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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 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