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: --- 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...自由产卵海洋无脊椎动物的物种形成遗传基础迄今尚未得到充分阐明。尽管基因拷贝数变异（gene copy number variations, GCNVs）与核苷酸变异或可触发这类生物的物种形成，但支撑这一假说的实证证据仍较为匮乏。本研究针对西太平洋鲍属物种形成相关的基因拷贝数变异基因组特征展开探寻。全基因组测序数据显示，在物种形成早期阶段，亲缘关系密切的盘鲍（Haliotis discus）和马氏鲍（H. madaka）中存在大量基因拷贝数变异。此外，携带基因拷贝数变异的基因所表现出的种间遗传分化程度显著高于其他基因，提示核苷酸分化同样在存在拷贝数变异的基因中不断积累。部分基因的拷贝数变异还在其他近缘鲍属物种中被检测到，表明这类变异既可能源自祖先遗传，也可能由新发突变产生。本研究结果表明，GCNVs在... ### 数据集标题： --- 用于从BAM文件中检测3种等位基因序列的Perl脚本及其分析结果。本脚本为笔者自主编写的定制化脚本，理解难度或较高，若存在困惑可随时联系笔者。有关本研究的其他分析方法详见正文。本研究使用的全基因组测序数据已在附录A的表[A1](https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.9816#ece39816-tbl-0001 "表格链接")中提供。 ### 数据与文件结构说明 **VCF_haplotype_detect_pipeline_american_abalone.pl** 本Perl脚本用于从北美鲍的BAM文件中检测3种等位基因序列。 **VCF_haplotype_detect_pipeline_Japanese_abalone.pl** 本Perl脚本用于从日本鲍的BAM文件中检测3种等位基因序列。 **haplotype_all_counts_american_species_dryad.xlsx** 北美鲍物种的3种等位基因序列计数...