Dataset: Population genetic surveys of Zostera marina
Deployment: BML_Stachowicz

A re-sampling of historical population genetic surveys of Zostera marina from Bodega, Tomales, and San Francisco Bays USA

Principal Investigator:

John J. Stachowicz (University of California-Davis, UC Davis)

Co-Principal Investigator:

Richard K. Grosberg (University of California-Davis, UC Davis)

Susan L. Williams (University of California-Davis BML, UC Davis-BML)

Contact:

Laura K. Reynolds (University of California-Davis, UC Davis)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Connecting genetic diversity to ecosystem functioning: links between genetic diversity, relatedness and trait variation in a seagrass community (Genetic Div to Ecosys Functioning)

Current State:

Final no updates expected

Version:

12 Oct 2016

Version Date:

2016-10-12

Data URL:

https://www.bco-dmo.org/dataset-deployment/661449/data

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Description

A re-sampling of historical population genetic surveys of Zostera marina from Bodega (BB), Tomales (TB), and San Francisco Bays (SFB) USA. Plant (Zostera marina) samples were collected from Bodega Bay, Tomales Bay, and San Francisco Bay in 2013. DNA was extracted and amplified in the Stachowicz and Grosberg labs at UCDavis, and fragments were analyzed at the UCDavis core facility during 2014-2015. Data are presented as number of base pairs.

Methods & Sampling

Dataset acquisition description

Both sampling and analyses are described in the manuscript in press in the journal Heredity, titled "Temporal stability in patterns of genetic diversity and structure of a marine foundation species (Zostera marina)".

Briefly, we re-sampled Z. marina populations previously described genetically in the literature. Because the goal of sampling these populations was to compare changes over time within each region, we designed the re-sampling to match the previously published studies as closely as possible. Consequently, sampling schemes (haphazard collection (SFB) vs. quadrat sampling (TB and BB)) differed between regions. DNA from all samples was analyzed at 12 microsatellite loci.

Data Processing Description

Dataset Processing Description

We amplified 12 previously characterized microsatellite loci (CT12, CT19 (Reusch 2000), CT3, GA2, GA3 (Reusch et al. 1999), CL32 Contig 2, ZMC 12075, ZMC 13053, ZMC 19017, (Oetjen & Reusch 2007), CL 559 Contig 1, CL172 Contig 1, ZMC 19062 (Oetjen et al. 2010)). We analyzed fragments on an ABI 3010XL at the UC Davis DNA sequencing facility, and visualized the fragments using STRand software (Toonen & Hughes 2001).

BCO-DMO Processing:
- modified parameter names to conform with BCO-DMO naming conventions; appended "a1" (allele 1) or "a2" (allele 2).
- added columns containing the full name/meaning for region, meadow, and tidal height codes.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1234345	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: ABI 3010XL

Supplied Description:

We analyzed fragments on an ABI 3010XL at the UC Davis DNA sequencing facility, and visualized the fragments using STRand software (Toonen & Hughes 2001).

