http://lod.bco-dmo.org/id/dataset/924886
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2024-04-12
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
RADseq data from Atlantic silversides used for linkage and QTL mapping.
2024-04-24
publication
2024-04-24
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-04-24
publication
https://doi.org/10.26008/1912/bco-dmo.924886.1
Nina Overgaard Therkildsen
Cornell University
principalInvestigator
Hannes Baumann
University of Connecticut
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Therkildsen, N. O., Akopyan, M., Baumann, H. (2024) RADseq data from Atlantic silversides used for linkage and QTL mapping. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-04-24 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.924886.1 [access date]
Dataset Description: <p>* Raw&nbsp; data&nbsp; from&nbsp; the&nbsp; RADseq&nbsp; libraries&nbsp; are&nbsp; available&nbsp; under&nbsp; NCBI&nbsp; BioProject accession number PRJNA771889 (see related dataset section).<br />
* SNP genotype call files (VCF format) are available at doi:10.6084/m9.figshare.19521955.v1 (see related dataset section) and as supplemental files to this dataset.</p> Methods and Sampling: <p>We generated three crosses for linkage mapping, including two F1 families resulting from reciprocal crossing of wild-caught silversides from two adaptively divergent parts of the distribution range (Georgia and New York), and one F2 family from intercrossing laboratory-reared progeny from one of the F1 families. Because linkage mapping measures recombination during gamete production in the parents, the F1 families give us separate information about the wild-caught male and female founder fish from each separate population (the F0 progenitors), and the F2 map reflects recombination in the hybrid F1 progeny.</p>
<p>In the spring of 2017, spawning ripe founders were caught by beach seine from Jekyll Island, Georgia (31°03’N, 81°26’W) and Patchogue, New York (40°45’N, 73°00’W) and transported live to the Rankin Seawater Facility at University of Connecticut's Avery Point campus. For each family, we strip-spawned a single male and a single female onto mesh screens submerged in seawater-filled plastic dishes, then transferred the fertilized embryos to rearing containers (20 L) placed in large temperature-controlled water baths with salinity (30 psu) and photoperiod held constant (15 L:9 D). Water baths were kept at 20°C for the New York mother and at 26°C for Georgia mother families, which increased hatching success by mimicking the ambient spawning temperatures at the two different latitudes. Post hatch, larvae were provided ad libitum rations of newly hatched brine shrimp nauplii (Artemia salina, brineshrimpdirect.com). At 22 days post hatch (dph), we sampled 138 full-sib progeny from each of the two F1 families to be genotyped. The remaining offspring from the Georgia-mother F1 family were reared to maturity in groups of equal density (40–50 individuals) in 24°C water baths. In spring 2018, one pair of adult F1 siblings from the Georgia family were intercrossed to generate the F2 mapping population. At 70 dph, we sampled 221 full-sib F2 progeny for genotyping. In total, we analyzed 503 individuals: the two founders (male and female) and 138 offspring from each of the two F1 families, plus two additional F1 siblings from the Georgia mother F1 family and their 221 F2 offspring. All animal care and euthanasia protocols were carried out in accordance with the University of Connecticut's Institutional Animal Care and Use Committee (A17-043).</p>
<p>We extracted DNA from each individual with a Qiagen DNeasy tissue kit following the manufacturer's instructions and used double-digest restriction-site associated DNA (ddRAD) sequencing (Peterson et al., 2012) to identify and genotype single nucleotide polymorphisms (SNPs) for linkage map construction. We created two ddRAD libraries, each with a random subset of ~250 barcoded individuals, using restriction enzymes MspI and PstI (New England BioLabs cat. R0106S and R3140S, respectively), following library construction steps as in Peterson et al. (2012). We size-selected libraries for 400– 650 bp fragments with a Pippin Prep instrument (Sage Science) and sequenced the libraries across six Illumina NextSeq500 lanes (75 bp single- end reads) at the Cornell Biotechnology Resource Centre. Raw reads were processed in Stacks v2.53 (Catchen et al., 2013) with the module process_radtags to discard low-quality reads and reads with ambiguous barcodes or RAD cut sites. The reads that passed the quality filters were demultiplexed to individual fastq files. To capture genomic regions potentially not included in the current reference genome assembly, we ran the ustacks module to assemble RAD loci de novo (rather than mapping to the reference genome). We required a minimum of three raw reads to form a stack (i.e., minimum read depth, default -m option) and allowed a maximum of four mismatches between stacks to merge them into a putative locus (-M option).</p>
