Project 906: R. A. Jenner, C. N. Dhubhghaill, M. P. Ferla, M. A. Wills. 2009. Eumalacostracan phylogeny and total evidence: limitations of the usual suspects. BMC Evolutionary Biology. 9:21.
Specimen: Gammarus roeselii
View: lateral

Abstract

Background
The phylogeny of Eumalacostraca (Crustacea) remains elusive, despite over a century of interest. Recent morphological and molecular phylogenies appear highly incongruent, but this has not been assessed quantitatively. Moreover, 18S rRNA trees show striking branch length differences between species, accompanied by a conspicuous clustering of taxa with similar branch lengths. Surprisingly, previous research found no rate heterogeneity. Hitherto, no phylogenetic analysis of all major eumalacostracan taxa (orders) has either combined evidence from multiple loci, or combined molecular and morphological evidence.
Results
We combined evidence from four nuclear ribosomal and mitochondrial loci (18S rRNA, 28S rRNA, 16S rRNA, and cytochrome c oxidase subunit I) with a newly synthesized morphological dataset. We tested the homogeneity of data partitions, both in terms of character congruence and the topological congruence of inferred trees. We also performed Bayesian and parsimony analyses on separate and combined partitions, and tested the contribution of each partition. We tested for potential long-branch attraction (LBA) using taxon deletion experiments, and with relative rate tests. Additionally we searched for molecular polytomies (spurious clades). Lastly, we investigated the phylogenetic stability of taxa, and assessed their impact on inferred relationships over the whole tree. We detected significant conflict between data partitions, especially between morphology and molecules. We found significant rate heterogeneity between species for both the 18S rRNA and combined datasets, introducing the possibility of LBA. As a test case, we showed that LBA probably affected the position of Spelaeogriphacea in the combined molecular evidence analysis. We also demonstrated that several clades, including the previously reported and surprising clade of Amphipoda plus Spelaeogriphacea, are 'supported' by zero length branches. Furthermore we showed that different sets of taxa have the greatest impact upon the relationships within molecular versus morphological trees.
Conclusion
Rate heterogeneity and conflict between data partitions mean that existing molecular and morphological evidence is unable to resolve a well-supported eumalacostracan phylogeny. We believe that it will be necessary to look beyond the most commonly utilized sources of data (nuclear ribosomal and mitochondrial sequences) to obtain a robust tree in the future.


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Project DOI: 10.7934/P906, http://dx.doi.org/10.7934/P906
This project containsMatrices
  • 2 Media
  • 1 Matrix
  • 26 Taxa
  • 2 Specimens
  • 177 Characters


Download Project SDD File
Total scored cells: 3972
Total media associated with cells: 0
Total labels associated with cell media: 0
Characters
Total characters: 177
Total characters with associated media: 0
Total characters with media with labels: 0
Total character states: 439
Total character states with associated media: 0
Total character states with media with labels:0
Total unordered/ordered characters:177/0
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MorphoBank Project 906


    Members

    member name taxa specimens media media
    notes
    chars character
    media
    labels
    cell scorings
    (scored, NPA, "-")
    cell
    medialabels
    rules
    Jo Wolfe
    Project Administrator
    Last logged in 03/10/14
    26220177003972
    (3697, 0, 275)
    000
    Ronald Jenner
    Full membership
    Last logged in Never
    00000000
    (0, 0, 0)
    000
    Matthew Wills
    Full membership
    Last logged in Never
    00000000
    (0, 0, 0)
    000


    Taxonomic Overview for Matrix 'M2011' (24 Taxa)

    taxon unscored
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    scored
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    NPA
    cells
    "-" cellscell images labels on
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    [1] Stomatopoda
    Last Modified in 12/05/13
    3160159015003
    [2] Bathynellacea
    Last Modified in 12/05/13
    31129127019003
    [3] Anaspidacea
    Last Modified in 12/05/13
    316716608003
    [4] Euphausiacea
    Last Modified in 12/05/13
    217217104003
    [5] Amphionidacea
    Last Modified in 12/05/13
    4212912906003
    [6] Dendrobranchiata
    Last Modified in 12/05/13
    116916808003
    [7] Procaridea
    Last Modified in 12/05/13
    1915515503003
    [8] Caridea
    Last Modified in 12/05/13
    017217007003
    [9] Euzygida
    Last Modified in 12/05/13
    2714514505003
    [10] Reptantia
    Last Modified in 12/05/13
    017416908003
    [11] Mysida
    Last Modified in 12/05/13
    118217402003
    [12] Lophogastrida
    Last Modified in 12/05/13
    1416116102003
    [13] Mictacea
    Last Modified in 12/05/13
    37125125015003
    [14] Bochusacea
    Last Modified in 12/05/13
    45125118014003
    [15] Isopoda
    Last Modified in 12/05/13
    1166161015003
    [16] Amphipoda
    Last Modified in 12/05/13
    2164156019003
    [17] Thermosbaenacea
    Last Modified in 12/05/13
    13153150014003
    [18] Cumacea
    Last Modified in 12/05/13
    1116215907003
    [19] Tanaidacea
    Last Modified in 12/05/13
    3174164010003
    [20] Spelaeogriphacea
    Last Modified in 12/05/13
    31146133013003
    [21] Leptostraca
    Last Modified in 12/05/13
    4163162011003
    [22] Brachypoda
    Last Modified in 12/05/13
    23129129025003
    [23] Anostraca
    Last Modified in 12/05/13
    15139137025003
    [24] Notostraca
    Last Modified in 12/05/13
    21136136020003


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    Specimen list2626
    Taxon list2684
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