Dataset: Rockfish microhaplotype sequence accessions from samples near Carmel and Monterey Bays, CA, 2013-2016 (Larval Dispersal in Kelp Rockfish project)

This dataset has not been validatedFinal no updates expectedVersion 1 (2018-02-27)Dataset Type:Other Field Results

Principal Investigator: Mark Carr (University of California-Santa Cruz)

Co-Principal Investigator: Christopher Edwards ()

Co-Principal Investigator: Dr John Carlos Garza (University of California-Santa Cruz)

BCO-DMO Data Manager: Nancy Copley (Woods Hole Oceanographic Institution)

Program: Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO)

Project: Integrative evaluation of larval dispersal and delivery in kelp rockfish using inter-generational genetic tagging, demography and oceanography (Larval Dispersal in Kelp Rockfish)

Abstract

This dataset contains NCBI accessions and collection metadata for samples collected in September 2010 along the coast of Monterey and Carmel, California.

Cite Dataset

2018-02-21: The data are currently stored in the Dryad repository as the following two packages. The files may also be accessed here via the 'Get Data' button (above).

Dryad package: Kelp-rockfish genotypes, DOI: 10.5061/dryad.6cp14g8
Data from: "Larval dispersal connects marine reserves and replenishes fished populations along the central California coast." Baetscher DS, Anderson EC, Saarman E, Malone D, Carr MH, Garza JC (2018?) Molecular Ecology (in press).
NOTE: not all files are publicly available until the associated publication is published.

This data repository contains the following:  Genotypes for 96 microhaplotypes - this file contains the genotypes for 6,108 kelp rockfish sequenced at 96 amplicon loci using paired-end Illumina sequencing. Genotypes were filtered for read depth (minimum 20 reads total per locus/individual) and allele balance (0.4 ratio of read depth for allele 1:allele 2 in a heterozygote). Samples with missing data at more than 10 percent of loci were excluded from this data set. Variant call format file generated using Freebayes software from 2,293 rockfish samples sequenced at 96 microhaplotype loci. Samples include four species of rockfishes: kelp (Sebastes atrovirens), copper (S. caurinus), black-and-yellow (S. chrysomelas), and gopher (S. carnatus). This file contains 1,495 variant sites across the 96 loci.

Dryad package: Rockfish microhaplotype sequences, DOI: 10.5061/dryad.5863d
Data from: Baetscher DS, Clemento AJ, Ng TC, Anderson EC, Garza JC (2017) Microhaplotypes provide increased power from short-read DNA sequences for relationship inference. Molecular Ecology Resources, https://doi.org/10.1111/1755-0998.12737
Consensus sequences and primer information for 192 targeted amplicons, the Binary Alignment/Map (BAM) files and variant call format (VCF) files for all retained regions genotype files for 144 kelp rockfish species and an R Notebook documenting all statistical analyses.

Related Datasets

IsRelatedTo
Dataset: Fish lengths - adults
Carr, M., Edwards, C., Garza, J. C. (2021) Species, sample date, location individual size and sample disposition of adult fish surveyed near Carmel and Monterey Bays, CA, 2013-2016 (Larval Dispersal in Kelp Rockfish project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2017-08-15 doi:10.26008/1912/bco-dmo.684426.2
IsRelatedTo
Dataset: Fish surveys 1999-2015
Carr, M., Edwards, C., Garza, J. C. (2021) Survey of fish species, number and size from transects near Carmel and Monterey Bays, CA, 1999-2015 (Larval Dispersal in Kelp Rockfish project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-03-17 doi:10.26008/1912/bco-dmo.684484.1
IsSupplementedBy
Dataset: Fish species code key
Carr, M., Edwards, C., Garza, J. C. (2021) Fish species code key for data collected along the shore of Monterey and Carmel from 1999-2015 (Larval Dispersal in Kelp Rockfish project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-03-17 doi:10.26008/1912/bco-dmo.684512.1
IsSupplementedBy
Dataset: Survey locations
Carr, M., Edwards, C., Garza, J. C. (2021) Locations of fish surveys in the Monterey and Carmel nearshore from 1999-2015 (Larval Dispersal in Kelp Rockfish project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-08-16 doi:10.26008/1912/bco-dmo.712843.1
IsSupplementedBy
Dataset: Site Code Key
Carr, M., Tinker, T. (2021) Site code key for kelp forest community data collected along the coast of Monterey and Carmel, CA from 1999-2015 (Kelp Forest Resilience project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-08-16 doi:10.26008/1912/bco-dmo.661175.1

Related Publications

Results
Baetscher, D. S., Anderson, E. C., Gilbert‐Horvath, E. A., Malone, D. P., Saarman, E. T., Carr, M. H., & Garza, J. C. (2019). Dispersal of a nearshore marine fish connects marine reserves and adjacent fished areas along an open coast. Molecular Ecology, 28(7), 1611–1623. doi:10.1111/mec.15044
Results
Baetscher, D. S., Clemento, A. J., Ng, T. C., Anderson, E. C., & Garza, J. C. (2017). Microhaplotypes provide increased power from short-read DNA sequences for relationship inference. Molecular Ecology Resources, 18(2), 296–305. doi:10.1111/1755-0998.12737

Carr, M., Garza, J. C., Edwards, C. (2018) Rockfish microhaplotype sequence accessions from samples near Carmel and Monterey Bays, CA, 2013-2016 (Larval Dispersal in Kelp Rockfish project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-02-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/684944 [access date]

Terms of Use

This dataset is licensed under Creative Commons Attribution 4.0.


If you wish to use this dataset, it is highly recommended that you contact the original principal investigators (PI). Should the relevant PI be unavailable, please contact BCO-DMO (info@bco-dmo.org) for additional guidance. For general guidance please see the BCO-DMO Terms of Use document.

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