Bio263 Who is our Closest Relative


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My first lecture on the second year Bio263 module on human evolution. An overview of human evolution and palaeoanthropology. Taxonomy and humanity's place in nature. Who is our closest living relative? Evidence from morphology and molecules.
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  • The genetic divergence time between two species, t(x), varies across the genome and is always greater than or equal to the speciation time, tspecies, which is the time of last gene flow between the species’ ancestors. The average genetic divergence (tgenome) thus always exceeds tspecies.
  • Bio263 Who is our Closest Relative

    1. 1. Human Evolution Bio263 Genes and Genomes Who is our closest relative? <ul><li>Professor Mark Pallen </li></ul>
    2. 2. Human Evolution Genes and Genomes <ul><ul><li>Lecture 1: Who is our closest relative </li></ul></ul><ul><ul><ul><li>An overview of human evolution and palaeoanthropology. Taxonomy and humanity’s place in nature. Who is our closest living relative? Evidence from morphology and molecules. </li></ul></ul></ul><ul><ul><li>Lecture 2: Becoming human </li></ul></ul><ul><ul><ul><li>What have comparisons between human and ape genomes taught us about what it means to be human? </li></ul></ul></ul>
    3. 3. Human Evolution sources of data Anatomically modern humans Homo neanderthalensis Ancient DNA Morphology Fossil Record Morphology Molecular phylogenetic & genomic studies Morphology Extinct hominins Living primates Population genetics studies with mtDNA, Y-chromosome & autosomal genes Homo sapiens
    4. 4. Evolutionary history versus evolutionary biology <ul><li>How is Homo sapiens related to other species? </li></ul><ul><li>When did we split from our closest relatives? </li></ul><ul><li>When and where did our species originate? </li></ul><ul><li>How did humans people the world? </li></ul><ul><li>Was there any gene flow between our ancestors and other archaic human species? </li></ul><ul><li>What were the genetic changes that made us “human”? </li></ul><ul><li>What evolutionary processes were at work in our genomes? </li></ul><ul><li>What adaptive changes have occurred since we became “anatomically modern humans”? </li></ul>
    5. 5. Where did we originate and who are our closest relatives? <ul><li>Charles Darwin: Origin of Species 1859 </li></ul><ul><ul><li>“ Light will be thrown on the origin of man and his history” </li></ul></ul><ul><li>Charles Darwin: Descent of Man 1871 </li></ul><ul><ul><li>speculated that humans originated in Africa </li></ul></ul><ul><ul><li>“ 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.” </li></ul></ul>
    6. 6. Where did we originate and who are our closest relatives? <ul><li>Evidence as to Man's Place in Nature Huxley 1863 </li></ul><ul><li>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”. </li></ul>
    7. 7. What people used to think in the 1960s Zallinger The March of Progress Pliopithecus - Proconsul - Dryopithecus - Oreopithecus – Ramapithecus - Australopithecus africanus - Australopithecus robustus - Australopithecus boisei - Homo habilis - Homo erectus - Early Homo sapiens - Neanderthal Man - Cro-Magnon Man - Modern Man
    8. 9. Human lineage thought to have diverged from African apes 15-28 Ma
    9. 10. A misreading of Darwin…
    10. 12. But who is our closest relative among living primates?
    11. 13. Chimps and gorillas were assumed to be sister taxa <ul><li>Shared traits: knuckle walking, thin enamel </li></ul><ul><li>Humans have </li></ul><ul><ul><li>Bipedalism, S-shaped spine, bowl-like pelvis </li></ul></ul><ul><ul><li>Giant brains, chins, small snout </li></ul></ul><ul><ul><li>Hairless: “the naked ape” </li></ul></ul><ul><ul><li>Tools, culture, language </li></ul></ul><ul><li>Only doubt was did humans branch off before or after orangs? </li></ul><ul><li>But no chimp or gorilla fossils </li></ul>g c h
    12. 14. Insights from immunology <ul><li>Nuttall 1904, anti-human antiserum reacted more strongly with chimp and gorilla serum than with orang or gibbon </li></ul><ul><li>Goodman, early 1960s </li></ul><ul><ul><li>human and great ape albumins hard to distinguish immunologically </li></ul></ul><ul><ul><ul><li>“ Hominoid slowdown”, when compared to bovines </li></ul></ul></ul><ul><ul><li>Confirmed human, chimp, gorilla relationship to the exclusion of orangs </li></ul></ul><ul><ul><ul><li>But human-African ape distance same as chimp-gorilla </li></ul></ul></ul><ul><ul><li>Similar results with serum protein electrophoresis </li></ul></ul>
    13. 15. The Cladistics Revolution
    14. 16. All taxa to be monophyletic birds crocodilians tortoises turtles lizards snakes tuatara mammals amphibians archosaurs diapsids amniotes sauropsids tetrapods Amniotes are a monophyletic group Reptiles are a paraphyletic group Warm-blooded animals are a polyphyletic group
    15. 17. A taxonomic adjustment
    16. 18. A recent split! Vincent M. Sarich and Allan C. Wilson &quot;Immunological time scale for hominid evolution&quot; Science 158, 1967, p. 1200-1203. &quot;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.
