Dataset: Glaucus species COI and 16S positions and bases

Name: Glaucus Study II: locality data, GenBank and museum voucher numbers, with molecular synapomorphies from a global sample set (Neuston Phylogeny project)
Published: 2014-02-21
Keywords: oceans

Cite This Dataset

Project:

Community Phylogeny and Global Phylogeography of the Neuston (Neuston Phylogeny)

Principal Investigator:

Diarmaid O'Foighil (University of Michigan)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI)

Version:

2014-02-21

Version Date:

2014-02-21

Validated:

Yes

Current State:

Final no updates expected

Glaucus Study II: locality data, GenBank and museum voucher numbers, with molecular synapomorphies from a global sample set (Neuston Phylogeny project)

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Description

These samples are part of a study that suggests the premise that continents like Europe and the Americas cause barriers to gene flow for the nudibranchs found in the uppermost layer (neuston) of the ocean. The nudibranch Glaucus atlanticus, found in all oceans, was studied to assess the genetic differentiation of mulitiple specimens from a global sampling effort.

This dataset contains molecular diagnostic traits (synapomorphies) for Glaucus atlanticus and Glaucus marginatus morphospecies in mitochondrial 16S rRNA and COI obtained with CAOS-analyzer. Both the position in the alignments and the base letter are included. Only diagnostics with values of 1.00 are included (pure diagnostics). Note that Churchill et al. (2013) were unsuccessful in obtaining mt COI genotyes for Glaucus bennettae sp. nov. [Appendix I, from....????]

Methods & Sampling

Glaucus atlanticus specimens were collected between 2006 and 2012 either from the beach or in the open ocean from neuston tows. The specimens were then preserved in 95% ethanol and identified. Where possible, 15 - 20 individuals were chosen from each ocean gyre for genetic analysis. Genomic DNA was extracted and mitochondrial cytochrome oxidase I (COI) was amplified using the universal primers LCO1490 and HCO2198 using the general PCR protocol. Details of the extraction, amplification and analyses can be found in the methods section of the Churchill (2014).

Data Processing Description

See [reference?] for methodology.

Relevant References:

Celia K. C. Churchill, Ángel Valdés and Diarmaid Ó Foighil (2014) Afro-Eurasia and the Americas present barriers to gene flow for the cosmopolitan neustonic nudibranch Glaucus atlanticus. Marine Biology DOI 10.1007/s00227-014-2389-7.

Celia K. C. Churchill, Alvin Alejandrino, A´ngel Valde´s and Diarmaid O´ Foighil (2013) Parallel changes in genital morphology delineate cryptic diversification of planktonic nudibranchs. Proc R Soc B:280: 20131224.http://dx.doi.org/10.1098/rspb.2013.1224.

Celia K. C. Churchill, Ellen E. Strong and Diarmaid O´Foighil (2011) Hitchhiking juveniles in the rare neustonic gastropod Recluzia cf. jehennei (Janthinidae). Journal of Molluscan Studies (2011) 0: 1-4. doi:10.1093/mollus/eyr020

Data Files

File
Glaucus_bases.csv (Comma Separated Values (.csv), 9.27 KB) MD5:599c30a2554653803f48170d45e4beb4 Primary data file for dataset ID 505436

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0850625

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
OFoighil_2014			OFoighil_2014	Diarmaid O'Foighil (Principal Investigator)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Automated Sequencer

Supplied Description:

ABI 3730xl (Applied Biosystems, Inc.)

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
species	species of nudibranch Glaucus	unitless	species
marker	genetic component analysed	unitless	no_bcodmo_term
position	position of sequence alignments	unitless	no_bcodmo_term
base	genetic base letter: A=adenine; T=thymine; C=cytosine; G=guanine	unitless	no_bcodmo_term

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Database

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Dataset: Glaucus species COI and 16S positions and bases