Skip to main content
SpringerLink
Log in

Merging Ecology and Genomics to Dissect Diversity in Wild Tomatoes and Their Relatives

  • Chapter
  • First Online:
Ecological Genomics

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 781))

Abstract

To understand the origin, history, and function, of natural biological variation, from nucleotide to community levels, is a fundamental promise of ecological genomics. The most fruitful systems for this work are those that possess both ecological and genomic resources. Such systems provide an opportunity to precisely dissect genetic and developmental mechanisms, and to connect genotypes to phenotypes, as well as to directly demonstrate the ecological and evolutionary relevance of this phenotypic variation. Here we synthesize findings emerging from our efforts to understand two fundamental evolutionary processes − speciation and adaptation – using ecological genomics approaches. Many of these studies have been in the wild tomato clade (Solanum section Lycopersicon), a group that has both exceptional diversity and genomic tools. We also highlight the expanding taxonomic reach of this work, especially in two genera – Capsicum and Jaltomata – that are closely related to Solanum. Parallel approaches in these ecologically and reproductively diverse clades enable us to examine novel questions and traits that are not captured within Solanum, while leveraging the power of comparative studies to understand shared ecological and evolutionary patterns. By synthesizing findings from phenotypic, ecophysiological, genetic, and comparative perspectives, our ultimate goal is to understand the complex mechanistic and evolutionary contributions to the formation of new traits and species diversity.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 219.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 279.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 279.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Alimi NA, Bink MCAM, Dieleman JA et al (2012) Genetic and QTL analyses of yield and a set of physiological traits in pepper. Euphytica 100(2):181–201

    Google Scholar 

  • Andersson C (1999) Glycoalkaloids in tomatoes, eggplants, pepper and two Solanum species growing wild in the Nordic countries. Nordic Council of Ministers, Copenhagen

    Google Scholar 

  • Anderson JT, Willis JH, Mitchell-Olds T (2011) Evolutionary genetics of plant adaptation. Trends Genet 27:258–266

    PubMed  CAS  Google Scholar 

  • Balbi V, Devoto A (2008) Jasmonate signaling network in Arabidopsis thaliana: crucial regulatory nodes and new physiological scenarios. New Phytol 177:301–318

    PubMed  CAS  Google Scholar 

  • Barboza G (2011) Lectotypifications, synonymy, and a new name in Capsicum (Solanoideae, Solanaceae). Phytokeys 2:91

    Google Scholar 

  • Barrett SCH (2002) Sexual interference of the floral kind. Heredity 88:154–159

    PubMed  CAS  Google Scholar 

  • Bedinger PA, Chetelat RT, McClure B et al (2011) Interspecific reproductive barriers in the tomato clade: opportunities to decipher mechanisms of reproductive isolation. Sex Plant Reprod 24:171–187

    PubMed  Google Scholar 

  • Bernacchi D, Tanksley SD (1997) An interspecific backcross of Lycopersicon esculentum x L. hirsutum: linkage analysis and a QTL study of sexual compatibility factors and floral traits. Genetics 147:861–877

    PubMed  CAS  Google Scholar 

  • Blum E, Mazourek M, O’Connell M, Curry J, Thorup T, Liu K, Paran I (2003) Molecular mapping of capsaicinoid biosynthesis genes and quantitative trait loci analysis for capsaicinoid content in Capsicum. Theor Appl Genet 108(1):79–86

    PubMed  CAS  Google Scholar 

  • Boughman JW, Rundle HD, Schluter D (2005) Parallel evolution of sexual isolation in sticklebacks. Evolution 59:361–373

    PubMed  Google Scholar 

  • Bradshaw H, Schemske D (2003) Allele substitution at a flower colour locus produces a pollinator shift in monkeyflowers. Nature 426:176–178

    PubMed  CAS  Google Scholar 

  • Campbell DR (2009) Using phenotypic manipulations to study multivariate selection of floral trait associations. Ann Bot 103:1557–1566

    PubMed  Google Scholar 

  • Causier B, Schwarz-Sommer Z, Davies B (2010) Floral organ identity: 20 years of ABCs. Semin Cell Dev Biol 21:73–79

    PubMed  CAS  Google Scholar 

  • Choi KH, Hong CB, Kim WT (2002) Isolation and characterization of drought-induced cDNA clones from hot pepper (Capsicum annuum). J Plant Biol 45:212–218

    CAS  Google Scholar 

  • Collins NC, Tardieu F, Tuberosa R (2008) Quantitative trait loci and crop performance under abiotic stress: where do we stand? Plant Physiol 147:469–486

