DOI: 10.5061/dryad.h7vb0
title: Data from: Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact

description: Ecophenotypic differentiation among replicate ecotype pairs within a
 species complex is often attributed to independent outcomes of parallel
 divergence driven by adaptation to similar environmental contrasts.
 However, the extent to which parallel phenotypic and genetic divergence
 patterns have emerged independently is increasingly questioned by
 population genomic studies. Here, we document the extent of genetic
 differentiation within and among two geographic replicates of the coastal
 and marine ecotypes of the European anchovy (Engraulis encrasicolus)
 gathered from Atlantic and Mediterranean locations. Using a genome-wide
 data set of RAD-derived SNPs, we show that habitat type (marine vs.
 coastal) is the most important component of genetic differentiation among
 populations of anchovy. By analysing the joint allele frequency spectrum
 of each coastal-marine ecotype pair, we show that genomic divergence
 patterns between ecotypes can be explained by a postglacial secondary
 contact following a long period of allopatric isolation (c. 300 kyrs). We
 found strong support for a model including heterogeneous migration among
 loci, suggesting that secondary gene flow has eroded past differentiation
 at different rates across the genome. Markers experiencing reduced
 introgression exhibited strongly correlated differentiation levels among
 Atlantic and Mediterranean regions. These results support that partial
 reproductive isolation and parallel genetic differentiation among
 replicate pairs of anchovy ecotypes are largely due to a common divergence
 history prior to secondary contact. They moreover provide comprehensive
 insights into the origin of a surprisingly strong fine-scale genetic
 structuring in a high gene flow marine fish, which should improve stock
 management and conservation actions.
description: LeMoan_Atlantic_anchovy_working_dataset_MAC1_1SNPperRADThe Atlantic subdataset containing 5260 SNPs typed 41 non-admixed individuals that were classified either as pure marine (30 PM) or pure coastal (11 PC) ecotypes using a 95% assignment probability threshold in NewHybrids. The minor allele count (MAC) threshold is 1 and only one SNP per RAD was kept.ATL_mac_1.vcfLeMoan_Mediterranean_anchovy_working_dataset_MAC1_1SNPperRADThe Mediterranean subdataset containing 6554 SNPs typed in 48 non-admixed individuals that were classified either as pure marine (17 PM) or pure coastal (31 PC) ecotypes using a 95% assignment probability threshold in NewHybrids. The minor allele count (MAC) threshold is 1 and only one SNP per RAD was kept.MED_mac_1.vcfLeMoan_4_pops_no_hybrid_anchovy_working_dataset_MAC1_1SNPperRADThe 4 populations dataset containing 3056 SNPs typed in 89 non-admixed individuals that were classified either as pure marine or pure coastal ecotypes using a 95% assignment probability threshold in NewHybrids. The minor allele count (MAC) threshold is 1 and only one SNP per RAD was kept.4pop_no_hybrid_mac_1.vcfLeMoan_4_pops_all_samples_anchovy_working_dataset_MAC2_1SNPperRADThe global SNP dataset used in NewHybrids analysis and in the PCA analysis containing hybrids (Figure 1A). The VCF file contains 5638 SNPs typed in 128 individuals. The minor allele count (MAC) threshold is 2 and only one SNP per RAD was kept.4pop_all_samples_mac_2.vcfLeMoan_Atlantic_anchovy_JAFSThe JAFS dadi input file for the Atlantic ecotype pair.ATL.fsLeMoan_Mediterranean_anchovy_JAFSThe JAFS dadi input file for the Mediterranean ecotype pair.MED.fs