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Human Evolution Bio263 Genes and Genomes
Who is our closest relative?
Professor Mark Pallen
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Human EvolutionGenes and Genomes
• Lecture 1: Who is our closest relativeAn overview of human evolution and
palaeoanthropology. Taxonomy and humanity’s place in nature. Who is our closest living relative? Evidence from morphology and molecules.
• Lecture 2: Becoming humanWhat have comparisons between human and ape
genomes taught us about what it means to be human?
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Anatomically Anatomically modern modern humanshumans
Homo neanderthalensi
s
Ancient DNAMorphology
Fossil RecordMorphology
Molecular phylogenetic & genomic studies Morphology
Extinct hominins
Living primates
Population genetics studieswith mtDNA, Y-chromosome & autosomal genes
Homo sapiens
Human Evolutionsources of data
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Evolutionary history versus evolutionary biologyHow is Homo sapiens
related to other species?
When did we split from our closest relatives?
When and where did our species originate?
How did humans people the world?
Was there any gene flow between our ancestors and other archaic human species?
What were the genetic changes that made us “human”?
What evolutionary processes were at work in our genomes?
What adaptive changes have occurred since we became “anatomically modern humans”?
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Where did we originate and who are our closest relatives?
Charles Darwin: Origin of Species 1859• “Light will be thrown on the origin of
man and his history” Charles Darwin: Descent of Man 1871
• speculated that humans originated in Africa
• “In each great region of the world the living mammals are closely related to the extinct species of the same region. It is, therefore, probable that Africa was formerly inhabited by extinct apes closely allied to the gorilla and chimpanzee; and as these two species are now man's nearest allies, it is somewhat more probable that our early progenitors lived on the African continent than elsewhere.”
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Where did we originate and who are our closest relatives?
Evidence as to Man's Place in Nature Huxley 1863 Thomas H. Huxley concluded that “it is quite certain that the
Ape which most nearly approaches man, in the totality of his organization, is either the chimpanzee or the gorilla”.
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What people used to think in the 1960s
Zallinger The March of ProgressPliopithecus - Proconsul - Dryopithecus - Oreopithecus – Ramapithecus - Australopithecus africanus - Australopithecus robustus - Australopithecus boisei - Homo habilis - Homo erectus - Early Homo sapiens - Neanderthal Man - Cro-Magnon Man - Modern Man
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Human lineage thought to have diverged from African apes 15-28 Ma
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A misreading of Darwin…
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But who is our closest relative among living primates?
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Chimps and gorillas were assumed to be sister taxa
Shared traits: knuckle walking, thin enamel
Humans have Bipedalism, S-shaped
spine, bowl-like pelvisGiant brains, chins,
small snoutHairless: “the naked
ape”Tools, culture,
languageOnly doubt was did
humans branch off before or after orangs?
But no chimp or gorilla fossils
g c h
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Insights from immunologyNuttall 1904, anti-human antiserum reacted
more strongly with chimp and gorilla serum than with orang or gibbon
Goodman, early 1960shuman and great ape albumins hard to
distinguish immunologically“Hominoid slowdown”, when compared to bovines
Confirmed human, chimp, gorilla relationship to the exclusion of orangsBut human-African ape distance same as chimp-gorilla
Similar results with serum protein electrophoresis
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The Cladistics Revolution
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birdscrocodilianstortoises turtles
lizardssnakes tuataramammals
amphibians
archosaurs
diapsids
amniotes
sauropsids
tetrapods
Amniotes are a monophyletic group
Reptiles are a paraphyletic group
Warm-blooded animals are a polyphyletic group
All taxa to be monophyletic
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A taxonomic adjustment
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Vincent M. Sarichand Allan C. Wilson
"Immunological time scale for hominid evolution"
Science 158, 1967, p. 1200-1203.
"that if, man and Old World monkeys shared a common ancestor 30 million years ago, then man and apes shared a common ancestor no more than 5 million years ago”
this challenge to paleontological opinion purely on the basis of biochemistry of living species was initially either ridiculed or ignored.
