Dataset: Acropora palmata mutations

Name: Mutations at microsatellite loci of Acropora palmata in the Caribbean and North-West Atlantic from 2015-2016 (Coral Hybridization project)
Published: 2017-10-19
Keywords: biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.666321.2

Spatial Extent: N:26.7075 E:-64.677 S:12.0831 W:-88.199

Project:

Collaborative research: Is hybridization among threatened Caribbean coral species the key to their survival or the harbinger of their extinction? (Coral Hybridization)

Principal Investigator:

Iliana B. Baums (Pennsylvania State University, PSU)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2017-10-19

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Mutations at microsatellite loci of Acropora palmata in the Caribbean and North-West Atlantic from 2015-2016 (Coral Hybridization project)

Abstract:

Somatic mutations that occurred at 5 microsatellite loci in Acropora palmata collected throughout the Caribbean. These data were deposited in DRYAD: http://dx.doi.org/10.5061/dryad.f6600 and published in the paper Devlin-Durante et al, Mol Ecol. (2016).

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2017-10-19	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.666321.2	2021-02-24

Methods & Sampling

Adult Acropora palmata colonies were sampled (1 cm2) 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.

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:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- nd (no data) was entered into all blank cells
- replaced spaces and / with underscores
- sorted records by region

VERSIONS: 2017-10-26: Replaced version 1 (2016-11-30) with version 2 (2017-10-19). Some latitudes and longitudes were added to allow visualization of the data on the mapserver.

Data Files

File
Apalmata_mutations_sort.csv (Comma Separated Values (.csv), 25.80 KB) MD5:4bd4ffe8e62b446059d18a1613959e94 Primary data file for dataset ID 666321

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1537959

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Baums_Carib		2015-10-01	Penn_State_U		data info

Instruments

Automated DNA Sequencer

Supplied Name: automated sequencer (ABI 3730)

Supplied Description:

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.

Thermal Cycler

Supplied Name: ABI 3730

Supplied Description:

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. 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. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
ancestral_allele_2	the second ancestral alleles of the gene	basepairs	no_bcodmo_term
reef	the sampling reef	unitless	site
locus	the microsatellite locus that had a mutated allele (166; 181; 182; 192;207)	basepairs	no_bcodmo_term
ancestral_allele_1	the first ancestral alleles of the genet	basepairs	no_bcodmo_term
full_mutation	Sometimes ancestral alleles were no longer detected (full mutations)	unitless	no_bcodmo_term
region	sampling region	unitless	region
mutational_change_allele_4_bp	Mutational Change Allele 4 (bp) The mutational change (in bp) from the ancestral alleles to the new allele is given.	basepairs	no_bcodmo_term
mutational_change_allele_3_bp	Mutational Change Allele 3 (bp) The mutational change (in bp) from the ancestral alleles to the new allele is given.	basepairs	no_bcodmo_term
sample_count_for_genet	Genets had from 2 to 94 samples (sample count for genet)	samples	no_bcodmo_term
genet_id	Genets are identified by their Genet ID	unitless	no_bcodmo_term
origin_allele_4	designation of origin of how additional allele 4 arose (i.e from ancestral Allele 1 or Allele 2). Sometimes one ancestral allele mutated twice giving rise to Alleles 3 and 4.	basepairs	no_bcodmo_term
origin_allele_3	designation of origin of how additional allele 3 arose (i.e from ancestral Allele 1 or Allele 2). Sometimes one ancestral allele mutated twice giving rise to Alleles 3 and 4.	basepairs	no_bcodmo_term
mutation_step_allele_3	Count of mutation steps from ancestral allele to mutated allele. Each mutation step is an addition or loss of 3 bp.	basepairs	no_bcodmo_term
mutation_step_allele_4	Count of mutation steps from ancestral allele to mutated allele. Each mutation step is an addition or loss of 3 bp.	basepairs	no_bcodmo_term
database_id	Baums lab sample Database ID (unique for each sample)	unitless	sample
allele_3	any additional alleles detected	basepairs	no_bcodmo_term
allele_4	any additional alleles detected	basepairs	no_bcodmo_term
lon	longitude; east is positive	decimal degrees	lon
lat	latitude; north is positive	decimal degrees	lat

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Dataset: Acropora palmata mutations