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Introgression and the origin of maize in Mexico and the Southwest US

Introgression and the origin of maize in Mexico and the Southwest US

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Introgression and the origin of maize in Mexico and the Southwest US

  1. 1. Introgression and the origin of maize in Mexico and the Southwest US Jeffrey Ross-Ibarra @jrossibarra • www.rilab.org Dept. Plant Sciences • Center for Population Biology • Genome Center University of California Davis
  2. 2. acknowledgements Matt Hufford (Iowa State) Rute Fonseca (Copenhagen) Joost van Heerwaarden (Wageningen) Tom Gilbert (Copenhagen) John Doebley (Wisconsin)
  3. 3. maize origins
  4. 4. maize origins
  5. 5. maize origins
  6. 6. Meyerowitz 1994 Current Biology Duvick et al. 1999 US 6639132 B1 maize origins Tripsacum extinct maize
  7. 7. Meyerowitz 1994 Current Biology Duvick et al. 1999 US 6639132 B1 maize origins Tripsacum F1 extinct maize
  8. 8. Meyerowitz 1994 Current Biology Duvick et al. 1999 US 6639132 B1 maize origins Tripsacum F1 extinct maize
  9. 9. Meyerowitz 1994 Current Biology Duvick et al. 1999 US 6639132 B1 maize origins F1 Tripsacum F1 extinct maize
  10. 10. single origin from teosinte Matsuoka et al. 2002 PNAS Piperno et al. 2009 PNAS mays parv mex
  11. 11. paradox of maize ancestry Fig. 2. A view of the enormous boulder that formed the Xihuatoxtla Shelter. Matsuoka et al. 2002 PNAS Piperno et al. 2009 PNAS mays parv mex 1,400 mm annually with over 90% falling during the June-to- October rainy season. The potential vegetation of the region is tropical deciduous forest, seen today in remnants scattered throughout the region. Vegetational reconstructions indicate that a species-diverse seasonal tropical forest flourished there B.P.), but the reworking of the rock shelter deposits in the early 20th century has left them thoroughly mixed over most of the site. At a fourth site, the Temaxcalapa Shelter, we recovered a large number of chipped stone artifacts from the eroded slope in front of the shelter, including preceramic-aged spear points.We SEE COMMENTARY
  12. 12. landrace and teosinte sampling van Heerwaarden et al. 2011 PNAS
  13. 13. SNPs show highland similarity to teosinte van Heerwaarden et al. 2011 PNAS
  14. 14. admixture explains patterns of diversity mexicana parviglumis South/Caribbean West Highland 2500 2000 m 1500 1000 500 0 van Heerwaarden et al. 2011 PNAS
  15. 15. admixture explains patterns of diversity H Genetic distance to parviglumis Heterozygosity 0.0 0.2 0.4 0.6 0.8 1.0 0.20 0.25 0.30 0.35 0.40 0.45 admixture proportion F van Heerwaarden et al. 2011 PNAS 0.0 0.2 0.4 0.6 0.8 1.0 0.25 0.26 0.27 0.28 0.29 admixture proportion observed observed
  16. 16. Pesach Lubinsky Norm Ellstrand hybrids commonly observed Pesach Lubinsky
  17. 17. admixture along the genome maize mexicana Mb % population admixed Chromosome 4 Hufford et al. 2013 PLoS Genetics
  18. 18. El Porvenir Opopeo Santa Clara Nabogame Puruandiro Xochimilco Tenango del Aire San Pedro Ixtlan Allopatric admixture localized, asymmetric El Porvenir Opopeo Santa Clara Nabogame Puruandiro Xochimilco Tenango del Aire San Pedro Ixtlan Allopatric Hufford et al. 2013 PLoS Genetics Pyhäjärvi et al. 2013 GBE