<p>Because the founders contain all the possible alleles that can occur in the progeny (except from any new mutations), we assembled a catalogue of loci with cstacks using only the four wild-caught F0 progenitors. We built the catalogue with both sets of founders to allow cross-referencing of common loci across the resulting F1 maps and we allowed for a maximum of four mismatches between loci (-n option). We matched loci from all progeny against the catalogue with sstacks, transposed the data with tsv2bam to be organized by sample rather than locus, called variable sites across all individuals, and genotyped each individual at those sites with gstacks using the default SNP model (marukilow) with a genotype likelihood ratio test critical value (α) of 0.05. Finally, we ran the populations module three times to generate a genotype output file for each mapping cross. For each run of populations, we specified the type of test cross (-- map-&nbsp; type option cp or F2), pruned unshared SNPs to reduce haplotype-wise missing data (-H option), and exported loci present in at least 80% of individuals in that cross (-r option) to a VCF file, without restricting the number of SNPs retained per locus.</p>
<p>&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756316 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756316
completed
Nina Overgaard Therkildsen
Cornell University
607-255-2014
Department of Natural Resources 208 Fernow Hall
Ithaca
NY
14853
USA
nt246@cornell.edu
pointOfContact
Hannes Baumann
University of Connecticut
860-405-9297
Department of Marine Sciences 1080 Shennecossett Road
Groton
CT
06340-6048
USA
hannes.baumann@uconn.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
bioproject_accession
biosample_accession
taxonomic_name
mother_f0_sampling_location
lat_mother
lon_mother
father_f0_sampling_location
lat_father
lon_father
SRA_study_accession
SRA_experiment_accession
SRA_run_accession
library_ID
title
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design_description
filetype
sample_name
filename
Illumina NextSeq500
theme
None, User defined
NCBI BioProject accession
NCBI BioSample accession
taxon
site
latitude
longitude
NCBI SRA study accession (SRP)
NCBI SRA experiment accession (SRX)
NCBI SRA run accession (SRR)
sample description
instrument
instrument model
datatype
sample identification
file_name
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative research: The genomic underpinnings of local adaptation despite gene flow along a coastal environmental cline
https://befel.marinesciences.uconn.edu/2018/03/07/research-news-new-nsf-grant-to-study-silverside-genes/
Collaborative research: The genomic underpinnings of local adaptation despite gene flow along a coastal environmental cline
<p>NSF Abstract:</p>
<p>Oceans are large, open habitats, and it was previously believed that their lack of obvious barriers to dispersal would result in extensive mixing, preventing organisms from adapting genetically to particular habitats. It has recently become clear, however, that many marine species are subdivided into multiple populations that have evolved to thrive best under contrasting local environmental conditions. Nevertheless, we still know very little about the genomic mechanisms that enable divergent adaptations in the face of ongoing intermixing. This project focuses on the Atlantic silverside (Menidia menidia), a small estuarine fish that exhibits a remarkable degree of local adaptation in growth rates and a suite of other traits tightly associated with a climatic gradient across latitudes. Decades of prior lab and field studies have made Atlantic silverside one of the marine species for which we have the best understanding of evolutionary tradeoffs among traits and drivers of selection causing adaptive divergence. Yet, the underlying genomic basis is so far completely unknown. The investigators will integrate whole genome sequencing data from wild fish sampled across the