1. Wheat by Thomas Hart Benton (1967), from The Emergence of Agriculture, B. Smith Molecular Data and Crop Evolution Graduate Seminar Wrap-up and summary

2. Crop evolution is a special and difficult case in systematics synthetic field: systematics, archaeology, genetics (breeders), anthropology synthetic field: systematics, archaeology, genetics (breeders), anthropology from wild progenitors to fully domesticated races (and everything in between) from wild progenitors to fully domesticated races (and everything in between) domestication is a whole plant concerted selection process (habit, flowering, breeding system, physiology, seed dormancy, life cycle, secondary compounds) domestication is a whole plant concerted selection process (habit, flowering, breeding system, physiology, seed dormancy, life cycle, secondary compounds)

3. Non-shattering habitNon-shattering habit Reduced seed dormancyReduced seed dormancy Reduced plant size, determinate growth habitReduced plant size, determinate growth habit Shorter life cyclesShorter life cycles Less branching, fewer flowersLess branching, fewer flowers Altered photoperiodic or vernalization requirementsAltered photoperiodic or vernalization requirements Reductions in defense mechanisms and defense compoundsReductions in defense mechanisms and defense compounds Changes in flower, seed, and fruit color...Changes in flower, seed, and fruit color... Whole plant concerted selection process

4. Autopolyploidy where fertility is relatively unimportantAutopolyploidy where fertility is relatively unimportant Allopolyploidy where fertility is importantAllopolyploidy where fertility is important Clonal propagationClonal propagation Inbreeding tolerance or derivation from outcrossingInbreeding tolerance or derivation from outcrossing Sex expression, apomixisSex expression, apomixis Whole plant concerted selection process but, much of this change is due to few major genes and often convergent

5. Domesticated between 7,000 and 12,000 years agoDomesticated between 7,000 and 12,000 years ago Despite independent domestication of the four major complexes: Rice (Asia), Wheat/Oats (Near East), Corn (America), Sorghum (Africa)Despite independent domestication of the four major complexes: Rice (Asia), Wheat/Oats (Near East), Corn (America), Sorghum (Africa) All were converted from small-seeded shattering grasses to large-seeded grasses with non-shattering habitAll were converted from small-seeded shattering grasses to large-seeded grasses with non-shattering habit Paterson et al. (1995) studied shattering, seed mass, daylength- insensitive flowering time in sorghum, rice, and cornPaterson et al. (1995) studied shattering, seed mass, daylength- insensitive flowering time in sorghum, rice, and corn Conservation across 65 my in grasses of genes affecting these traits was unexpectedConservation across 65 my in grasses of genes affecting these traits was unexpected Convergent domestication in Poaceae

6. Crop evolution is a special and difficult case in systematics synthetic field: systematics, archaeology, genetics (breeders), anthropology synthetic field: systematics, archaeology, genetics (breeders), anthropology from wild progenitors to fully domesticated races (and everything in between) from wild progenitors to fully domesticated races (and everything in between) domestication is a whole plant concerted selection process domestication is a whole plant concerted selection process domestication can have intense divergent selection domestication can have intense divergent selection

7. Then... throw in divergent selection Turnip (Brassica campestris) AA Genome, wild Selection for seed Annual oil seed Selection for leafiness chinensispekinensis Biennial habit, bulbing Turnip napus (AACC) napocampestris (AAAACC) nigra (BB) juncea (AABB) Raph. sativus (RR) Brassicoraphanus (AARR)

8. Phylogenetic issues 1. Recent origin from close relatives (<12Ky) or, why molecular phylogenetics of crop plants is not easy

9. back in time As you go back in time to earlier generations, the genetic connections appear as a network within the population of interbreeding individuals 1 Population Are you studying taxonomic units in which gene trees provide an “emerging” species tree?

10. back in time But further back, they appear as dichotomous branching ropes Are you studying taxonomic units in which gene trees provide an “emerging” species tree? Designation of species, subspecies, etc., although important, impedes research!

11. (Modified after O’Hara, 1993, Syst Biol 42) Designation of species, subspecies, etc., although important, impedes research! Are you studying taxonomic units in which gene trees provide an “emerging” species tree? Situation in crop plants is probably much like that proposed by O’Hara as common in natural speciation Genetic discontinuity to present Genetic discontinuity ephemeral

12. Phylogenetic issues 1.Recent origin from close relatives (<12Ky) 2.Morphological, but not molecular, variation great or, why molecular phylogenetics of crop plants is not easy therefore the search for “markers” [RFLPs, RAPDs, SSRs, ISSRs, AFLPs, etc.] therefore the search for “markers” [RFLPs, RAPDs, SSRs, ISSRs, AFLPs, etc.] issues with how to analyze & interpret these “trees”, “phylograms”, “networks”, “PCA diagrams” issues with how to analyze & interpret these “trees”, “phylograms”, “networks”, “PCA diagrams”

