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Data server object:  dataset4_Krug_2012




  
    Philine spp. collection data and NCBI accessions links for 16S haplotype sequences from Krug et al (2012) Biol. Invasions (PLDvFST project)
    
  
  
    
    

Philine spp. collection data and NCBI accessions links for 16S haplotype sequences from Krug et al (2012) Biol. Invasions (PLDvFST project)

Website: https://www.bco-dmo.org/dataset/682248
Data Type: Other Field Results
Version:
Version Date: 2017-01-26

Project
» Quantifying larval behavior to reconcile genetic connectivity with biophysical model predictions (PLDvFST)
ContributorsAffiliationRole
Krug, PatrickCalifornia State University Los Angeles (Cal State LA)Principal Investigator
Copley, NancyWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager


Dataset Description

Sequences were generated for 10 Philine species sampled globally. Collection information, accessions and links to the GenBank pages are provided.

Detailed collection information and archival data for specimens of Philine spp.  ID codes are in-house labels. National Center for Bioinformatics (NCBI) accession numbers for unique 16S haplotypes are listed with a given haplotype. Museum voucher numbers are for the California Academy of Sciences (CASIZ), British Museum of Natural History (BMNH), or Auckland War Memorial Museum (AK). CA = California; OR = Oregon, U.S.A. Samples in parentheses were positively identified in the present study. Samples are from invaded sites are shown under 'invasion' column. Dashes indicate specimens that were not available for accessioning in a museum collection. 'Additional specimens' denotes vouchered material that was not sequenced in the present study.

Related Reference: Krug, P.J., Asif, J., Baeza, I., Morley, M., Blom, W., and T. Gosliner. 2012. Molecular identification of two species of the carnivorous sea slug Philine, invaders of the U.S. west coast. Biological Invasions, 14: 2447-2459. doi: 10.1007/s10530-012-0242-9.


Acquisition Description

Purified PCR products were directly cycle-sequenced in both directions using PCR primers and Big Dye Terminator 3.1 Cycle Sequencing chemistry at the High-Throughput Genomics Unit, University of Washington or on an ABI PrismTM 377 DNA Sequencer (Applied Biosystems).  Chromatograms were edited and primer sequences removed in GeneiousPro 4.8 software.

For full details on sampling and analytical methodology, see Krug et al (2012).


Processing Description

Sequences were edited to remove primer sequences.

BCO-DMO Processing notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- added links to NCBI accessions
- spelled out genus names
- replaced hyphens with 'did_not_amplify'


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Parameters

ParameterDescriptionUnits
specimen_idin-house specimen identifier unitless
speciesspecimen identifier code unitless
invasionwhether the specimens were from an invaded site or not unitless
haplotype_16Shaplotype 16S identifier unitless
accession_16S16S gene GenBank accession number unitless
accession_16S_linklink to 16S gene GenBank accession page unitless
vouchermuseum voucher number: CASIZ = California Academy of Sciences; BMNH = British Museum of Natural History; AK = Auckland War Memorial Museum unitless
collection_localityplace of collection unitless
date_collecteddate collected unitless
collectorcollector's name unitless


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Instruments

Dataset-specific Instrument Name
Generic Instrument Name
Automated DNA Sequencer
Dataset-specific Description
Big Dye Terminator 3.1 Cycle Sequencing chemistry at the High-Throughput Genomics Unit, University of Washington or on an ABI PrismTM 377 DNA Sequencer (Applied Biosystems).
Generic Instrument 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.

Dataset-specific Instrument Name
Generic Instrument Name
PCR Thermal Cycler
Generic Instrument Description
General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. (adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)


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Deployments

Krug_lab

Website
Platform
Cal State LA
Start Date
2011-09-01
End Date
2016-07-31
Description
Studies on ecology and evolution of marine animals, focusing on larval stages.


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Project Information

Quantifying larval behavior to reconcile genetic connectivity with biophysical model predictions (PLDvFST)

Coverage: Florida and Caribbean


Dispersal is a critical life-history trait linking ecological and evolutionary processes. Transport of planktonic larvae affects colonization success and population persistence for benthic animals, and influences genetic subdivision of populations, local adaptation, and speciation. However, recent studies question the long-held assumption that pelagic larval duration (PLD) determines how far larvae are advected. This has applied significance, as oceanographic models used to predict exchange among marine protected areas often use PLD as the key larval parameter. The investigators' data for Caribbean gastropods show genetic breaks that are not congruent with model predictions, and levels of structure that are inconsistent with larval lifespan, highlighting a need for new theory. This research will integrate molecular and larval ecology to test the link between dispersal and larval duration in a phylogenetic framework, and determine whether Individual Based Models (IBMs) accurately predict exchange for Caribbean reef ecosystems. The PI will collect multi-locus genetic data and quantify larval behavior for 14 related, ecologically similar species of sea slugs with PLDs from 0-30 days. The PI predicts that larval behavior explains why some species are under- or over-dispersed relative to their PLD; this work will reveal key parameters needed for biophysical-coupling models to predict connectivity for coastal invertebrates. The proposal will address 3 inter-related objectives: (1) Are genetic connectivity estimates from mtDNA and nuclear markers congruent, and consistent with model predictions? Data for mitochondrial and nuclear loci will be used to test for selection on mtDNA, estimate rates of gene flow and times of divergence, and assess levels of connectivity within each species. Matrices of model-predicted exchange will be compared with genetic similarity matrices to test whether breaks in gene flow occur where predicted. (2) Are genetic connectivity and PLD correlated? More broadly, the PI will test the assumption that larval period determines dispersal, using comparative methods in a phylogenetic framework to correct for effects of relatedness among species. The PI will compare models of trait evolution with Bayesian Markov chain Monte Carlo (MCMC) methods to determine if gene flow is correlated or uncorrelated with PLD, using a molecular phylogeny and multi-locus genetic data. (3) Does larval behavior explain genetic structure in species with long PLD? At least two of the focal species selected for this study are under-dispersed, with genetically isolated demes despite a 30-day PLD. Conversely, at least one short-PLD species has no genetic structure over large regions of the Caribbean. The PI will build on past work quantifying larval behavior to ask if species-specific differences in larval swimming facilitate local retention, making species deviate from expected connectivity patterns. The PI will also test whether pre-competent larvae respond to habitat cues in a way that influences dispersal, as occurs in fish. This work will reconcile life-history theory, oceanographic models, and genetics by mechanistically explaining breaks in connectivity; the results will deepen our understanding of how larval behavior can determine the pace of divergence among populations.  


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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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This document is created by info v 4.1f 5 Oct 2018 from the content of the BCO-DMO metadata database.    2020-02-29  08:22:54