    PubMed  CAS  Google Scholar 

  • Courtney WH III, Lambeth VN (1977) Glycoalkaloid content of mature green fruit of Lycopersicon species (tomatoes, interspecific breeding). Hort Sci 12(6):550–551

    CAS  Google Scholar 

  • Covey PA, Kondo K, Welch L et al (2010) Multiple features that distinguish unilateral incongruity and self-incompatibility in the tomato clade. Plant J 64:367–378

    PubMed  CAS  Google Scholar 

  • Coyne JA, Orr HA (2004) Speciation. Sinauer Associates, Sunderland

    Google Scholar 

  • Darwin C (1862) On the contrivances by which British and foreign orchids are fertilized by insects, and on the good effects of intercrossing. John Murray, London

    Google Scholar 

  • Darwin C (1876) The effects of cross- and self-fertilization in the vegetable kingdom. John Murray, London

    Google Scholar 

  • Darwin SC, Knapp S, Peralta IE (2003) Taxonomy of tomatoes in the Galápagos Islands: native and introduced species of Solanum section Lycopersicon (Solanaceae). Syst Biodivers 1:29–53

    Google Scholar 

  • Dawkins R, Krebs JR (1979) Arms races between and within species. Proc R Soc B 205:489–511

    CAS  Google Scholar 

  • De Bodt S, Maere S, Van de Peer Y (2005) Genome duplication and the origin of angiosperms. Trends Ecol Evol 20:591–597

    PubMed  Google Scholar 

  • de Nettancourt (2000) Incompatibility and incongruity in wild and cultivated plants, 2nd edn. Springer, Berlin/Heidelberg/New York

    Google Scholar 

  • De Pascale S, Ruggiero C, Barbieri G, Maggio A (2003) Physiological responses of pepper to salinity and drought. J Am Soc Hortic Sci 128:48–54

    Google Scholar 

  • Dell’Olivo A, Hoballah ME, Gübitz T, Kuhlemeier C (2011) Isolation barriers between Petunia axillaris and Petunia integrifolia (Solanaceae). Evolution 65:1979–1991

    PubMed  Google Scholar 

  • Drummond (1986) Coevolution of ithomiine butterflies and solanaceous plants. In: D’Arcy WG (ed) The Solanaceae: biology and systematics. Columbia University Press, New York, pp 303–327

    Google Scholar 

  • Egea C, Perez MDG, Candela ME (1996) Capsidiol accumulation in Capsicum annuum stems during the hypersensitive reaction to Phytophthora capsici. J Plant Physiol 149(6):762–764

    CAS  Google Scholar 

  • Ehrlich P, Raven P (1964) Butterflies and plants – a study in coevolution. Evolution 18:586–608

    Google Scholar 

  • Eisen JA, Fraser CM (2003) Phylogenomics: intersection of evolution and genomics. Science 300:1706–1707

    PubMed  CAS  Google Scholar 

  • Ellegren H, Smeds L, Burri R et al (2012) The genomic landscape of species divergence in Ficedula flycatchers. Nature 491:756–760

    PubMed  CAS  Google Scholar 

  • Endress PK (2011) Evolutionary diversification of the flowers in angiosperms. Am J Bot 98:370–396

    PubMed  Google Scholar 

  • Farmer EE, Ryan CA (1992) Octadecanoid precursors of jasmonic acid activate the synthesis of wound-inducible proteinase inhibitors. Plant Cell 4:129–134

    PubMed  CAS  Google Scholar 

  • Feder M, Mitchell-Olds T (2003) Evolutionary and ecological functional genomics. Nat Rev Genet 4:651–657

    PubMed  CAS  Google Scholar 

  • Fishman L, Kelly JA, Willis JH (2002) Minor quantitative trait loci underlie floral traits associated with mating system divergence in Mimulus. Evolution 56:2138–2155

    PubMed  Google Scholar 

  • Foolad M (2007) Genome mapping and molecular breeding of tomato. Int J Plant Genom 2007:52

    Google Scholar 

  • Foolad MR, Zhang LP, Subbiah P (2003) Genetics of drought tolerance during seed germination in tomato: inheritance and QTL mapping. Genome 46:536–545

    PubMed  CAS  Google Scholar 

  • Fulton M, Hodges SA (1999) Floral isolation between Aquilegia formosa and Aquilegia pubescens. Proc R Soc B 266:2247–2252

    Google Scholar 

  • Futuyma DJ, Moreno G (1988) The evolution of ecological specialization. Annu Rev Ecol Evol Syst 19:207–233

    Google Scholar 

  • Gentry AH (1982) Patterns of neotropical plant species diversity. Evol Biol 15:1–84

