DOI: 10.5061/dryad.n1432
title: Data from: Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes

description: Understanding the processes that shape patterns of genetic structure
 across space is a central aim of landscape genetics. However, it remains
 unclear how geographic features and environmental variables shape gene
 flow, particularly for marine species in large complex seascapes. Here, we
 evaluated the genomic composition of the two-band anemonefish Amphiprion
 bicinctus across its entire geographic range in the Red Sea and Gulf of
 Aden, as well as its close relative, Amphiprion omanensis endemic to the
 southern coast of Oman. Both the Red Sea and the Arabian Sea are complex
 and environmentally heterogeneous marine systems that provide an ideal
 scenario to address these questions. Our findings confirm the presence of
 two genetic clusters previously reported for A. bicinctus in the Red Sea.
 Genetic structure analyses suggest a complex seascape configuration, with
 evidence of both Isolation by Distance (IBD) and Isolation by Environment
 (IBE). In addition to IBD and IBE, genetic structure among sites was best
 explained when two barriers to gene flow were also accounted for. One of
 these coincides with a strong oligotrophic-eutrophic gradient at around
 16-20˚N in the Red Sea. The other agrees with an historical bathymetric
 barrier at the straight of Bab al Mandab. Finally, these data support the
 presence of inter-specific hybrids at an intermediate suture zone at
 Socotra and indicate complex patterns of genomic admixture in the Gulf of
 Aden with evidence of introgression between species. Our findings
 highlight the power of recent genomic approaches to resolve subtle
 patterns of gene flow in marine seascapes.
description: de_novo_assembly
 _filesThis files contains the
 principal output files from the de_novo.pl pipeline from
 Stacks.Biocode_Information_sheetThis file contains information about each of the raw data files that were uploaded to the SRA repository. The last column of the file includes the name of the site of each sample as in the publication.4559_loci_fileVCF file with information of all 4559 SNPs used for analyses in the publication. It can be converted to other formats such as Structure or Genodive.data matrix_Information-theoretic approachData file used for the Information-theoretic approach. The results of this section of the paper can be duplicated by using this file and the associated R script (please see the Information_theoretic_aproach_script.R accompanying file)Information_theoretic_aproach_scriptR script used for the Information-Theoretic approach section.candidate_loci_k2List of candidate loci obtained with the lfmm function when the number of latent factors was set to K = 2. Note that Locus ID in this file is the same locus ID in the vcf file provided.candidate_loci_k3List of candidate loci obtained with the lfmm function when the number of latent factors was set to K = 3. Note that Locus ID in this file is the same locus ID in the vcf file provided.tremix_MLtree_with_m5_ML tree file from treemix. This is the resulting tree with five migration events that is shown in figure 5. The first line of this file is the Newick format ML tree, and the remaining lines contain the migration edges. The first column for these lines is the weight on the edge, followed by the jackknife estimate of the weight, the jackknife estimate of the standard error, and the p-values. Then come the subtree below the origin of the migration edge, and the subtree below the destination of the migration edge.threepop_test_results_fileResults from the three population test run in trimix. The output is four columns. These are the populations used to calculate the f3 statistic, the f3 statistic, the standard error in the f3 statistic, and the Z-score.