Human origins and evolution

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Human origins and evolution

• Gil McVean, Department of Statistics, Oxford

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Questions about human origins

• What defines a human?
• What does the fossil record tell us?
• What are the genetic changes that make us human?
• What are the genetic changes that make people(s)
  different?

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What makes us human?

• Upright posture, bipedalism
• Advanced tool-making capability
• Big brain, relative to body size, and small
  canine teeth
• Global dispersal
• Use of fire to modify environment
• Language and consciousness (self-awareness)
• Complex culture

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Human brain size

• Humans have an encephalisation quotient of about
  6.5 8.0
• The biggest of any mammal!

Mammals Ebrain 0.12 x Mbody 2/3
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What is culture?

• Language
• Beliefs
• Rituals
• Law
• Morality
• Manners
• Visual arts

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Great ape phylogeny

• Human and chimp ancestors split about 6 MYA

Hacia JG (2001)
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A recent X?

• Suggestion of a more recent divergence time for X
  chromosome
• Patterson et al (2006)

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Some terminology

• Hominid is a term used to describe Humans and any
  lineages that share a common ancestor with humans
  more recently than the human-chimp split

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An overview of the fossils
Human chimp split
Origin of H. sapiens sapiens
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Australopithecus

• 3.9 3 MYA
• Both gracile and robust forms (latter called
  Paranthropus)
• Evidence for sexual dimorphism within these
  species

Australopithecus robustus
Australopithecus africanus
Australopithecus afarensis (Lucy)
Australopithecus boisei
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The Laetoli footprints

• First evidence of bipedalism
• 3.7 MYA
• Three sets of tracks in volcanic ash

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Lucy

• 3.2 MYA from Ethiopia
• Lucy was bipedal, an adaptation for travel across
  savannah woodlands and grasslands
• Big teeth, still not a big brain.

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Early Homo species
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Homo habilis

• 2.6 1.4 MYA
• Some, but not all, have slightly bigger brains
• Maker of tools (Oldowan tools)

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Striding out, standing tall, and at last, a big
brain
Brain size versus height

• Turkana boy (1.5 million years ago) the earliest
  individual with estimated brain size (909cc)
  significantly above primate allometry curve.
• Homo ergaster

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H. ergaster lived in Eurasia at same time as in
Africa

• Dmanisi fossils date to 1.7 mya
• Caucasus Mountains, Republic of Georgia (well
  north of the tropics)
• Associated Oldowan tools
• H. ergaster is the first species of hominin
  adapted for endurance running.

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Why leave Africa? The role of Pleistocene climate
change

• Middle Pleistocene climate colder and more
  variable long cold glacial periods punctuated by
  short, warmer interglacials
• Migrations of many species between Africa and
  Eurasia during interglacials

Warm
Onset of Lower Pleistocene glaciations at 2
million years ago with formation of permanent ice
sheets and sharp cooling. Africa becomes drier.
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What is life in the Pleistocene like for early
Homo species?

• Hunting game as well as scavenging
• Control of fire
• Possibly from 2MYA
• Improving the tool kit
• more elaborate Acheulean stone tools e.g.
  handaxe for butchering
• Increasingly complex social behaviour

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Homo erectus did cross sea barriers

• Archaeology on Flores, dates to 840,000 years ago
• H. florensiensis (Hobbits) on Flores date to as
  recently as 20,000 yrs ago

Hobbit on left compared with modern human
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Homo sapiens neanderthalensis

• From H. heidelbergensis (0.75 0.25 MYA)
• Only found in Europe and near East
• Diverged from AMH lineage about 0.8 MYA
• More robust than AMH, but shared many features of
  culture
• Music
• Jewellery
• Complex tools
• Ritual (burial of dead)
• Language ability?

