DOI: 10.5061/dryad.nvx0k6f0n
title: Complex patterns of genetic population structure in the mouthbrooding marine catfish, Bagre marinus, in the Gulf of Mexico and U.S. Atlantic

description: Patterns of genetic variation reflect interactions among microevolutionary
 forces that vary in strength with changing demography. For marine species,
 these patterns are often interpreted under the expectation that larval
 movement drives connectivity because most marine species exhibit broadcast
 spawning dispersal strategies. Here, patterns of variation within and
 among samples of the mouth brooding gafftopsail catfish (Bagre marinus,
 Family Ariidae) captured in the U.S Atlantic and throughout the Gulf of
 Mexico were analyzed using genomics to generate neutral and non-neutral
 SNP data sets. Because genomic resources are lacking for ariids, linkage
 disequilibrium network analysis was used to examine patterns of putatively
 adaptive variation. Finally, historical demographic parameters were
 estimated from site frequency spectra. The results show four
 differentiated groups, corresponding to the (1) U.S. Atlantic, and the (2)
 northeastern, (3) northwestern, and (4) southern Gulf of Mexico. Patterns
 of genetic variation for the neutral data resemble that of other fishes
 that use the same estuarine habitats as nurseries, regardless of the
 presence/absence of a dispersive larval phase, supporting the idea that
 adult/juvenile behavior and habitat are important predictors of
 contemporary patterns of genetic structure. The non-neutral data presented
 two contrasting signals of structure, one due to increases in diversity
 moving west to east and north to south, and another to increased
 heterozygosity in the Atlantic. Demographic analysis suggested recently
 reduced long-term effective population size in the Atlantic is likely an
 important driver of patterns of genetic variation and is consistent with a
 known reduction in population size potentially due to an epizootic.
description: <strong>Sampling and library prep</strong>
 Fin clips were obtained from 382 mixed-age samples of gafftopsail
 catfish collected from nine geographic sampling locations (hereafter
 locations; Figure 1) from 2015 to 2018: one in the Atlantic in Indian
 River Lagoon, Florida and adjacent coastal waters (ATL) and eight in the
 Gulf. Locations in the Gulf were near Tampa Bay, Florida (FLGS), North of
 Tampa Bay, Florida (FLGN), near Mobile Bay, Alabama, (MB), in Mississippi
 Sound, Mississippi (MISS), in Chandeleur Sound, LA (CS), off Louisiana
 west of the Mississippi River (LA), in Corpus Christi Bay, Texas (CC) and
 in the Bay of Campeche, Mexico (CAMP). All locations were selected because
 they represent inshore habitats used by mouth brooding males for
 parturition and by juveniles as nursery habitat, except CAMP which was
 opportunistically sampled further offshore. Sampling took place as part of
 surveys routinely conducted by state or academic entities, the latter
 following approved animal care protocols. All fin clips were preserved in
 20% DMSO-0.25M EDTA-saturated NaCl buffer (Seutin et al., 1991) and stored
 at room temperature until time of extraction. DNA was
 extracted using Mag-Bind Tissue DNA kits (Omega Bio-Tek, Norcross, GA) and
 500-1000 ng of high-quality genomic DNA used in a modified version of the
 ddRAD genomic library preparation method (Peterson<em> </em>et
 al., 2012). Briefly, genomic DNA was digested with two restriction
 endonucleases (<em>Eco</em>RI, <em>Msp</em>I), and
 a barcoded adapter was ligated to <em>Eco</em>RI sites while a
 common adapter was ligated to <em>Msp</em>I sites. Following
 adapter ligation, individuals were pooled by index and size-selected using
 a Pippin Prep size-selection system (Sage Science, Beverly, MA) to a
 standard size range (338 – 412 base pairs). Polymerase chain-reaction
 (PCR) amplification of fragments was performed to incorporate adaptors
 necessary for annealing to an Illumina flow cell and index-specific
 identifiers. Index pools were then combined into libraries of
 approximately 150 individuals spread across the geographic range of
 sampling and duplicate individuals (technical replicates), and three
 libraries were sequenced (paired-end) each on a lane of an Illumina HiSeq
 4000 DNA sequencer at GeneWiz<sup>®</sup>, New Jersey,
 USA. <strong>Genotyping</strong>
 RAD sequences retrieved from each run were demultiplexed
 using <em>process_radtags </em>(Catchen et al., 2011) and
 quality trimming, reduced-representation reference assembly, read mapping
 and SNP calling were performed using the <em>dDocent</em>
 pipeline (Puritz et al., 2014). The ten individuals with the highest
 number of reads were selected from each lane for <em>de
 novo</em> reduced-representation reference assembly, using the
 overlapping read (OL) assembly option in <em>dDocent</em>.
