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". BMC Ecology and Evolution 23, 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 Mobula alfredi reference mitogenome OP562409 [https://www.ncbi.nlm.nih.gov/nuccore/OP562409].