DOI: 10.5061/dryad.xpnvx0ks9
title: Data from: A comparison of the life history and distribution of vermilion rockfish (<em>Sebastes miniatus</em>) and its cryptic pair, sunset rockfish (<em>S. crocotulus</em>) along the Pacific Coast

description: 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.
description: # 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 Dataset DOI:
 [10.5061/dryad.xpnvx0ks9](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](https://github.com/GTseq/GTseq-Pipeline/blob/a988cc4caa627034ad51ee521b912f797aa5e8f9/GTseq_Genotyper_v3.pl#L7)) * 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