Plant Systematics and Evolution

, Volume 287, Issue 1–2, pp 85–97 | Cite as

A phylogenetic investigation of Carthamus combining sequence and microsatellite data

  • Victoria G. Bowles
  • Reinhold Mayerhofer
  • Corey Davis
  • Allen G. Good
  • Jocelyn C. Hall
Original Article


Carthamus (Asteraceae) includes both crop (Carthamus tinctorius, safflower) and weedy species. Despite previous studies, many outstanding questions remain regarding the phylogenetic surroundings of safflower, especially in relation to weedy species. Here we investigated relationships within Carthamus using a tiered approach examining sequence and microsatellite data. First, nuclear and chloroplast sequences were analyzed from 37 accessions of 16 species. Maximum parsimony, maximum likelihood, and Bayesian inference confirm two well supported clades, corresponding to sect. Atractlyis and sect. Carthamus, the latter of which includes safflower. Because sequence data provided limited resolution within the clades, microsatellite markers were used to investigate relationships within sect. Carthamus. Both sequence and microsatellite data reveal that most traditionally recognized species are not monophyletic. Microsatellite data indicate that Carthamus palaestinus is the closest relative of cultivated safflower.


Carthamus Microsatellite Phylogeny Safflower 



We would like to thank the staff of the Molecular Biology Service Unit at the University of Alberta for all their help and support with sequencing and microsatellites. Marion Mayerhofer provided much appreciated assistance with growing plants from seed and tissue collection. We also thank members of the Hall Lab for their comments on earlier versions of this manuscript and anonymous reviewers for their help in improving the manuscript. The research was funded by SemBioSys Genetics Inc. and an NSERC CRD grant to A.G.G.


