February 12, 2010 | David F. Coppedge

For His Birthday, Darwin Gets a Scrambled Arthropod Tree

If Darwin lost his tree last year (01/22/2009), it would seem any corrections or rearrangements would be academic.  Nevertheless, eight evolutionary biologists at Duke University tried rearranging one of the biggest branches on Darwin’s tree of common ancestry – the highly diverse group known as arthropods (animals with jointed appendages).  Arthropods comprise the largest number of species and the largest count of animals on the planet.  It includes the insects, spiders, crustaceans, millipedes, shrimp and much more.  The team’s results were advance-published on the Nature website right before Darwin’s 201st birthday,1 accompanied by a press release from Duke University.
    This is just the latest in a century-long project to make sense of the arthropod family tree.  The authors admitted an “often-heated, century-long debate on arthropod relationships.”  Early attempts were based entirely on morphology (physical traits).  More recent methods have included genetic and protein comparisons, but the authors said “The molecular phylogeny of Arthropoda has proven difficult to resolve.”  The puzzles are reflected by some of the names: Paradoxopoda (paradoxical feet), Miracrustacea (surprising crustaceans) and Xenocarida (strange shrimp).  The researchers quadrupled their earlier data set for the latest phylogeny.  They claimed overall strong agreement between molecular and morphological phylogenies, but the press release stated, “Some of the relationships are so surprising that new names had to be coined for five newly-discovered groupings.”
    Even though the paper and press release present a tone of success in finally resolving the family tree, some statements indicate this is just the latest rest stop on a work in progress.  The success comes at a price; some relationships are counterintuitive or controversial.  The authors, moreover, had to select data they thought was more indicative of signal over noise.  Here are some excerpts that show any claimed success is strained:

  • The remarkable antiquity, diversity and ecological significance of arthropods have inspired numerous attempts to resolve their deep phylogenetic history, but the results of two decades of intensive molecular phylogenetics have been mixed.
  • More typically, analyses based on limited samples of taxa and genes have generated results that are inconsistent, weakly supported and highly sensitive to analytical conditions.
  • These results provide a statistically well-supported phylogenetic framework for the largest animal phylum and represent a step towards ending the often-heated, century-long debate on arthropod relationships.
  • Until recently, arthropod molecular phylogenetics relied mainly upon nuclear ribosomal DNA and mitochondrial sequences.  Our data come from the complementary DNA of single-copy nuclear protein-coding genes, which represent the largest source of data for phylogenetics.
  • Uncertainty about homology at sites bracketing small insertion�deletion (indel) regions resulted in exclusion of approximately 6.5% of all sites.
  • Of the six newly named groups shown in bold in Fig. 1, only two had more than 70% bootstrap support in single-gene analyses (one gene each; Supplementary Table 3).
  • Bootstrap values derived for amino acids were sometimes lower than those derived from nucleotides.
  • At the deepest level, our phylogeny strongly supports Mandibulata (Pancrustacea plus Myriapoda), a controversial result that is robust to expanded outgroup sampling.
  • Our strong support for Mandibulata contradicts several molecular studies that have placed Myriapoda as sister group to the Chelicerata (Euchelicerata plus Pycnogonida), a grouping so contrary to morphology that it was recently dubbed Paradoxopoda.
  • Although our phylogeny resolves many problems within Mandibulata, it does not resolve the status of Chelicerata, the group including Pycnogonida (sea spiders) and Euchelicerata (horseshoe crabs, scorpions and spiders).
  • Xenocarida includes two unusual and morphologically dissimilar classes of crustacean, Remipedia and Cephalocarida.  We place the xenocarids and hexapods in the newly named clade Miracrustacea (’surprising crustaceans’).  Both Xenocarida and Miracrustacea are found in the maximum-likelihood trees for all four methods of analysis, although support varies.
  • Bootstrap support for both Xenocarida and Miracrustacea is strong for noLRall1+nt2 and degen1 analyses (93�100%), moderately strong for codon analysis (79�89%) and weak for amino-acid analysis (17�54%).
  • Our results strongly support the monophyly of Hexapoda, in contrast to mitochondrial studies that place Collembola (springtails) among ‘crustaceans’ rather than other hexapods.
  • The sister group to Miracrustacea is another unanticipated group, Vericrustacea (‘true crustaceans’), which joins Malacostraca (crabs, shrimp and so on), Branchiopoda (fairy shrimp, water fleas and so on) and some members of the polyphyletic ‘Maxillopoda’, namely Thecostraca (barnacles) and Copepoda.
  • Within the Vericrustacea are two other groupings not anticipated by morphology: the Multicrustacea (‘numerous crustaceans’: Malacostraca plus Thecostraca plus Copepoda) and the Communostraca (‘common shelled ones’: Malacostraca plus Thecostraca).
  • Significantly, our analysis adds Mystacocarida to Oligostraca.  The mystacocarids are small, enigmatic crustaceans that live between sand grains along marine shores.  Oligostracans are a disparate, ancient clade, and there is little in their gross morphology other than reduction in the number of body segments that would suggest a close relationship among them.
  • Our results differ from morphology-inspired hypotheses in uniting Pauropoda with Symphyla rather than with Diplopoda, a result that is also seen in recent analyses of nuclear ribosomal sequences.

