Genetics and the making of Homo sapiens

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Genetics and the making of Homo sapiens

• Sean B. Carrol

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Outline

• Human Evolution
• Fossil record
• Comparative Anatomy
• Development
• Trait evolution in model systems
• Molecular phylogeny
• Genome-wide
• Individual Loci
• How to find causative changes
• Methodological Challenges
• Future advances

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What makes humans different than Apes?

• Evolution or Intelligent Design?
• Traditional methods
• Lots of gaps
• Sparse fossil record
• Molecular Comparisons
• Surprising similarity - 99
• But still many differences

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Fossil vs Molecular evidence

• Fossil record
• Many individual fossils
• Fragmentary evidence
• Inferred relationships
• Molecular phylogenies
• Few extant species
• Abundant sequence information

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Comparative Anatomy

• Speech centers can be identified
• by functional MRI
• Studies of specific lesions
• Similar anatomical features in other primates
• What makes humans capable of speech?

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Comparative neuroanatomy of humans and chimpanzees
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Development

• Final form is programmed in development
• Human skulls start larger and less developed
  than Chimps but end up about the same size
• Different features seem to have evolved
  independently
• Their appearance in the fossil record is not
  coordinated
• Does Ontogeny recapitulate Phylogeny?

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Genetics of human evolution

• Questions
• What specific genetic changes account for
  evolutionary differences in form and function?
• Are few specific changes responsible?
• How can we identify the genetic origins of the
  differences?

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Lessons from model organisms

1. Quantitative traits are usually polygenic
2. Rate of evolution unrelated to number of genes
3. Morphological variation is associated with
   developmental regulation
4. Mutations that lead to trait variation are often
   in regulatory DNA
5. Quantitative trait alleles often differ at
   multiple nucleotides
6. Intra-species variation and inter-species
   differences often involve the same genes

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Arithmetic

• Total genome size Human 3 x 109 bps
• Average human/chimp variation in single copy DNA
  1.2
• Assuming a common ancestor half of variation
  occurs in human lineage
• 3 x 109 x (1.2 / 2) 1.8 x 106 changes
• Divided between
• single base pair changes
• Insertions and Deletions (indels)
• Many changes may be in repeated or unselected DNA
  and thus be functionally neutral
• How to identify the rare meaningful changes from
  neutral variation noise?

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Potential Genetic Origins of Inter-Species
Differences

• How many genes define the differences between
  humans and chimps?
• 10, 100, 1000?
• Which genes are responsible for which traits?
• What types of changes are responsible?
• Gene duplications?
• Coding sequence differences?
• Regulatory changes ?

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Candidate genes an come from

• Comparative genomics
• Population genetics selective sweeps
• Expression profiling

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Model Systems

• Mice and humans have mostly the same genes
• 80 of mouse genes have a 11 human ortholog
• 99 of mouse genes have a human homolog
• regions of duplication and segmental expansion
  specific to mice
• many duplicated genes involved in reproduction,
  immunity and olfaction

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Population genetics - Selective sweeps

• An individual mutation subject to selection (eg.
  resistance to malaria) arises in a population
• Under strong selection most members of the
  population soon carry the mutation along with
  linked unselected polymorphisms
• Over time recombination and mutation reduce
  genetic homogeneity

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Protein coding genes are a small fraction of
total DNA

• 30,000 genes x 400 AAs x 3bp/AA 3.5 x 107 bps
• 3.5 x 107 bps / 3 x 109 bps/genome 1.5
• 1.5 x 1.8 x 106 changes 270,000 sites
• If 1/4 of coding sequence changes are silent
• 200,000 AA replacements
• Which of these changes are adaptive?

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Up to 35 of AA changes may have been positively
selected

• Sequence multiple monkey genes from multiple
  monkeys
• Sequence human homologs from distinct human
  populations
• Compare of sequence divergence (inter-species) to
  polymorphism (intra-species)
• Note the proportion of missense(AA replacement)
  to silent mutations
• An excess of missense mutations indicates
  positive selection

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Can we assume that coding sequences contain the
answer?

• No direct demonstration of functional differences
  due to AARs
• Positively selected proteins generally do not
  affect development
• Most DNA is not so highly conserved as coding
  sequences and has not been investigated so
  thoroughly
• Important changes may be in more variable
  regulatory sequences

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Evolution of gene expression patterns and
control

• 98 of the genome is non coding
• Non coding sequences are also under positive
  selection
• Selected regulatory sequences may be 2X coding
  sequences (2-4 of the genome)
• No good way to comprehensively analyze
• Computers can find coding sequences automatically
• Stop codons frequent in noncoding DNA (3 in 64
  triplets)
• Open reading frames (ORFs) are identifiable
• Splice junctions are specified by sequence
• No genetic code for regulation

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How can we find regulatory changes

• RNA expression profiles large scale surveys
• Carefully examine individual Candidate genes
• Subclone and analyze promoters in heterologous
  systems

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RNA expression profiles large scale surveys

• Make individual DNAs that represent homologous
  coding sequences
• Immobilized them in a predetermined order in 2
  dimensional arrays
• Isolate RNA from different
• Species
• Individuals
• Tissues
• Developmental stages
• Make fluorescent copies of that RNA
• Hybridize fluorescent copies to DNA array
• Quantify relative expression levels

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The Expression Levels of All The Genes of An
Organism Can Be Monitored Simultaneously
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Candidate genes

• Can come from
• Comparative genomics
• Population genetics selective sweeps
• Expression profiling
• In depth studies of
• Developmental expression profiles in model
  systems
• Function in organisms, tissues, cells and
  molecules

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FOXP2 - a Candidate Speech Gene

• Identified as an inherited mutation in individual
  humans with a speech disorder
• Identified as correlated with vocalization in
  songbirds
• Comparatively - Species with more elaborate
  songs have higher levels
• Developmentally - RNA expression coincides
  temporally with singing behavior
• Human population genetics suggests recent
  positive selection

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Summary

• Structural and functional differences between
  species arise from multiple genetic contributions
  
• Changes in regulatory sequences likely play an
  important role, but are currently difficult to
  assess.
• Continued development of strategies based on
  comparative and functional genomics, population
  genetics and genetic and biochemical studies of
  individual candidate genes and regulatory regions
  will be necessary to address important questions
  in human biology.