Human Evolution Genes and GenomesMajor Population Movements: Peopling of the World

Professor Mark Pallen

OverviewAfricaEuropeIndiaChinaAmericas

African language groups

http://en.wikipedia.org/wiki/File:African_language_families_en.svgMark Dingemanse Creative Commons Attribution 2.5 license

The SanAka “Bushmen”Hunter-gatherers

from Southern Africa

Speak click languages

Probably related to other click-language groups from East Africa

Bushmen represent early branching lineage of AMHIn 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 individualMore variation among Bushmen than among Eurasians!

vast majority of Bushmen SNPs are changes that accumulated since Bushmen lineage diverged from other human populations

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

Bantu Expansion Geographic expansion of Bantu Niger-

Kordofanian-speakers within the past 5000 years, perhaps driven by change to drier climate and adoption of new cropsFirst from Nigeria and Cameroon

into equatorial rainforestsThen into eastern and southern

Africa Evidenced by Bantu Niger-

Kordofanian ancestry in many African populations and widespread distribution of Bantu-related languages independent waves of migration of

western African and East African Bantu-speakers into southern Africa

Settlement History of EuropeFive episodes over the past 50,000 years 1.Pioneer colonisation in Upper Palaeolithic (50

kya)2.Late Glacial re-colonisation from southern

refugia after Last Glacial Maximum (~20kya)3.Postglacial re-colonization of deserted areas

after Younger Dryas cold snap (11.5kya)4.Arrival of Near Easterners with Neolithic

package (10–4 kya)5.small-scale migrations along continent-wide

economic exchange networks from Copper Age

European mtDNA haplogroups

(Torroni et al 2006 Trends in Genetics)

European mtDNA haplogroupsset of mtDNA haplotypes in Europe is much poorer

than in East Asiasuggesting small founding population as a minor shoot

off the main trunk of migration eastwards. Modern European mtDNA haplotypes are mainly

branches of the N and R haplogroups. Age of European mtDNA haplotypes suggests that

Europe was probably populated by anatomically modern humans relatively late, compared to South East AsiaDistribution of certain haplotypes across Europe

reveals an important role of Southern European refugia, in particular, Iberian peninsular in repopulating Europe after the Ice Ages.

Y chromosomes in Europe

(Semino et al 2000)

Western R1bY-haplotype

Middle-Eastern J Y-haplotype

EasternR1a Y-

haplotype•Western European (R1b), •Eastern European (R1a) and •Central European (I)

E C I J R1b R1a P/Q

Central IY-haplotype

•J haplotype is of Middle-Eastern origin and

•E haplotype is of African origin

Major proto-European Palaeolithic Y-haplotypes (~30,000 years old):

Recently (<10,000 years ago) introgressed haplotypes:

African E Y-haplotype

An E/W gradient in Europe?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

Recent post-Neolithic migrations were in all possible directions, so they should have blurred rather than formed the gradient

Such an E/W gradient could have formed only under quite specific conditionsNeolithic demic diffusion model: the postglacial (<10kY)

Neolithic farmers have spread westwards and mixed with local hunter-gatherers who had different gene frequencies

Cultural diffusion model: the farming & other techniques have spread due to cultural contact and have not involved much people movement

The gradient in multiple genes in Europe supports the DDM

The Proto-Indo-Europeans1786, William Jones in Kolkata noted similarities

between Sanskrit and Greek/Latin; later added Gothic, Persian, Celtic

1813, Thomas Young coined term Indo-European1833, Franz Bopp’s Comparative Grammarmid 19th C, August Schleicher’s Stammbaumtheorie;

parallels with Darwinian evolution noted by Darwin and Schleicher

Saussure’s laryngeal theory; confirmed by discovery of Hittite

Attempts to construct Proto-Indo-European But when and where was Proto-Indo-European (PIE)

spoken?

Nowadays most people speak an Indo-European languageDark green: countries where most speak IE languageLight green: countries where IE language has official status

Reconstructions of PIE societyanimal husbandry: domesticated cattle, horses, and dogsagriculture and cereal cultivationclimate with winter snow; boats, wheels for cartssky god; oral heroic poetry; patrilineal kinship system

Schleicher’s reconstruction

Rival Hypotheses for PIE origins Anatolian Hypothesis

Proposed by Colin Renfrew. Indo-European languages

spread peacefully into Europe from Asia Minor from ~ 7000 BCE with advance of farming (“wave of advance”).

Armenian hypothesis PIE spoken during the 4th

millennium BC in Armenian highlands

Kurgan HypothesisProposed by Marija

Gimbutas After kurgans (burial

mounds) of the Eurasian steppes

Indo-Europeans as a nomadic tribe of Pontic-Caspian steppe (Eastern Ukraine/Southern Russia)

Tamed the horse, expanded in waves of invasion during 3rd millennium BCE.

