Dataset: Acropora palmata genotypes

Name: Acropora palmata genotypes derived from microsatellite markers collected from multiple reefs in the Florida Keys National Marine Sanctuary from 2005-2014 (Surviving Climate Change project)
Published: 2016-01-22
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:25.1236 E:-80.2973 S:25.0096 W:-80.3748

Project:

RAPID: surviving climate change - the role of acclimatization in reef-building corals (Surviving Climate Change)

Principal Investigator:

Iliana B. Baums (Pennsylvania State University, PSU)

Co-Principal Investigator:

Dana E. Williams (University of Miami Rosenstiel School of Marine and Atmospheric Science, UM-RSMAS)

Contact:

Meghann Durante (Pennsylvania State University, PSU)

Data Manager:

Danie Kinkade (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

BCO-DMO Data Manager:

Danie Kinkade (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

2016.01.22

Version Date:

2016-01-22

Restricted:

Validated:

Yes

Current State:

Preliminary and in progress

Acropora palmata genotypes derived from microsatellite markers collected from multiple reefs in the Florida Keys National Marine Sanctuary from 2005-2014 (Surviving Climate Change project)

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Description

Acropora palmata multilocus genotypes derived from five microsatellite markers.

Methods & Sampling

Adult Acropora palmata colonies were sampled (1 cm^2) with hammer and chisel and tissues were preserved in 96% non-denature Ethanol. DNA was extracted using the DNEasy tissue kit (Qiagen) following manufacturer’s instructions. Two multiplex Polymerase Chain Reactions (PCR) were performed per sample using fluorescently labeled primers to assay five loci containing AAT repeats. These five microsatellite loci have previously been demonstrated to be mendelian and coral-specific using controlled crosses (Baums et al., 2005). PCR products were visualized with an automated sequencer (ABI 3730). An internal size standard (Gene Scan 500-Liz, Applied Biosystems CA) ensured accurate sizing. Electropherograms were analyzed with GeneMapper Software 3.0 (Applied Biosystems, CA). Alleles were scored as PCR product size.

See Baums IB, Hughes CR, Hellberg MH (2005) for details.

Data Processing Description

Electropherograms of microsatellite alleles were scored for allele sizes (basepairs) in Genemapper vers. (Applied Biosystems) and transferred to spreadsheets.

BCO-DMO Processing Notes:

- As per PI, edited column "Region" to the value 'Florida' (previously, this column's valuess
were all set to 'region'). It is expected that the dataset may grow with new regions in the
future.

- Added PI-provided lat/lon for each "Reef" location.

- Each locus allele size was split into separate columns (i.e., allele size 1 was the first 3 digits,
and allele size 2 were the second consecutive digits of a six digit column. These were separated into
separate columns per allele size at each locus).

- Edited loci headers to include the word 'locus' and whether the column held values for
allele size one or two (e.g., column headers for '166' was edited to 'locus_166_allele1' and locus_166_allele2'.

- Edited entire header to BCO-DMO format (e.g., lowercase names, underscores where needed)

- Edited lat/lon values to four decimal precision consistently.

- Edited spaces in reef names to underscores

- Split date into year, month, day fromat

Data Files

File
host_genotype.csv (Comma Separated Values (.csv), 7.71 KB) MD5:eac3312f36cb9f0d77456cde4b1b1fdc Primary data file for dataset ID 636335

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1516763

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Baums_FL_Keys_NMS		2005-05-01	Florida Keys National Marine Sanctuary	Iliana B. Baums (Principal Investigator)	data info

Instruments

Automated DNA Sequencer

Supplied Name: automated sequencer

Supplied Description:

Applied Biosystems 3730 DNA Analyzer

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
region	Region where coral colony was sampled.	dimensionless	region
reef	Reef where coral colony was sampled.	dimensionless	site
colony	Colony identification number.	dimensionless	sample
sample	Sample identification number cosisting of colony identification number and replicate number (A-Z).	dimensionless	replicate
lat	Latitude component of geographic sampling location, where positive is North.	decimal degrees	lat
lon	Longitude component of geographic sampling location, where positive is East.	decimal degrees	lon
ID_database	Baums Database access number	dimensionless	individual
ID_host_clonal	Unique identifier of host genet	dimensionless	individual
locus_166_allele1	Allele size 1 for locus 166.	base pairs	no_bcodmo_term
locus_166_allele2	Allele size 2 for locus 166.	base pairs	no_bcodmo_term
locus_181_allele1	Allele size 1 for locus 181.	base pairs	no_bcodmo_term
locus_181_allele2	Allele size 2 for locus 181.	base pairs	no_bcodmo_term
locus_182_allele1	Allele size 1 for locus 182.	base pairs	no_bcodmo_term
locus_182_allele2	Allele size 2 for locus 182.	base pairs	no_bcodmo_term
locus_192_allele1	Allele size 1 for locus 192.	base pairs	no_bcodmo_term
locus_192_allele2	Allele size 2 for locus 192.	base pairs	no_bcodmo_term
locus_207_allele1	Allele size 1 for locus 207.	base pairs	no_bcodmo_term
locus_207_allele2	Allele size 2 for locus 207.	base pairs	no_bcodmo_term
year	year of sample collection.	YYYY	year
day_local	day of sample collection.	DD	day_local
month_local	month of sample collection.	MM	month_local

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Dataset: Acropora palmata genotypes