autosomal marker studies have provided a higher level of resolution in confirming the Asian origin of indigenous Americans </li></ul><ul><li>Beringia constituted land connection between Asia and North America during the last glacial maximum (LGM) ~20kya </li></ul>
  23. 41. Peopling of the Americas <ul><li>BUT date and nature of earliest colonisation of Americas still contested </li></ul><ul><ul><li>land mass of Beringia buried in ice age, so no “donor” population survives </li></ul></ul><ul><li>Curiously, earliest archaeological dates for settlement in the Americas come from South America </li></ul><ul><ul><li>Monte Verde in Chile ~14kya </li></ul></ul><ul><ul><li>Pedra Furada in Brazil <30 kya, but questioned by many scholars. </li></ul></ul><ul><li>Clovis culture stool tools in N. America ~13 kya </li></ul>
  24. 42. Peopling of Americas Americas were populated by three main waves or “blitzkriegs” of immigrants from Asia, corresponding to language groups Eskimo-Aleut Na-Dene Amerind Modern population DNA-based genetics data provides no support for these three migrations Shallow consensus on single migration event Clovis culture Three language groups Led to late 20 th C Three Migrations Theory
  25. 43. mtDNA in Siberia <ul><li>Both M and N haplogroups are present & widespread in Native Siberian populations </li></ul><ul><li>Interestingly, mtDNA of Native Americans clusters within the Siberian mtDNA trees </li></ul>Native Americans
  26. 44. mtDNA in Americas <ul><li>Native American population contain a rare haplogroup X not present in most Asian populations </li></ul><ul><li>mtDNA haplotype frequencies in Native Americans are quite different from that in Asia. </li></ul>
  27. 45. Peopling of Americas & Y haplotypes (Jobling and Tyler-Smith 2003) Reduced variation in Y haplotypes common in Native Americans compared to Asia; poor resolution using Y chromosomes. E E E E E E E E E E Q Q Q Q Q Q Q P N N N N N N N O O O O O O O O O O O J J J J C C C C C C C C C C C C C C J J F F R R R R R R R A B B C C C D D B R M M F R R R R K K K I I R
  28. 46. Some early Americans did not look like modern Native Americans Kennewick Man 9.3 kya skeleton from Kennewick in Washington state Initially thought to look like a Caucasian, then Ainu from Japan; uncertain whether allied to any modern population; controversies over Native American rights to remains Luzia 11.5 kya skeleton from Lapa Vermelha, Brazil Resembles Africans, Indigenous Australians, Melanesians and the Negritos of South East Asia Does not resemble Native Americans/Siberians
  29. 47. Some early Americans did not look like modern Native Americans <ul><li>the migratory hypothesis , which suggests that the biological variation among South American groups was the result of a variable number of migratory waves (Palaeo-Americans, then Amerindians) </li></ul><ul><li>the local diversification hypothesis , i.e. that all South American groups descend from the same ancestral population or from populations related to each other, with local random (i.e. genetic drift) and non-random factors (i.e. selection and phenotypic plasticity) as the main causes of the diversification. </li></ul>
  30. 48. Migration Routes still unresolved
  31. 50. Palaeo-eskimo genome <ul><li>Rasmussen et al 2010 </li></ul><ul><li>first genome sequence of an ancient human from ~4kya permafrost-preserved hair from a male from the first known culture to settle in Greenland. </li></ul><ul><li>the mtDNA and Y-chromosome DNA haplotypes fit within haplogroups typical of north-east Asia </li></ul><ul><li>population admixture analyses show no European component in the Saqqaq genome </li></ul><ul><li>PCA plots reveal close affiliation to contemporary north-east Siberian populations </li></ul>
  32. 52. Summary <ul><li>Africa: San, Bantu </li></ul><ul><li>Europe: Gene gradients and Indo-Europeans </li></ul><ul><li>India: tribal and castes, ANI and ASI </li></ul><ul><li>China: Han migrations north-south </li></ul><ul><li>Americas: peopling via Beringia, but routes and modes unclear </li></ul>

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