Evolution of human diversity

The history of Homo sapiens

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The primates

Chimpanzee

OrangutanGorilla

Human

Millions years ago

GibbonMacaque

HumanChimpanzeeBonoboGorillaOrangutanGibbon

HumanBonobo ChimpanzeeOrangutanMacaque Gorilla!2

The last most recent common ancestor of humans and chimps

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} 6 – 7 MYA – fossils } Problems assigning fossils to lineages

} 5 – 6 MYA – sequence comparisons } Different models give different results (up to 2x)

} Not earlier than 8 MYA } As distant from humans, as from chimps

} we do not come from chimps or any other modern primate

Complex relations

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} Many primate fossils found, some existed at the same time } Difficult to establish phylogeny

} Ancestors or side lineages?

Sahelanthropus tchadensis - Toumaï} Close to the MRCA of humans

and chimps? } Skull the size of chimp, but

proportions more “human” } About the time of speciation } Could be a side lineage?

} Only a fragment of one skull found

} ~ 6-7 MYA

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Orrorin tugenensis

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} Discovered: 2001 } ~ 5 - 6 MYA } Ancestor of Homo?

} If so, was Australopithecus a side lineage? } Some characteristics more human-like than

Australopithecus

} Bipedal? } based on bone structure – at least

partially

} Habitat – forest or savanna? } forest or border

Ardipithecus ramidus - Ardi

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} Discovered in 1994, published in 2009 } 4.4 MYA } Oldest hominin } At least partially bipedal } Ancestor of Australopithecus (?)

Ardipithecus ramidus - Ardi

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Ardipithecus

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Debate

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} It is difficult to assign the older fossils to a lineage } human lineage (hominins)? } chimpanzee lineage? } another lineage, with no surviving descendants

Evolution is not a straight line!

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Australopithecus

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} Many species found } gracile and robust

} 4 – 2 MYA } Most famous: A. afarensis

} Lucy (~3.6 mln lat) } Mrs. Ples

} A. africanus } The Taung child

} A. boisei - Olduvai

Australopithecus sediba

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} Described in 2010, Age: ~ 2 MY } Many traits between Australopithecus and Homo

Australopithecus sediba

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Skull volume closer to Australopithecus (~420 cm3), but some morphological traits closer to Homo - lateral asymmetry – language?

http://www.sciencemag.org

Human ancestry?

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} Australopithecus afarensis -> Homo habilis } A. sediba – side lineage

!} A. africanus -> A. sediba -> Homo

} A. afarensis – side lineage

Homo

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} ~ 2.3 MYA } older than A. sediba – one had to be a side branch

} The Olduvai culture tools (1.9 MYA) – Homo habilis

} Homo erectus, H. ergaster (“pithecanthropus”) – 1.5 MYA, extinct 70 000 YBP } First to leave Africa } First to use fire } Hunting (spears) } Social structures

Narzędzie sprzed 1,8 mln. lat z Olduvai British Museum

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Homo

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} Fossils found in Republic of Georgia (Dmanisi) (~1.8 MYA) suggest that H. habilis, H. ergaster and H. rudolfensis could be the same species as H. erectus

} Based on morphological variation (no ancient DNA that old)

The cradle of humanity

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Australopithecus afarensis (Lucy) oldest Homo fossils (a jawbone ~ 2.3 MY)

Australopithecus, Homo habilis, H. erectus, H. sapiens

Australopithecus africanus A. sediba

The cradle of humanity

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The first migrations from Africa

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About 2 MYA …

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Multiregional hypothesis = regional continuity

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Multiregional evolution

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} Human ancestors left Africa ~ 2 million years ago and evolved in parallel on different continents

} Gene flow (continuity) between regional populations } if that were the case, TMRCA of modern humans should

be ~ 2 MYA } mtDNA studies showed TMRCA ~ 200 000 years

The OAR model (Out of Africa Replacement)

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OAR

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} Out of Africa } ~ 200 000 an ancestral population (already

anatomically modern H. sapiens) migrated from Africa to other continents

} New migrants displaced the previous hominids, without mixing and drove them to extinction

} All modern humans are descendants of this last wave of migration

} mtDNA is highly polymorphic } inherited as a single genetic unit (uniparental

inheritance) } sets of polymorphism inherited together as

haplotypes } haplogroups (clusters of haplotypes sharing

common polymorphisms) correlate with population history - used in anthropology, forensics etc.

mtDNA polymorphism

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mtDNA haplogroups

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mtDNA tree

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Y chromosome haplogroups

Jobling & Tyler-Smith (2003) Nature Rev. Genet. 4, 598-612!32

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Conclusions} mtDNA and chromosome Y trees are both rooted

in African populations } TMRCA -100 000—200 000 years } Supports OAR (recent African descent)

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Human genetic diversity is low

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} Two  chimpanzees  (e.g.  Central  and  Western  African)  have  up  to  5  x  more  genetic  differences  than  most  distant  humans  

} Human  genetic  diversity  highest  in  Africa  } Bottlenecks  

} Migrations  -­‐  serial  founder  effect  } Natural  disaster  70  000  years  ago  (Toba  volcano)? } Population  reduced  in  Africa  before  migrations  (~170  000years  ago,  climate  change)?