    Google Scholar 

  • Gonzalez-Vigil E, Hufnagel DE, Kim J et al (2012) Evolution of TPS20-related terpene synthases influences chemical diversity in the glandular trichomes of the wild tomato relative Solanum habrochaites. Plant J 71:921–935

    Google Scholar 

  • Goodwillie C, Ritland C, Ritland K (2006) The genetic basis of floral traits associated with mating system evolution in Leptosiphon (Polemoniaceae): an analysis of quantitative trait loci. Evolution 60:491–504

    PubMed  CAS  Google Scholar 

  • Grandillo S, Chetelat R, Knapp S et al (2011) Solanum sect. Lycopersicon. In: Wild crop relatives: genomic and breeding resources. Springer, New York, pp 129–215

    Google Scholar 

  • Grant V (1949) Pollination systems as isolating mechanisms in angiosperms. Evolution 3:82–97

    PubMed  CAS  Google Scholar 

  • Guisan A, Zimmermann NE (2000) Predictive habitat distribution models in ecology. Ecol Model 135:147–186

    Google Scholar 

  • Haak DC, McGinnis LA, Levey DJ, Tewksbury JJ (2012) Why are not all chilies hot? A trade-off limits pungency. Proc R Soc B 279:2012–2017

    PubMed  Google Scholar 

  • Hansen DM, Olesen JM, Mione T et al (2007) Coloured nectar: distribution, ecology, and evolution of an enigmatic floral trait. Biol Rev 82:83–111

    PubMed  Google Scholar 

  • Harborne JB (1986) Systematic significance of variations in defense chemistry in the Solanaceae. In: Solanaceae: biology and systematics. Columbia University Press, New York, pp 328–344

    Google Scholar 

  • Harrison MA (2012) Cross-talk between phytohormone signaling pathways under both optimal and stressful environmental conditions. In: Phytohormones and abiotic stress tolerance in plants. Springer, Berlin/Heidelberg/New York, pp 49–76

    Google Scholar 

  • Hause B, Stenzel I, Miersch O et al (2000) Tissue-specific oxylipin signature of tomato flowers: allene oxide cyclase is highly expressed in distinct flower organs and vascular bundles. Plant J 24:113–126

    PubMed  CAS  Google Scholar 

  • Heijmans K, Morel P, Vandenbussche M (2012) MADS-box genes and floral development: the dark side. J Exp Bot 63:5397–5404

    PubMed  CAS  Google Scholar 

  • Heiser CB (1987) The fascinating world of the nightshades: tobacco, mandrake, potato, tomato, pepper, eggplant, etc. Dover publications, New York

    Google Scholar 

  • Hileman LC, Sundstrom JF, Litt A, Chen M, Shumba T, Irish VF (2006) Molecular and phylogenetic analyses of the MADS-Box gene family in tomato. Mol Biol Evol 23:2245–2258

    PubMed  CAS  Google Scholar 

  • Hoballah ME, Gubitz T, Stuurman J, Broger L, Barone M, Mandel T, Dell’Olivo A, Arnold M, Kuhlemeier C (2007) Single gene-mediated shift in pollinator attraction in Petunia. Plant Cell 19:779–790

    PubMed  CAS  Google Scholar 

  • Hodges SA, Whittall JB, Fulton M, Yang JY (2002) Genetics of floral traits influencing reproductive isolation between Aquilegia formosa and Aquilegia pubescens. Am Nat 159:S51–S60

    PubMed  Google Scholar 

  • Holle M, Rick CM, Hunt DG (1979) Catalog of collections of green-fruited Lycopersicon species and Solanum pennellii found in watersheds of Peru. Report Tomato Genetics Cooperative

    Google Scholar 

  • Hollocher H, Wu CI (1996) The genetics of reproductive isolation in the Drosophila simulans clade: X vs autosomal effects and male vs female effects. Genetics 143:1243–1255

    PubMed  CAS  Google Scholar 

  • Hopkins R, Rausher MD (2011) Identification of two genes causing reinforcement in the Texas wildflower Phlox drummondii. Nature 469:411–414

    PubMed  CAS  Google Scholar 

  • Hopkins R, Rausher MD (2012) Pollinator-mediated selection on flower color allele drives reinforcement. Science 335:1090–1092

    PubMed  CAS  Google Scholar 

  • Hsiao TC (1973) Plant responses to water stress. Annu Rev Plant Physiol 24(1):519–570

    CAS  Google Scholar 

  • Irish VF (2006) Duplication, diversification, and comparative genetics of angiosperm MADS-box genes. In: Soltis DE, LeebensMack JH, Soltis PS, Callow JA (eds) Advances in botanical research: incorporating advances in plant pathology, vol 44, Developmental genetics of the flower. Elsevier, Boston, pp 129–161

