Data to support Whitney JL, Coleman RR, Deakos MH "Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian Reef Manta Rays"

Datasets supporting the manuscript: Whitney JL, Coleman RR, Deakos MH "Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian Reef Manta Rays". <em>BMC Ecology and Evolution </em><strong>23</strong>, 31 (2023). https://doi.org/10.1186/s12862-023-02130-0 Nuclear data: "Mobula-alfredi_nuclear_reference_RAD_contigs.fasta" is a fasta of 359,751 contigs that serve as the reference for nuclear alignment of genotypes to RAD loci. Contigs begin and end with GATC cut site. Mobula-alfredi_nuclear_all_2048snps_38genotypes.vcf is a VCF file with all 2048 nuclear SNPs in final filtered SNP dataset. 38 genotypes are included from Maui Nui and Hawaii Island. This 2048 SNPs includes both 2038 neutral and 10 outlier SNPs. Mobula-alfredi_nuclear_neutral_2038snps_38genotypes.vcf is a VCF file with 2038 neutral nuclear SNPs genotyped in 38 individuals from Maui Nui and Hawaii Island. Mobula-alfredi_nuclear_outliers_10snps_38genotypes.vcf is a VCF file with 10 outlier SNPs genotyped in 38 individuals from Maui Nui and Hawaii Island. Structure (.str) files are also provided in addition to VCFs. In all files Population prefixes M=Maui Nui and K=Hawaii Island. Mitochondrial data: Mobula-alfredi_mitogenome_34haplotypes_9sites_min4x.vcf is a VCF file with 9 variant sites across the mitogenome haplotyped in 34 individuals from Maui Nui and Hawaii Island. Mobula-alfredi_mitogenome_34haplotypes_allsites_min4x.fasta is a FASTA file with whole mitogenomes aligned to OP562409 [https://www.ncbi.nlm.nih.gov/nuccore/OP562409]. Sites with less than 4x coverage were masked with Ns. Mobula-alfredi_mitogenome_reference_OP562409.fasta is a FASTA file containing the <em>Mobula alfredi</em> reference mitogenome OP562409 [https://www.ncbi.nlm.nih.gov/nuccore/OP562409].本数据集支撑以下学术论文的研究数据：Whitney JL、Coleman RR、Deakos MH发表于《BMC生态与进化》2023年第23卷第31期的《基因组证据显示夏威夷礁蝠鲼存在小型岛屿居留种群及性别偏向性行为》，DOI: 10.1186/s12862-023-02130-0。 核基因组数据： "Mobula-alfredi_nuclear_reference_RAD_contigs.fasta"为包含359,751个RAD（限制性酶切位点相关DNA，Restriction site-Associated DNA）重叠群的FASTA格式文件，作为基因型与RAD位点进行核基因组比对的参考序列。所有重叠群的首尾均带有GATC酶切位点。 "Mobula-alfredi_nuclear_all_2048snps_38genotypes.vcf"（变异检测格式文件，Variant Call Format，简称VCF）为最终过滤后的单核苷酸多态性（Single Nucleotide Polymorphism，SNP）数据集，包含全部2048个核基因组SNP位点，纳入了来自茂宜岛群和夏威夷岛的38份基因型数据。该2048个SNP位点包含2038个中性SNP与10个离群SNP。 "Mobula-alfredi_nuclear_neutral_2038snps_38genotypes.vcf"为VCF文件，包含来自茂宜岛群和夏威夷岛的38个个体的2038个中性核基因组SNP的基因型数据。 "Mobula-alfredi_nuclear_outliers_10snps_38genotypes.vcf"为VCF文件，包含来自茂宜岛群和夏威夷岛的38个个体的10个离群核基因组SNP的基因型数据。 除VCF文件外，本数据集还提供了Structure格式（.str）文件。所有文件的种群前缀规则为：M代表茂宜岛群，K代表夏威夷岛。 线粒体基因组数据： "Mobula-alfredi_mitogenome_34haplotypes_9sites_min4x.vcf"为VCF文件，包含来自茂宜岛群和夏威夷岛的34个个体的线粒体基因组上的9个变异位点，已完成单倍型分型。 "Mobula-alfredi_mitogenome_34haplotypes_allsites_min4x.fasta"为FASTA格式文件，包含比对至参考序列OP562409（https://www.ncbi.nlm.nih.gov/nuccore/OP562409）的完整线粒体基因组序列。测序覆盖度低于4x的位点均用N字符进行了遮蔽。 "Mobula-alfredi_mitogenome_reference_OP562409.fasta"为FASTA格式文件，包含阿尔弗雷德蝠鲼（Mobula alfredi）的线粒体参考基因组序列OP562409（https://www.ncbi.nlm.nih.gov/nuccore/OP562409）。