A recent split!
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Kimura and the neutral theory1968, Motoo KimuraNeutral mutations
predominate in evolutionDownplays the role of
natural selection in DNA and protein evolution
Neutral changes should show clock-like behaviour
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DNA sequence data…
Make a treePolymorphic sites
Sequence-based phylogenies
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Early molecular phylogeneticsDuring 1970s and 1980s several studies
support existence of human-chimp-gorilla cladeFibrinopeptidesMyoglobinHaemoglobinsCarbonic anhydrases
But sequences all very similar—only one amino-acid change supported human-chimp clade
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The trichotomy
g c h
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King and Wilson (1975) found high melting temperature for human-
chimp duplex, consistent with 99% sequence identity
Sibley & Ahlquist 1984Chimp-human duplex more stable than
gorilla-chimp or human-gorilla
Resolving the trichotomy: DNA-DNA hybridisation
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Contradictory results with single-gene phylogeniesBUT phylogenetic analysis of concatenated
sequences or meta-analysis of multiple phylogenies provide solid support for human-chimp clade
Resolving the trichotomy: DNA sequence data
Ruvolo 1997
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Some gene sequences incongruent, as a result of lineage sorting and because two successive splits very close in time
Resolving the trichotomy: DNA sequence data
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Resolving the trichotomy: DNA sequence data
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Resolving the trichotomy: Morphology
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Resolving the trichotomy: Morphology
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Our cousins resolved
g c h
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Our cousins resolved
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Another taxonomic adjustment
Sub-tribe Hominina or “hominins” reserved for species on human lineage after divergence from chimps
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But when and how…?
Estimates of divergence time depend on models of genetic change (rate constant or variable) and on calibration points
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Human/chimp divergence corrected for the difference in the mutation rate
varies considerably across the genome.
HumanChimp
τ-speciation
τ-gene divergence
X-chromosome shows significantly lower
divergence, compared to the rest of the genome.
This may tell us something about the human/chimpanzee
speciation(Patterson et al 2006 Nature)
But when and how…?
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(Patterson et al 2006 Nature)
The observed variation in human/chimpanzee
divergence can be explained by a
secondary hybridisation of the two species after
the initial speciation event
Human/chimp speciation
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The myth of 98.3%Goodman argues that as
chimps and humans share >98.3% of their non-coding DNA and ~99.5% of protein-coding sequences, chimps and bonobos should join us in genus Homo.
Jared Diamond argues that humans represent a third species of chimpanzee
Field observations of chimps and bonobos undermine human uniqueness in tool use, tool creation, sexuality etc.
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http://www.greatapeproject.org
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“As most people know, chimpanzees share about 98% of our DNA, but bananas share about 50%, and we are not 98% chimp or 50% banana, we are entirely human and unique in that respect. It is simply a mistake to use an entirely human construct, which is rights, and apply it to an animal, which is not human. Rights come with responsibility and I have never seen a chimp fined for stealing a plate of bananas”
Steve Jones
We are not 98% chimp!
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We are not 6 million years from a chimp!
6 million years
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We are not 6 million years from a chimp!
but 12 million years!
http://www.sciencemag.org/ardipithecus/
Study of Ardipithecus ramidus (4.4Ma) suggest the last human-chimp ancestor was probably more human-like than chimp-like.
“Ar. ramidus lacks any characters typical of suspension, vertical climbing, or knuckle-walking. Ar. ramidus indicates that despite the genetic similarities of living humans and chimpanzees, the ancestor we last shared probably differed substantially from any extant African ape. Hominids and extant African apes have each become highly specialized through very different evolutionary pathways.”
LCA
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Human EvolutionGenes and Genomes
• Lecture 1: Molecules and MorphologyAn overview of human evolution and
palaeoanthropology. Taxonomy and humanity’s place in nature. Who is our closest living relative? Evidence from morphology and molecules.
• Lecture 2: Becoming humanWhat have comparisons between human and ape
genomes taught us about what it means to be human?