    Google Scholar 

  • Jewell C, Papineau AD, Freyre R, Moyle LC (2012) Patterns of reproductive isolation in Nolana (Chilean Bellflower). Evolution 66:2628–2636

    PubMed  Google Scholar 

  • Juenger TE, McKay JK, Hausmann N et al (2005) Identification and characterization of QTL underlying whole-plant physiology in Arabidopsis thaliana: delta13C, stomatal conductance and transpiration efficiency. Plant Cell Environ 28:697–708

    CAS  Google Scholar 

  • Juvik JA, Stevens MA, Rick CM (1982) Survey of the genus Lycopersicon for variability in α-tomatine content. HortScience 17(5):764–766

    CAS  Google Scholar 

  • Kang J, Shi F, Jones A et al (2010) Distortion of trichome morphology by the hairless mutation of tomato affects leaf surface chemistry. J Exp Bot 61:1053

    PubMed  CAS  Google Scholar 

  • Karban R, Baldwin IT (1997) Induced responses to herbivory. University of Chicago Press, Chicago

    Google Scholar 

  • Kawecki TJ, Ebert D (2004) Conceptual issues in local adaptation. Ecol Lett 7:1225–1241

    Google Scholar 

  • Kay KM, Sargent RD (2009) The role of animal pollination in plant speciation: integrating ecology, geography, and genetics. Ann Rev Ecol Evolut Syst 40:637–656

    Google Scholar 

  • Kennedy GG (2003) Tomato, pests, parasitoids, and predators: tritrophic interactions involving the genus Lycopersicon. Annu Rev Entomol 48:51–72

    PubMed  CAS  Google Scholar 

  • Kennedy GG (2007) Resistance in tomato and other Lycopersicon species to insect and mite pests. Genet Improv Solanaceous Crops 2:488–519

    Google Scholar 

  • Kennedy GG, Sorenson CF (1985) Role of glandular trichomes in the resistance of Lycopersicon hirsutum f. glabratum to Colorado potato beetle (Coleoptera: Chrysomelidae). J Econ Entomol 78(3):547–551

    Google Scholar 

  • Kessler A, Halitschke R, Poveda K (2011) Herbivory-mediated pollinator limitation: negative impacts of induced volatiles on plant-pollinator interactions. Ecology 92:1769–1780

    PubMed  Google Scholar 

  • Kim H-J, Baek K-H, Lee S-W et al (2008) Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome. BMC Plant Biol 8:101–101

    PubMed  Google Scholar 

  • Kim J, Kang K, Gonzales-Vigil E et al (2012) Striking natural diversity in glandular trichome acylsugar composition is shaped by variation at the Acyltransferase2 locus in the wild tomato Solanum habrochaites. Plant Physiol 160:1854–1870

    PubMed  CAS  Google Scholar 

  • Knapp S (2010) On “various contrivances”: pollination, phylogeny and flower form in the Solanaceae. Philos Trans R Soc B 365:449–460

    Google Scholar 

  • Lefebvre V, Palloix A (1996) Both epistatic and additive effects of QTLs are involved in polygenic induced resistance to disease: a case study, the interaction pepper – Phytophthora capsici Leonian. Theor Appl Genet 93:503–511

    PubMed  CAS  Google Scholar 

  • Levey DJ, Tewksbury JJ, Izhaki I, Tsahar E, Haak DC (2007) Evolutionary ecology of secondary compounds in ripe fruit: case studies with capsaicin and emodin. In: Dennis AJ, Schupp EW, Green RJ, Westcott DA (eds) Seed dispersal: theory and its application in a changing world. CABI, Wallingford, pp 37–58

    Google Scholar 

  • Li C (2003) The tomato suppressor of prosystemin-mediated responses: gene encodes a fatty acid desaturase required for the biosynthesis of jasmonic acid and the production of a systemic wound signal for defense gene expression. Plant Cell 15:1646–1661

    PubMed  CAS  Google Scholar 

  • Li (2010) Exploration of wild relatives of tomato for enhanced stress tolerance. Thesis, Wageningen University, Wageningen

    Google Scholar 

  • Li W, Chetelat RT (2010) A pollen factor linking inter- and intraspecific pollen rejection in tomato. Science 330:1827–1830

    PubMed  CAS  Google Scholar 

  • Li L, Zhao Y, McCaig B et al (2004) The tomato homolog of CORONATINE-INSENSITIVE1 is required for the maternal control of seed maturation, jasmonate-signaled defense responses, and glandular trichome development. Plant Cell 16:126