distribution range with breeding experiments in the laboratory to decipher these genomic underpinnings. This will provide one of the most comprehensive assessments of the genomic basis for local adaptation in the oceans to date, thereby generating insights that are urgently needed for better predictions about how species can respond to rapid environmental change. The project will provide interdisciplinary training for a postdoc as well as two graduate and several undergraduate students from underrepresented minorities. The findings will also be leveraged to develop engaging teaching and outreach materials (e.g. a video documentary and popular science articles) to promote a better understanding of ecology, evolution, and local adaptation among science students and the general public.</p>
<p>The goal of the project is to characterize the genomic basis and architecture underlying local adaptation in M. menidia and examine how the adaptive divergence is shaped by varying levels of gene flow and maintained over ecological time scales. The project is organized into four interconnected components. Part 1 examines fine-scale spatial patterns of genomic differentiation along the adaptive cline to a) characterize the connectivity landscape, b) identify genomic regions under divergent selection, and c) deduce potential drivers and targets of selection by examining how allele frequencies vary in relation to environmental factors and biogeographic features. Part 2 maps key locally adapted traits to the genome to dissect their underlying genomic basis. Part 3 integrates patterns of variation in the wild (part 1) and the mapping of traits under controlled conditions (part 2) to a) examine how genomic architectures underlying local adaptation vary across gene flow regimes and b) elucidating the potential role of chromosomal rearrangements and other tight linkage among adaptive alleles in facilitating adaptation. Finally, part 4 examines dispersal - selection dynamics over seasonal time scales to a) infer how selection against migrants and their offspring maintains local adaptation despite homogenizing connectivity and b) validate candidate loci for local adaptation. Varying levels of gene flow across the species range create a natural experiment for testing general predictions about the genomic mechanisms that enable adaptive divergence in the face of gene flow. The findings will therefore have broad implications and will significantly advance our understanding of the role genomic architecture plays in modifying the gene flow - selection balance within coastal environments.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
GenomAdapt
largerWorkCitation
project
eng; USA
oceans
-81.43
-73
31.02
40.75
2017-05-01
2018-05-09
Eastern coastline of North America
0
BCO-DMO catalogue of parameters from RADseq data from Atlantic silversides used for linkage and QTL mapping.
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/925094.rdf
Name: bioproject_accession
Units: units
Description: <p>NCBI BioProject accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/925095.rdf
Name: biosample_accession
Units: units
Description: <p>NCBI BioSample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/925096.rdf
Name: taxonomic_name
Units: units
Description: <p>Taxonomic name of specimen</p>
http://lod.bco-dmo.org/id/dataset-parameter/925097.rdf
Name: mother_f0_sampling_location
Units: units
Description: <p>Sampling location ()Jekyll Island, GA for the wild-caught mother of the F0 cross used to generate F1 and F2 offspring (the generation of each sample is listed in the filename column).</p>
http://lod.bco-dmo.org/id/dataset-parameter/925098.rdf
Name: lat_mother
Units: units
Description: <p>Latitude of sampling location of wild-caught mother</p>
http://lod.bco-dmo.org/id/dataset-parameter/925099.rdf
Name: lon_mother
Units: units
Description: <p>Longitude of sampling location of wild-caught mother</p>
http://lod.bco-dmo.org/id/dataset-parameter/925100.rdf
Name: father_f0_sampling_location
Units: units
Description: <p>Sampling location (Patchogue, NY) for the wild-caught father of the F0 cross used to generate F1 and F2 offspring (the generation of each sample is listed in the filename column).</p>
http://lod.bco-dmo.org/id/dataset-parameter/925101.rdf
Name: lat_father
Units: units
Description: <p>Latitude of sampling location of wild-caught father</p>
http://lod.bco-dmo.org/id/dataset-parameter/925102.rdf
Name: lon_father
Units: units
Description: <p>Longitude of sampling location of wild-caught father</p>
