Data from: A comparison of the life history and distribution of vermilion rockfish (Sebastes miniatus) and its cryptic pair, sunset rockfish (S. crocotulus) along the Pacific Coast
Data files
Oct 09, 2025 version files 23.64 MB
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metadata_all_samples.csv
4.94 MB
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raw_genotypes_all.csv
18.67 MB
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README.md
3.60 KB
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vermilion_sunset_primer_probe_file.csv
16.47 KB
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vermilion_sunset_rubias_references.RDS
10.14 KB
Abstract
We used advanced genomics techniques to separate an economically and ecologically important cryptic species pair, vermilion rockfish and sunset rockfish (Genus: Sebastes), into its constituent species. Over 30,000 tissue specimens were analyzed to clarify species-specific life history traits and improve the information available for research and management. Vermilion rockfish were observed from Canada to Mexico, generally in waters shallower than 130 m, while sunset rockfish were encountered from Point Arena, California, to Mexico and were common in both shallow waters and offshore banks to at least 300 m. Sunset rockfish grew faster and reached larger maximum sizes, but vermilion rockfish exhibited older maximum ages. As a result of spatial and depth-based management, which disproportionately protected deeper waters, vermilion rockfish have likely been subjected to greater commercial and recreational fishing pressure than sunset rockfish throughout most of the 21st century. Improved understanding of the unique life and catch histories of the two species may have implications for how this and other cryptic species pairs are assessed and managed in the future.
Dataset DOI: 10.5061/dryad.xpnvx0ks9
Description of the data and file structure
This repository contains the data required to replicate analyses in Harms et al, which used advanced genomics techniques to separate an economically and ecologically important cryptic species pair, vermilion rockfish and sunset rockfish (Genus Sebastes), into its constituent species. Upon acceptance, all associated code for processing these samples will be available on GitHub. All files are in CSV or RDS format, which can be read by R using read.csv() or readRDS(), respectively.
Files and variables
File: vermilion_sunset_primer_probe_file.csv
Description: primer/probe file for processing raw sequence data using Nate Campbell's GTseq pipeline
Variables
- locus name
- allele 1
- allele 2
- forward probe sequence
- reverse probe sequence
- correction value allele 1
- correction value allele 2
File: vermilion_sunset_rubias_references.RDS
Description: a reference used in Rubias to call individuals
- sample_type – column required by Rubias to identify these samples as the reference
- indiv – unique identifier for each individual
- repunit – species call for each reference individual
- collection – population call for each individual
- Allele calls for each locus, split by allele
File: raw_genotypes_all.csv
Description: raw genotypes for all individuals sequenced for this project
Variables
- sample_ID – unique individual identifier
- Sequencing Plate – unique plate identifier for sequencing
- Raw Reads – number of total sequence reads
- On Target Reads – number of cumulative reads at the desired loci
- % On Target – ratio of the previous two columns
- % GT – % of how many loci were genotyped
- IFI – the IFI score (Individual Fuzziness Index) for each sample. This is a measure of DNA cross-contamination and is calculated using read counts from the background signal at homozygous and No-Call loci. (from Nate Campbell’s readme)
- allele calls for each locus
File: metadata_all_samples.csv
Description: associated metadata from every individual sequenced, including the final species ID call. Missing data: NA
Variables
- Specimen.Num – unique identifier for each individual
- FishInfoID.FishID – unique identifier for each individual as determined by certain surveys
- Field.ID – species ID call made in the field
- Survey – name/type of survey
- Year – collection year
- Vessel – boat name
- Site.Cell.ID – unique identifier for site
- Set.Haul.ID – unique identifier for haul
- FC.Blotter.Num – unique identifier for physical fin clip
- LatDD – latitude in decimal degrees
- LonDD.v2 – longitude in decimal degrees
- Depth..m. – depth in meters
- Sex – field sex identification
- Fork. length..cm. – fork length in centimeters
- Wt..kg. – weight in kilograms
- Otolith Barcode – unique identifier for otolith (if collected)
- Ages –estimated age from otolith analysis
- Ager – name of ager
- Rubias Species Call – species call from Rubias analysis
- Rubias Pop Call – population call from Rubias analysis
- On Target Reads – number of cumulative reads at the desired loci
- % GT - % of how many loci were genotyped