    PubMed  CAS  Google Scholar 

  • Li Y, Costello J, Holloway A, Hahn M (2008) “Reverse ecology” and the power of population genomics. Evolution 62:2984–2994

    PubMed  Google Scholar 

  • Lin JZ, Ritland K (1997) Quantitative trait loci differentiating the outbreeding Mimulus guttatus from the inbreeding M. platycalyx. Genetics 146:1115–1121

    PubMed  CAS  Google Scholar 

  • Liu Z, Mara C (2010) Regulatory mechanisms for floral homeotic gene expression. Semin Cell Dev Biol 21:80–86

    PubMed  Google Scholar 

  • Magwene PM, Willis JH, Kelly JK (2011) The statistics of bulk segregant analysis using next generation sequencing. PLoS Comput Biol 7(11):e1002255

    PubMed  CAS  Google Scholar 

  • Malmberg RL, Mauricio R (2005) QTL-based evidence for the role of epistasis in evolution. Genet Res 86:89–95

    PubMed  CAS  Google Scholar 

  • Martin B, Nienhuis J, King G, Schaefer A (1989) Restriction fragment length polymorphisms associated with water use efficiency in tomato. Science 243:1725–1728

    PubMed  CAS  Google Scholar 

  • Masly JP, Presgraves DC (2007) High-resolution genome-wide dissection of the two rules of speciation in Drosophila. PLoS Biol 5:e243

    PubMed  Google Scholar 

  • McCormack JE, Faircloth BC, Crawford NG et al (2012) Ultra-conserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res 22:746–754

    PubMed  CAS  Google Scholar 

  • McDowell ET, Kapteyn J, Schmidt A et al (2011) Comparative functional genomic analysis of Solanum glandular trichome types. Plant Physiol 155:524–539

    PubMed  CAS  Google Scholar 

  • McKay J, Richards J, Nemali K et al (2008) Genetics of drought adaptation in Arabidopsis thaliana II. QTL analysis of a new mapping population KAS-1x TSU-1. Evolution 62:3014–3026

    PubMed  Google Scholar 

  • Medina-Tapia N, Ayala-Berdon J, Morales-Perez L, Miron Melo L, Schondube JE (2012) Do hummingbirds have a sweet-tooth? Gustatory sugar thresholds and sugar selection in the broad-billed hummingbird Cynanthus latirostris. Comp Biochem Physiol A Mol Integr Physiol 161:307–314

    PubMed  CAS  Google Scholar 

  • Miller RJ, Mione T, Phan H-L, Olmstead RG (2011) Color by numbers: nuclear gene phylogeny of Jaltomata (Solanaceae), sister genus to Solanum, supports three clades differing in fruit color. Syst Bot 36:153–162

    Google Scholar 

  • Mitchell-Olds T, Schmitt J (2006) Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis. Nature 441:947

    PubMed  CAS  Google Scholar 

  • Mitchell-Olds T, Willis JH, Goldstein DB (2007) Which evolutionary processes influence natural genetic variation for phenotypic traits? Nat Rev Genet 8:845–856

    PubMed  CAS  Google Scholar 

  • Moyle LC (2007) Comparative genetics of potential prezygotic and postzygotic isolating barriers in a Lycopersicon species cross. J Hered 98:123–135

    PubMed  CAS  Google Scholar 

  • Moyle LC (2008) Ecological and evolutionary genomics in the wild tomatoes (Solanum sect. Lycopersicon). Evolution 62(12):2995–3013

    PubMed  Google Scholar 

  • Moyle LC, Graham EB (2005) Genetics of hybrid incompatibility between Lycopersicon esculentum and L. hirsutum. Genetics 169:355–373

    PubMed  CAS  Google Scholar 

  • Moyle LC, Graham EB (2006) Genome-wide associations between hybrid sterility QTL and marker transmission ratio distortion. Mol Biol Evol 23:973–980

    PubMed  CAS  Google Scholar 

  • Moyle LC, Muir CD (2010) Reciprocal insights into adaptation from agricultural and evolutionary studies in tomato. Evol Appl 3:409–421

    Google Scholar 

  • Moyle LC, Nakazato T (2008) Comparative genetics of hybrid incompatibility: sterility in two Solanum species crosses. Genetics 179:1437–1453

    PubMed  Google Scholar 

  • Moyle LC, Nakazato T (2009) Complex epistasis for Dobzhansky-Muller hybrid incompatibility in Solanum. Genetics 181:347–351

    PubMed  Google Scholar 

  • Moyle LC, Nakazato T (2010) Hybrid incompatibility “snowballs” between Solanum species. Science 329:1521–1523

