Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

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

Please refer to the paper for methodological details. If you have further questions, please contact the corresponding author (Dr. Erica Goetze): egoetze[at]hawaii[dot]edu.

From the cruise report:
Sample collection. Plankton samples were collected with 0.71m diameter bongo nets (200, 333 µm), and with an RMT1 midwater trawl (333 µm) that has a nominal mouth area of 1m2. A total of 50 plankton tows were conducted along the cruise leg (Table 1), with 35 tows conducted using the bongo and 14 samples collected with the RMT net. The bongo tows were oblique tows that sampled from between 211 to 488 m depth and the surface (324m average maximum depth of tow). The bongo samples will be used for quantitative estimates of animal abundance along the cruise leg (target species only, tows conducted with timedepth-recorder and flowmeter). The RMT tows were also oblique tows that sampled between 62 to 216 m depth and the surface (153 m average maximum depth of tow). All tows except one (station 42) were conducted at night, in order to efficiently sample the migratory community.

Sample handling and preservation. All plankton from the 200 µm mesh bongo net was preserved immediately in 100% ethyl alcohol for use in molecular studies, including DNA sequencing and microsatellite genotyping (and possibly RAD tag sequencing), in addition to estimates of abundance of target species. Plankton material from the 333 µm mesh bongo net and the RMT net was sorted live immediately following collection, and animals were individually identified, and preserved in acetone, RNALater, cryopreserved, and in some cases used for live imaging prior to preservation. These animals will be used for molecular, genomic and transcriptomic analyses. Both RNA/DNA ratios and prosome length - dry weight relationships will be used as measures of animal condition in copepods. In total, over 17,000 animals from 40 target species were individually sorted and preserved for this panel of measurements. Following live sorting and imaging of the 333 µm samples, the remaining plankton was preserved either in 4% buffered formalin or 100% ethyl alcohol for morphological studies.

SEQUENCE DATA FILES
Illumina HiSeq reads are available NCBI Sequence Read Archive (SRA). Libraries were prepared following the ezRAD protocol (Toonen et al. 2013). Sequences from Illumina HiSeq 2500, with quality trimming and adaptor removal using TrimGalore (as follows).

#ADAPTERS
#Illumina TruSeq HT dual-indexed Adapters (96 barcode combinations)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG #Read1 w/ 8 digit wildcard i7 #barcode
GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTNNNNNNNNGTGTAGATCTCGGTGGTCGCCGTATCATT  #Read2 w/ wildcard i5 barcode (reverse complemented)

#TrimGalore Command
#first make directory for cleaned files
mkdir cleaned_for_stacks

##FOR R1 loop for trim_galore##
declare -a TEST=(site09_12 site09_15 site09_18 site09_21 site09_24 site09_13 site09_16 site09_19 site09_22 site09_14 site09_17 site09_20 site09_23)

for i in "${TEST[@]}"; do perl ~/ddocent/trim_galore —-phred33 —-dont_gzip -a gatcggaagagcacacgtctgaactccagtcacnnnnnnnnatctcgtatgccgtcttctgcttg --stringency 5 -e 0.1 -r1 100 --output_dir ./cleaned_for_stacks $i.R1.fq; done

##FOR R2 loop for trim_galore##
declare -a TEST=(site09_12 site09_15 site09_18 site09_21 site09_24 site09_13 site09_16 site09_19 site09_22 site09_14 site09_17 site09_20 site09_23)

for i in "${TEST[@]}"; do perl ~/ddocent/trim_galore —-phred33 —-dont_gzip -a gatcggaagagcgtcgtgtagggaaagagtgtnnnnnnnngtgtagatctcggtggtcgccgtatcatt --stringency 5 -e 0.1 -r1 100 --output_dir ./cleaned_for_stacks $i.R2.fq; done

Contact: Erica Goetze for any questions, or for subsequent use of these data.

BCO-DMO Processing Notes:
added conventional header with dataset name, PI name, version date
modified parameter names to conform with BCO-DMO naming conventions
combined SRA metadata with collection information
converted latitude and longitude to decimal degrees
added links to NCBI GenBank BioProject and BioSample pages

Description from NSF award abstract:
Marine zooplankton show strong ecological responses to climate change, but little is known about their capacity for evolutionary response. Many authors have assumed that the evolutionary potential of zooplankton is limited. However, recent studies provide circumstantial evidence for the idea that selection is a dominant evolutionary force acting on these species, and that genetic isolation can be achieved at regional spatial scales in pelagic habitats. This RAPID project will take advantage of a unique opportunity for basin-scale transect sampling through participation in the Atlantic Meridional Transect (AMT) cruise in 2014. The cruise will traverse more than 90 degrees of latitude in the Atlantic Ocean and include boreal-temperate, subtropical and tropical waters. Zooplankton samples will be collected along the transect, and mitochondrial and microsatellite markers will be used to identify the geographic location of strong genetic breaks within three copepod species. Bayesian and coalescent analytical techniques will test if these regions act as dispersal barriers. The physiological condition of animals collected in distinct ocean habitats will be assessed by measurements of egg production (at sea) as well as body size (condition index), dry weight, and carbon and nitrogen content. The PI will test the prediction that ocean regions that serve as dispersal barriers for marine holoplankton are areas of poor-quality habitat for the target species, and that this is a dominant mechanism driving population genetic structure in oceanic zooplankton.

Note: This project is funded by an NSF RAPID award. This RAPID grant supported the shiptime costs, and all the sampling reported in the AMT24 zooplankton ecology cruise report (PDF).

Online science outreach blog at: https://atlanticplankton.wordpress.com