  19. 19. El Porvenir Opopeo Santa Clara Nabogame Puruandiro Xochimilco Tenango del Aire San Pedro Ixtlan Allopatric admixture localized, asymmetric El Porvenir Opopeo Santa Clara Nabogame Puruandiro Xochimilco Tenango del Aire San Pedro Ixtlan Allopatric Inv4n Hufford et al. 2013 PLoS Genetics Pyhäjärvi et al. 2013 GBE
  20. 20. El Porvenir Opopeo Santa Clara Nabogame Puruandiro Xochimilco Tenango del Aire San Pedro Ixtlan Allopatric admixture localized, asymmetric El Porvenir Opopeo Santa Clara Nabogame Puruandiro Xochimilco Tenango del Aire San Pedro Ixtlan Allopatric Inv4n Hufford et al. 2013 PLoS Genetics Pyhäjärvi et al. 2013 GBE
  21. 21. El Porvenir Opopeo Santa Clara Nabogame Puruandiro Xochimilco Tenango del Aire San Pedro Ixtlan Allopatric admixture localized, asymmetric El Porvenir Opopeo Santa Clara Nabogame Puruandiro Xochimilco Tenango del Aire San Pedro Ixtlan Allopatric * * * * * Inv4n Hufford et al. 2013 PLoS Genetics Pyhäjärvi et al. 2013 GBE
  22. 22. introgressions overlap with mexicana QTL Lauter et al. 2004 Genetics Moose et al. 2004 Genetics b1 in maize Inv4n Hufford et al. 2013 PLoS Genetics
  23. 23. introgressions show mexicana phenotypes Introgression No Introgression Hufford et al. 2013 PLoS Genetics macrohairs pigmentaton
  24. 24. introgressions grow faster at low temp Introgressed Not Introgressed Hufford et al. 2013 PLoS Genetics
  25. 25. admixture confounds ancestral inference compare to wild ancestor inferred origin origin
  26. 26. admixture confounds ancestral inference compare to wild ancestor inferred origin origin compare to wild ancestor origin gene flow inferred origin
  27. 27. Gene frequency a solution: ancestral reconstruction Nicholson et al 2002 J Roy Stat Soc. B wild ancestor 1 0
  28. 28. origin Gene frequency a solution: ancestral reconstruction Nicholson et al 2002 J Roy Stat Soc. B wild ancestor 1 0 1 0
  29. 29. wild ancestor origin derivative 1 derivative 2 Gene frequency a solution: ancestral reconstruction 1 drift 1 drift Nicholson et al 2002 J Roy Stat Soc. B 1 0 1 0 0 0
  30. 30. ancestral reconstruction resolves origins wild ancestor origin gene flow inferred origin
  31. 31. ancestral reconstruction resolves origins ancestral reconstruction origin inferred origin gene flow wild ancestor origin gene flow inferred origin
  32. 32. because the adaptive differences between highland and lowland maize are profound (14, 29). In other crops, uncertainty about ancestral allele frequen-cies. frequencies observed in parviglumis because the adaptive differences between highland and maize are profound (14, 29). In other crops, uncertainty 0.1 0.2 0.3 0.4 maize origins in lowland west Mexico frequen-cies. parviglumis B A B C Compared to wild teosinte Compared to ancestral maize 0.1 0.2 0.3 0.4 0.1 0.2 0.3 0.4 Lowland Lowland 0.3 0.4 0.1 0.2 0.3 0.4 0.1 0.2 0.3 0.4 Genetic distance from ancestor density F F F F F parameter F for 10 genetic groups with respect to (A) mexicana and (B) parviglumis. Only lowland included. van (Heerwaarden C) Drift of all et 10 al. genetic 2011 PNAS groups with respect to inferred ancestral frequencies. Light blue represents between lowlands (<1,500 m, solid line) and highlands (>2,000 m). C genetic groups with respect to (A) mexicana and (B) parviglumis. Only lowland accessions of genetic groups with respect to inferred ancestral frequencies. Light blue represents West m, solid line) and highlands (>2,000 m).
