DOI: 10.5061/dryad.s1rn8pk40
title: Speciation history of European (Anguilla anguilla) and American eel (A. rostrata), analyzed using genomic data

description: Speciation in the ocean could differ from terrestrial environments due to
 fewer barriers to gene flow. Hence, sympatric speciation might be common,
 with American and European eel being candidates for exemplifying this.
 They show disjunct continental distributions on both sides of the
 Atlantic, but spawn in overlapping regions of the Sargasso Sea from where
 juveniles are advected to North American, European and North African
 coasts. Hybridization and introgression is known to occur, with hybrids
 almost exclusively observed in Iceland. Different speciation scenarios
 have been suggested, involving either vicariance or sympatric ecological
 speciation. Using RAD sequencing and whole-genome sequencing data from
 parental species and F1 hybrids, we analyzed speciation history based on
 the Joint Allele Frequency Spectrum (JAFS) and PSMC (pairwise sequentially
 Markovian coalescent) plot. JAFS supported a model involving a split
 without gene flow 150,000 – 160,000 generations ago, followed by
 secondary contact 87,000 – 92,000 generations ago, with 64% of the genome
 experiencing restricted gene flow. This supports vicariance rather than
 sympatric speciation, likely associated with Pleistocene
 Glaciation cycles and ocean current changes. Whole genome PSMC
 analysis of F1 hybrids from Iceland suggested divergence 200,000
 generations ago and indicated subsequent gene flow rather than strict
 isolation. Finally, simulations showed that results from both approaches
 (JAFS and PSMC) were congruent. Hence, there is strong evidence against
 sympatric speciation in North Atlantic eels. These results reiterate the
 need for careful consideration of cases of possible sympatric speciation,
 as even in seemingly barrier-free oceanic environments palaeoceanographic
 factors may have promoted vicariance and allopatric speciation.
description: The data encompasses a Genepop (Atlantic_eels_Genepop.txt) and a
 VCF file (Atlantic_eels.vcf) consisting of 9,481 SNPs in European and
 American eel filtered from a previously published dataset generated by RAD
 sequencing (Jacobsen MW, Pujolar JM, Bernatchez L<i>, et al.</i> (2014) Genomic footprints of speciation in Atlantic eels (<i>Anguilla anguilla</i> and <i>A. rostrata</i>). <i>Molecular Ecology</i> <b>23</b>, 4785–4798).  In addition, commands (*.sh files) are included for simulations of pure and hybrid eel genomes using ms (Hudson RR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. <i>Bioinformatics</i> <b>18</b>, 337-338).
description: In the SNP dataset (Genepop and VCF files) the following
 individuals are European eel: LEG11 LEG9 RHG12 RHG13 RHG14 RHG16 RHG17
 RHG3 RHG5 RHG6 RHG8 LEG12 RHG9 VG11 VG12 VG13 VG14 VG15 VG16 VG17 VG18
 VG19 LEG13 VG20 LEG14 LEG15 LEG16 LEG20 LEG7 LEG8. The
 following individuals are American eels: NEG19 RBA14 RBA15 RBA16 RBA17
 RBA19 RBA1 RBA21 RBA22 RBA2 RBA4 NEG20 RBA5 RBA6 RBA7 RBG11 RBG20 RBG27
 RBG28 STJ33 STJ34 NEG24 NEG25 NEG29 NEG30 NEG4 RBA12 RBA13.
 For the simulation commands IM denotes "Isolation with
 migration", SI denotes "Strict isolation", and SCG denotes
 "Secondary contact with exponential growth". AM denotes American
 eel, EU denotes European eel and F1 denotes F1 hybrids between the two
 species.