Status Matrix
updated on December 7, 2007
The interactive Status Matrix tracks the progress of the molecular project, showing for each planned exemplar whether specimens have been obtained (column labelled Collected?), and the status for each of the 26 genes. The gene regions named here are defined and discussed, in the same order, in the Regier Lab primers and protocols. The “sets” column refers to the successive batches in which the specimens are processed. Sets A through C’ are included in the pilot studies, as explained in Molecular Updates 1 & 2. No special plug-ins are required to view the matrix.
| View a superfamily summary to focus on one superfamily at a time. |
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| View the whole matrix, and hide or show columns as desired. |
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The exemplars listed, representing all the families and subfamilies of Lepidoptera, are currently deemed likely to be included in the study at some point. However, the optimal sampling plan (Project Proposal) cannot be specified a priori, but must be successively approximated in light of results as they are obtained. Therefore, some of the taxa now listed may not be sequenced, while others not presently listed may be added. It is unlikely that additional genes will be included, but design efficiency will probably dictate that many taxa be sequenced for only a subset of genes. |
Key to sets
Charlie points out that he described the sets in Molecular Update #1 last year.
Excerpted:
Entries marked A and A’ are for bombycoids and B for macroleps.
In the search for increased resolution, we are, first, sequencing the other 21 genes in selected bombycoids (taxa marked A’ in the Status Matrix). The bombycoids are already relatively densely sampled, so this will be mainly a test of the effect of adding more genes.
Second, using just the initial five genes, we are greatly expanding taxon sampling, across the macroleps and putative outgroups (B’ taxa in the Status Matrix). This will be a test of the efficacy of increased taxon sampling, with gene sampling held constant.
In the third pilot project (taxon set C in the Status Matrix) we are sequencing all 26 genes for 32 species spread across the lower Ditrysia, to better characterize the relative utility of the individual genes at greater depths in the phylogeny.
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We have begun the survey across families, using three gene regions judged from extensive previous evidence to be safe bets for inclusion in the first-pass gene sample. These are CAD, DDC and Period. The exemplars in progress so far are labeled C’, D,E and F in the Status Matrix.
Sets?
Do we have a key to the column marked “Set”? Felix was just asking which Tortricids are being included in the analyses and I bet this column might help him understand.