| Contributors | Affiliation | Role |
|---|---|---|
| Halanych, Kenneth M. | Auburn University | Principal Investigator |
| Mahon, Andrew | Central Michigan University | Co-Principal Investigator |
| Copley, Nancy | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
This dataset was published as Supplementary Table 1 from Halanych et al (2013). It contains GenBank accession links of hemichordate and echinoderm specimens collected globally from 2001 to 2013.
Related Reference: Halanych, K.M., J.T. Cannon, A.R. Mahon, B.J. Swalla, C.R. Smith. 2013. Tubicolous acorn worms from Antarctica. Nature Communications DOI://10.1038/ncomms3738
Related Dataset: Halanych_2013: Video of acorn worm tubes
Scientific research expeditions were aboard the RVIB Nathaniel B. Palmer in 2008 to the Antarctic Peninsula and 2013 to the Ross Sea. Benthic samples were obtained from the Ross Sea by a Blake trawl with a 2-m opening. Sampled were sorted and preserved on deck. Sequencing and phylogenetic protocols of 18S and 16S ribosomal DNA used the standard procedures3. PCR amplification used primers 16Sar 50-CGCCTGTTTATCAAAAA CAT-30 and 16Sbr 50-CCGGTCTGAACTCAGATCACGT-30 for 16S ribosomal DNA and 18e 50-CTGGTTGATCCTGCCAGT-30 and 18 P 50-TAATGATCCTTCCGCAGGTTCACCT-30 .
Maximum likelihood and Bayesian analyses (both used the best fitting model GTR+I+G) were conducted with RaxML version 7.3.9 (ref. 19) (5,000 bootstrap replicates) and MrBayes version 3.2.0 (ref. 20) (four independent runs for 5,000,000 generations sampled every 100 generations), respectively.
BCO-DMO Processing notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- removed trailing blank spaces
- replaced cells with hyphen with nd (no data)
- added links to NCBI accession pages
| File |
|---|
Halanych_2013_T1.csv (Comma Separated Values (.csv), 12.43 KB) MD5:a568f54b8bbb02145f894536079187e5 Primary data file for dataset ID 671551 |
| Parameter | Description | Units |
| taxon | more specific taxonomic group | unitless |
| species | taxonomic genus and species name | unitless |
| accession_rDNA_18S | 18S NCBI GenBank accession number | unitless |
| accession_rDNA_16S | 16S NCBI GenBank accession number | unitless |
| link_accession_rDNA_18S | link to 18S NCBI GenBank accession | unitless |
| link_accession_rDNA_16S | link to 16S NCBI GenBank accession | unitless |
| Dataset-specific Instrument Name | Illumina MiSeq (San Diego, CA) at Auburn University |
| Generic Instrument Name | Automated DNA Sequencer |
| Generic Instrument Description | General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. |
| Dataset-specific Instrument Name | |
| Generic Instrument Name | Thermal Cycler |
| Generic Instrument Description | A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html) |
| Website | |
| Platform | Auburn University lab |
| Start Date | 2011-08-01 |
| End Date | 2016-07-31 |
| Description | Invertebrate genomics |
Extracted from the NSF award abstract:
The research will explore the genetics, diversity, and biogeography of Antarctic marine benthic invertebrates, seeking to overturn the widely accepted suggestion that benthic fauna do not constitute a large, panmictic population. The investigators will sample adults and larvae from undersampled regions of West Antarctica that, combined with existing samples, will provide significant coverage of the western hemisphere of the Southern Ocean. The objectives are: 1) To assess the degree of genetic connectivity (or isolation) of benthic invertebrate species in the Western Antarctic using high-resolution genetic markers. 2) To begin exploring planktonic larvae spatial and bathymetric distributions for benthic shelf invertebrates in the Bellinghausen, Amundsen and Ross Seas. 3) To continue to develop a Marine Antarctic Genetic Inventory (MAGI) that relates larval and adult forms via DNA barcoding.
| Funding Source | Award |
|---|---|
| NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) | |
| NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) |