 Similarity threshold for clustering (c = 0.8), minimum within individual
 coverage (K1 = 5) and minimum number of individuals a read must occur in
 to be included (K2 = 2) were chosen after comparing mapping statistics for
 ten individuals randomly chosen from each library and mapped to references
 generated for c = 0.8, K1 = 2 – 10, and K2 = 1 – 10 using
 <em>BWA</em> (Li & Durbin, 2009) to maximize the
 number of reads mapped as a proper pair and minimize reads where forward
 and reverse reads mapped to different contigs. The constructed
 reduced-representation reference encompassed a total 10,874,990 base pairs
 across 37,872 fragments (mean 287 bp; mode 307 bp).
 Reads were mapped to the reduced-representation reference using
 <em>BWA</em> (Match=1, mismatch penalty=3 and gap penalty=5;
 Li, 2013) and SNPs called using <em>freebayes</em> (Garrison
 & Marth, 2012). The resulting data set was filtered to remove low
 quality and artefactual SNPs, paralogs, and low-quality individuals using
 <em>vcftools</em> (Danecek et al., 2011) and custom scripts
 following O’Leary et al. (2018), allowing for the retention of SNPs with
 more than 2 alleles. Genotypes with quality &lt; 20 and &lt; 5
 reads were coded as missing, retaining loci with quality &gt; 20,
 genotype call rate &gt; 90%, and mean depth 15 – 300. Loci were also
 filtered based on allelic balance (remove SNPs &lt; 0.25 and
 &gt;0.75), mapping quality ratios (remove SNPs &lt; 0.25 and
 &gt;1.75), strand balance (remove SNPs with &gt; 100x more forward
 alternate reads than reverse alternate reads and &gt; 100x more
 forward reverse reads than reverse alternate reads), paired status,
 depth/quality ratio (&lt; 0.2), and excess heterozygosity (remove SNPs
 &gt; 0.5 and that deviate significantly from the expectations of
 Hardy-Weinberg Equilibrium). Individuals with &gt; 25% missing data
 were removed. Finally, <em>rad_haplotyper </em>(Willis et al.,
 2017) was used to merge SNPs on the same fragments into SNP-containing
 loci (hereafter microhaplotypes), by using a random sample of 20 reads per
 locus and recording all possible haplotypes and then discarding haplotypes
 that are not possible given the SNPs present in the final dataset. Loci
 are flagged as paralogs if too may haplotypes are called given SNP
 genotypes. Genotyping error is flagged if an individual as too few
 haplotypes given SNP genotypes). The resulting haplotyped data set was
 further filtered to remove loci haplotyped in &lt; 90% of individuals,
 flagged as potential paralogs in &gt; 4 individuals, or as affected by
 genotyping error in &gt; 10 individuals. Technical replicates were
 compared to assess genotyping error, and loci systematically affected by
 genotyping error or flagged as deviating significantly from the
 expectations of Hardy-Weinberg Equilibrium (HWE) in &gt; 5 sites were
 removed.
description: # Complex patterns of genetic population structure in the mouthbrooding
 marine catfish, Bagre marinus, in the Gulf of Mexico and U.S. Atlantic
 [https://doi.org/10.5061/dryad.nvx0k6f0n](https://doi.org/10.5061/dryad.nvx0k6f0n) The three genepop files consist of a complete dataset as well as the dataset split into neutral and outlier loci. A metadata text file is also included to describe the catch locations of the samples. ## Description of the data and file structure The complete genepop dataset (BMA_by_pop_genepop.gen) consisted of 367 gafftopsail catfish (Bagre marinus, Family Ariidae) samples genotyped at 5,554 microhaplotype loci (14,682 SNPs) collected from the western North Atlantic Ocean ranging from Indian River Lagoon, Florida to the Bay of Campeche, Mexico. The neutral genepop file (BMA_by_pop_only-neutral_genepop.gen) is a subset of the complete file which contains 5,421 loci while the outlier genepop (BMA_by_pop_all-outl_genepop.gen) contains 133 loci. The sample names for these files consist of a species indicator, library designation, ligation well and sample name. The sample names are included in the tab deliminated metadata (SampleInfo.txt) file along with the catch coordinates, population designation and estuary they were sampled in. Missing data in the genepop files is designated with "000000" as alleles are coded with three digits. ## Metadata Key SAMPLE_ID: The name assigned to the sample LAT: The latitude of the vessel when the sample was brought on board LONG: The longitude of the vessel when the sample was brought on board POP: The geographic population assignment of the sample based upon catch location ESTUARY: The estuary in which the sample was collected ## Sharing/Access information Further metadata for these samples can be found at: * [https://data.griidc.org/data/R6.x805.000:0005](https://data.griidc.org/data/R6.x805.000:0005) ## Code/Software Further information about the code used to produce and analyze this data can be found at: * [https://github.com/marinegenomicslab/gafftop_popgen_2024](https://github.com/marinegenomicslab/gafftop_popgen_2024)