DOI: 10.5061/dryad.xd2547djs
title: Life history implications of kinship structure in an Atlantic Herring schooling aggregation

description: Kinship in natural marine fish systems has been little explored in part
 due to costs of genomic analysis. This is especially true for very
 abundant and commercially exploited marine fish with broadcast spawning.
 Recent advances in genomics have however, facilitated an improved
 understanding of population structure in marine systems at fine geographic
 scales. Here, we identify kinship structure in an aggregation of Atlantic
 Herring (Clupea harengus) juveniles. We identified 11 and potentially up
 to 14 half-sib pairs using a suite of 92 sequenced microsatellite DNA
 markers and the R package CKMRsim in a sample of N=1391 herring
 individuals comprising two cohorts (ages 0+ and 1+) collected from the
 2018 Fall research survey of the Southern Gulf of St. Lawrence. We also
 discuss the detection of potential full-sibs in the data by way of
 association from the half-sib pairs. This study suggests the presence of
 kinship structure in a juvenile herring aggregation three months or more
 post hatching with implication for our understanding of herring early life
 history.
description: Unprocessed microsatellite data from Atlantic herring tissue
 samples from Gulf of St. Lawrence collected in 2018. DNA extraction was
 done using Glassmilk protocol and sequenced on Illumina HiSeq 2500 - High
 Throughput for 92 microsatellite markers on 1391 individuals (980 Age 0+
 and 411 Age 1+). 
description: # Life history implications of kinship structure in an Atlantic Herring
 schooling aggregation Dataset DOI:
 [10.5061/dryad.xd2547djs](10.5061/dryad.xd2547djs) ## Description of the
 data and file structure Usage notes \- The files are of minimally
 processed microsatellite data from 980 Age 0+ and 411 Age 1+ Atlantic
 herring sequenced on Illumina HiSeq 2500 - High Throughput for 92
 microsatellite loci. \- Data analysis: CKMRsim to estimate proportion of
 sibship structure in the data. Refer to Dec12_Herringpop2HS_markdown.html
 for R-markdown. ### Files and variables #### File:
 herring\_genos\_used\_two\_col\_Age1.csv **Description:** Raw
 microsatellite data from 411 age 1+ Atlantic herring sequenced on Illumina
 HiSeq 2500 - High Throughput for 92 microsatellite loci. ##### Variables:
 * Missing data are shown as "0". * Each column is an allele
 composed of n and n-b (e.g., CHR1 and CHR1-b constitute a locus). * Ch in
 the sample ID (NMFS_DNA ID) refers to* Clupea harengus* * File is in comma
 delimited UTF-8 format. #### File: README\_files.txt
 **Description:** Readme file. ##### Variables * Data from: Life history
 implications of kinship structure in an Atlantic herring schooling
 aggregation : #### File: herring\_genos\_used\_two\_col\_Age0.csv
 **Description:** Raw microsatellite data from 980 age 0+ Atlantic herring
 sequenced on Illumina HiSeq 2500 - High Throughput for 92 microsatellite
 loci ##### Variables * Missing data are shown as "0". * Each
 column is an allele composed of n and n-b (e.g., CHR1 and CHR1-b
 constitute a locus). * Ch in the sample ID (NMFS_DNA ID) refers to* Clupea
 harengus* * File is in comma delimited UTF-8 format. #### File:
 July3rd\_Annotated\_HerringExample\_markdown.html
 **Description:** Markdown showing sample analysis. ## Code/software File
 can be opened in text editor such as sublime text or notepad++ as well as
 excel and Rstudio.  Packages required: *CKMRsim* *ggplot2* ## Access
 information Other publicly accessible locations of the data: * None Data
 was derived from the following sources: * Kho, James, McCracken, Gregory
 R., McDermid, Jenni L., and Ruzzante, Daniel E. (2025). Data from: Life
 history implications of kinship structure in an Atlantic herring schooling
 aggregation, Dryad, Dataset *Reuse and replication efforts may vary
 depending on manipulation of data for downstream analyses including
 filtering parameters (i.e. threshold for missing data) and formatting