http://lod.bco-dmo.org/id/dataset-parameter/925103.rdf
Name: SRA_study_accession
Units: units
Description: <p>NCBI SRA study accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/925104.rdf
Name: SRA_experiment_accession
Units: units
Description: <p>NCBI SRA experiment accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/925105.rdf
Name: SRA_run_accession
Units: units
Description: <p>NCBI SRA run accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/925106.rdf
Name: library_ID
Units: units
Description: <p>Short, unique identifier for the sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/925107.rdf
Name: title
Units: units
Description: <p>Short description that identifies the dataset in NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/925108.rdf
Name: library_strategy
Units: units
Description: <p>The library preparation type used for the sample (details in Akopyan et al. 2022</p>
http://lod.bco-dmo.org/id/dataset-parameter/925109.rdf
Name: library_source
Units: units
Description: <p>The type of DNA used to prepare the sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/925110.rdf
Name: library_selection
Units: units
Description: <p>NCBI Controlled vocabulary of terms describing selection or reduction method use in library construction</p>
http://lod.bco-dmo.org/id/dataset-parameter/925111.rdf
Name: library_layout
Units: units
Description: <p>Either paired-end or single-end reads</p>
http://lod.bco-dmo.org/id/dataset-parameter/925112.rdf
Name: platform
Units: units
Description: <p>Manufacturer of the sequencing instrument</p>
http://lod.bco-dmo.org/id/dataset-parameter/925113.rdf
Name: instrument_model
Units: units
Description: <p>Model of the sequencing instrument</p>
http://lod.bco-dmo.org/id/dataset-parameter/925114.rdf
Name: design_description
Units: units
Description: <p>Type of experimental design for original study</p>
http://lod.bco-dmo.org/id/dataset-parameter/925115.rdf
Name: filetype
Units: units
Description: <p>Type of file wiith raw sequencing data</p>
http://lod.bco-dmo.org/id/dataset-parameter/925116.rdf
Name: sample_name
Units: units
Description: <p>Name of the sample. Sample names containing F0 were wild-caught founders of the cross. Sample names including F1 are from F1 offspring. File names containing F1_x_ are F1 offspring intercrossed with other F1 to generate F2. Sample names containing F2 are for F2 offspring.</p>
http://lod.bco-dmo.org/id/dataset-parameter/925117.rdf
Name: filename
Units: units
Description: <p>Name of the fastq file. File names containing F0 were wild-caught founders of the cross. File names including F1 are from F1 offspring. File names containing F1_x_ are F1 offspring intercrossed with other F1 to generate F2. File names containing F2 are for F2 offspring.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
166388
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/ff49bacb-1557-4ecd-bcde-6b94efc2a1af/content
download
https://doi.org/10.26008/1912/bco-dmo.924886.1
download
onLine
dataset
<p>We generated three crosses for linkage mapping, including two F1 families resulting from reciprocal crossing of wild-caught silversides from two adaptively divergent parts of the distribution range (Georgia and New York), and one F2 family from intercrossing laboratory-reared progeny from one of the F1 families. Because linkage mapping measures recombination during gamete production in the parents, the F1 families give us separate information about the wild-caught male and female founder fish from each separate population (the F0 progenitors), and the F2 map reflects recombination in the hybrid F1 progeny.</p>
<p>In the spring of 2017, spawning ripe founders were caught by beach seine from Jekyll Island, Georgia (31°03’N, 81°26’W) and Patchogue, New York (40°45’N, 73°00’W) and transported live to the Rankin Seawater Facility at University of Connecticut's Avery Point campus. For each family, we strip-spawned a single male and a single female onto mesh screens submerged in seawater-filled plastic dishes, then transferred the fertilized embryos to rearing containers (20 L) placed in large temperature-controlled water baths with salinity (30 psu) and photoperiod held constant (15 L:9 D). Water baths were kept at 20°C for the New York mother and at 26°C for Georgia mother families, which increased hatching success by mimicking the ambient spawning temperatures at the two different latitudes. Post hatch, larvae were provided ad libitum rations of newly hatched