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

Website: https://www.bco-dmo.org/dataset/749774
Version: 1
Version Date: 2018-11-19

Project
» An Integrative Investigation of Population Connectivity Using a Coral Reef Fish (Elacatinus Dispersal I)
ContributorsAffiliationRole
Buston, PeterBoston University (BU)Principal Investigator
D'Aloia, Cassidy C.Boston University (BU)Co-Principal Investigator
Biddle, MathewWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Table of Contents


Coverage

Spatial Extent: N:16.981 E:-88.019983 S:16.625067 W:-88.077183
Temporal Extent: 2018 - 2018

Dataset Description

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


Acquisition Description

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. (in press), Marine Ecology Progress Series.


Processing Description

Genotype data were analyzed using custom Perl scripts as described in D’Aloia et al. (2017), 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.

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Related Publications

D’Aloia, C. C., Bogdanowicz, S. M., Harrison, R. G., & Buston, P. M. (2016). Cryptic genetic diversity and spatial patterns of admixture within Belizean marine reserves. Conservation Genetics, 18(1), 211–223. doi:10.1007/s10592-016-0895-5
D’Aloia, C., Xuereb, A., Fortin, M., Bogdanowicz, S., & Buston, P. (2018). Limited dispersal explains the spatial distribution of siblings in a reef fish population. Marine Ecology Progress Series. doi:10.3354/meps12792

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Parameters

ParameterDescriptionUnits
sample_IDidentifier for the sample unitless
site_ididentifier for the site unitless
individual_IDidentifier for the individual unitless
latapproximate latitude in degrees north decimal degrees
lonapproximate longitude in degrees east decimal degrees
Elor_564_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_564_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_2975_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_2975_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3015_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3015_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_605_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_605_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_639_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_639_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_7629_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_7629_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_781_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_781_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_8417_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_8417_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_4010_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_4010_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3025_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3025_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_7401_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_7401_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_476_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_476_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_5163_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_5163_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_a618_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_a618_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_2609_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_2609_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_179_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_179_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_13691_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_13691_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_5115_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_5115_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1592_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1592_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1698_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1698_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_5782_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_5782_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_517_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_517_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1687_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1687_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_6561_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_6561_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_483_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_483_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_4648_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_4648_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_5404_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_5404_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_2848_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_2848_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_4362_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_4362_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_6213_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_6213_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_525_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_525_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_905_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_905_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_25488_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_25488_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1556_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1556_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3690_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3690_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_5676_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_5676_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_6085_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_6085_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_6616_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_6616_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_13590_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_13590_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1078_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1078_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_5726_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_5726_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_7548_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_7548_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_6357_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_6357_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_976_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_976_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3103_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3103_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_8832_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_8832_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1161_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1161_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1408_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1408_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_12215_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_12215_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3569_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3569_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_9671_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_9671_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_8933_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_8933_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3013_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3013_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_6056_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_6056_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_10743_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_10743_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_6856_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_6856_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_2023_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_2023_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3612_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3612_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3686_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3686_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3843_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_3843_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_4139_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_4139_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_7908_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_7908_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_533_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_533_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1079_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_1079_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_4622_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_4622_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_8200_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_8200_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_8924_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_8924_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_503_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Elor_503_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Goby14528_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Goby14528_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Goby21378_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Goby21378_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Goby25362_afield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless
Goby25362_bfield name is the microsatellite locus name. Data is Haplotype id for each microsatellite allele unitless

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Instruments

Dataset-specific Instrument Namemultiplex PCR protocol
Generic Instrument NamePCR Thermal Cycler
Dataset-specific Descriptionindividuals were sequenced at 71 microsatellite loci using a multiplex PCR protocol for targeted amplicon sequencing.
Generic Instrument DescriptionGeneral 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

Belize_2010

Websitehttps://www.bco-dmo.org/deployment/704795
Platformlab Buston
DescriptionBuston lab expeditions to Belize beginning in 2010.


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Project Information

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

Website: http://people.bu.edu/buston/lab/Welcome.html
Coverage: Belizean Barrier Reef System (16.803 degrees North 88.096 degrees West)

Understanding the patterns, causes and consequences of larval dispersal is a major goal of 21st century marine ecology. Patterns of dispersal determine the rates of larval exchange, or connectivity, between populations. Both physical factors (e.g., water movement) and biological factors (e.g., larval behavior) cause variation in population connectivity. Population connectivity, in turn, has major consequences for all aspects of an organism's biology, from individual behavior to metapopulation dynamics, and from evolution within metapopulations to the origin and extinction of species. Further, understanding population connectivity is critical for the design of effective networks of marine reserves, creation of vital tools in conservation, and the development of sustainable fisheries. Over the last decade, three methods, each of which tells something slightly different, have emerged as leading contenders to provide the greatest insights into population connectivity. First, coupled biophysical models make assumptions regarding water flow, larval behavior and ecology, to predict population connectivity. Second, indirect genetic methods use spatial distributions of allele frequencies to infer population connectivity. Third, direct genetic methods use parentage analyses, tracing recruits to specific adults, to measure population connectivity. Despite advances, lack of integration means that we do not know the predictive skill of biophysical models, or the extent to which patterns of dispersal predict spatial genetic structure. The overall objective of this proposal is to conduct an integrated investigation of population connectivity, using all three methods in one tractable system: the neon goby, Elacatinus lori, on the Belizean Barrier Reef. There are three motives for this choice of study system: i) fourteen highly polymorphic microsatellite loci have been developed, facilitating the assignment of recruits to parents using parentage analyses and the measurement of dispersal; ii) the physical oceanography of the Belizean Barrier Reef is well-studied, facilitating the development and testing of coupled biophysical models; and, iii) E. lori has a relatively small biogeographic range, facilitating analysis of the spatial distribution of allele frequencies throughout its range. Broader Impacts. The grant will support one postdoc and two graduate students who will be trained in scientific diving, marine fieldwork, population genetics, biophysical modeling, and mathematical modeling, and will gain collaborative research experience. PIs will incorporate research findings in their courses, which cover all these topics. The grant will also broaden participation of under-represented groups by supporting six undergraduates from groups traditionally underrepresented in STEM fields. In each year of the project there will be an All Participants meeting to reinforce the network of participants. A project website will be developed, in English and Spanish, on the theme of larval dispersal and population connectivity. This will include a resource for K-12 marine science educators developed in collaboration with a marine science educator. All PIs will ensure that results are broadly disseminated to the scientific community and general public via appropriate forms of media.

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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE) OCE-1260424

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