overview
These data support: Gillespie, Yoder, and Wharton. 2005. Predicted Secondary Structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): Impact on Sequence Alignment and Phylogeny Estimation. J. Mol. Evol. 61: 114-137.
data
- Online reports (matrix, column composition, basepair-frequency tables etc.) are available in the interleave index.
- The present model version is Death_Star_3.10.Nex.
- The above model with an additional 6 outgroup taxa is 28S_Ichneumonidae.OG.0.01.NEX.
- The present stem index file is Ichs_Index.3.10a.txt.
- There are currently no older models available for download.
- There are currently no older stemfiles available for download.
ongoing work
Since acceptance of the GWY 2005 we've modified the jRNA scripts to make POY analyses more robust and flexible. We've re-run most of the published POY analyses using these scripts and found identical or near identical results. As mentioned in our paper, our primary goal was to present a structural model for these data, not to provide a final say with respect to phylogenetic relationships among the taxa involved. Much further work can be done with respect to analysis of the provided datasets and we encourage those interested to make use of the scripts in combination with the provided datasets. In particular, analyses of the combined data-set (278 taxa) for the D2-D3 are of interest. Our preliminary findings show that under parsimony Braconidae are resolved as nearly-monophyletic (very few taxa misplaced), but arising within Ichneumonidae. We find that analyzing the same data, with outgroups removed, recovers near monophyly of Ichneumonidae and Braconidae, suggesting that outgroup choice is likely worth exploring.
We have also modified our matrix to place the NHRs back within the regions they were taken from, as opposed to being placed at the end of the file. This dataset is available on request. The online reports for this data are available here.
results
Results of phylogenetic analyses are available in their respective folders here.
figures
Use the "view-image" function of your browser (right-click->"view image" (ctrl-click for Mac) in Mozilla/Netscape) or download the images to examine them at full resolution.
18S concensus diagram
coming end of August, 2005
Figures are numbered as in GYW.
figure 1
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figure 7
figure 8
figure 9ab
figure 9cd
figure 10
