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Datasets
The Santos Lab is happy to offer downloadable datasets and sequence alignments of molecules commonly utilized in Symbiodinium diversity and phylogenetic studies. These alignments are for use as a scaffold to which novel sequences may be added and preliminary phylogenies constructed. Given the rate that new sequences are generated, these alignments are not representative of all sequences available from sources such as NCBI, and are not intended to encompass all Symbiodinium diversity (either within the genus or any particular clade). The alignments are made available in NEXUS format (for use in programs such as PAUP*) and can be converted to other formats. To download a file, right-click the link and save it to your computer. For additional sequence alignments of molecules commonly used in Symbiodinium phylogenetics, you may also want to check the NCBI PopSet and TreeBase databases.
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Other Datasets Malacostraca complete mitochondrial sequences: Nucleotide and amino acid alignments utilized in Ivey and Santos (2007) Gene 394:35-44. Zip Archive
Symbiodinium ITS intragenomic data: alignments and chromatograms from Thornhill et al. (2007) Molecular Ecology 16:5326-5340. Zip Archive (46 MB)
Symbiodinium microsatellite data: files for computational analysis via Structure of Symbiodinium Clade B populations from Gorgonia ventalina in the Florida Keys utilized in Kirk et al. (2009) Marine Biology 156:1609-1623. Zip Archive
Symbiodinium microsatellite data: colony info, allelic variation and AMOVA hierarchical structure for analyses with GenAlEx from Symbiodinium Clade B populations of M. faveolata and M. annularis from Thornhill et al. (2009) PLoS One 4:e6262. Zip Archive
Montastrea spp. mitochondrial sequence data: Nucleotide alignments of the mtDNA intergenic region for M. faveolata and M. annularis from the Florida Keys and Bahamas utilized in Thornhill et al. (2010) Marine Ecology Progress Series 420:113-123. Zip Archive
Coral-associated apicomplexan sequence data for various coral species from Kirk et al. (2013) Coral Reefs 32:847-858. Zip Archive
Coral-associated apicomplexan sequence data for brooding vs. broadcast-spawning coral species from Kirk et al. (2013) PLoS One 8:e80618. Zip Archive
Mitogenome amino acid (AA) and nucleotide (nt) alignments, tree files, and scripts used in Havird and Santos (2014) PLoS One 9:e84080. NOTE: the archive is ~20 GB in size when compressed with 7Zip and will expand into a directory of ~120 GB. If you would like either the complete dataset or a subset of the data without downloading the whole archive, please contact Justin C. Havird directly.
Cyclooxygenase (COX) sequence alignments and tree files from Havird et al. (2015) Journal of Molecular Evolution 80:193-208. Zip Archive
Halocaridina rubra larval data for analyses in R statistical environment from Havird et al. (2015) The Biological Bulletin 229:134-142. Zip Archive
Developmental transcriptomic data for Halocaridina rubra from Havird and Santos (2016) Integrative and Comparative Biology. NOTE: the archive is ~700 MB in size when compressed with 7Zip and will expand into a directory of ~1.4 GB. If you would like a subset of the data without downloading the whole archive, please contact Justin C. Havird directly. 7Zip Archive
Crab RNA-Seq data from Havird et al. (2016) Comparative Biochemistry and Physiology - Part A 19:34-44. NOTE: the archive is ~1.1 GB in size when compressed with Zip and will expand into a directory of ~4.2 GB. If you would like a subset of the data without downloading the whole archive, please contact Justin C. Havird directly. Zip Archive
R scripts and associated code for analyses presented in Hoffman et al. (2018) Hydrobiologia 806:265-282. Diversity and the environmental drivers of spatial variation in Bacteria and micro-Eukarya communities from the Hawaiian anchialine ecosystem. Zip Archive
R scripts and associated code for analyses presented in Hoffman et al. (2018) Aquatic Microbial Ecology 82:87-104. Comparing the community structure of Bacteria and micro-Eukarya from the Hawaiian anchialine ecosystem during wet and dry seasons. Zip Archive
R scripts and associated code for analyses presented in Hoffman et al. (2020) Integrative and Comparative Biology - Phenotypic comparability from genotypic variability among physically structured microbial consortia. Zip Archive
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