Wheat by Thomas Hart Benton (1967), from The Emergence of Agriculture, B. Smith

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

2. Crop evolution is a special and difficult case in systematics • synthetic field: systematics, archaeology, genetics (breeders), anthropology • 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)

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

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

5. Convergent domestication in Poaceae • Domesticated 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) • All 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 corn • Conservation across 65 my in grasses of genes affecting these traits was unexpected

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

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

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

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

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

11. Genetic discontinuity to present Genetic discontinuity ephemeral 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 Designation of species, subspecies, etc., although important, impedes research! (Modified after O’Hara, 1993, Syst Biol 42)

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

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

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

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

16. Phylogenetic issues or, why molecular phylogenetics of crop plants is not easy Recent origin from close relatives (<12Ky) Morphological, but not molecular, variation great Sampling critical (wild progenitors, landraces, outgroups) • 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 • No M. sylvestris! Robinson et al 2001

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

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

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

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

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

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 • < 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

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

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

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

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

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

33. http://www.infojardin.com/fichas/hortalizas-verduras/col-china-coles-chinas-repollo-chino.htmhttp://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_chayote2_f.jpg