    PubMed  CAS  Google Scholar 

  • Moyle LC, Payseur BA (2009) Reproductive isolation grows on trees. Trends Ecol Evol 24:591–598

    PubMed  Google Scholar 

  • Muir CD, Moyle LC (2009) Antagonistic epistasis for ecophysiological trait differences between Solanum species. New Phytol 183:789–802

    PubMed  Google Scholar 

  • Nakazato T, Bogonovich M, Moyle LC (2008) Environmental factors predict adaptive phenotypic differentiation within and between two wild Andean tomatoes. Evolution 62(4):774–792

    PubMed  CAS  Google Scholar 

  • Nakazato T, Warren DL, Moyle LC (2010) Ecological and geographic modes of species divergence in wild tomatoes. Am J Bot 97:680–693

    PubMed  Google Scholar 

  • Nesbitt TC, Tanksley SD (2002) Comparative sequencing in the genus Lycopersicon: implications for the evolution of fruit size in the domestication of cultivated tomatoes. Genetics 162(1):365–379

    PubMed  CAS  Google Scholar 

  • Olmstead RG, Bohs L, Migid HA, Santiago-Valentin E, Garcia VF, Collier SM (2008) A molecular phylogeny of the Solanaceae. Taxon 57(4):1159–1181

    Google Scholar 

  • Orr HA (1995) The population genetics of speciation- the evolution of hybrid incompatibilities. Genetics 139:1805–1813

    PubMed  CAS  Google Scholar 

  • Owen CR, Bradshaw HD (2011) Induced mutations affecting pollinator choice in Mimulus lewisii (Phrymaceae). Arthropod-Plant Interact 5:235–244

    Google Scholar 

  • Payseur BA, Place M (2007) Searching the genomes of inbred mouse strains for incompatibilities that reproductively isolate their wild relatives. J Hered 98:115–122

    PubMed  CAS  Google Scholar 

  • Peralta I, Knapp S, Spooner D (2007) The taxonomy of tomatoes: a revision of wild tomatoes (Solanum L. section Lycopersicon (Mill.) Wettst.) and their outgroup relatives (Solanum sections Juglandifolium (Rydb.) Child and Lycopersicoides (Child) Peralta). Syst Bot Monogr 84:1–186

    Google Scholar 

  • Posto AL (2009) The genetics of pre-and postzygotic reproductive isolation in Solanum (Masters of Science Thesis, Indiana University, Department of Biology)

    Google Scholar 

  • Presgraves DC (2008) Sex chromosomes and speciation in Drosophila. Trends Genet 24:336–343

    PubMed  CAS  Google Scholar 

  • Presgraves DC (2010) The molecular evolutionary basis of species formation. Nat Rev Genet 11:175–180

    PubMed  CAS  Google Scholar 

  • Ramsey J, Bradshaw HD, Schemske DW (2003) Components of reproductive isolation between the monkeyflowers Mimulus lewisii and M. cardinalis (Phrymaceae). Evolution 57(7):1520–1534

    PubMed  Google Scholar 

  • Rick CM (1963) Barriers to interbreeding in Lycopersicon peruvianum. Evolution 17:216–232

    Google Scholar 

  • Rick CM (1973) Potential genetic resources in tomato species: clues from observations in native habitats. Basic Life Sci 2:255–269

    PubMed  CAS  Google Scholar 

  • Rick CM (1979) Biosystematic studies in Lycopersicon and closely related species of Solanum. In: Hawkes JG, Lester RN, Skelding AD (eds) The biology and taxonomy of the Solanaceae. Academic Press for the Linnean Society, London, pp 667–678

    Google Scholar 

  • Rick, Lamm (1995) Biosystematic studies on the status of Lycopersicon chilense. Am J Bot 42(7):663–675

    Google Scholar 

  • Rick CM, Quiros CF, Harry Lange W, Allen Stevens M (1976) Monogenic control of resistance in the tomato to the tobacco flea beetle: probable repellance by foliage volatiles. Euphytica 25:521–530

    Google Scholar 

  • Rijpkema A, Gerats T, Vandenbussche M (2006) Genetics of floral development in Petunia. In: Soltis DE, LeebensMack JH, Soltis PS, Callow JA (eds) Advances in botanical research: incorporating advances in plant pathology, vol 44: developmental genetics of the flower., pp 237–278

    Google Scholar 

  • Rodriguez-Saona CR, Musser RO, Vogel H et al (2010) Molecular, biochemical, and organismal analyses of tomato plants simultaneously attacked by herbivores from two feeding guilds. J Chem Ecol 36:1043–1057

