Letter | Published:

Arthropod phylogeny based on eight molecular loci and morphology

Nature volume 413, pages 157161 (13 September 2001) | Download Citation



The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists1,2. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny3,4,5,6,7 and has inspired new considerations of character evolution8,9. Novel hypotheses such as a crustacean–hexapod affinity4,10,11,12 were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order13, and eye and brain ultrastructure and neurogenesis14,15. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures16,17 and constructed a parallel computer cluster with 256 central processing units18 to analyse molecular data on a scale not previously possible. The optimal ‘total evidence’ cladogram supports the crustacean–hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1.

    Evolution of the Annelida, Onychophora and Arthropoda. Smithson. Misc. Collect. 97, 1–159 (1938).

  2. 2.

    , , , & Arthropod Fossils and Phylogeny (ed. Edgecombe, G. D.) 33–105 (Columbia Univ. Press, New York, 1998).

  3. 3.

    , & Arthropod phylogeny: A combined approach. Cladistics 9, 1–39 (1993).

  4. 4.

    & Molecular phylogeny of arthropods and the significance of the Cambrian “explosion” for molecular systematics. Am. Zool. 38, 918–928 (1998).

  5. 5.

    Arthropod Fossils and Phylogeny (ed. Edgecombe, G. D.) 9–32 (Columbia Univ. Press, New York, 1998).

  6. 6.

    , , , & Arthropod cladistics: Combined analysis of histone H3 and U2 snRNA sequences and morphology. Cladistics 16, 155–203 (2000).

  7. 7.

    & A review of arthropod phylogeny: New data based on ribosomal DNA sequences and direct character optimization. Cladistics 16, 204–231 (2000).

  8. 8.

    , , , & Molecular evidence for the gnathobasic derivation of arthropod mandibles and for the appendicular origin of the labrum and other structures. Dev. Genes Evol. 208, 142–150 (1998).

  9. 9.

    , & The pattern of Distal-less expression in the mouthparts of crustaceans, myriapods and insects: new evidence for a gnathobasic mandible and the common origin of Mandibulata. Int. J. Dev. Biol. 42, 801–810 (1998).

  10. 10.

    & Ribosomal DNA phylogeny of the major extant arthropod classes and the evolution of myriapods. Nature 376, 165–167 (1995).

  11. 11.

    , , , & First molecular evidence for the existence of a Tardigrada + Arthropoda clade. Mol. Biol. Evol. 13, 76–84 (1996).

  12. 12.

    & Phylogenetic analysis of arthropods using two nuclear protein-encoding genes supports a crustacean + hexapod clade. Proc. R. Soc. Lond. B 267, 1011–1019 (2000).

  13. 13.

    , & Gene translocation links insects and crustaceans. Nature 392, 667–668 (1998).

  14. 14.

    Are the insects terrestrial crustaceans? A discussion of some new facts and arguments and the proposal of the proper name ‘Tetraconata’ for the monophyletic unit Crustacea + Hexapoda. Ann. Soc. Entomol. France 37, 85–103 (2001).

  15. 15.

    Crustacean–insect relationships: The use of brain characters to derive phylogeny amongst segmented invertebrates. Brain Behav. Evol. 52, 186–206 (1998).

  16. 16.

    Optimization alignment: The end of multiple sequence alignment in phylogenetics? Cladistics 12, 1–9 (1996).

  17. 17.

    & POY (2000). Program and documentation available at ftp://amnh.org/pub/molecular.

  18. 18.

    Homegrown computer roots out phylogenetic networks. Nature 404, 214 (2000).

  19. 19.

    & The basic body plan of arthropods: Insights from evolutionary morphology and developmental biology. J. Evol. Biol. 10, 353–367 (1997).

  20. 20.

    , & Arthropod Relationships (eds Fortey, R. A. & Thomas, R. H.) 97–107 (Chapman & Hall, London, 1998).

  21. 21.

    & Molecular phylogeny of the major arthropod groups indicates polyphyly of crustaceans and a new hypothesis for the origin of hexapods. Mol. Biol. Evol. 14, 902–913 (1997).

  22. 22.

    et al. Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. Aust. J. Zool. 46, 419–437 (1998).

  23. 23.

    A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38, 7–25 (1989).

  24. 24.

    Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Syst. Biol. 44, 321–331 (1995).

  25. 25.

    & Arthropod Relationships (eds Fortey, R. A. & Thomas, R. H.) 169–187 (Chapman & Hall, London, 1998).

  26. 26.

    NONA v. 2.0 (1998). Program and documentation available at ftp://unt.edu.ar/pub/parsimony.

  27. 27.

    & Pattern of phylogenetic relationships among members of the tribe Melitaeini (Lepidoptera: Nymphalidae). Cladistics 16, 347–363 (2000).

  28. 28.

    The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42, 795–803 (1988).

  29. 29.

    Analyzing large data sets in reasonable times: Solutions for composite optima. Cladistics 15, 415–428 (1999).

  30. 30.

    , , & Constructing a significance test for incongruence. Syst. Biol. 44, 570–572 (1995).

Download references


We thank all those who have assisted us with morphological discussions, laboratory work (especially K. Demeo), collecting specimens, and given any other form of help or advice. D. Colgan and G. Wilson have been valued collaborators. S. Thurston provided technical illustration. J. Shultz and L. Prendini shared specimens and unpublished sequence data. Funding was mainly provided by the Fundamental Biology Program of NASA.

Author information


  1. *Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA

    • Gonzalo Giribet
  2. †Australian Museum, 6 College Street, Sydney, New South Wales 2010, Australia

    • Gregory D. Edgecombe
  3. ‡Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024, USA

    • Ward C. Wheeler


  1. Search for Gonzalo Giribet in:

  2. Search for Gregory D. Edgecombe in:

  3. Search for Ward C. Wheeler in:

Corresponding author

Correspondence to Gonzalo Giribet.

Supplementary information

About this article

Publication history






Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.