How do new adaptations arise

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How do new adaptations arise?

• Modularity, recombination, and functional duality

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Cytochrome c
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Cytochrome c protein structure
TUNA
RICE
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Folds and Fold Super Families
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Universal sharing patterns in proteomes and
evolution of protein fold architecture and life.
Caetano-Anollés et al.1, Wang et al.2

• 104 modules of protein fold domains
• Folds are highly conserved
• Genome sequencing reveals proteome
• Propose a genomic demography

• J Mol Evol (2005) 60484498
• Structure (2009) 1766-78

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Evolution and conservation of domains in diverse
proteins
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Universal Sharing Patterns in Proteomes and
Evolution of Protein FoldArchitecture and LifeJ
Mol Evol (2005) 60484498Gustavo
Caetano-Anolle, Derek Caetano-Anolle
Sequence data for DNA was used to infer
functional domains (32 species)
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How are folds modified through evolution?
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Types of modules evolved at different rates
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Phylogenetic tree of fold architectures
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Major patterns in protein folding modules

• A core of basic tools is common across archaea,
  bacteria, eukaria
• Higher organisms are a mosaic of old and
  new protein domains
• Cladistic analysis of variants reinforces the
  phylogenetic hypotheses previously proposed
• The evolution of multicellularity was accompanied
  by many and major novelties in protein
  architecture

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Origins of eumetazoan genes
Putnam, et al. 2007. Sea anemone genome reveals
ancestral eumetazoan gene repertoire and genomic
organization. Science 31786-94.
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Mosaic evolution of integrin signaling
Putnam, et al. 2007. Sea anemone genome reveals
ancestral eumetazoan gene repertoire and genomic
organization. Science 31786-94.
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Can adaptation be demonstrated at the level of
genes?

• Compare synonymous and non-synonymous
  substitutions (ratio ?)
• Ratio, ? gt 1 for 873 genes in human lineage
• Difference between Purifying and Positive
  selection
• Examples of convergence (lysozymes)

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Phylogenetic evidence for molecular convergence
in primate, ruminant, and avian lysozymes
Who digests bacteria in the foregut?
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How do new genes arise?
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Evidence for lateral gene transfer from Archaea
to Entamoeba histolytica
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What is another form of lateral gene transfer?

• Hybridization
• Introgression
• Another creative process module recombination
• Exon shuffling
• Domain accretion

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Origin of new genes via intron-mediated exon
shuffling
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Origin of a new Drosophila gene,
jingweiRetrotransposition to form a chimeric gene
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Gene duplication Modification of one copy

• Uneven crossing over OR polyploidy, followed by
• Modification of one or more copies, leading to
• Gene families
• Such as globins of types a-, ß-, ?-, ?-, e-

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Gene evolution within and between species

• Modification through descent can occur
• When genes are duplicated and modified within a
  species over time PARALOGOUS
• Or, When genes diverge following speciation
  ORTHOLOGOUS

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Orthology and paralogy in gene families
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How often does duplication occur?

• In vertebrates, gt1700 events based on 749 gene
  families
• Gene families may have blocks of up to 1000
  copies (human ribosomal RNA genes)
• One estimate is 0.01 duplication per gene per
  million years

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Use of age distribution of gene duplication
events to infer whole-genome duplications