    PubMed  CAS  Google Scholar 

  • Römer P, Hahn S, Jordan T et al (2007) Plant pathogen recognition mediated by promoter activation of the pepper Bs3 resistance gene. Science 318:645–648

    PubMed  Google Scholar 

  • Sablowski R (2010) Genes and functions controlled by floral organ identity genes. Semin Cell Dev Biol 21:94–99

    PubMed  CAS  Google Scholar 

  • Salinas M, Capel C, Alba JM et al (2012) Genetic mapping of two QTL from the wild tomato Solanum pimpinellifolium L. controlling resistance against two-spotted spider mite (Tetranychus urticae Koch). Theor Appl Genet 126:83–92

    PubMed  Google Scholar 

  • Sánchez-Peña P, Oyama K, Núñez-Farfán J, Fornoni J, Hernandez-Verdugo S, Marquez-Guzman J, Garzón-Tiznado JA (2006) Sources of resistance to whitefly (Bemisia spp.) in wild populations of Solanum lycopersicum var.cerasiforme (Dunal). Spooner GJ Anderson et RK Jansen in Northwestern Mexico. Genet Resour Crop Evol 53(4):711–719

    Google Scholar 

  • Schemske DW, Bradshaw HD (1999) Pollinator preference and the evolution of floral traits in monkeyflowers (Mimulus). Proc Natl Acad Sci USA 96:11910–11915

    PubMed  CAS  Google Scholar 

  • Schemske DW, Mittelbach GG, Cornell HV, Sobel JM, Roy K (2009) Is there a latitudinal gradient in the importance of biotic interactions? Annu Rev Ecol Evol Syst 40:245–269

    Google Scholar 

  • Schilmiller AL, Howe GA (2005) Systemic signaling in the wound response. Curr Opin Plant Biol 8:369–377

    PubMed  CAS  Google Scholar 

  • Sicard A, Lenhard M (2011) The selfing syndrome: a model for studying the genetic and evolutionary basis of morphological adaptation in plants. Ann Bot 107:1433–1443

    PubMed  Google Scholar 

  • Smaczniak C, Immink RGH, Angenent GC, Kaufmann K (2012) Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies. Development 139:3081–3098

    PubMed  CAS  Google Scholar 

  • Smith SD, Rausher MD (2011) Gene loss and parallel evolution contribute to species difference in flower color. Mol Biol Evol 28:2799–2810

    PubMed  CAS  Google Scholar 

  • Smith SD, Ané C, Baum DA (2008) The role of pollinator shifts in the floral diversification of Iochroma (Solanaceae). Evolution 62:793–806

    PubMed  Google Scholar 

  • Song B, Mitchell Olds T (2011) Evolutionary and ecological genomics of non-model plants. J Syst Evol 49:17–24

    PubMed  Google Scholar 

  • Stebbins GL (1957) Self fertilization and population variability in the higher plants. Am Nat 91:337–352

    Google Scholar 

  • Stellari GM, Mazourek M, Jahn MM (2009) Contrasting modes for loss of pungency between cultivated and wild species of Capsicum. Heredity 104(5):460–471

    PubMed  Google Scholar 

  • Stewart C, Mazourek M, Stellari GM, O’Connell M, Jahn M (2007) Genetic control of pungency in C. chinense via the Pun1 locus. J Exp Bot 58(5):979–991

    PubMed  CAS  Google Scholar 

  • Stinchcombe JR, Hoekstra HE (2007) Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity 100(2):158–170

    PubMed  Google Scholar 

  • Tao Y, Xhen SN, Hartl DL, Laurie CC (2003a) Genetic dissection of hybrid incompatibilities between Drosophila simulans and D. mauritiana. I. Differential accumulation of hybrid male sterility effects on the X and autosomes. Genetics 164:1383–1397

    PubMed  CAS  Google Scholar 

  • Tao Y, Zeng ZB, Li J, Hartl DL, Laurie CC (2003b) Genetic dissection of hybrid Incompatibilities between Drosophila simulans and D. mauritiana. II. Mapping hybrid male sterility loci on the third chromosome. Genetics 164:1399–1418

    PubMed  CAS  Google Scholar 

  • Tewksbury J, Manchego C, Haak DC, Levey D (2006) Where did the chili get its spice? Biogeography of capsaicinoid production in ancestral wild chili species. J Chem Ecol 32:547–564

    PubMed  CAS  Google Scholar 

  • Tewksbury JJ, Reagan KM, Machnicki NJ, Carlo TA, Haak DC, Peñaloza ALC, Levey DJ (2008) Evolutionary ecology of pungency in wild chilies. Proc Natl Acad Sci USA 105(33):11808–11811