  1. Alvarez AE, van de Wiel CCM, Smulders MJM, Vosman B (2001) Use of microsatellites to evaluate genetic diversity and species relationships in the genus Lycopersicon. Theor Appl Genet 103:1283–1292CrossRefGoogle Scholar
  2. Ashri A, Efron Y (1964) Inheritance studies with fertile interspecific hybrids of three Carthamus L. species. Crop Sci 4:510–514CrossRefGoogle Scholar
  3. Ashri A, Knowles PF (1960) Cytogenetics of safflower (Carthamus L.) species and their hybrids. Agron J 52:11–17Google Scholar
  4. Ashri A, Rudich J (1965) Unequal reciprocal natural hybridization rates between two Carthamus L. species. Crop Sci 5:190–191CrossRefGoogle Scholar
  5. Bassiri A (1977) Identification and polymorphism of cultivars and wild ecotypes of safflower based on isoenzyme patterns. Euphytica 26:709–719CrossRefGoogle Scholar
  6. Chapman MA, Burke JM (2007) DNA sequence diversity and the origin of cultivated safflower (Carthamus tinctorius L.; Asteraceae). BMC Plant Biol 7:60CrossRefPubMedGoogle Scholar
  7. Deshpande RB (1952) Wild safflower (Carthamus oxyacantha Bieb.)—a possible oilseed crop for the desert and arid regions. Indian J Genet Plant Breed 12:10–14Google Scholar
  8. Doyle JF, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15Google Scholar
  9. Ellstrand NC, Prentice HC, Hancock JF (1999) Gene flow and introgression from domesticated plants into their wild relatives. Annu Rev Ecol Syst 30:539–563CrossRefGoogle Scholar
  10. Estilai A, Knowles PF (1976) Cytogenetic studies of Carthamus divaricatus with 11 pairs of chromosomes and its relationship to other Carthamus species (Compositae). Am J Bot 63:771–782CrossRefGoogle Scholar
  11. Fitch WM (1971) Towards defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  12. Garnatje T, Garcia S, Vilatersana R, Vallès J (2006) Genome size variation in the Carthamus (Asteraceae, Cardueae): systematic implications and additive changes during allopolyploidization. Ann Bot 97:461–467CrossRefPubMedGoogle Scholar
  13. Goldstein DB, Pollock DD (1997) Launching microsatellites: a review of mutation processes and methods of phylogenetic inference. J Hered 88:335–342PubMedGoogle Scholar
  14. Goldstein DB, Linares AR, Cavalli-Sforza LL, Feldman MW (1995) An evaluation of genetic distances for use with microsatellite loci. Genetics 139:463–471PubMedGoogle Scholar
  15. Hamilton MB, Pincus EL, Fiore AD, Fleisher RC (1999) Universal linker and ligation procedures for construction of genomic DNA libraries. Biotechniques 27:500–507PubMedGoogle Scholar
  16. Hanelt P (1963) Monographische Ubersicht der Gattung Carthamus L. (Compositae). Feddes Repert 67:41–180Google Scholar
  17. Hillis DM, Huelsenbeck JP (1992) Signal, noise and reliability in molecular phylogenetic analyses. J Hered 83:189–195PubMedGoogle Scholar
  18. Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754–755CrossRefPubMedGoogle Scholar
  19. Imrie BC, Knowles PF (1970) Inheritance studies in interspecific hybrids between Carthamus flavescens and C. tinctorius. Crop Sci 10:349–352CrossRefGoogle Scholar
  20. Johnston AM, Tanaka DL, Miller PR, Brandt SA, Mielsen DC, Lafond GP, Riveland NR (2002) Oilseed crops for semiarid cropping systems in the northern Great Plains. Agron J 94:231–240CrossRefGoogle Scholar
  21. Keil DJ (2006) Carthamus. In: Barkley TM, Brouillet L, Jeude H, Strother JL, Gandhi K, Kiger RW, Yatskievych K, Sarucchi JL (eds) Flora of North America, vol. 19. New York, pp 178–181Google Scholar
  22. Khidir MO, Knowles PF (1970) Cytogenetic studies of Carthamus species (Compositae) with 32 pairs of chromosomes II. Intersectional hybridization. Can J Genet Cytol 12:90–99Google Scholar
  23. Knowles PF (1976) Safflower. In: Simmonds NW (ed) Evolution of crop plants. Longman, New York, pp 31Google Scholar
  24. Knowles PF, Schank SC (1964) Artificial hybrids of Carthamus nitidus Boiss. and C. tinctorius L. (Compositae). Crop Sci 4:596–599CrossRefGoogle Scholar
  25. López-González G (1989) Acerca de la Clasificación natural del género Carthamus L., s.l. Anal Jardín Bot Madrid 47:11–34Google Scholar
  26. Maddison DR, Maddison WP (2005) MacClade version 4.07. Computer program and documentation. Sinauer, SunderlandGoogle Scholar
  27. Maddison WP, Maddison DR (2009) Mesquite: a modular system for evolutionary analysis. Version 2.72.
  28. Mason-Gamer RJ, Kellogg EA (1996) Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Graminae). Syst Biol 45:524–545Google Scholar
  29. McPherson MA, Good AG, Topinka AKC, Hall LM (2004) Theoretical hybridization potential of transgenic safflower (Carthamus tinctorius L.) with weedy relatives in the New World. Can J Plant Sci 84:923–934Google Scholar
