Little Penguin (Eudyptula minor) RADseq illumina sequencing RAW output

PEN_C5N7WANXX_s_7_fastq.txt.gz - compressed RAW read data from illumina Hiseq 2000 generated from a RADseq library digested with Pst1 and Msp1 and sequenced with SE 100bp reads.

PEN_key.txt - contains metadata associated with the RAW data. This is a list of samples including one blank and four duplicate samples which were included in the sequencing. It also includes the unique library barcode for each sample and the location of the sample on the sequencing plate. For other sample related metadata see Supplementary material 1 from publication.

PEN_SNPcallingOUTPUT.zip - Remaining folders and files containing other output associated with SNP calling using the UNEAK Tassel pipeline version 3.0.169. SNP calling was performed using a default error rate, a minor allele frequency cut-off of > 0.05 and a minimum call rate of 80% (Supplementary material S2). Inferred loci with a read depth of<10 or that did not occur in at least 90% of individuals were removed. We only selected a single SNP per fragment and SNPs with a minor allele ratio of < 0.2 were called as homozygotes for the major allele.

hapMap.zip - Post SNP calling files contains genotypes, tag pair sequences (HapMap.fas.txt), number of allele calls for each locus for each sample (HapMap.hmc.txt) and locus specific information (HapMap.hmp.txt)

This project was approved by the Flinders University Ethics Committee (E388) and supported by a scientific permit to conduct the research (Y26040).

Colombelli-Négrel, D., Slender, A., Bradford, T. et al. Subtle genetic clustering among South Australian colonies of little penguins (Eudyptula minor). Conserv Genet 21, 747–756 (2020). https://doi.org/10.1007/s10592-020-01284-4

Related dataset: Genetic data of little penguins collected at eight colonies in South Australia between 2011 and 2014

DOI: https://doi.org/10.25451/flinders.16545477