Their final paragraph contains the most significant caution lights:

In conclusion, our phylogenomic study provides a strongly supported phylogenetic framework for the arthropods, but the problem of reconstructing and interpreting morphological evolution within this diverse group remains.  Our phylogeny highlights the large gaps in the morphological spectrum of extant arthropods that have complicated the task of morphology-based systematists.  Our result has significant implications, as it requires taxonomists to acknowledge crustaceans as a paraphyletic grade of primitively aquatic mandibulates and to classify hexapods as a terrestrial clade within Pancrustacea.  In particular, the position of Xenocarida (Remipedia plus Cephalocarida) as the sister group to Hexapoda, and the relatively derived placement of supposedly ‘primitive’ groups such as Branchiopoda, promises to alter views on the evolution of morphology and morphogenesis in Arthropoda.

The press release called this work a “scientific and technological tour de force” with a result that “at least the shape of the tree seems right.”  Questions not addressed by the paper, though, might be posed by a philosopher, historian, logician, or skeptical inquirer.  Why should molecular evidence outweigh morphological evidence, or vice versa?  Which kind of molecular evidence should be given priority when different schemes conflict?  Would a different research team, with different strategies, agree with these results?  Are some of the groupings contrived?  Do the new groupings really carve nature at its joints, or do they reflect researcher bias to force-fit uncooperative data into predetermined schemes? 

1.  Regier et al, “Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences,” Nature advance online publication 10 February 2010; doi:10.1038/nature08742.

Details are necessary to show how arbitrary and contrived the practice of evolutionary tree-building is.  If this is how tree-building goes for the greatest group of animals in the world, should we be impressed with claims for any other group?  But it doesn’t matter.  Since we have already shown that tree-building is hopeless (07/25/2002) and the branching tree is a fallen icon of evolution anyway (01/22/2009), it would be charitable to call this work that the Dukes have hazarded an exercise in futility.
    They might just as well try to build a family tree for the tools in a hardware store.  Look at their capricious and arbitrary name game.  Does it help understand relationships to name a group Miracrustacea?  Are you impressed by the Latin name for “surprising crustaceans”?  What if phylogenists in a hardware store invented a group name for crowbars and screwdrivers called Xenocapulus (strange handles)?  Latin is a poor mask for vanity.
    Maybe it makes them feel good to be busy, but constructing paper trees for Darwin seems hardly a useful scientific quest.  Darwin trees aren’t good for wood, construction, shade, the environment, or anything.  Their usefulness for understanding is highly doubtful.  Scientists should do better than to obsess over vain projects that are rootless and fruitless.

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