Lecture 1: Genomics approaches for analyses of population structure

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

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

Anopheles gambiae

?

X chromosome polymorphism

♀ ( ♂ ) – share allele

♀ ( ♂ ) – share allele

~1% ♀ ( ♂ ), ♀ ( ♂ ) - don’t share

Affymetrix microarray:

142K oligonucleotides 25 bp each.

Normal use: RNA We used: DNA

Multiple samples per race.

S: -------------- M: --------------S: -------------- M: --------------S: -------------- M: --------------

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

S: -------------- M: --------------

S: -------------- M: --------------

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Support from Re-Sequencing?

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.






“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.

Selection for starvation / oxidation resistances

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)

X

0 5 10 15 20

Nu

mb

er o

f sig

nifi

can

t sfp

s pe

r 1M

b

0

5

10

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2L

0 5 10 15 20

0

5

10

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2R

0 5 10 15 20

3L

Mb

0 5 10 15 20

0

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203R

0 5 10 15 20 25

4

0 1

Genome - Enabled Hitch-Hiking Mapping

Two QTLs primarily accounted for selection response… but are they real?

Confirmed by pyrosequencing!






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

Sequence divergence matters

95% sequence identity 1 b out of 25 are divergent

2853369 PMs on the array 371642 are matches

28 (p<0.05 Bonferroni);

72 (FDR<1%);

362 (FDR<5%).

Preliminary conclusions

14 probes would be significant P<0.01

(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)

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.






Chips EvolutionA. thaliana A. arenosa

p = 0.01 1 2 3 4 5138537 88691 104753 82545 117708

0.389 0.385 0.369 0.382 0.377

Chips Evolution

A. thaliana + A. arenosa = F1 hybrid

A. suecica

Probes % of F1 / A. suecica classified as:

A. thaliana 2 / 9

mix 88 / 69

A. arenosa 10 / 22

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?

Follow up comments

Chips? Ilumina454Solexa $5K = 40M reads / 30b =

= 1.2G or8 x Drosophila

coverage

4 reads H Ni 25x + 4 reads L Ni 25x

Documents

Lecture 1: Genomics approaches for analyses of population structure