Skip to main content
Log in

Phylogenetic position of Dictyostelium inferred from multiple protein data sets

  • Articles
  • Published:
Journal of Molecular Evolution Aims and scope Submit manuscript

Abstract

The phylogenetic position of Dictyostelium inferred from 18S rRNA data contradicts that from protein data. Protein trees always show the close affinity of Dictyostelium with animals, fungi, and plants, whereas in 18S rRNA trees the branching of Dictyostelium is placed at a position before the massive radiation of protist groups including the divergence of the three kingdoms. To settle this controversial issue and to determine the correct position of Dictyostelium, we inferred the phylogenetic relationship among Dictyostelium and the three kingdoms Animalia, Fungi, and Plantae by a maximum-likelihood method using 19 different protein data sets. It was shown at the significance level of 1 SE that the branching of Dictyostelium antedates the divergence of Animalia and Fungi, and Plantae is an outgroup of the Animalia-Fungi-Dictyostelium clade.

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Adachi J, Hasegawa M (1992) Computer science monographs, No. 27, MOLPHY: programs for molecular phylogenetics I. PROTML: maximum likelihood inference of protein phylogeny. Institute of Statistical Mathematics, Tokyo

    Google Scholar 

  • Berger MP, Munson PJ (1991) A novel randomized iterative strategy for aligning multiple protein sequences. CABIOS 7:479–484

    Article  CAS  PubMed  Google Scholar 

  • Cavalier-Smith T (1993) Kingdom Protozoa and its 18 phyla. Microbiol Rev 57:953–994

    CAS  PubMed  Google Scholar 

  • Cubitt AB, Carrel F, Dharmawardhane S, Gaskins C, Hadwiger J, Howard P, Mann SKO, Okaichi K, Zhou K, Firtel RA (1992) Molecular genetic analysis of signal transduction pathways controlling multicelluar development in Dictyostelium. Cold Spring Harbor Symp Quanti Biol LVII:177–192

    Google Scholar 

  • Douglas SE, Murphy CA, Spencer DF, Gray MW (1991) Cryptomonad algae are evolutionary chimaeras of two phylogenetically distinct unicellular eukaryotes. Nature 350:148–151

    Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Google Scholar 

  • Hasegawa M, Iida Y, Yano T, Takaiwa F, Iwabuchi M (1985) Phylogenetic relationships among eukaryotic kingdoms inferred from ribosomal RNA sequences. J Mol Evol 22:32–38

    Google Scholar 

  • Hasegawa M, Hashimoto T, Adachi J, Iwabe N, Miyata T (1993) Early branchings in the evolution of eukaryotes: ancient divergence of Entamoeba that lacks mitochondria revealed by protein sequence data. J Mol Evol 36:380–388

    CAS  PubMed  Google Scholar 

  • Hashimoto T, Nakamura Y, Nakamura F, Shirakura T, Adachi J, Goto N, Okamoto K, Hasegawa M (1994) Protein phylogeny gives a robust estimation for early divergences of eukaryotes: phylogenetic place of a mitochondria-lacking protozoan, Giardia lamblia. Mol Biol Evol 11:65–71

    Google Scholar 

  • Hendriks L, De Baere R, Van de Peer Y, Neefs J, Goris A, De Wachter R (1991) The evolutionary position of the rhodophyte Porphyra umbilicalis and the basidiomycete Leucosporidium scottii among other eukaryotes as deduced from complete sequences of small ribosomal subunit RNA. J Mol Evol 32:167–177

    Google Scholar 

  • Johnson RL, Gundersen R, Hereld D, Pitt GS, Tugendreich S, Saxe III CL, Kimmel AR, Devreotes PN (1992) G-protein-linked signaling pathways mediate development in Dictyostelium. Cold Spring Harbor Symp Quanti Biol LVII:169–176

    Google Scholar 

  • Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 29:170–179

    CAS  PubMed  Google Scholar 

  • Kishino H, Miyata T, Hasegawa M (1990) Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J Mol Evol 30:151–160

    Google Scholar 

  • Klein PS, Sun TJ, Saxe III CL, Kimmel AR, Johnson RL, Devreotes PN (1988) A chemoattractant receptor controls development in Dictyostelium discoideum. Science 241:1467–1472

    Google Scholar 

  • Loomis WF, Smith DW (1990) Molecular phylogeny of Dictyostelium discoideum by protein sequence comparison. Proc Natl Acad Sci USA 87:9093–9097

    Google Scholar 

  • Margulis L, Schwartz KV (1988) Five kingdoms: an illustrated guide to the phyla of life on earth, 2nd ed. WH Freeman, New York

    Google Scholar 

  • McCarroll R, Olsen, GJ, Stahl YD, Woese CR, Sogin ML (1983) Nucleotide sequence of the Dictyostelium discoideum small-subunit ribosomal ribonucleic acid inferred from the gene sequence: evolutionary implications. Biochemistry 22:5858–5868

    Google Scholar 

  • Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443–453

    CAS  PubMed  Google Scholar 

  • Nikoh N, Hayase N, Iwabe N, Kuma K, Miyata T (1994) Phylogenetic relationship of the kingdoms Animalia, Plantae, and Fungi inferred from twenty-three different protein species. Mol Biol Evol 11:762–768

    Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Simmer JP, Kelly RE, Rinker AG, Zimmermann BH, Scully JL, Kim H, Evans DR (1990) Mammalian dihydroorotaste: nucleotide sequence, peptide sequences, and evolution of the dihydroorotase domain of the multifunctional protein CAD. Proc Natl Acad Sci USA 87:174–178

    Google Scholar 

  • Sogin ML, Elwood HJ, Gunderson JH (1986) Evolutionary diversity of eukaryotic small-subunit rRNA genes. Proc Natl Acad Sci USA 83:1383–1387

    Google Scholar 

  • Sogin ML, Gunderson JH, Elwood HJ, Alonso RA, Peattie DA (1989) Phylogenetic meaning of the kingdom concept: an unusual ribosomal RNA from Giardia lamblia. Science 243:75–77

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Additional information

Correspondence to: T. Miyata

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kuma, Ki., Nikoh, N., Iwabe, N. et al. Phylogenetic position of Dictyostelium inferred from multiple protein data sets. J Mol Evol 41, 238–246 (1995). https://doi.org/10.1007/BF00170678

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00170678

Key words

Navigation