Dataset: Goby_Sibship_2018

Name: Genotype data for E. lori individuals sequenced at 71 microsatellites from a 41 km-long transect of the Belize Barrier reef during 2018
Published: 2018-10-22
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.749774.1

Spatial Extent: N:16.981 E:-88.019983 S:16.625067 W:-88.077183

Temporal Extent: 2018 - 2018

Project:

An Integrative Investigation of Population Connectivity Using a Coral Reef Fish (Elacatinus Dispersal I)

Principal Investigator:

Peter Buston (Boston University, BU)

Co-Principal Investigator:

Cassidy C. D'Aloia (Boston University, BU)

BCO-DMO Data Manager:

Mathew Biddle (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2018-10-22

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Genotype data for E. lori individuals sequenced at 71 microsatellites from a 41 km-long transect of the Belize Barrier reef during 2018

Abstract:

Genotype data for E. lori individuals sequenced at 71 microsatellites from a 41 km-long transect of the Belize Barrier reef during 2018.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2018-10-22	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.749774.1	2021-05-20

Description

Genotype data for E. lori individuals sequenced at 71 microsatellites.

Methods & Sampling

We surveyed a 41 km-long transect of the Belize Barrier reef, centered at Carrie Bow Cay, by SCUBA to conduct a genetic parentage study of the reef fish Elactinus lori. To collect settlers, we sampled ~ 100 individuals every kilometer. Individuals were collected from the outsides of sponges using slurp guns and placed them in plastic bags. At the surface, settlers were anesthetized with MS-222. For genetic analyses, DNA was extracted using a HotSHOT protocol; individuals were sequenced at 71 microsatellite loci using a multiplex PCR protocol for targeted amplicon sequencing. For full details see D’Aloia et al. (2018), Marine Ecology Progress Series.

Data Processing Description

Genotype data were analyzed using custom Perl scripts as described in D’Aloia et al. (2016), Conservation Genetics.

BCO-DMO Processing Notes:

Every other column of data was for another allele, therefore we appended "_a" to the first and "_b" to the second column.
renamed the individual_ID column to sample_ID
created two additional columns, sample_id and individual_ID, from the sample_ID column by splitting on the underscore.
mapped sample_id value to latitude and longitude coordinates for the sample_ID.
sorted data on sample_ID and individual_ID.
added BCO-DMO conventional header.

Data Files

File
goby_sibship.csv (Comma Separated Values (.csv), 1.33 MB) MD5:50536b3dafed50dbd4d1048c75bbd7be Primary data file for dataset ID 749774

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1260424

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Belize_2010			lab Buston	Peter Buston (Principal Investigator)	data info

Instruments

Thermal Cycler

Supplied Name: multiplex PCR protocol

Supplied Description:

individuals were sequenced at 71 microsatellite loci using a multiplex PCR protocol for targeted amplicon sequencing.

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
sample_ID	identifier for the sample	unitless	sample
site_id	identifier for the site	unitless	site
individual_ID	identifier for the individual	unitless	sample
lat	approximate latitude in degrees north	decimal degrees	lat
lon	approximate longitude in degrees east	decimal degrees	lon
Elor_564_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_564_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_2975_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_2975_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3015_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3015_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_605_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_605_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_639_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_639_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_7629_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_7629_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_781_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_781_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_8417_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_8417_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_4010_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_4010_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3025_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3025_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_7401_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_7401_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_476_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_476_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_5163_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_5163_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_a618_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_a618_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_2609_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_2609_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_179_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_179_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_13691_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_13691_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_5115_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_5115_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1592_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1592_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1698_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1698_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_5782_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_5782_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_517_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_517_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1687_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1687_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_6561_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_6561_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_483_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_483_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_4648_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_4648_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_5404_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_5404_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_2848_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_2848_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_4362_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_4362_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_6213_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_6213_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_525_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_525_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_905_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_905_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_25488_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_25488_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1556_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1556_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3690_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3690_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_5676_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_5676_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_6085_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_6085_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_6616_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_6616_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_13590_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_13590_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1078_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1078_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_5726_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_5726_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_7548_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_7548_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_6357_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_6357_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_976_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_976_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3103_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3103_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_8832_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_8832_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1161_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1161_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1408_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1408_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_12215_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_12215_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3569_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3569_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_9671_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_9671_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_8933_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_8933_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3013_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3013_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_6056_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_6056_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_10743_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_10743_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_6856_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_6856_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_2023_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_2023_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3612_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3612_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3686_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3686_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3843_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_3843_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_4139_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_4139_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_7908_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_7908_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_533_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_533_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1079_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_1079_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_4622_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_4622_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_8200_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_8200_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_8924_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_8924_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_503_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Elor_503_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Goby14528_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Goby14528_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Goby21378_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Goby21378_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Goby25362_a	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term
Goby25362_b	field name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele	unitless	no_bcodmo_term

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Dataset: Goby_Sibship_2018