DOI: 10.5061/dryad.18931zd8c
title: Data from: Possible involvement of ghost introgressions in the striking diversity of Vomeronasal type 1 receptor genes in East African cichlids

description: Cichlids that have undergone adaptive radiation are genetically close but
 exhibit extreme ecological and morphological diversity, making them useful
 for understanding speciation mechanisms. Vomeronasal type 1 receptors
 (V1R) are highly conserved among teleost fish at the amino acid sequence
 level and believed to play a fundamental role in reproduction. We
 previously reported the surprisingly high sequence diversity of V1Rs among
 certain cichlid species, suggesting a possible role for V1Rs in their
 speciation. In this study, we investigated the process of evolutionary
 diversification of all 6 V1Rs (V1R1-6) by using the genome data of 528
 cichlid species, encompassing nearly all lineages. In the case of V1R2,
 two highly divergent alleles (1.17%: variant sites/coding sequence (CDS)
 length) without recombination were preserved and shared among cichlids
 found in all of the East African Great Lakes. In the case of V1R6,
 numerous highly variable alleles that could be derived from multiple
 recombination events between two highly divergent alleles (1.39%: variant
 sites/CDS length) were found among the Lake Victoria cichlids.
 Additionally, we identified highly divergent alleles of V1R1 within the
 tribe Tropheini, and of both V1R3 and V1R6 within Trematocarini and
 Ectodini. Because one of the two divergent alleles of these V1Rs emerged
 rapidly during cichlid evolution, they are likely to have been derived
 from introgression. However, despite extensive investigations, we could
 not identify the source lineages for these introgressions, implying that
 they may have become extinct. This study revealed the potential role of
 introgression in explaining the remarkable diversity of V1Rs in East
 African cichlids.
description: # Possible involvement of ghost introgressions in the striking diversity
 of Vomeronasal type 1 receptor genes in East African cichlids Dataset DOI:
 [10.5061/dryad.18931zd8c](10.5061/dryad.18931zd8c) ## Files * ###
 \*\_unphased.fasta We used short-read data from 28 tribes, 528 species,
 and 907 samples of cichlids deposited within the NCBI Sequence Read
 Archive (Figure S1, Table S1). Low-quality reads were removed using fastp
 v0.23.2 (Chen et al., 2018), and the filtered reads were mapped to the
 reference genome (Table S2) using bwa-mem2 v2.2.1 (Vasimuddin et al.,
 2019) and sorted and indexed using samtools v.1.15 (Danecek et al., 2021).
 The V1R gene regions were then extracted from the sorted BAM files using
 samtools v1.15 (Danecek et al., 2021). Variants were called from the
 extracted BAM files using the HaplotypeCaller tool of GATK v4.3.0 (McKenna
 et al., 2010). The first round of hard filtering for SNPs and INDELs was
 performed using the VariantFiltration tool of GATK v4.3.0 (McKenna et al.,
 2010) based on the following parameters: SNPs (QD&lt;2.0, QUAL&lt;30.0,
 SOR&gt;4.0, FS&gt;60.0, MQ&lt;40.0, MQRankSum&lt;-12.5, and
 ReadPosRankSum&lt;-8.0) and INDELs (QD&lt;2.0, QUAL&lt;30.0, FS&gt;200.0,
 SOR&gt;10.0, and ReadPosRankSum&lt;-20.0). Based on the resulting VCF
 file, quality recalibration of the BAM files was performed with the
 BaseRecalibrator and ApplyBQSR tools from GATK v4.3.0 (McKenna et al.,
 2010). The second round of hard filtering was conducted similarly to the
 first round. The filtered VCF files were used to generate V1R gene
 sequences in fasta format using bcftools v1.15 (Danecek et al., 2021) *
 ### \*\_phased.fasta Sequences containing heterozygous variants were
 phased using HapCUT2 v1.3.3 (Edge et al., 2017). ## Code/software Scripts
 for obtaining V1R gene sequences of cichlids are available on
 Github([https://github.com/taki-sh/RegionCall](https://github.com/taki-sh/RegionCall))