Data from: Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water ...

• Main Authors: Deagle, Bruce E., Faux, Cassandra, Kawaguchi, So, Meyer, Bettina, Jarman, Simon N.
• Format: Dataset
• Language: English
• Published: Dryad 2015
• Subjects: genotyping-by-sequencing; repetitive DNA; Antarctic; East Antarctica; Southern Ocean; Antarc*; Antarctic Krill; Antarctica; Euphausia superba
• Online Access: https://dx.doi.org/10.5061/dryad.3023m; https://datadryad.org/stash/dataset/doi:10.5061/dryad.3023m

Antarctic krill (Euphausia superba; hereafter krill) are an incredibly abundant pelagic crustacean which has a wide, but patchy, distribution in the Southern Ocean. Several studies have examined the potential for population genetic structuring in krill, but DNA-based analyses have focused on a limited number of markers and have covered only part of their circum-Antarctic range. We used mitochondrial DNA and restriction site-associated DNA sequencing (RAD-seq) to investigate genetic differences between krill from five sites, including two from East Antarctica. Our mtDNA results show no discernible genetic structuring between sites separated by thousands of kilometres, which is consistent with previous studies. Using standard RAD-seq methodology, we obtained over a billion sequences from >140 krill, and thousands of variable nucleotides were identified at hundreds of loci. However, downstream analysis found that markers with sufficient coverage were primarily from multicopy genomic regions. Careful ... : 1 RAD-seq project info V22_Unique_RAD_TagsSequences of the unique RAD tags3a_BSP_pipeline_logParameters used to generate BAM/SAM files4 Variant call format files V2Variant call format files derived from the RAD sequencing5_VCF_extract_filesData extracted from Variant Call Format files6_R_code_count_PCAData and R code for principal component analysis (PCA) of the count data from the ‘Core Dataset’7_MtDNA_sequencesMtDNA sequence data for 142 krill. Two fragments were sequenced: 655 bp Cytochrome c Oxidase subunit I (COI) and 569 bp NADH Dehydrogenase subunit 1 (ND1).Extra_Figure5_SequencesSequences of the RAD tags used to produce trees in Figure 5 of the paper (FASTA format)Figure 5 sequences.zip ...