|Bowen, Brian||University of Hawaii at Manoa (HIMB)||Principal Investigator, Contact|
|York, Amber D.||Woods Hole Oceanographic Institution (WHOI BCO-DMO)||BCO-DMO Data Manager|
This dataset contains GenBank accession numbers for various genomic and mtDNA loci sequences from reef fish. The fish were sampled in multiple locations in the Indian Ocean, Pacific Ocean, and the Red Sea between 2005 to 2015.
These data were published in the data sections of the following publications:
Coleman, R.R., J.A. Eble, J.D. DiBattista, L.A. Rocha, J.E. Randall, M.L. Berumen, B.W. Bowen. 2016. Regal phylogeography: range-wide survey of the marine angelfish Pygoplites diacanthus reveals evolutionary partitions between the Red Sea, Indian Ocean, and Pacific Ocean. Molecular Phylogenetics and Evolution 100:243 – 253. doi: 10.1016/j.ympev.2016.04.005.
DiBattista J.D., J. Whitney, M.T. Craig, J.-P. A. Hobbs, L.A. Rocha, K.A. Feldheim, M.L. Berumen, B.W. Bowen. 2016. Surgeons and suture zones: hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes. Molecular Phylogenetics and Evolution 101:203 – 215. doi: 10.1016/j.ympev.2016.04.036.
DiBattista, J.D., M.R. Gaither, J.-P. A. Hobbs, L.A. Rocha, B.W. Bowen. 2016. Angelfishes, paper tigers, and the devilish taxonomy of the Centropyge flavissima complex. Journal of Heredity 107:647 – 653. doi: 10.1093/jhered/esw062.
Tenggardjaja, K. A., Bowen, B. W., & Bernardi, G. (2014). Vertical and horizontal genetic connectivity in Chromis verater, an endemic damselfish found on shallow and mesophotic reefs in the Hawaiian Archipelago and adjacent Johnston Atoll. PLoS One, 9 (12), e115493. doi: 10.1371/journal.pone.0115493
Tenggardjaja, K.A., B.W. Bowen, G. Bernardi. 2016. Reef fish dispersal in the Hawaiian Archipelago: comparative phylogeography of three endemic damselfishes. Journal of Marine Biology: Article ID 3251814. doi: 10.1155/2016/3251814.
Methodology: Various genomic and mtDNA loci were sequenced from reef fishes.
Sampling and analytical procedures: Samples were taken as fine clips, then sequenced and analyzed to detect population structure and evolutionary genetic divergences. Species were collected with scuba gear, nets, and spears.
Raw sequence data was aligned with GENEIOUS R6 (Biomatters, LTD, Auckland, NZ) or GENEIOUS v.8.0.3 (Gene Codes, Ann Arbor, MI, USA). Sequence analyses were performed with BEAST v.2.2.0 and ARLEQUIN v. 3.5.
For details of these analyses, see the references listed in the "Description" section of this page.
BCO-DMO Data Manager Processing Notes:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* added columns for max/min latitude and longitudes for species collections
* added column with DOIs for the journal references
* modified dataset so each row contains one range of accessions.
* replaced commas in the data with semicolons to support .csv format of data
|Species_Names||Name of species sampled||unitless|
|Sequence_Description||Description of type of sequence||unitless|
|Collection_Location||Location species were collected||unitless|
|Sequence_Analysis_Method||Sequence method and instrument||unitless|
|Genbank_Accession_Range||Range of accession numbers at National Center for Biotechnology Information (NCBI) Genbank||unitless|
|Genbank_First_Accession_Link||Link to the first accession in the accession range at National Center for Biotechnology Information (NCBI) Genbank||unitless|
|Collection_Max_Lat||Maximum species collection latitude||decimal degrees|
|Collection_Min_Lat||Minimum species collection latitude||decimal degrees|
|Collection_Max_Lon||Maximum species collection longitude||decimal degrees|
|Collection_Min_Lon||Minimum species collection longitude||decimal degrees|
|Journal_Publications||Journal publications these accessions were published in||untiless|
|Journal_Publication_DOI||Digital object identifier (DOI) for the journal publications these accessions were published in||untiless|
|Dataset-specific Instrument Name|| |
ABI 3730XL Genetic Analyzer
|Generic Instrument Name|| |
Automated DNA Sequencer
|Dataset-specific Description|| |
ABI 3730XL Genetic Analyzer (Applied Biosystems, Foster City, CA, USA)
|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.
This document is created by info v 4.1f 5 Oct 2018 from the content of the BCO-DMO metadata database. 2020-08-08 07:42:00