Lecture 1: Genomics approaches for analyses of population structure

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Lecture 1 Genomics approaches for analyses of
population structure

• Tom Turner Matt Hahn
• UI Bloomington
• Kristy Harmon Larry Harshman
• UN Lincoln
• Eric von Wettberg, Sharon Strauss Tom Turner
• Brian Dilkes, Shelley McMahon Peter Chang
• UA Tucson
  USouthCal

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Four topics of the talk

• Genomics of mosquito incipient speciation
• Genome-enabled hitchhiking mapping in flies
• Genomics of local adaptations in diploid
  mustards
• Genomics of tetraploidy in mustards

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• Anopheles gambiae
• ?
• X chromosome polymorphism
• ? ( ? ) share allele
• ? ( ? ) share allele
• 1 ? ( ? ), ? ( ? ) - dont share

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• Affymetrix microarray
• 142K oligonucleotides 25 bp each.
• Normal use RNA
• We used DNA
• Multiple samples per race.
• S -------------- M --------------
• S -------------- M --------------
• S -------------- M --------------

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What Component of the Genome Is Not Shared
between the Races?

• S -------------- M --------------
• S -------------- M --------------
• S -------------- M --------------

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Support from Re-Sequencing?
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Conclusions Genomics of Mosquito Incipient
Speciation

• natural hybrid zones are a powerful tool of
  genetic (genomic) analysis
• three speciation islands ( X and II) contain
  67 genes (including olfactory receptors with
  signatures of natural selection)
• the rest of the genome is shared between the
  races.

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Four topics of the talk

• Genomics of mosquito incipient speciation
• Genome-enabled hitchhiking mapping in flies
• Genomics of local adaptations in diploid
  mustards
• Genomics of tetraploidy in mustards

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Normal Approaches for the Analysis of Variation

• Identify two interesting genotypes
• Cross them to generate mapping population
• Genotype hundred(s) of recombinant individuals /
  genotypes
• Analyze QTLs.
• long, boring, labor-intensive.

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Selection for starvation / oxidation resistances
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How to analyze numerous dense markers?

• Microsatellites? AFLPs? ? SNPs
• 2b out of 100 are different between flies.
• 3 selected 3 control
• X 3 chips 9 X 3 chips 9
• ? high false discovery rate (up to 50)
• ? analyze CLUMPS of significances (1Mb)

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Genome - Enabled Hitch-Hiking Mapping

• Two QTLs primarily accounted for selection
  response but are they real?
• Confirmed by pyrosequencing!

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Four topics of the talk

• Genomics of mosquito incipient speciation
• Genome-enabled hitchhiking mapping in flies
• Genomics of local adaptations in diploid
  mustards
• Genomics of tetraploidy in mustards

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Sequence divergence, how much does it matter?

• Arabidopsis lyrata
• 95 seq. identity
• tiling Arabidopsis array
• 3M PM/MM features
• 2 populations on normal
• 2 on serpentine X 3 chips
• ? 12 arrays

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Sequence divergence matters

• 95 sequence identity ?
• ? 1 b out of 25 are divergent
• 2853369 PMs on the array ?
• ? 371642 are matches
• 28 (plt0.05 Bonferroni)
• 72 (FDRlt1)
• 362 (FDRlt5).

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Preliminary conclusions

• 14 probes would be significant Plt0.01
• (assuming 2853369 tests)
• 5 (3) highly significant probes map to AT5G17740
  (AAA-type ATPase family protein,
• members of gene family have been implicated in
  salt stress adaptation)

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Other candidate genes

• - similar to early-responsive to
  dehydrationprotein-related" gene
• a receptor-like kinase that has
  serine/threoninekinase activity whose expression
  is induced by high salt stress
• many golgi/ER and transport related genes,
  including cation transporters.

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Four topics of the talk

• Genomics of mosquito incipient speciation
• Genome-enabled hitchhiking mapping in flies
• Genomics of local adaptations in diploid
  mustards
• Genomics of tetraploidy in mustards

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Chips ? Evolution

• A. thaliana A. arenosa

p 0.01 1 2 3
4 5 138537 88691 104753
82545 117708 0.389 0.385
0.369 0.382 0.377
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Chips ? Evolution

• A. thaliana A. arenosa F1 hybrid
• A. suecica
• Probes of F1 / A. suecica classified as
• thaliana 2 / 9
• mix 88 / 69
• A. arenosa 10 / 22

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Chips ? Evolution

• False discoveries or deletions within species?
• Deletions after tetraploid formation (9-10 of
  both parents) ? genes / pathways / ecology?
• Evolution of allele-specific expression ?
• genes / pathways / chromosomal positions?

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Follow up comments

• Chips? ? Ilumina
• 454
• Solexa
• ? 5K 40M reads / 30b
• 1.2G or
• 8 x Drosophila coverage
• ? 4 reads H Ni 25x 4 reads L Ni 25x