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Homo sapiens sapiens

• Anatomically modern humans (AMH)
• Modern anatomy at 200,000 years ago (Ethiopia
  Omo I and II)
• Out-of-Africa event 70,000 years ago

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Out of Africa diversity among early modern Homo
sapiens

1. Skhul 5, Israel, 90,000 Yrs
2. Cro-Magnon 1, France, 23-27 KYrs
3. Kow Swamp, robust Aboriginal Australian, 9-13 KYrs

Shared features Cranial vault height high and
domed, brow ridges lighter or absent, chin present
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Dispersal of AMHs out of Africa

• Into Middle East by 90,000 years ago, and then
  retreat. (Neanderthal distribution expands)
• Reach Australia by 60,000 years ago, apparently
  via south Asian coastal route.
• 40,000 years ago substantial presence of moderns
  in Europe and Asia (little evidence in
  archaeological record at earlier dates)
• Last Neanderthals about 25,000 years ago
• Bottleneck in dispersal out of Africa -
  implicated by genetic data
• Note that this bottleneck is not associated with
  speciation, only with modest structure between
  sub-Saharan and other human populations.

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What does genetic variation tell us about human
evolution?

• Modern humans appear in the fossil record about
  200K years ago
• The mitochondrial Eve dates back to about 150K
  years ago
• The Y-chromosome Adam dates back to about 70K
  years ago
• AMHs left Africa about 70KYA
• For most of our genome, however, the common
  ancestor is about 500K 1M years ago
• This predates the origin of Homo sapiens
  considerably

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Did early humans interbreed with Neanderthals?
Neanderthals
mtDNA sequences say no
Ovchinnikov et al (2000)
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But

• There is some evidence for this in the presence
  of unusual haplotypes found in Europe composed of
  SNPs not found in non-European populations

Plagnol and Wall (2006)
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Deeper trees in the human genome

• There is growing evidence that some regions of
  our genome have truly ancient common ancestors
• Dystrophin has an ancient haplotype found
  primarily outside Africa suggesting a
  colonisation of gt160KYA
• There is an inversion found primarily in
  Europeans that is roughly 3MY old

Haplotype 1
Haplotype 2
Stefansson et al (2005)
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What are the genetic differences that make us
human?
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Chromosomal changes

• Human chromosome 2 is a fusion of two chromosomes
  in great apes
• There are several inversion differences between
  the chromosomes

Feuk et al (2005)
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Gene loss

• Loss of enzymes that make sialic acid
• Sugar on cell surface that mediates a variety of
  recognition events involving pathogenic microbes
  and toxins
• Myosin heavy chain
• Associated with gracilization

Wang et al (2006)
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Gene evolution

• FOXP2 is a highly conserved gene (across the
  mammalia), expressed in the brain. Mutations in
  the gene in humans are associated with specific
  language impairment
• Across the entire mammalian phylogeny, there have
  only been a very few amino acid changing
  substitutions
• However, two amino acid changes have become fixed
  in the lineage leading to modern humans since the
  split with the chimpanzee lineage

Enard et al. (2002)
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What are the genetic differences that make people
and peoples different?
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How do we differ? Let me count the ways

• Single nucleotide polymorphisms
• 1 every few hundred bp
• Short indels (insertion/deletion)
• 1 every few kb
• Microsatellite (STR) repeat number
• 1 every few kb
• Minisatellites
• 1 every few kb
• Repeated genes
• rRNA, histones
• Large inversions, deletions
• Y chromosome, Copy Number Variants (CNVs)

TGCATTGCGTAGGC TGCATTCCGTAGGC
TGCATT---TAGGC TGCATTCCGTAGGC
TGCTCATCATCATCAGC TGCTCATCA------GC
100bp
1-5kb
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Detecting recent adaptive evolution

• Lets look closely at the dynamics of the
  fixation process for adaptive mutations
• The fixation of a beneficial mutation is
  associated with a change in the patterns of
  linked neutral genetic variation
• This is known as the hitch-hiking effect (Maynard
  Smith and Haigh 1974)
• Looking for the signature of hitch-hiking can be
  a good way of detecting very recent fixation
  events

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Diversity is not evenly distributed across genes
II

• Adaptive evolution wipes out diversity nearby
  due to the hitch-hiking effects of a selective
  sweep
• e.g. Duffy-null locus in sub-Saharn africa,
  protects against P. vivax

FYO mutation
African
Pop1
Pop2
European
Ancestral allele
Derived allele
Missing data
Hamblin and Di Rienzo (2000)
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Long haplotypes

• A selective sweep at the Lactase gene in Europeans

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Strong population differentiation

• SLC24A5

Lamason et al (Science 2005)
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Classes of selected genes
Voight et al. (2005)