Download Human origins and evolution - Department of Statistics Oxford

Human origins and evolution
Gil McVean, Department of Statistics, Oxford
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?
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
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
What is culture?
• Language
• Beliefs
• Rituals
• Law
• Morality
• Manners
• Visual arts
Great ape phylogeny
• Human and chimp ancestors split about 6 MYA
Hacia JG (2001)
A recent X?
• Suggestion of a more recent divergence time for X chromosome
– Patterson et al (2006)
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
An overview of the fossils
Origin of H. sapiens sapiens
Human – chimp split
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
The Laetoli footprints
• First evidence of bipedalism
• 3.7 MYA
• Three sets of tracks in volcanic ash
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.
Early Homo species
Homo habilis
• 2.6 – 1.4 MYA
• Some, but not all, have slightly bigger brains
• Maker of tools (Oldowan tools)
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
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.
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.
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
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
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?
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
Out of Africa: diversity among early modern Homo sapiens
(a) Skhul 5, Israel,
90,000 Yrs
(b) Cro-Magnon 1,
France, 23-27
KYrs
(c) Kow Swamp,
robust Aboriginal
Australian, 9-13
KYrs
Shared features:
Cranial vault
height high and
domed, brow
ridges lighter or
absent, chin
present
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.
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
Did early humans interbreed with Neanderthals?
Neanderthals
mtDNA sequences say no…
Ovchinnikov et al (2000)
But…
• There is some evidence for this in the presence of unusual
haplotypes found in Europe composed of SNPs not found in nonEuropean populations
Plagnol and Wall (2006)
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 >160KYA
• There is an inversion found primarily in Europeans that is roughly
3MY old
Haplotype 1
Haplotype 2
Stefansson et al (2005)
What are the genetic differences
that make us human?
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)
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)
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)
What are the genetic differences
that make people and peoples
different?
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
TGCATTGCGTAGGC
TGCATTCCGTAGGC
TGCATT---TAGGC
TGCATTCCGTAGGC
TGCTCATCATCATCAGC
TGCTCATCA------GC
• Minisatellites
– 1 every few kb
≤100bp
• Repeated genes
– rRNA, histones
1-5kb
• Large inversions, deletions
– Y chromosome, Copy Number Variants (CNVs)
Detecting recent adaptive evolution
• Let’s 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
Diversity is not evenly distributed across genes II
• Adaptive evolution ‘wipes out’ diversity nearby due to the hitchhiking effects of a selective sweep
– e.g. Duffy-null locus in sub-Saharn africa, protects against P. vivax
FY*O mutation
African
Pop1
Pop2
European
Hamblin and Di Rienzo (2000)
Ancestral allele
Derived allele
Missing data
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Long haplotypes
• A selective sweep at the Lactase gene in Europeans
Strong population differentiation
• SLC24A5
Lamason et al (Science 2005)
Classes of selected genes
Voight et al. (2005)