DOI: 10.5061/dryad.w9ghx3fmj
title: Going against the flow: barriers to gene flow impact patterns of connectivity in cryptic coral reef gobies throughout the western Atlantic

description: Aim: Complex oceanographic features have historically caused difficulty in
 understanding gene flow in marine taxa. Here, we evaluate the impact of
 potential phylogeographic barriers to gene flow and assess demography and
 evolutionary history of a coral reef goby species complex. Specifically,
 we test how the Amazon River outflow and ocean currents impact gene flow.
 Location: Western Atlantic. Taxon: The bridled goby (Coryphopterus
 glaucofraenum) and sand-canyon goby (C. venezuelae) species complex.
 Methods: We used mitochondrial DNA and 2401 genomic SNPs to investigate
 evolutionary history and test hypotheses of how major barriers impact
 species-level differentiation. We used clustering algorithms and pairwise
 FST to assess population differentiation caused by minor barriers within
 and among regions. Finally, we tested alternate hypotheses of demographic
 history via coalescent simulations to determine the most plausible spread
 across the Western Atlantic. Results: We found two unique clades of C.
 glaucofraenum along the Brazilian coast and Atol das Rocas (AR) that are
 more closely related to C. venzuelae. Further genetic structure within the
 Caribbean and separately along the Brazilian coast led to at least two
 distinct populations in each location. Coalescent simulations indicated
 that an ancestral population of C. venezuelae split from C. glaucofraenum
 in the Caribbean, dispersed to Brazil, then spread to AR. Main
 Conclusions: Species-level genetic differentiation has resulted from the
 Amazon River outflow and isolation of AR. Population differentiation
 within the Caribbean matched previous studies indicating an east-west
 pattern of divergence. Brazilian population differentiation was impacted
 by the cold-water upwelling at Cabo Frio. Overall, this research
 highlights how barriers to gene flow impact speciation and genetic
 structure within western Atlantic gobies and provides insight into the
 role oceanographic features have in the speciation process of fishes.
description: A reduced-sample SNP dataset was generated using 103 total
 individuals from 16 populations across the range of both <i>C.
 glaucofraenum </i>and <i>C. venezuelae </i>including
 three individuals of <i>C. tortugae</i> as an outgroup.
 Genomic DNA was converted into nextRAD genotyping-by-sequencing libraries
 (SNPsaurus, LLC) as in Russello, Waterhouse, Etter, & Johnson
 (2015). The nextRAD libraries were sequenced on an Illumina HiSeq 4000
 with one lane of single-end 150 bp reads (University of Oregon). After de
 novo assembly and initial filtering, there were 9,003 SNPs. Following
 additional locus filtration for 10x coverage, 20% missing data and HWE,
 samples were thinned to include only one SNP per fragment resulting in a
 final dataset of 2,401 SNPs.  Detailed information on the standard
 SNPsaurus SNP generation and filtering can be found in Supplemental
 Document 1. To identify loci under selection we used the program Bayescan
 v.2.1 (Foll & Gaggiotti, 2008) using default parameters for a
 neutral model: 100,000 iterations and 10 prior odds. The maximum allowable
 false discovery rate (FDR) was set to 0.05. We ran Bayescan within each
 putative species (i.e. Brazilian C. <i>glaucofraenum </i>(with
 southern Brazil vs. central and northern Brazil); <i>C.
 venezualae</i>; and Caribbean <i>C. glaucofraenum</i>;
 see Results)<i>.  </i>All outlier loci were removed from
 downstream analyses.
description: The data file is provided in STRUCTURE format where missing
 values are denoted as "-9" and SNPs are defined as G = 1, C = 2,
 A = 3, and T = 4. Individuals have two fragments, comprising one diploid
 individual. There is a metadata file which provides location information
 for each individual.