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 ~1% ♀ ( ♂ ), ♀ ( ♂ ) - don’t share

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

What Component of the Genome Is Not Shared between the Races? S: 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 3 controlX 3 chips = 9  high false discovery rate (up to 50%)  analyze CLUMPS of significances (1Mb)

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 PMs on the array   are matches 28 (p<0.05 Bonferroni); 72 (FDR<1%); 362 (FDR<5%).

Preliminary conclusions 14 probes would be significant P<0.01 (assuming 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 A. arenosa p =

Chips  Evolution A. thaliana + A. arenosa = F1 hybrid A. suecica Probes % of F1 / A. suecica classified as: A.thaliana 2 / 9 mix88 / 69 A. arenosa10 / 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