  30. Mündel HH, Blacksaw RE, Byers JR, Huang HC, Johnson DL, Keon R, Kubik J, McKenzie R, Otto B, Roth B, Stanford K (2004) Safflower production on the Canadian prairies: revisited in 2004. Agriculture and Agri-Food Canada, Lethbridge Research Center, AlbertaGoogle Scholar
  31. Nauta MJ, Weissing FJ (1996) Constraints on allele size at microsatellite loci: implications for genetic differentiation. Genetics 143:1021–1032PubMedGoogle Scholar
  32. Nylander JAA (2004) MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala UniversityGoogle Scholar
  33. Petren K, Grant BR, Grant PR (1999) A phylogeny of Darwin’s finches based on microsatellite DNA length variation. Proc R Soc Lond Ser B Biol Sci 266:321–329CrossRefGoogle Scholar
  34. Richard M, Thorpe RS (2001) Can microsatellites be used to infer phylogenies? Evidence from population affinities of the western Canary Island lizard (Gallotia galloti). Mol Phylogenet Evol 20:351–360CrossRefPubMedGoogle Scholar
  35. Ritz LR, Glowatzki-Mullis ML, MacHugh DE, Gaillard C (2000) Phylogenetic analysis of the tribe Bovini using microsatellites. Anim Genet 31:178–185CrossRefPubMedGoogle Scholar
  36. Ronquist F, Huelsenbeck JP (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574CrossRefPubMedGoogle Scholar
  37. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar
  38. Sasanuma T, Sehgal D, Sasakuma T, Raina SN (2008) Phylogenetic analysis of Carthamus species based on the nucleotide sequence of the nuclear SACPD gene and chloroplast trnL–trnF IGS region. Genome 51:721–727CrossRefPubMedGoogle Scholar
  39. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234CrossRefPubMedGoogle Scholar
  40. Sehgal D, Rajpal VR, Raina SN (2008) Chloroplast DNA diversity reveals the contribution of two wild species to the origin and evolution of diploid safflower (Carthamus tinctorius L.). Genome 51:638–643CrossRefPubMedGoogle Scholar
  41. Sehgal D, Raina SN, Devarumath RM, Sasanuma T, Sasakuma T (2009) Nuclear DNA assay in solving issues related to ancestry of the domesticated diploid safflower (Carthamus tinctorius L.) and the polyploid (Carthamus) taxa, and phylogenetic and genomic relationships in the genus Carthamus L. (Asteraceae). Mol Phylogenet Evol 53:631–644CrossRefPubMedGoogle Scholar
  42. Shaw J, Lickey EB, Beck JT, Farmer SB, Liu WS, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL (2005) The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 92:142–166CrossRefGoogle Scholar
  43. Shaw J, Lickey EB, Schilling EE, Small RL (2007) Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am J Bot 94:275–288CrossRefGoogle Scholar
  44. Smith JR (1996) Safflower. AOCS Press, Champaign, pp 2–4Google Scholar
  45. Swofford DL (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer, SunderlandGoogle Scholar
  46. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of 3 noncoding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109CrossRefPubMedGoogle Scholar
  47. Vilatersana R, Susanna A, Garcia-Jacas N, Garnatje T (2000a) Generic delimitation and phylogeny of the CarduncellusCarthamus complex (Asteraceae) based on ITS sequences. Plant Syst Evol 221:89–105CrossRefGoogle Scholar
  48. Vilatersana R, Susanna A, Garcia-Jacas N, Garnatje T (2000b) Karyology, generic delineation and dysploidy in the genera Carduncellus, Carthamus and Phonus (Asteraceae). Bot J Linn Soc 134:425–438CrossRefGoogle Scholar
  49. Vilatersana R, Garnatje T, Susanna A, Garcia-Jacas N (2005) Taxonomic problems in Carthamus (Asteraceae): RAPD markers and sectional classification. Bot J Linn Soc 147:375–383CrossRefGoogle Scholar
  50. Vilatersana R, Brysting AK, Brochmann C (2007) Molecular evidence for hybrid origins of the invasive polyploids Carthamus creticus and C. turkestanicus (Cardueae, Asteraceae). Mol Phylogenet Evol 44:610–621CrossRefPubMedGoogle Scholar
  51. Weising KN, Nybom H, Wolff H, Kahl G (2005) DNA fingerprinting in plants: principles, methods and applications, 2nd edn. Taylor & Francis, Boca Raton, pp 41–45Google Scholar
  52. White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR protocols: a guide to methods and applications. Academic Press, San Diego, pp 315–322Google Scholar
  53. Yao XH, Ye Q, Fritsch PW, Crux BC, Huang H (2008) Phylogeny of Sinojackia (Styracaceae) based on DNA sequence and microsatellite data: implications for taxonomy and conservation. Ann Bot 101:651–659CrossRefPubMedGoogle Scholar
  54. Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD Dissertation, The University of Texas, AustinGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Victoria G. Bowles
    • 1
  • Reinhold Mayerhofer
    • 1
  • Corey Davis
    • 1
  • Allen G. Good
    • 1
  • Jocelyn C. Hall
    • 1
  1. 1.Biological SciencesUniversity of AlbertaEdmontonCanada

Personalised recommendations