Transcript Variation and Evolution of Genetic Networks

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: -------------S: -------------S: --------------
M: -------------M: -------------M: --------------
What Component of the Genome Is Not
Shared between the Races?
S: -------------S: -------------S: --------------
M: -------------M: -------------M: --------------
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.
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
“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
X 3 chips = 9
3 control
X 3 chips = 9
 high false discovery rate (up to 50%)
 analyze CLUMPS of significances (1Mb)
20
X
4
15
10
5
0
0
5
10
15
20
Number of significant sfps per 1Mb
20
0
1
2L
2R
15
10
5
0
0
5
10
15
20
0
5
10
15
20
20
3R
3L
15
10
5
0
0
5
10
15
20
0
Mb
5
10
15
20
25
Genome - Enabled Hitch-Hiking Mapping
Two QTLs primarily accounted for selection
response… but are they real?
Confirmed by pyrosequencing!
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
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 dehydration
protein-related" gene;
- a receptor-like kinase that has serine/threonine
kinase activity whose expression is induced by
high salt stress;
- many golgi/ER and transport related genes,
including cation transporters.
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
Chips  Evolution
A. thaliana
p = 0.01
A. arenosa
1
2
3
138537 88691 104753
0.389
0.385 0.369
4
82545
0.382
5
117708
0.377
Chips  Evolution
A. thaliana + A. arenosa = F1 hybrid
A. suecica
Probes % of F1 / A. suecica classified as:
A. thaliana
mix
A. arenosa
2
88
10
/
/
/
9
69
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? 
Ilumina
454
Solexa
 $5K = 40M reads / 30b =
= 1.2G or
8 x Drosophila coverage
 4 reads H Ni 25x + 4 reads L Ni 25x