Anatolia

http://www.nature.com/nature/journal/v426/n6965/pdf/426391a.pdf

mtDNA in IndiaBasu 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 NorthCame later from the North West

M

U

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

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 7th century AD

C

C-haplotype is most common in

Mongolians. Traces of Mongolian influence?

CASTEThe Dravidian speaking groups inhabit southern India,Indo-European speakers inhabit northern India and Tibeto-Burman speakers are confined to northeastern India. TRIBALSmall group of Austro-Asiatic speakers in fragmentedgeographical areas of eastern and central India.Andamanese

Demic diffusion in Asia

(Wen et al 2004 Nature)

Three north-to-south migrations:

Han migrations

AD 265–316

AD 618–907

AD 1127–1279

•The first wave involving 0.9 million (~ one-sixth of southern population at that time) during Western Jin Dynasty (AD 265–316)•The second migration, more extensive than the first, during Tang Dynasty (AD 618–907)•The third wave, including 5m immigrants, occurred during Southern Song Dynasty (AD 1127–1279), fleeing Mongols?

Proportion of Northern Han

genes in Southern Han

population

Y mtDNA82% 56%Male-biased migration?

The spread of Han Chinese culture and language explained by two alternative models1.demic diffusion model, which involves mass movement of people2.cultural diffusion model, which refers to cultural impact with limited genetic exchange.

Han Chinese, the world’s largest tribe, with 1.4 bn members

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)

Peopling of the AmericasAsian origin of the earliest Americans amply

established by numerous classical marker studies by the mid-twentieth century:blood group, serum protein, enzyme

polymorphismsMore recently, mtDNA sequences, Y-chromosome

and autosomal marker studies have provided a higher level of resolution in confirming the Asian origin of indigenous Americans

Beringia constituted land connection between Asia and North America during the last glacial maximum (LGM) ~20kya

Peopling of the Americas BUT date and nature of earliest colonisation of Americas still contested

land mass of Beringia buried in ice age, so no “donor” population survives

Curiously, earliest archaeological dates for settlement in the Americas come from South AmericaMonte Verde in Chile ~14kyaPedra Furada in Brazil <30 kya, but questioned by many scholars.

Clovis culture stool tools in N. America ~13 kya

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

migrationsShallow consensus on single migration event

Clovis cultureThree language groupsLed to late 20th C Three Migrations Theory

mtDNA in Siberia

Native Americans

•Both M and N haplogroups are present & widespread in Native Siberian populations

•Interestingly, mtDNA of Native Americans clusters within the Siberian mtDNA trees

mtDNA in Americas

•Native American population contain a rare haplogroup X not present in most Asian populations

•mtDNA haplotype frequencies in Native Americans are quite different from that in Asia.

Peopling of Americas & Y haplotypes

E

EE

EE

E

E

E

E

E

QQ

Q

Q

Q

QQ

P

NNNNNN

N

O

O

O

O

O

O

O

O

O

OO

J

J

J

J

C

CC

C

C

C

C

C

CC

C

C

C

C

JJ

F

F

R

RR

R

R

R

R

AB

B

C

C

C

D

D

BR

M

M

F

R

R

R

R

K

K

K

I

I

R

(Jobling and Tyler-Smith 2003)

Reduced variation in Y haplotypes common in Native Americans compared to Asia; poor resolution using Y chromosomes.

Some early Americans did not look like modern Native Americans

Kennewick Man9.3 kya skeleton from Kennewick in Washington stateInitially thought to look like a Caucasian, then Ainu from Japan; uncertain whether allied to any modern population; controversies over Native American rights to remains

Luzia11.5 kya skeleton from Lapa Vermelha, BrazilResembles Africans, Indigenous Australians, Melanesians and the Negritos of South East AsiaDoes not resemble Native Americans/Siberians

Some early Americans did not look like modern Native Americans

• 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) • 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.

Migration Routes still unresolved

Palaeo-eskimo genomeRasmussen et al 2010first genome sequence of an ancient human

from ~4kya permafrost-preserved hair from a male from the first known culture to settle in Greenland.

the mtDNA and Y-chromosome DNA haplotypes fit within haplogroups typical of north-east Asia

population admixture analyses show no European component in the Saqqaq genome

PCA plots reveal close affiliation to contemporary north-east Siberian populations

SummaryAfrica: San, BantuEurope: Gene gradients and Indo-Europeans

India: tribal and castes, ANI and ASI

China: Han migrations north-southAmericas: peopling via Beringia, but routes and modes unclear