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Table S1 Information about the filtering process for the American eel and European eel samples.

Table S2 Information about alignment of filtered reads for the American eel and European samples.

Table S3 Summary information on reads after p-STACKS (p-stacks; M = 10) for American and European eel samples.

Table S4 Filtering on the final number of loci after populations.

Table S7 Individual NCBI codes of the used RAD sequenced samples.

Note S1 Information about the annotation of the genome prior to analyses of nonsynonymous and synonymous substitutions in SNPeff (Cingolani et al. 2012).

Fig S1 Plots of FST across the 30 longest scaffolds using a minor allele frequency (MAF) > 0.05.

mec12896-sup-0002-TableS5.xlsxapplication/msexcel96KTable S5 Genes represented by one or several SNPs with FST > 0.8 in either the genes themselves (including both introns and exon) or ≤5000 bp upstream the gene.
mec12896-sup-0003-TableS6.xlsapplication/msexcel757KTable S6 Genes or upstream regions represented by lositan SNP outliers, candidates for positive selection.

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