13. From Dr. Marc Ghislain’s presentation at the 2 nd Solanaceae Genome workshop 2005, Ischia - Italy Is this the appropriate “diagram” for this kind of marker data? cluster analysis in Solanum

14. Gene pool structure analyses I From Dr. Marc Ghislain’s presentation at the 2 nd Solanaceae Genome workshop 2005, Ischia - Italy Or this? factorial analysis in Solanum

15. from Harter et al 2004 One of the better analyses using genetic data as it uses a model based approach to ID placement of wild and domesticated Helianthus strains

16. Phylogenetic issues 1.Recent origin from close relatives (<12Ky) 2.Morphological, but not molecular, variation great 3.Sampling critical (wild progenitors, landraces, outgroups) or, why molecular phylogenetics of crop plants is not easy how many times this semester were you frustrated by the lack of sampling of critical taxa, or different samplings from study to study? how many times this semester were you frustrated by the lack of sampling of critical taxa, or different samplings from study to study?

17. Nuclear ribosomal ITS Robinson et al 2001 No M. sylvestris! No M. sylvestris! =

18. Phylogenetic issues 1.Recent origin from close relatives (<12Ky) 2.Morphological, but not molecular, variation great 3.Sampling critical 4.Hybridization, introgression, polyploidy common or, why molecular phylogenetics of crop plants is not easy gene trees will not equal “species” tree (whatever the latter means) gene trees will not equal “species” tree (whatever the latter means)

19. Eubanks, 1997 Hybridization and introgression jumped at almost immediately, even when wrong

20. Is this the prevailing “icon” for crop plants, rather than a branching “species” tree?

21. Prevalence of polyploidy (both allo- and auto-) presents homology issues in use of nuclear genes or anonymous markers

22. All these genome transfers requires multiple data sets from different genomes in most phylogenetic studies of crop plants

23. Phylogenetic issues 1.Recent origin from close relatives (<12Ky) 2.Morphological, but not molecular, variation great 3.Sampling critical 4.Hybridization, introgression, polyploidy common 5.Biogeography is complex (both natural and human induced movements) or, why molecular phylogenetics of crop plants is not easy

24. How should we biogeographically interpret (or analyze!) the distribution of these MDH alleles or phenotypes ? Artocarpus (breadfruit)

25. Phylogeography of G3pdh haplotypes in Manihot (cassava) Should there be more phylogeographical analysis of molecular data ?

26. Should there be more clock calibrations for determining timing of species formation or even domestication? Sechium edule - chayote (Cucurbitaceae)

27. Where do we go from here? 200 plant species have been domesticated out of approximately 275,000 angiosperms 200 plant species have been domesticated out of approximately 275,000 angiosperms < 20 crops in 8 families provide most of the world’s food (wheat, rice, corn, beans, sugarcane, sugar beet, cassava, potato, sweet potato, banana, coconut, soybean, peanut, barley, and sorghum - Harlan, 1992) < 20 crops in 8 families provide most of the world’s food (wheat, rice, corn, beans, sugarcane, sugar beet, cassava, potato, sweet potato, banana, coconut, soybean, peanut, barley, and sorghum - Harlan, 1992) only 8 plant families stand between most humans and starvation only 8 plant families stand between most humans and starvation

28. Where do we go from here? major crops (and some minor - sunflower) are well known from systematic and genomic perspectives major crops (and some minor - sunflower) are well known from systematic and genomic perspectives their study often revolutionizes systematics in terms of techniques their study often revolutionizes systematics in terms of techniques providing new methods do address questions of evolution and speciation in plants providing new methods do address questions of evolution and speciation in plants sequenced genomes, libraries, EST approaches, FISH and GISH chromosomal analyses sequenced genomes, libraries, EST approaches, FISH and GISH chromosomal analyses

29. Can we go beyond these markers? From Darwin’s Harvest

30. Tragopogon - goat’s beard (Modified after Pires & al, 2004, AJB 91) Fluorescent in situ hybridization (FISH) mainly used on crop plants but some wild species

31. Future of crop evolution? What do we want to learn? Why is it important? Questions

32. Wheat by Thomas Hart Benton (1967), from The Emergence of Agriculture, B. Smith Molecular Data and Crop Evolution Graduate Seminar Wrap-up and summary

33. http://www.infojardin.com/fichas/hortalizas-verduras/col-china-coles- chinas-repollo-chino.htm http://gettle.org/gallery/d/242-1/Chayote.jpg http://www.uc.cl/sw_educ/hortalizas/imagenes/chayote/diversidad_ch ayote2_f.jpg