This codebook.txt file was generated on 20180430 by Mattias Johansson


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GENERAL INFORMATION
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1. Title of Dataset 
Data from "Seasonal distribution and environmental associations among late larval and juvenile rockfish (Sebastes spp.) off Oregon and Washington: new insights based on genetics"

2. Author Information


  Principal Investigator Contact Information
        Name: Mattias L. Johansson
           Research Performed At: Oregon State University
           Address: Coastal Oregon Marine Experiment Station, Newport, OR 97365
           Current Institution: University of North Georgia
           Address: Biology Department, 3820 Mundy Mill Rd., Oakwood, GA 30566
           Email: m.l.johansson@gmail.com


  Associate or Co-investigator Contact Information
        Name: Marisa N.C. Litz
           Institution: Oregon State University
           Address: Cooperative Institute for Marine Resources Studies, Newport, OR 97365
           Email: marisalitz123@gmail.com


  Associate or Co-investigator Contact Information
           Name: Richard D. Brodeur
           Institution: NOAA Fisheries
           Address: Fish Ecology Division, Northwest Fisheries Science Center, Newport, OR 97365
           Email: rick.brodeur@noaa.gov


  Associate or Co-investigator Contact Information
           Name: Tristan A. Britt
           Institution: Oregon State University
           Address: Cooperative Institute for Marine Resources Studies, Newport, OR 97365
           Email: marisalitz123@gmail.com


  Associate or Co-investigator Contact Information
           Name: Camilo A. Vanegas
           Institution: Oregon State University
           Address: Coastal Oregon Marine Experiment Station, Newport, OR 97365
           Email: camiloavanegas90@gmail.com


  Associate or Co-investigator Contact Information
           Name: John R. Hyde
           Institution: NOAA Fisheries
           Address: Southwest Fisheries Science Center, La Jolla, CA USA 92037
           Email: john.hyde@noaa.gov


  Associate or Co-investigator Contact Information
           Name: Michael A. Banks
           Institution: Oregon State University
           Address: Coastal Oregon Marine Experiment Station, Newport, OR 97365
           Email: michael.banks@oregonstate.edu


3. Date of data collection (single date, range, approximate date) 2008
The samples were collected from May-September 2005-2008. The molecular data was generated in 2008. 

4. Geographic location of data collection (where was data collected?): 
Hatfield Marine Science Center, Newport, OR

5. Information about funding sources that supported the collection of the data:
This research was funded by the NOAA Northwest Fisheries Science Center Stock Assessment Improvement Program, the Oregon State University Cooperative Institute for Marine Resources Studies, the NSF Research Experiences for Undergraduates program, and the NOAA NWFSC Conservation Biology Division. 

6. Abstract
Cytochrome B sequence data (FASTA format) from the paper ÒSeasonal distribution and environmental associations among late larval and juvenile rockfish (Sebastes spp.) off Oregon and Washington: new insights based on geneticsÓ. The data was generated from a sample of 2534 unknown, field collected late-larval and juvenile rockfishes from the Pacific Ocean off Oregon and Washington. These unknowns identified by comparison with a data set of sequences generated from known (morphologically identified) adult fishes. This project demonstrates the utility of using sequence data to identify larval and juvenile rockfishes, which are known to be difficult or impossible to identify to species morphologically.

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SHARING/ACCESS INFORMATION
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1. Licenses/restrictions placed on the data:
Creative Commons Attribution 4.0 (CC BY 4.0)

2. Links to publications that cite or use the data:
Taylor CA, Watson W, Chereskin T, Hyde J, and Vetter R. 2004. Retention of larval rockfishes, Sebastes, near natal habitat in the Southern California Bight, as indicated by molecular identification methods. CALCOFI Rep. 45:152-166.

Hyde JR and Vetter RD. 2007. The origin, evolution, and diversification of rockfishes of the genus Sebastes (Cuvier). Mol. Phylogenet. Evol. 44: 790-811.

3. Links to other publicly accessible locations of the data:
Some of the sequences in this data file are also available through GenBank. See Hyde and Vetter, 2007 for Accession Numbers.

4. Recommended citation for the data:
Johansson, Mattias L.; Litz, Marisa N.C.; Brodeur, Richard D.; Britt, Tristan A.; Vanegas, Camilo A.; Hyde, John R.; Banks, Michael A. (2018): Seasonal distribution and environmental associations among late larval and juvenile rockfish (Sebastes spp.) off Oregon and Washington: new insights based on genetics. Oregon State University Libraries. Dataset. 


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DATA & FILE OVERVIEW
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1. File List
   A. Filename: HydeSamples.txt       
      Short description: FASTA file format, all reference sequences (sequenced from adult rockfishes)       
       Number of rows: 364

        
   B. Filename: Identical_as_Consensus.txt       
      Short description: FASTA file format, field samples (sequences used for molecular identification), identical samples represented by a single consensus sequence       
      Number of cases/rows: 776

        
   C. Filename: AllRFIDSequences.txt       
      Short description: FASTA file format, field samples (sequences used for molecular identification), all samples included.
      Number of rows: 2534


2. Relationship between files:        
HydeSamples contains unique data, derived from morphologically-identified adult samples. Identical_as_Consensus and AllRFIDSequences contain essentially the same data, with the difference that Identical_as_Consensus only contains one copy of each of the sequences that were identical in our analysis. AllRFIDSequences contains duplicates, where duplicates exist.



3. There are no other versions of this dataset.
  

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METHODOLOGICAL INFORMATION
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1. Description of methods used for collection/generation of data: 

Johansson ML, Litz MNC, Brodeur RD, Britt TA, Vanegas CA, Hyde JR, Banks MA. In Review. Seasonal distribution and environmental associations among late larval and juvenile rockfish (Sebastes spp.) off Oregon and Washington: new insights based on genetics. Fishery Bulletin.

2. Methods for processing the data: 
Sequences generated on an ABI3739XL sequencer, aligned and edited in Sequencher v5.0

3. Instrument- or software-specific information needed to interpret the data:
FASTA files. Readable by common DNA sequence editing software

4. Standards and calibration information, if appropriate:
None

5. Environmental/experimental conditions:
None

6. Describe any quality-assurance procedures performed on the data:
Forward and reverse reads for each sample matched and uncertainties manually edited in Sequencher v5.0.
Low-quality portions of sequences removed. 

7. People involved with sample collection, processing, analysis and/or submission:
Mattias Johansson, Tristan Britt, Marisa Litz, Camilo Vanegas