Dataset: Population genomics study on the planktonic copepod Pleuromamma xiphias: RADSeq data and metadata (Plankton Population Genetics project)

This dataset includes RADSeq data as well as NCBI Short Read Archive (SRA) BioProject and BioSample accessions and collection metadata from animals collected on Atlantic Meridional Transect 22 (AMT22) in Oct. - Nov. 2012. Field work was conducted on the RRS James Cook cruise JC079. See NCBI GenBank Bioproject PRJNA368728 [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA368728]

The sequences are embargoed until 2019-12-01. Please check back after that date.

README for processed data files associated with the article: “Genetic isolation between populations in distinct pelagic habitats of the oceanic copepod Pleuromamma xiphias” – Authors: Lauren Van Woudenberg, Matthew Iacchei, Jonathon Whitney, Katja T. C. A. Peijnenburg, Erica Goetze (2017?). in preparation for submission to Molecular Ecology.

Data files included in this archive:
(1) Supplementary Table 1. Overview of RADSeq data for all animals included in the study. VanWoudenberg_et_al_PLXI_RADSeq.xlsx

(2) VCF file used in downstream analyses, including mitochondrial clade 3 animals only. 289 total animals included. M4n3_5X_60%indiv_40%miss_final.vcf.

(3) VCF file used in downstream analyses, for analyses regarding mitochondrial clades 2 & 3 and SNP clusters 1 & 2. 112 total animals included. MTclades_M4n3_5X_60%indiv_40%miss.vcf

(4) Summary table and metadata of the sequence files submitted to the NCBI Sequence Read Archive (SRA), with BioProject and BioSample numbers. VanWoudenberg_et_al_2017_SRA_metadata.xlsx