    PubMed  CAS  Google Scholar 

  • Thaler JS, Owen B, Higgins VJ (2004) The role of the jasmonate response in plant susceptibility to diverse pathogens with a range of lifestyles. Plant Physiol 135:530–538

    PubMed  CAS  Google Scholar 

  • Thaler JS, Humphrey PT, Whiteman NK (2012) Evolution of jasmonate and salicylate signal crosstalk. Trends Plant Sci 17:260–270

    PubMed  CAS  Google Scholar 

  • Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641

    Google Scholar 

  • True JR, Weir BS, Laurie CC (1996) A genome-wide survey of hybrid incompatibility factors by the introgression of marked segments of Drosophila mauritiana chromosomes into Drosophila simulans. Genetics 142:819–837

    PubMed  CAS  Google Scholar 

  • Turelli M, Moyle LC (2007) Asymmetric postmating isolation: Darwin’s corollary to Haldane’s rule. Genetics 176:1059–1088

    PubMed  Google Scholar 

  • Turelli M, Orr HA (2000) Dominance, epistasis and the genetics of postzygotic isolation. Genetics 154:1663–1679

    PubMed  CAS  Google Scholar 

  • Turesson G (1925) The plant species in relation to habitat and climate. Hereditas 6:147–236

    Google Scholar 

  • Turner LM, Hoekstra HE (2006) Adaptive evolution of fertilization proteins within a genus: variation in ZP2 and ZP3 in deer mice (Peromyscus). Mol Biol Evol 23:1656–1669

    PubMed  CAS  Google Scholar 

  • Walia H, Josefsson C, Dilkes B, Kirkbride R, Harada J, Comai L (2009) Dosage-dependent deregulation of an AGAMOUS-LIKE gene cluster contributes to interspecific incompatibility. Curr Biol 19:1128–1132

    PubMed  CAS  Google Scholar 

  • Walsh BM, Hoot SB (2001) Phylogenetic relationships of Capsicum (Solanaceae) using DNA sequences from two noncoding regions: the chloroplast atpB-rbcL spacer region and nuclear waxy introns. Int J Plant Sci 162:1409–1418

    CAS  Google Scholar 

  • Wang Y, Diehl A, Wu F et al (2008) Sequencing and comparative analysis of a conserved syntenic segment in the solanaceae. Genetics 180:391–408

    PubMed  CAS  Google Scholar 

  • Wasternack C, Hause B (2002) Jasmonates and octadecanoids: signals in plant stress responses and development. Prog Nucleic Acid Res Mol Biol 72:165–221

    PubMed  CAS  Google Scholar 

  • Xu X, Martin B, Comstock JP et al (2008) Fine mapping a QTL for carbon isotope composition in tomato. Theor Appl Genet 117:221–233

    PubMed  CAS  Google Scholar 

  • Xu S, Schlueter PM, Scopece G, Breitkopf H, Gross K, Cozzolino S, Schiestl FP (2011) Floral isolation is the main reproductive barrier among closely related sexually deceptive orchids. Evolution 65:2606–2620

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

Members of the Moyle lab, and two anonymous reviewers, provided helpful feedback. T. Mione kindly shared Jaltomata seed material and unpublished data, and T. Carlo kindly shared unpublished Capsicum data. The C.M. Rick Tomato Genetics Resource Center (tgrc.ucdavis.edu) provided access to their collections and collection information database. This work was supported by National Science Foundation (Division of Environmental Biology/Dimensions of Biodiversity) award 1136707 (to L.C.M. and D.C.H). J.L.K. was supported by the IU Biology Floyd Plant and Fungal Biology Summer Fellowship, Amherst College Graduate Fellowship, and an NIH Genetics, Cellular, and Molecular Sciences training grant, award 5T32GM007757.

Author information

Authors and Affiliations

  1. Department of Biology, Indiana University, Bloomington, IN, 47405, USA

    David C. Haak, Jamie L. Kostyun & Leonie C. Moyle

Authors
  1. David C. Haak
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jamie L. Kostyun
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Leonie C. Moyle
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Leonie C. Moyle .

Editor information

Editors and Affiliations

  1. Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Quebec, Québec, Canada

    Christian R. Landry

  2. Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Quebec, Québec, Canada

    Nadia Aubin-Horth

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Haak, D.C., Kostyun, J.L., Moyle, L.C. (2014). Merging Ecology and Genomics to Dissect Diversity in Wild Tomatoes and Their Relatives. In: Landry, C., Aubin-Horth, N. (eds) Ecological Genomics. Advances in Experimental Medicine and Biology, vol 781. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7347-9_14

Download citation

Publish with us

Policies and ethics

Search

Navigation