Dataset: Data from: Iacchei, M., E. Butcher, E. Portner, Goetze, E. (in press) It’s about time: Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices.

This dataset consists of mitochondrial sequence data and specimen information for two species of copepods, Haloptilus longicornis and Pleuromamma xiphias, collected at an open ocean time series site in the North Pacific Subtropical Gyre (station ALOHA, 22.45N, 158W) during 11 of the routine Hawai'i Ocean Time-series (HOT) research cruises from September of 2012 to October of 2013 (HOT-246 to HOT-256). Data for Haloptilus longicornis include a 546 base-pair fragment of mitochondrial cytochrome c oxidase subunit II for each of 483 individuals (mean of 44 animals per cruise). Data for Pleuromamma xiphias include a 551 base-pair fragment of mitochondrial cytochrome c oxidase subunit I for each of 510 individuals (mean of 46 animals per cruise). Information is also provided on the HOT cruise number, date, and specific tow from which each individual was collected. Life stage and sex of each animal are also noted when identifiable

These data are associated with the forthcoming publication:
Iacchei, M., E. Butcher, E. Portner, Goetze, E. (in press) It’s about time: Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices.  Limnology and Oceanography  

The unique haplotypes in these data are also available under NCBI accession numbers KY560470 - KY560514 [Haloptilus longicornis], KY560515 - KY560565 [Pleuromamma xiphias].

The following files have been included in this dataset (note that the sequence IDs in these files differ from the NCBI sequence IDs):
HOT-HALO.fasta: A fasta-formatted text file containing sequences for a portion of the mitochondrial cytochrome c oxidase subunit II gene (COII; 546 bp) for 483 Haloptilus longicornis individuals collected at Station ALOHA.

HOT-PLXI.fasta: A fasta-formatted text file containing sequences for a portion of the mitochondrial cytochrome c oxidase subunit I gene (COI; 551 bp) for 510 Pleuromamma xiphias individuals collected at Station ALOHA.

HALO.csv and PLXI.csv: Converted to csv from an Excel file consisting of one worksheet for Haloptilus longicornis and one worksheet for Pleuromamma xiphias. In each worksheet, column headings designate:
sample_id: the sample ID number associated with the original organism collected, DNA extraction, and PCR amplification.
sequence_id: the sample ID number associated with sequences analysed for the project.
genus: Genus of the collected organism.
species: Species of the collected organism.
cruise: The cruise number for the Hawai'i Ocean Time Series (HOT) cruise on which the specimen was collected.
tow: The net tow number on which the specimen was collected.
collection_date: The date on which the specimen was collected, formatted as yyyy-mm-dd.
stage_sex: The life stage (Copepodite or Adult) of the individual, and the sex (Copepodite, Female, Male).
stage: The life stage (Copepodite or Adult) of the individual. Column added by BCO-DMO from the original stage_sex column for ease of use.
sex: The sex (Copepodite, Female, or Male) of the individual. Column added by BCO-DMO from the original stage_sex column for ease of use.
mtCO*_sequence: The mtDNA sequence (COII for Haloptilus longicornis; COI for Pleuromamma xiphias) associated with that individual. This sequence matches the sequence associated with the Sequence ID number in the respective fasta file.