Population bottleneck

An episode of reduction in population size, leading to reduced allelic diversity

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Founder effect

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} A new population started by a small subgroup of original population can have radically different allele frequencies

} Some rare human genetic diseases are frequent in particular isolated populations

} Reduction in human genetic diversity – serial founder effect } genetic diversity decreases with

increasing distance from African ancestors

The island of the colorblind

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} In 1775 the Pingelap atoll was devastated by a typhoon, killing ~90% of the population, ~20 people survived

} One of them was the ruler Nahnmwarki Mwanenised, who was a carrier of the rare autosomal recessive achromatopsia

} Currently 10% of islanders are colorblind, a 30% are carriers } In the USA the incidence of achromatopsia is 1:33 000

} Achromatopsia (nonfunctional cones) is not daltonism!

• The ‘Star cluster’ of Y haplotypes in Mongolia ~1,000 (700-1300) years ago • Currently in ~8% men in Central-Eastern Asia, ~0.5% worldwide • Genghis Khan?

Zerjal et al. (2003) Am. J. Hum. Genet. 72, 717-721

Recent changes in diversity

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Neanderthals} Earliest fossil traces (Asia) ~ 400 000 years b.p. } Lived in Europe, extinct~30 000 years b.p. } Modern humans colonized Europe~ 40 000 - 50

000 years b.p. } Were Neanderthals ancestors of Europeans, did

they interbreed with humans?

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Neanderthals

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} Human and Neanderthal lineages split ~ 600 000 years ago } Was in Europe before H. sapiens (earlier migration) } Culture (burials), tools, probably speech

Wikimedia commons, Anthropological Institute, University of Zürich

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The Neanderthal genome project

} mtDNA fragments of several specimens (1997) } ~ 106 bp of nDNA (2006) } 60% of nuclear genome (2010) } more complete genome of several specimens

(2013)

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Krings M., Stone A., Schmitz R.W., Krainitzki H., Stoneking M., and Pääbo S. (1997), Cell, 90:19-30.

mtDNA

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Knight A. (2003): Journal of Human Evolution, 44:627-32.

mtDNA tree

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mtDNA - conclusions} Neanderthal mtDNA outside the human tree } Not closer to Europeans than to other populations } No sign of interbreeding in Neanderthal maternal

lineage } Low population genetic diversity

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nDNA results - evolution

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Genome sequencing conclusions

} Human and Neanderthal lineages split long before the last common ancestor of modern humans

} Neanderthals were not our ancestors } What about interbreeding?

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The 2010 genome analysis

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} Confirmed the final split of lineages ~270 000 - 440 000 years ago

} SNP polymorphic sites – Neanderthal alleles found in human genomes, but only from Europe, Asia, and Oceania

} No Neanderthal SNPs in African genomes

Did humans and Neanderthals interbreed?

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} ~ 4% of polymorphisms in Eurasian genomes of Neanderthal origin !

} Low level of interbreeding between Neanderthals and ancestors of Eurasian populations

Scenarios

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} Amount of Neanderthal alleles is the same in Europe, Asia and Papua New Guinea } Interbreeding with the ancestors of E, A i PNG,

somewhere in the Middle East } Intermixing was rare

} wavefront effect – rapid expansion of migrant population amplifies the alleles intermixed from the encountered local populations

Not just Neanderthals

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} Fossils from the Denisova cave (Altai mountains) } Contemporary of Neanderthals

} probably a sister group } Traces of interbreeding in human populations from Oceania

} intermixing episode during migration to SE Asia

Interbreeding

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} Recent Denisovan genome sequence (2013) suggests interbreeding with H. sapiens, H. neanderthalensis and a fourth unknown hominid

The Sima de los Huesos mystery

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} DNA from a 400 000 years old bone fragment from Northern Spain- mtDNA closer to Denisovan than Neanderthal } bones and teeth look closer to Neanderthal } ancestor of Denisovans and Neanderthals? } a separate lineage?

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Conclusions

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} OAR is essentially supported, but more complex than thought

} Migrants could interbreed with earlier populations

Not so simple story

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} mtDNA of modern Europeans is different from European mtDNA from before 10 000 years ago } neolithic migrations (~7 000 YBP) } subsequent migrations

} also early and late Neanderthal mtDNA is different } significant inbreeding among Neanderthals - small

population size (cause of extinction?)

European prehistory

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} First settlement from Africa (~ 50 000 YBP) } Glacial period - repeopling from southern refugia and

postglacial recolonization (18 000 - 10 000 YBP) } Neolithic farmer migration from Near East (7 000 YBP) } later migrations

} Indo-European migration 4 000 - 1 000 YBP

European prehistory

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} 3 ancestral populations } West European Hunter-Gatherers (earliest) } Ancient North Eurasians (Siberia), also contributed to Native

Americans } Early European Farmers (Middle East, Neolithic revolution)

} Based on ancient DNA sequences from 7 000 - 8 000 year old skeletons

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Descendants of the first Europeans?

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} All European populations are a mixture of pre-neolithic (hunter-gatherer) and neolithic (farming) ancestry

} The only signs of continuity from pre-neolithic times - the Basque

Out of Africa - human genetic diversity

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Genetic diversity gradient

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More than genes

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} Genetic diversity correlates with language diversity

The diversity of languages

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classification based on phonemes (sounds)

phoneme diversity

Atkinson, Science (2011) 332: 346-349

The spread of language

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The question of race

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} Lewontin’s argument } variation within group higher than between groups } traits allowing to distinguish races - ~6% of all variability

} Traditional classification of races is based on traits that are not a good measure of genetic similarity } skin colour (~6 genes), nose and eye shape – under selection

} Some traits do show correlation (covariance) } gradients, not groups

} A continuum of genetic variability reflecting population history is real

The question of race

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} A continuum of genetic variability reflecting population history is real

} But it does not allow to create meaningful divisions } A monophyletic group that would include all the

descendants of a common ancestor of Africans would also include all non-Africans