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

Supplied Name	Supplied description	Supplied Units	Standard Name
region_code	Code assigned to region where samples were collected	unitless	site
region	Region where samples were collected	unitless	site
meadow_code	Code assigned to meadow within the region where samples were collected	unitless	site
meadow	Meadow within the region where samples were collected	unitless	site
tidal_height_code	Code assigned to tidal height. NA = Not applicable because samples were collected over a gradient	unitless	site_descrip
tidal_height	Description of tidal height of area sampled	unitless	site_descrip
CL32_Con2_a1	Locus CL32 Contig 2 (Oetjen & Reusch 2007 Molecular Ecology); allele 1; reported in number of base pairs.	unitless	no_bcodmo_term
CL32_Con2_a2	Locus CL32 Contig 2 (Oetjen & Reusch 2007 Molecular Ecology); allele 2; reported in number of base pairs.	unitless	no_bcodmo_term
CL559_Con1_a1	Locus CL 559 Contig 1 (Oetjen et al. 2010 Marine Biology); allele 1; reported in number of base pairs.	unitless	no_bcodmo_term
CL559_Con1_a2	Locus CL 559 Contig 1 (Oetjen et al. 2010 Marine Biology); allele 2; reported in number of base pairs.	unitless	no_bcodmo_term
ZMC12075_a1	Locus ZMC 12075 (Oetjen & Reusch 2007 Molecular Ecology); allele 1; reported in number of base pairs.	unitless	no_bcodmo_term
ZMC12075_a2	Locus ZMC 12075 (Oetjen & Reusch 2007 Molecular Ecology); allele 2; reported in number of base pairs.	unitless	no_bcodmo_term
ZMC13053_a1	Locus ZMC 13053 (Oetjen & Reusch 2007 Molecular Ecology); allele 1; reported in number of base pairs.	unitless	no_bcodmo_term
ZMC13053_a2	Locus ZMC 13053 (Oetjen & Reusch 2007 Molecular Ecology); allele 2; reported in number of base pairs.	unitless	no_bcodmo_term
CL172_Con1_a1	Locus CL172 Contig 1 (Oetjen et al. 2010 Marine Biology); allele 1; reported in number of base pairs.	unitless	no_bcodmo_term
CL172_Con1_a2	Locus CL172 Contig 1 (Oetjen et al. 2010 Marine Biology); allele 2; reported in number of base pairs.	unitless	no_bcodmo_term
ZMC19017_a1	Locus ZMC 19017 (Oetjen & Reusch 2007 Molecular Ecology); allele 1; reported in number of base pairs.	unitless	no_bcodmo_term
ZMC19017_a2	Locus ZMC 19017 (Oetjen & Reusch 2007 Molecular Ecology); allele 2; reported in number of base pairs.	unitless	no_bcodmo_term
ZMC19062_a1	Locus ZMC 19062 (Oetjen et al. 2010 Marine Biology); allele 1; reported in number of base pairs.	unitless	no_bcodmo_term
ZMC19062_a2	Locus ZMC 19062 (Oetjen et al. 2010 Marine Biology); allele 2; reported in number of base pairs.	unitless	no_bcodmo_term
CT12_a1	Locus CT12 (Reusch 2000 Molecular Ecology); allele 1; reported in number of base pairs.	unitless	no_bcodmo_term
CT12_a2	Locus CT12 (Reusch 2000 Molecular Ecology); allele 2; reported in number of base pairs.	unitless	no_bcodmo_term
CT19_a1	Locus CT19 (Reusch 2000 Molecular Ecology); allele 1; reported in number of base pairs.	unitless	no_bcodmo_term
CT19_a2	Locus CT19 (Reusch 2000 Molecular Ecology); allele 2; reported in number of base pairs.	unitless	no_bcodmo_term
CT3_a1	Locus CT3 (Reusch et al. 1999 Marine Biology); allele 1; reported in number of base pairs.	unitless	no_bcodmo_term
CT3_a2	Locus CT3 (Reusch et al. 1999 Marine Biology); allele 2; reported in number of base pairs.	unitless	no_bcodmo_term
GA2_a1	Locus GA2 (Reusch et al. 1999 Marine Biology); allele 1; reported in number of base pairs.	unitless	no_bcodmo_term
GA2_a2	Locus GA2 (Reusch et al. 1999 Marine Biology); allele 2; reported in number of base pairs.	unitless	no_bcodmo_term
GA3_a1	Locus GA3 (Reusch et al. 1999 Marine Biology); allele 1; reported in number of base pairs.	unitless	no_bcodmo_term
GA3_a2	Locus GA3 (Reusch et al. 1999 Marine Biology); allele 2; reported in number of base pairs.	unitless	no_bcodmo_term

Database

Contribute Data

Dataset: Population genetic surveys of Zostera marina
Deployment: BML_Stachowicz

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Population genetic surveys of Zostera marinaDeployment: BML_Stachowicz

Dataset acquisition description

Dataset Processing Description

Dataset: Population genetic surveys of Zostera marina
Deployment: BML_Stachowicz