DOI: 10.5061/dryad.38nh3
title: Data from: Population genomics reveals multiple drivers of population differentiation in a sex-role-reversed pipefish

description: A major goal of molecular ecology is to identify the causes of genetic and
 phenotypic differentiation among populations. Population genomics is
 suitably poised to tackle these key questions by diagnosing the
 evolutionary mechanisms driving divergence in nature. Here, we set out to
 investigate the evolutionary processes underlying population
 differentiation in the Gulf pipefish, Syngnathus scovelli. We sampled
 approximately 50 fish from each of 12 populations distributed from the
 Gulf coast of Texas to the Atlantic coast of Florida and performed
 restriction-site-associated DNA sequencing to identify SNPs throughout the
 genome. After imposing quality and stringency filters, we selected a panel
 of 6348 SNPs present in all 12 populations, 1753 of which were not
 physically linked. We identified a genome-wide pattern of isolation by
 distance, in addition to a more substantial genetic break separating
 populations in the Gulf of Mexico from those in the Atlantic. We also used
 several divergence outlier approaches and tests for genotype–environment
 correlations to identify 400 SNPs putatively involved in local adaptation.
 Patterns of phenotypic differentiation and variation diverged from the
 overall genomic pattern, suggesting that selection, phenotypic plasticity
 or demographic factors may be shaping phenotypes in distinct populations.
 Overall, our results suggest that population divergence is driven by a
 variety of factors in S. scovelli, including neutral processes and
 selection on multiple traits.
description: Female
 Phenotypes This file contains all
 of the raw female phenotype data. The column names refer to the following:
 PopID = Population ID; ID = Individual ID; SVL = snout-vent length (mm);
 std.length = standard length (tip of snout to start of tail, mm); depth =
 body depth (measured at urogenital opening, mm); SnoutLength = snout
 length (tip of snout to eye, mm); SnoutDepth = snout depth (measured at
 midpoint of snout, mm); HeadLength = head length (tip of snout to start of
 gills, mm); MBandArea = mean band area (mm^2); BandNum = number of bands
 (count). fem.pheno.txt
 
 Male
 Phenotypes This file contains all
 of the raw male phenotypic measurements. he column names refer to the
 following: PopID = Population ID; ID = Individual ID; SVL = snout-vent
 length (mm); std.length = standard length (tip of snout to start of tail,
 mm); depth = body depth (measured at urogenital opening, mm); SnoutLength
 = snout length (tip of snout to eye, mm); SnoutDepth = snout depth
 (measured at midpoint of snout, mm); HeadLength = head length (tip of
 snout to start of gills, mm) mal.pheno.txt
 
 Sample Location
 Coordinates This file contains the
 latitude ("lat") and longitude ("lon") for each
 collection site ("site"). marine_coordinates_revised.csv Draft Genome Assembly This is the draft genome assembly file, courtesy of Clay Small and William Cresko. allpaths_cms1.scaff.fa PLINK map file for subset of SNPs This file is the map file for the 1753 unlinked SNPs that are in Hardy Weinberg Equilibrium. subset.map PLINK ped file for subset of SNPs This file is the map file for the 1753 unlinked SNPs that are in Hardy Weinberg Equilibrium. subset.ped Sample_information This file contains the information linking the individuals to the raw sequence data. Each individual has a barcode and a plate ID. Barcodes are unique to each plate but repeated between plates. This file also contains the population of origin for each individual and the latitude/longitude for that population. This file contains data for additional populations not used in this study. Flanagan_popgen_sampleinfo.txt   PLINK map file for all SNPs This file is the map file for the 6384 SNPs identified. all.6384.plink.map PLINK ped file for subset of SNPs This file is the ped file for the 6384 SNPs identified. all.6384.plink.ped   <strong>Table of outliers</strong> Tabular data containing the following information for all outlier loci: RAD locus ID (locus), scaffold ID (scaffold), basepair on the scaffold (BP), analysis in which the SNP was identified as an outlier (analysis), SNP ID (SNP), and the sequence of the RAD locus containing the SNP (Sequence). AllOutliers.txt