Accumulation of gene copy number variations during the early phase of free-spawning abalone speciation

The genetic basis of speciation in free-spawning marine invertebrates is poorly understood. Although gene copy number variations (GCNVs) as well as nucleotide variations possibly trigger the speciation of these organisms, empirical evidence for such a hypothesis is limited. In this study, we searched for genomic signatures of GCNVs that may contribute to the speciation of Western Pacific abalone species. Whole-genome sequencing data suggested the existence of significant amounts of GCNVs in closely related abalones, Haliotis discus and H. madaka, in the early phase of speciation. In addition, the degree of interspecies genetic differentiation in the genes where GCNVs were estimated was higher than that in other genes, suggesting that nucleotide divergence also accumulates in the genes with GCNVs. GCNVs in some genes were also detected in other related abalone species, suggesting that these GCNVs are derived from both ancestral and de novo mutations. Our findings suggest that GCNVs have ..., , , # Title of Dataset:

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The perl scripts to detect 3 allele sequences from bam files and their results. These are custom scripts I created, so it might be difficult to understand. If you find it confusing, please feel free to contact me. Please see text for other analysis methods in this study. The WGS data used in this study are provided in Table [A1](https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.9816#ece39816-tbl-0001 \"Link to table\") in Appendix [A](https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.9816#ece39816-app-0001 \"Link to appendix\"). 

### Description of the data and file structure

**VCF_haplotype_detect_pipeline_american_abalone.pl**

This perl script was used to detect 3 allele sequences from bam files of North American abalones

**VCF_haplotype_detect_pipeline_Japanese_abalone.pl**

This perl script was used to detect 3 allele sequences from bam files of Japanese abalones

**haplotype_all_counts_american_species_dryad.xlsx**

Numbers of 3 allele sequences...