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How do new adaptations arise

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Sequence data for DNA was used to infer functional domains (32 species) ... Phylogenetic evidence for molecular convergence in primate, ruminant, and avian lysozymes ... – PowerPoint PPT presentation

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Title: How do new adaptations arise


1
How do new adaptations arise?
  • Modularity, recombination, and functional duality

2
Cytochrome c
3
Cytochrome c protein structure
TUNA
RICE
4
Folds and Fold Super Families
5
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

6
Evolution and conservation of domains in diverse
proteins
7
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)
8
How are folds modified through evolution?
9
Types of modules evolved at different rates
10
Phylogenetic tree of fold architectures
11
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

12
Origins of eumetazoan genes
Putnam, et al. 2007. Sea anemone genome reveals
ancestral eumetazoan gene repertoire and genomic
organization. Science 31786-94.
13
Mosaic evolution of integrin signaling
Putnam, et al. 2007. Sea anemone genome reveals
ancestral eumetazoan gene repertoire and genomic
organization. Science 31786-94.
14
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)

15
Phylogenetic evidence for molecular convergence
in primate, ruminant, and avian lysozymes
Who digests bacteria in the foregut?
16
How do new genes arise?
17
Evidence for lateral gene transfer from Archaea
to Entamoeba histolytica
18
What is another form of lateral gene transfer?
  • Hybridization
  • Introgression
  • Another creative process module recombination
  • Exon shuffling
  • Domain accretion

19
Origin of new genes via intron-mediated exon
shuffling
20
Origin of a new Drosophila gene,
jingweiRetrotransposition to form a chimeric gene
21
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-

22
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

23
Orthology and paralogy in gene families
24
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

25
Use of age distribution of gene duplication
events to infer whole-genome duplications
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