brine shrimp nauplii (Artemia salina, brineshrimpdirect.com). At 22 days post hatch (dph), we sampled 138 full-sib progeny from each of the two F1 families to be genotyped. The remaining offspring from the Georgia-mother F1 family were reared to maturity in groups of equal density (40–50 individuals) in 24°C water baths. In spring 2018, one pair of adult F1 siblings from the Georgia family were intercrossed to generate the F2 mapping population. At 70 dph, we sampled 221 full-sib F2 progeny for genotyping. In total, we analyzed 503 individuals: the two founders (male and female) and 138 offspring from each of the two F1 families, plus two additional F1 siblings from the Georgia mother F1 family and their 221 F2 offspring. All animal care and euthanasia protocols were carried out in accordance with the University of Connecticut's Institutional Animal Care and Use Committee (A17-043).</p>
<p>We extracted DNA from each individual with a Qiagen DNeasy tissue kit following the manufacturer's instructions and used double-digest restriction-site associated DNA (ddRAD) sequencing (Peterson et al., 2012) to identify and genotype single nucleotide polymorphisms (SNPs) for linkage map construction. We created two ddRAD libraries, each with a random subset of ~250 barcoded individuals, using restriction enzymes MspI and PstI (New England BioLabs cat. R0106S and R3140S, respectively), following library construction steps as in Peterson et al. (2012). We size-selected libraries for 400– 650 bp fragments with a Pippin Prep instrument (Sage Science) and sequenced the libraries across six Illumina NextSeq500 lanes (75 bp single- end reads) at the Cornell Biotechnology Resource Centre. Raw reads were processed in Stacks v2.53 (Catchen et al., 2013) with the module process_radtags to discard low-quality reads and reads with ambiguous barcodes or RAD cut sites. The reads that passed the quality filters were demultiplexed to individual fastq files. To capture genomic regions potentially not included in the current reference genome assembly, we ran the ustacks module to assemble RAD loci de novo (rather than mapping to the reference genome). We required a minimum of three raw reads to form a stack (i.e., minimum read depth, default -m option) and allowed a maximum of four mismatches between stacks to merge them into a putative locus (-M option).</p>
<p>Because the founders contain all the possible alleles that can occur in the progeny (except from any new mutations), we assembled a catalogue of loci with cstacks using only the four wild-caught F0 progenitors. We built the catalogue with both sets of founders to allow cross-referencing of common loci across the resulting F1 maps and we allowed for a maximum of four mismatches between loci (-n option). We matched loci from all progeny against the catalogue with sstacks, transposed the data with tsv2bam to be organized by sample rather than locus, called variable sites across all individuals, and genotyped each individual at those sites with gstacks using the default SNP model (marukilow) with a genotype likelihood ratio test critical value (α) of 0.05. Finally, we ran the populations module three times to generate a genotype output file for each mapping cross. For each run of populations, we specified the type of test cross (-- map-&nbsp; type option cp or F2), pruned unshared SNPs to reduce haplotype-wise missing data (-H option), and exported loci present in at least 80% of individuals in that cross (-r option) to a VCF file, without restricting the number of SNPs retained per locus.</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
<p>The NCBI accessions refer to raw sequencing files.</p>
<p>The .vcf files contain SNP genotype data processed as described under methods</p>
<p>Raw&nbsp; data&nbsp; from&nbsp; the&nbsp; RADseq&nbsp; libraries&nbsp; are&nbsp; available&nbsp; under&nbsp; NCBI&nbsp; BioProject accession number PRJNA771889 (see related datasets)</p>
<p>SNP genotype call files (VCF format) are available atfigshare (see related publications) and as supplemental files to this dataset.</p>
Specified by the Principal Investigator(s)
* Added lat/lon of sampling location for the mother and father
* Added SRA information: SRA study, experiment, run & sample name
* Adjusted field names to database requirements
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Illumina NextSeq500
Illumina NextSeq500
PI Supplied Instrument Name: Illumina NextSeq500 Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.