Cypridinidae Phylogeny - Revision history

128.111.227.119: /* Transcriptome Data */

2013-09-25T19:33:07Z

‎Transcriptome Data

2013-09-25T19:31:19Z

‎Compiled

2013-09-25T19:30:41Z

‎Data Sources

2013-09-25T18:12:56Z

‎Transcriptome Data

2013-09-25T17:44:13Z

2013-09-25T17:36:51Z

2013-09-25T17:36:08Z

2013-09-25T17:27:03Z

‎Transcriptome Data

2013-09-25T17:26:37Z

‎Transcriptome Data

2013-09-25T17:24:42Z

‎Data Sources

@@ Line 18: / Line 18: @@
 ** 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]]
 * We have multiple new transcriptomes that we used for finding luciferases

@@ Line 1: / Line 1: @@
 ==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]]
+* 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===
 * Cohen and Morin (2003)

@@ Line 1: / Line 1: @@
 ==Data Sources==
 ===Morphological matrix===
 * Cohen and Morin (2003)

@@ Line 15: / Line 15: @@
 ** 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]]
 ===GenBank Data===

@@ Line 5: / Line 5: @@
 * Requires conversion of species names to match other data
 ** Partly done, but needed for some data partitions
-* TO DO: Create separate partitions for binary and multi
 ===Lisa Torres Matrix===
@@ Line 24: / Line 24: @@
 ==TO DO==
 * Full mt genomes could be useful and might be present in transcriptomes. Make HMM set for ostracod mt genomes using V. hilgendorfii and Argulus(?)

@@ Line 23: / Line 23: @@
 ** Wakayama see table 1 [[http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.2006.00589.x/full#t1]]
-===TO DO===
+==TO DO==
 * Full mt genomes could be useful and might be present in transcriptomes. Make HMM set for ostracod mt genomes using V. hilgendorfii and Argulus(?)

← Older revision		Revision as of 17:36, 25 September 2013
Line 15:		Line 15:
	** 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]]
		+
		+	===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===
		+	* Full mt genomes could be useful and might be present in transcriptomes. Make HMM set for ostracod mt genomes using V. hilgendorfii and Argulus(?)

@@ Line 12: / Line 12: @@
 ===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
 * 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]]

← Older revision		Revision as of 17:26, 25 September 2013
Line 14:		Line 14:
	* Oakley et al (2013) included Skogsbergia lerneri and Vargula tsujii		* Oakley et al (2013) included Skogsbergia lerneri and Vargula tsujii
	** 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]]

← Older revision		Revision as of 17:24, 25 September 2013
Line 1:		Line 1:
−	=Data Sources=	+	==Data Sources==
		+	===Morphological matrix===
		+	* Cohen and Morin (2003)
		+	* Uploaded to MorphoBank
		+	* Requires conversion of species names to match other data
		+	** Partly done, but needed for some data partitions
		+	* TO DO: Create separate partitions for binary and multi
		+
		+	===Lisa Torres Matrix===
		+	* Thesis of Vanessa Gonzalez
		+	* 16S, COI, 12S and H3 genes
		+
		+	===Transcriptome Data===
		+	* Oakley et al (2013) included Skogsbergia lerneri and Vargula tsujii
		+	** OET13 included Regier (2010) data in S. lerneri