Population genomics of shy and white-capped albatrosses using DArTseq

This dataset includes population genomic data for shy albatross (Thalassarche cauta) and white-capped albatross (T. steadi). DNA samples from 6 breeding colonies (3 per species) were analysed using DArTseq (Diversity Arrays Technology reduced representation sequencing method: https://www.diversityarrays.com/) to generate single nucleotide polymorphism (SNP) genotypes for each sample. The dataset includes raw DNA sequence data, analysed data, and details of workflows used for analyses. Raw DNA sequence data are also available from NCBI SRA [accession numbers to be added once finalised].

This research was funded by Australia from its voluntary contribution to the Agreement on the Conservation of Albatrosses and Petrels. Data analyses were supported by Galaxy Australia, a service provided by Australian BioCommons and its partners (Galaxy Australia receives NCRIS funding through Bioplatforms Australia, as well as The University of Melbourne and Queensland Government RICF funding) and by use of the Nectar Research Cloud, a collaborative Australian research platform supported by the NCRIS-funded Australian Research Data Commons.

Data and metadata files associated with the project "Population genomics of Shy and White-capped Albatrosses" Reduced representation DNA sequencing data and associated population genomics analyses for shy and white-capped albatross. 1. Sample metadata: details of 90 shy and white-capped albatross samples used in this study. These samples are also included as BioSamples under NCBI BioProject PRJNA1467377: - Thalassarche_sample_metadata_tableS1.csv 2. DNA sequencing library metadata: details of 112 DNA libraries generated and sequenced during this study by Diversity Arrays Technology (https://www.diversityarrays.com/) using the DArTseq method. Duplicate libraries were included for 22 of the 90 samples to provide technical replicates: - Thalassarche_dartseq_library_metadata.csv 3. Raw DNA sequence data files. 112 files: one fastq file per DNA sequence library. Filenames include library IDs and can be matched to sample IDs using the library metadata file. Also includes metadata files from Diversity Arrays Technology.

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DArT.txt # readme file from Diversity Arrays Technology - targets_HWMGCDRXY_1.csv # metadata file from Diversity Arrays Technology 4. Output files from Diversity Arrays Technology DArTseq service, including SilicoDArT and SNP markers identified and genotyped from the raw sequence data, using DArT's proprietary pipeline. Provided here for reference, these were not used for population genomic analyses in this study: - Report_DThal21-6645_SilicoDArT_1.csv - Report_DThal21-6645_SNP_2.csv - Report_DThal21-6645_SNP_mapping_2.csv 5. Galaxy Australia Stacks2 analysis history folder. This history is also available from https://usegalaxy.org.au/u/annamac/h/shy-and-white-capped-albatross-snp-calling-stacks2-reference-based: - Shy-and-white-capped-albatross-SNP-ID---stacks2-reference-based.tar.gz 6. Stacks2 output file in vcf format, including SNP markers identified and genotyped from the raw sequence data: - Thalassarche-SNPs-stacks2.vcf 7. R code and sample metadata file used to filter SNP markers and conduct population genomics analyses, using the vcf file above as the input dataset: - Thalassarche-dartR-code_260327.Rmd - Thalassarche_sample_metadata_dartr.csv 8. R output file including autosomal SNP genotypes post-filtering. These are the SNP genotype data used for population genomic analyses in this study. This .rds file can be viewed in R (code included in .Rmd file above): - stacks-filtered-snps.rds 9. R output files including Z chromosome-linked SNP genotypes and Gametolog SNP genotypes post-filtering. Provided here for information, these were not used for population genomic analyses in this study. These .rds files can be viewed in R (code included in .Rmd file above): - Thalassarche-Z-linked-SNPs.rds - Thalassarche-gametolog-SNPs.rds