DOI: 10.5061/dryad.6t1g1jww2
title: The contribution of ancient admixture to reproductive isolation between European sea bass lineages

description: Understanding how new species arise through the progressive establishment
 of reproductive isolation barriers between diverging populations is a
 major goal in Evolutionary Biology. An important result of speciation
 genomics studies is that genomic regions involved in reproductive
 isolation frequently harbor anciently diverged haplotypes that predate the
 reconstructed history of species divergence. The possible origins of these
 old alleles remain much debated, as they relate to contrasting mechanisms
 of speciation that are not yet fully understood. In the European sea bass
 (Dicentrarchus labrax), the genomic regions involved in reproductive
 isolation between Atlantic and Mediterranean lineages are enriched for
 anciently diverged alleles of unknown origin. Here, we used
 haplotype-resolved whole-genome sequences to test whether divergent
 haplotypes could have originated from a closely related species, the
 spotted sea bass (Dicentrarchus punctatus). We found that an ancient
 admixture event between D. labrax and D. punctatus is responsible for the
 presence of shared derived alleles that segregate at low frequencies in
 both lineages of D. labrax. An exception to this was found within regions
 involved in reproductive isolation between the two D. labrax lineages. In
 those regions, archaic tracts originating from D. punctatus locally
 reached high frequencies or even fixation in Atlantic genomes but were
 almost absent in the Mediterranean. We showed that the ancient admixture
 event most likely occurred between D. punctatus and the D. labrax Atlantic
 lineage, while Atlantic and Mediterranean D. labrax lineages were
 experiencing allopatric isolation. Our results suggest that local adaptive
 introgression and/or the resolution of genomic conflicts provoked by
 ancient admixture have probably contributed to the establishment of
 reproductive isolation between the two D. labrax lineages.
description: <b><i>Whole-genome resequencing and
 haplotyping</i></b> We sequenced the whole
 genome of one <i>Dicentrarchus punctatus
 </i>individual<i> </i>from the Atlantic Ocean (Gulf of
 Cadiz, PUN) and 59 new <i>Dicentrarchus labrax </i>individual
 genomes. Fifty-two of them were wild individuals captured from the
 Atlantic Ocean (English Channel, 10 males ♂<sub>AT</sub>), the
 western Mediterranean Sea (Gulf of Lion, 14 females ♀<sub>WME
 </sub>and 9 males ♂<sub>WME</sub>) and the eastern
 Mediterranean Sea (Turkey, 10 males ♂<sub>NEM</sub> and Egypt,
 9 males ♂<sub>SEM</sub>). Some of these specimens were
 experimentally crossed to generate first generation hybrids, which were
 used to phase the genome of their parents using a phasing-by-transmission
 approach. Whole genome sequencing libraries were
 prepared separately for each individual using either the Illumina TruSeq
 DNA PCR-Free (40 individuals) or the TruSeq DNA Nano protocol (20
 individuals), depending on DNA concentration. Pools of 5 individually
 barcoded libraries were then sequenced on 12 separate lanes of an Illumina
 HiSeq3000 using 2x150bp PE reads. Alignment of
 individual PE reads to the sea bass reference genome was performed using
 BWA-mem v0.7.5a with default parameters. Duplicate reads were marked using
 Picard version 1.112 before being removed, producing a mean coverage depth
 of 33.8X per individual. We then followed GATK’s (version 3.3-0-g37228af)
 best practice pipeline from individual variant calling (using
 HaplotypeCaller), to joint genotyping, genotype refinement and variant
 filtering (using Filter Expression: QD&lt;10; MQ&lt;50;
 FS&gt;7; MQRankSum&lt;-1.5; ReadPosRankSum&lt;-1.5). We used
 the BQSR algorithm to recalibrate base quality scores using a set of
 high-quality variants identified in a previous study (Duranton <i>et
 al.</i> 2018), and to perform variant quality score recalibration
 using the VQSR algorithm. Hard filtering was then applied to exclude
 low-quality genotypes with a GQ score &lt; 30.
 Haplotype phasing in <i>D. labrax</i> was done after
 merging the 59 newly sequenced genomes with the 16 genomes already
 obtained in Duranton <i>et al.</i> (2018). Fifteen individuals
 that were involved in family crosses were submitted to
 phasing-by-transmission using the PhaseByTransmission algorithm in GATK
 with default parameters and a mutation rate prior of
 10<sup>-8</sup> for <i>de novo</i> mutations. For
 all individuals, variants located on a same read pair were directly phased
 using physical phasing information. Non-related <i>D.
 labrax</i> individuals were then statistically phased using Eagle2
 (version 2.4). The 22 parents phased with the phasing-by-transmission
 approach were used to build a European sea bass reference haplotype
 library, which was used in Eagle2 to improve statistical
 phasing. We finally filtered out SNPs in VCFtools using
 --max-missing-count 0 and the --phased option to exclude unphased
 variants. In this way, we generated a dataset of haplotype-resolved
 whole-genome sequences from 68 unrelated <i>D. labrax</i>
 individuals (14 AT, 31 WME, 11 SEM and 12 NEM), containing 5,074,249
 phased SNPs without missing data.
 <em><strong>The corresponding VCF file containing
 5,074,249 phased SNPs is called:</strong></em>
 HQ_68G_phased_LG.vcf.gz
 <strong><em>The genome-wide statistics calculated in
 non-overlapping 50kb:</em></strong>
 ALL_STATS_50Kb_Windows.txt  
description: <em><strong>The VCF file containing 5,074,249 phased
 SNPs from 68 Dicentrarchus labrax genomes without missing
 genotype:</strong></em>
 HQ_68G_phased_LG.vcf.gz
 <strong><em>The genome-wide statistics calculated in
 non-overlapping 50kb windows
 </em></strong><em><strong>from 68 Dicentrarchus
 labrax
 genomes</strong></em><strong><em>:</em></strong> ALL_STATS_50Kb_Windows.txt