Chan et al. (2012) J Phycol, 48(5): 1130-1142.

Supporting Material
Analysis of Alexandrium tamarense (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote

Cheong Xin Chan1,6, Marcelo B. Soares2, Maria F. Bonaldo2, Jennifer H. Wisecaver3, Jeremiah D. Hackett3, Donald M. Anderson4, Deana L. Erdner5 and Debashish Bhattacharya1
1Department of Ecology, Evolution and Natural Resources, and Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, U.S.A.
2Northwestern University, Children's Memorial Research Center, Chicago, IL 60614, USA
3Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85721, USA
4Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
5Marine Science Institute, University of Texas, Port Aransas, TX 78373, USA
6Present address: The University of Queensland, Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, Brisbane, QLD 4072, Australia


DATA: Alexandrium tamarense
Assembled EST contigs of A. tamarense (32,110) in FASTA Download (.fasta, 17MB)
A. tamarense proteins with significant hits [e-value <= 1e-10] only in dinoflagellates (6145; FASTA)
[reciprocal BLAST best-hits]
Download (.zip, 5.2MB)
A. tamarense proteins with significant hits [e-value <= 1e-10] in other taxa (4366; FASTA)
[reciprocal BLAST best-hits]
Download (.zip, 34MB)
Protein sequence alignments, after GBLOCKS refinement (3,705) in PHYLIP
(these are used to build the phylogenies)
Download (.zip, 17MB)
RAxML phylogenetic trees (3,705) in NEWICK Download (.zip, 9.3MB)
RAxML phylogenetic trees analyzed in the study (2,523) in NEWICK
Number of terminal taxa per tree (N) >= 20, Number of phyla >= 2
Download (.zip, 8.7MB)
RESULTS: Sorted RAxML trees
Trees supporting monophyly of dinoflagellates with other phyla (269; Fig. 2B)
Number of terminal taxa per tree (N) >= 20, Number of phyla >= 2, boostrap >= 90%
Download (.zip, 990KB)
Trees supporting monophyly of dinoflagellates with other phyla (446; Fig. 2C)
Number of terminal taxa per tree (N) >= 20, Number of phyla >= 2, boostrap >= 70%
Download (.zip, 1.7MB)
Trees supporting monophyly of dinoflagellates with other phyla (612; Fig. 2D)
Number of terminal taxa per tree (N) >= 20, Number of phyla >= 2, boostrap >= 50%
Download (.zip, 2.8MB)
Trees supporting monophyly of dinoflagellates with Plantae lineages (including interrupting taxa)
sorted by bootstrap >=90% and >=70% (e.g., Fig. S1 and S2)
Number of terminal taxa per tree (N) >= 20, Number of phyla >= 2
Download (.zip, 2.0MB)

Citation:
Chan CX, Soares MB, Bonaldo MF, Wisecaver JH, Hackett JD, Anderson DM, Erdner DL and Bhattacharya D (2012). Analysis of Alexandrium tamarense (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote. Journal of Phycology, 48(5): 1130-1142. | DOI:10.1111/j.1529-8817.2012.01194.x | PDF

Updated 12 October, 2012


©2011-12 Cheong Xin Chan and Debashish Bhattacharya.