Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Deployments
• Project Information
• Program Information
• Funding

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.

Haplotype data from 150bp amplicon sequencing on an Illumina MiSeq. All loci used in the generation of haplotype sequence data will be submitted to GenBank (National Center for Biotechnology Information).

Genotype data are generated with high-throughput DNA sequencing on an Illumina MiSeq instrument. Amplicons are prepared through polymerase chain reaction with primers designed from either expressed sequence tags in publicly available databases (e.g., Cyverse) or from sequences generated by double digest Restriction-Site Associated DNA (RAD) sequencing. Amplicon sequencing is using the procedure described in Campbell et al. 2015 (Molecular Ecology Resources 15: 855-867) termed genotyping in thousands by sequencing (GT-seq). Data are filtered by quality score and genotypes called for all locus by individual combinations with read depth ≥20. Genotyping accuracy is evaluated by confirmation of Mendelian segregation in known families. Haplotypes are called from constituent SNPs using FreeBayes software.

Standard filtering for quality scores and read depth have been applied to the raw instrument output to call haplotypes.

BCO-DMO Processing Notes:
- created table of files downloaded from Dryad
- added conventional header with dataset name, PI name, version date

Description from NSF award abstract:
The spatial structure and dynamics of coastal marine fish populations are strongly influenced by the transport and recruitment of larvae. However, the scale and patterns of larval dispersal are among the most difficult demographic parameters to quantify in marine systems, due to the inability to tag and track the movement of larvae. In particular, the extent of local retention of larvae versus regional dispersal to other locations and populations is currently a hotly debated topic in the field of marine ecology and has profound implications for the design and effectiveness of Marine Protected Areas (MPAs). The research will identify patterns of larval dispersal and use those patterns to test predictions of dispersal generated by state-of-the-art circulation models.

The PI team brings together ecologists, geneticists, statisticians, and oceanographers with expertise in population demography and field sampling, mark/recapture data from genetic tags, and empirical and model-based evaluation of oceanographic processes to answer the following questions:
1. Do observed patterns of dispersal and connectivity of larval kelp rockfish correspond to patterns predicted by high spatial resolution regional ocean circulation models? Model predictions will be tested empirically using larval settlement samples. Parentage analysis will be used to verify the occurrence of larvae derived from genetically tagged source populations.
2. Is there evidence for local retention of larval kelp rockfish within the study area? To test the hypothesis that local retention of juvenile kelp rockfish from source populations is greater than expected by existing larval transport models, the PIs will compare the proportion of recruits that are genetically identified to have been produced from within three focal sites with the proportion of larval production that was tagged in those sites.
3. Is the relative recruitment of recently settled kelp rockfish to focal sites in the study region proportionate to the relative larval production of those focal sites? The PIs will compare the proportion of tagged recruits with the proportion of larval production generated from tagged adults at varying spatial scales. They will use goodness of fit models to compare expected and observed connectivity matrices under varying hypotheses of larval dispersal. Alternatively, if the relative contribution of focal sites to larval replenishment of themselves, one another, and more distant populations is disproportionate to their relative production, can this discrepancy be explained by oceanographic processes that could facilitate particular trajectories of larval dispersal?

To determine if differences in self recruitment and connectivity can be attributed to local oceanographic features, the PIs will examine spatial and temporal correlations between these features and the spatial distribution and timing of recruitment.

Related websites:
http://piscoweb.org
http://research.pbsci.ucsc.edu/eeb/rclab/kelp-rockfish-pbt-project/  (broken link)​
http://rockfish.ucsc.edu/
http://oceanmodeling.ucsc.edu

The Partnership for Interdisciplinary Studies of Coastal Oceans is a long-term ecosystem research and monitoring program established with the goals of: 

• understanding dynamics of the coastal ocean ecosystem along the U.S. west coast
• sharing that knowledge so ocean managers and policy makers can make science based decisions regarding coastal and marine stewardship
• producing a new generation of scientists trained in interdisciplinary collaborative approaches

Over the last 10 years, PISCO has successfully built a unique research program that combines complementary disciplines to answer critical environmental questions and inform management and policy. Activities are conducted at the latitudinal scale of the California Current Large Marine Ecosystem along the west coast of North America, but anchored around the dynamics of coastal, hardbottom habitats and the oceanography of the nearshore ocean – among the most productive and diverse components of this ecosystem. The program integrates studies of changes in the ocean environment through ecological monitoring and experiments. Scientists examine the causes and consequences of ecosystem changes over spatial scales that are the most relevant to marine species and management, but largely unstudied elsewhere.

Findings are linked to solutions through a growing portfolio of tools for policy and management decisions. The time from scientific discovery to policy change is greatly reduced by coordinated, efficient links between scientists and key decision makers.

Core elements of PISCO are:

• Interdisciplinary ecosystem science
• Data archiving and sharing
• Outreach to public and decision-making user groups
• Interdisciplinary training
• Coordination of distributed research team

Established in 1999 with funding from The David and Lucile Packard Foundation, PISCO is led by scientists from core campuses Oregon State University (OSU); Stanford University’s Hopkins Marine Station; University of California, Santa Cruz (UCSC); and University of California, Santa Barbara (UCSB). Collaborators from other institutions also contribute to leadership and development of PISCO programs.  As of 2005, core PISCO activities are funded by collaborative grants from The David and Lucile Packard Foundation and the Gordon and Betty Moore Foundation. Core support, along with additional funding from diverse public and private sources, make this unique partnership possible.