  33. 33. maize origins in lowland west Mexico 1750m 1250m van Heerwaarden et al. 2011 PNAS
  34. 34. how did maize arrive and adapt to SW US? J. ROSS-IBARRA / UC DAVIS 2. Coastal route 1. Highland route SW Mexico Fonseca et al. 2015 Nature Plants Ronald Humeyestewa
  35. 35. ancient cobs to investigate chronology Fonseca et al. 2015 Nature Plants Hufford et al. 2012 Nature Genetics
  36. 36. DNA capture to enrich for subset of genome J. ROSS-IBARRA / UC DAVIS Fonseca et al. 2015 Nature Plants
  37. 37. ancient DNA data analysis: ANGSD J. ROSS-IBARRA / UC DAVIS error rate Fonseca et al. 2015 Nature Plants
  38. 38. SW shares ancestry with highland Mexico J. ROSS-IBARRA / UC DAVIS 6. Barplots of STRUCTURE q-matrices (2310 modern maize landraces and teosinte) from k=3 to k=10 where k is the number of groups assigned. Each individual Figure group is sorted from low to high elevation (top to bottom). The high elevation groups in the SW, Mexico and Guatemala share ancestry with each other and to varying extents parviglumis mexicana S. America C. America Mexico SWUS Fonseca et al. 2015 Nature Plants US
  39. 39. allele counts support both hypotheses SWUS highland coast teosinte HUFFORD ET AL. 2012 PLOS GENETICS VAN HEERWAARDEN ET AL 2011 PNAS Fonseca et al. 2015 Nature Plants J. ROSS-IBARRA / UC DAVIS
  40. 40. allele counts support both hypotheses SWUS highland coast teosinte K=5 a b c TMx25 TMx08 TPa06 TPa10 Ancient Mexico Reventador Chapalote Highlands Mex35 Mex25 Mex31 Mex30 Mex29 SW3K SW2K SW750 USA17 0.00 0.05 0.10 0.15 0.20 Teosintes USA Mexico Central/South America Chile Z. m. mexicana Z. m. parviglumis Coastal Drift parameter USA Mexico SW3K SW2K SW750 USA17 -0.2 -0.1 0.0 0.1 0.2 D Coastal Highlands Outgroup SW Coastal Highlands Outgroup SW HUFFORD ET AL. 2012 PLOS GENETICS VAN HEERWAARDEN ET AL 2011 PNAS Figure 1 Fonseca et al. 2015 Nature Plants J. ROSS-IBARRA / UC DAVIS
  41. 41. tree, admixture analyses support results K=5 TMx25 TMx08 TPa06 TPa10 Ancient Mexico Reventador Chapalote Highlands Mex35 Mex25 Mex31 Mex30 Mex29 SW3K SW2K SW750 USA17 0.00 0.05 0.10 0.15 0.20 Teosintes USA Mexico Central/South America Chile Z. m. mexicana Z. m. parviglumis Coastal Drift parameter USA Coastal Highlands SW 0.1 0.2 b c Figure 1 Fonseca et al. 2015 Nature Plants J. ROSS-IBARRA / UC DAVIS
  42. 42. ancient population genomics J. ROSS-IBARRA / UC DAVIS ~2000 years b.p. n=10 Changes in shape and size ~750 years b.p. n=12 Fonseca et al. 2015 Nature Plants
  43. 43. selection affects patterns of diversity
  44. 44. selection affects patterns of diversity SFS Proportion SNPs 0.7 0.525 0.35 0.175 0 1 2 3 4 Individuals Proportion SNPs 0.7 0.525 0.35 0.175 0 1 2 3 4 Individuals Taj D = 0 Taj D < 0
  45. 45. selection affects patterns of diversity SFS Proportion SNPs 0.7 0.525 0.35 0.175 0 1 2 3 4 Individuals Proportion SNPs 0.7 0.525 0.35 0.175 0 1 2 3 4 Individuals Taj D = 0 Taj D < 0 PBS 2000yr 700yr teosinte
  46. 46. methods identify known domestication loci J. ROSS-IBARRA / UC DAVIS median PBS values parviglumis SW750 SW2K dehyd1A parviglumis SW2K SW750 a b Fonseca et al. 2015 Nature Plants Figure 2
  47. 47. domestication loci John Doebley median PBS values parviglumis parviglumis) PBS(SW750 SW2K dehyd1A zagl1 su1 parviglumis SW750 SW2K parviglumis parviglumis SW2K b Fonseca et al. 2015 Nature Plants J. ROSS-IBARRA / UC DAVIS Liu et al. 2013 PLOS Genetics
  48. 48. domestication loci John Doebley median PBS values parviglumis parviglumis) PBS(SW750 SW2K dehyd1A zagl1 su1 parviglumis SW750 SW2K parviglumis parviglumis SW2K b Fonseca et al. 2015 Nature Plants J. ROSS-IBARRA / UC DAVIS Liu et al. 2013 PLOS Genetics
  49. 49. Fonseca et al. 2015 Nature Plants J. ROSS-IBARRA / UC DAVIS PBS(parviglumis) parviglumis SW750 SW2K dehyd1A su1 parviglumis SW750 SW2K parviglumis SW2K SW750 parviglumis SW2K SW750 Figure 2 Liu et al. 2013 PLOS Genetics median PBS values PBS(parviglumis) parviglumis SW750 SW2K dehyd1A zagl1 su1 parviglumis SW750 SW2K parviglumis parviglumis SW2K b adaptation loci Bill Belknap John Doebley
  50. 50. chronology of selection on starch pathway Fonseca et al. 2015 Nature Plants J. ROSS-IBARRA / UC DAVIS
  51. 51. concluding thoughts • introgression confounds simple estimates of origin • ancestral reconstruction provides resolution • introgression adapted maize to highlands • Southwest US maize originated in highlands with subsequent gene flow from Pacific Coast • ancient DNA allows chronology of gene flow, adaptation

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