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.
Abstract
BackgroundThe 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 contains | Matrices |
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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
MorphoBank Project 906
- Creation Date:
18 March 2013 - Publication Date:
10 March 2014 - Project views: 29907
- Matrix downloads: 7
Authors' Institutions
- University of Bath
Members
member name | taxa | specimens | media | media notes | chars | character
| cell scorings (scored, NPA, "-") | cell
| rules | ||||||
Jo Wolfe Project Administrator | 26 | 2 | 2 | 0 | 177 | 0 | 0 | 3972 (3697, 0, 275) | 0 | 0 | 0 | ||||
Ronald Jenner Full membership | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 (0, 0, 0) | 0 | 0 | 0 | ||||
Matthew Wills Full membership | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 (0, 0, 0) | 0 | 0 | 0 |
Taxonomic Overview for Matrix 'M2011' (24 Taxa)
taxon | unscored cells |
scored cells |
no cell support |
NPA cells |
"-" cells | cell images | labels on cell images |
member access |
[1] Stomatopoda Last Modified in 12/05/13 | 3 | 160 | 159 | 0 | 15 | 0 | 0 | 3 |
[2] Bathynellacea Last Modified in 12/05/13 | 31 | 129 | 127 | 0 | 19 | 0 | 0 | 3 |
[3] Anaspidacea Last Modified in 12/05/13 | 3 | 167 | 166 | 0 | 8 | 0 | 0 | 3 |
[4] Euphausiacea Last Modified in 12/05/13 | 2 | 172 | 171 | 0 | 4 | 0 | 0 | 3 |
[5] Amphionidacea Last Modified in 12/05/13 | 42 | 129 | 129 | 0 | 6 | 0 | 0 | 3 |
[6] Dendrobranchiata Last Modified in 12/05/13 | 1 | 169 | 168 | 0 | 8 | 0 | 0 | 3 |
[7] Procaridea Last Modified in 12/05/13 | 19 | 155 | 155 | 0 | 3 | 0 | 0 | 3 |
[8] Caridea Last Modified in 12/05/13 | 0 | 172 | 170 | 0 | 7 | 0 | 0 | 3 |
[9] Euzygida Last Modified in 12/05/13 | 27 | 145 | 145 | 0 | 5 | 0 | 0 | 3 |
[10] Reptantia Last Modified in 12/05/13 | 0 | 174 | 169 | 0 | 8 | 0 | 0 | 3 |
[11] Mysida Last Modified in 12/05/13 | 1 | 182 | 174 | 0 | 2 | 0 | 0 | 3 |
[12] Lophogastrida Last Modified in 12/05/13 | 14 | 161 | 161 | 0 | 2 | 0 | 0 | 3 |
[13] Mictacea Last Modified in 12/05/13 | 37 | 125 | 125 | 0 | 15 | 0 | 0 | 3 |
[14] Bochusacea Last Modified in 12/05/13 | 45 | 125 | 118 | 0 | 14 | 0 | 0 | 3 |
[15] Isopoda Last Modified in 12/05/13 | 1 | 166 | 161 | 0 | 15 | 0 | 0 | 3 |
[16] Amphipoda Last Modified in 12/05/13 | 2 | 164 | 156 | 0 | 19 | 0 | 0 | 3 |
[17] Thermosbaenacea Last Modified in 12/05/13 | 13 | 153 | 150 | 0 | 14 | 0 | 0 | 3 |
[18] Cumacea Last Modified in 12/05/13 | 11 | 162 | 159 | 0 | 7 | 0 | 0 | 3 |
[19] Tanaidacea Last Modified in 12/05/13 | 3 | 174 | 164 | 0 | 10 | 0 | 0 | 3 |
[20] Spelaeogriphacea Last Modified in 12/05/13 | 31 | 146 | 133 | 0 | 13 | 0 | 0 | 3 |
[21] Leptostraca Last Modified in 12/05/13 | 4 | 163 | 162 | 0 | 11 | 0 | 0 | 3 |
[22] Brachypoda Last Modified in 12/05/13 | 23 | 129 | 129 | 0 | 25 | 0 | 0 | 3 |
[23] Anostraca Last Modified in 12/05/13 | 15 | 139 | 137 | 0 | 25 | 0 | 0 | 3 |
[24] Notostraca Last Modified in 12/05/13 | 21 | 136 | 136 | 0 | 20 | 0 | 0 | 3 |
Project views
type | number of views | Individual items viewed (where applicable) |
Total project views | 29907 | |
Project overview | 4562 | |
Matrix views | 3064 | Matrix landing page (2735 views); Eumalacostracan phylogeny and total evidence: limitations of the usual suspects (329 views); |
Media views | 10010 | Media search (6207 views); M326554 (1992 views); M326556 (1811 views); |
Specimen list | 4703 | |
Taxon list | 5546 | |
Views for media list | 2013 | |
Documents list | 9 |
Project downloads
type | number of downloads | Individual items downloaded (where applicable) |
Total downloads from project | 385 | |
Matrix downloads | 7 | Eumalacostracan phylogeny and total evidence: limitations of the usual suspects (7 downloads); |
Project downloads | 378 |