Difference between revisions of "Cypridinidae Phylogeny"
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==Data Sources== | ==Data Sources== | ||
| + | ===Compiled=== | ||
| + | * THO is compiling all raw datasets on the Osiris demo server [[http://galaxy-dev.cnsi.ucsb.edu/osiris/u/ostratodd/h/cypridinidae-raw-data-sets]] | ||
| + | |||
===Morphological matrix=== | ===Morphological matrix=== | ||
* Cohen and Morin (2003) | * Cohen and Morin (2003) | ||
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* Requires conversion of species names to match other data | * Requires conversion of species names to match other data | ||
** Partly done, but needed for some data partitions | ** Partly done, but needed for some data partitions | ||
| − | + | ||
===Lisa Torres Matrix=== | ===Lisa Torres Matrix=== | ||
| Line 12: | Line 15: | ||
===Transcriptome Data=== | ===Transcriptome Data=== | ||
| − | * Oakley et al (2013) included Skogsbergia lerneri and Vargula tsujii | + | * Oakley et al (2013) included Skogsbergia lerneri and Vargula tsujii [[http://mbe.oxfordjournals.org/content/30/1/215/F1.expansion.html]] |
** OET13 included Regier (2010) data in S. lerneri | ** OET13 included Regier (2010) data in S. lerneri | ||
* von Reumont (2011) included 1 undescribed species. Based on collection locality in Mediterranean, this is likely Skogsbergia [[http://mbe.oxfordjournals.org/content/early/2011/12/20/molbev.msr270.full]] | * von Reumont (2011) included 1 undescribed species. Based on collection locality in Mediterranean, this is likely Skogsbergia [[http://mbe.oxfordjournals.org/content/early/2011/12/20/molbev.msr270.full]] | ||
| + | ** I downloaded these sequences and ran Hamster with arthNreg HMMS here [[http://galaxy-dev.cnsi.ucsb.edu/osiris/u/ostratodd/h/cypridininaebvr]] | ||
| + | * We have multiple new transcriptomes that we used for finding luciferases | ||
| + | |||
| + | ===GenBank Data=== | ||
| + | * 18S | ||
| + | ** Mainly from Oakley and Cunningham (2002) [[http://labs.eemb.ucsb.edu/oakley/todd/publications/72]] | ||
| + | ** Also Yamaguchi and Endo, but this only has V. hilgendorfii, which is also in O&C02 [[http://link.springer.com/article/10.1007/s00227-003-1062-3]] | ||
| + | *16S | ||
| + | ** Wakayama see table 1 [[http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.2006.00589.x/full#t1]] | ||
| + | |||
| + | ==TO DO== | ||
| + | * In MorphoBank, Create separate partitions for binary and multi | ||
| + | * Full mt genomes could be useful and might be present in transcriptomes. Make HMM set for ostracod mt genomes using V. hilgendorfii and Argulus(?) | ||
Latest revision as of 12:33, 25 September 2013
Contents
Data Sources[edit]
Compiled[edit]
- THO is compiling all raw datasets on the Osiris demo server [[1]]
Morphological matrix[edit]
- Cohen and Morin (2003)
- Uploaded to MorphoBank
- Requires conversion of species names to match other data
- Partly done, but needed for some data partitions
Lisa Torres Matrix[edit]
- Thesis of Vanessa Gonzalez
- 16S, COI, 12S and H3 genes
Transcriptome Data[edit]
- Oakley et al (2013) included Skogsbergia lerneri and Vargula tsujii [[2]]
- OET13 included Regier (2010) data in S. lerneri
- von Reumont (2011) included 1 undescribed species. Based on collection locality in Mediterranean, this is likely Skogsbergia [[3]]
- I downloaded these sequences and ran Hamster with arthNreg HMMS here [[4]]
- We have multiple new transcriptomes that we used for finding luciferases
GenBank Data[edit]
- 18S
- 16S
- Wakayama see table 1 [[7]]
TO DO[edit]
- In MorphoBank, Create separate partitions for binary and multi
- Full mt genomes could be useful and might be present in transcriptomes. Make HMM set for ostracod mt genomes using V. hilgendorfii and Argulus(?)