    17. 20. Kimura and the neutral theory <ul><li>1968, Motoo Kimura </li></ul><ul><li>Neutral mutations predominate in evolution </li></ul><ul><li>Downplays the role of natural selection in DNA and protein evolution </li></ul><ul><li>Neutral changes should show clock-like behaviour </li></ul>
    18. 21. Sequence-based phylogenies DNA sequence data… Make a tree Polymorphic sites
    19. 22. Early molecular phylogenetics <ul><li>During 1970s and 1980s several studies support existence of human-chimp-gorilla clade </li></ul><ul><ul><li>Fibrinopeptides </li></ul></ul><ul><ul><li>Myoglobin </li></ul></ul><ul><ul><li>Haemoglobins </li></ul></ul><ul><ul><li>Carbonic anhydrases </li></ul></ul><ul><li>But sequences all very similar—only one amino-acid change supported human-chimp clade </li></ul>
    20. 23. The trichotomy g c h
    21. 24. <ul><li>King and Wilson (1975) </li></ul><ul><ul><li>found high melting temperature for human-chimp duplex, consistent with 99% sequence identity </li></ul></ul><ul><li>Sibley & Ahlquist 1984 </li></ul><ul><ul><li>Chimp-human duplex more stable than gorilla-chimp or human-gorilla </li></ul></ul>Resolving the trichotomy: DNA-DNA hybridisation
    22. 25. <ul><li>Contradictory results with single-gene phylogenies </li></ul><ul><li>BUT phylogenetic analysis of concatenated sequences or meta-analysis of multiple phylogenies provide solid support for human-chimp clade </li></ul>Resolving the trichotomy: DNA sequence data Ruvolo 1997
    23. 26. <ul><li>Some gene sequences incongruent, as a result of lineage sorting and because two successive splits very close in time </li></ul>Resolving the trichotomy: DNA sequence data
    24. 27. Resolving the trichotomy: DNA sequence data
    25. 28. Resolving the trichotomy: Morphology
    26. 29. Resolving the trichotomy: Morphology
    27. 30. Our cousins resolved g c h
    28. 31. Our cousins resolved
    29. 32. Another taxonomic adjustment Sub-tribe Hominina or “hominins” reserved for species on human lineage after divergence from chimps
    30. 33. But when and how…? Estimates of divergence time depend on models of genetic change (rate constant or variable) and on calibration points
    31. 35. But when and how…? Human/chimp divergence corrected for the difference in the mutation rate varies considerably across the genome. 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) Human Chimp τ -speciation τ -gene divergence
    32. 36. Human/chimp speciation (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
    33. 37. The myth of 98.3% <ul><li>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 . </li></ul><ul><li>Jared Diamond argues that humans represent a third species of chimpanzee </li></ul><ul><li>Field observations of chimps and bonobos undermine human uniqueness in tool use, tool creation, sexuality etc. </li></ul>
    34. 38.
    35. 40. We are not 98% chimp! “ 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
    36. 41. We are not 6 million years from a chimp! 6 million years
    37. 42. We are not 6 million years from a chimp! but 12 million years! 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
    38. 43. Human Evolution Genes and Genomes <ul><ul><li>Lecture 1: Molecules and Morphology </li></ul></ul><ul><ul><ul><li>An overview of human evolution and palaeoanthropology. Taxonomy and humanity’s place in nature. Who is our closest living relative? Evidence from morphology and molecules. </li></ul></ul></ul><ul><ul><li>Lecture 2: Becoming human </li></ul></ul><ul><ul><ul><li>What have comparisons between human and ape genomes taught us about what it means to be human? </li></ul></ul></ul>