http://lod.bco-dmo.org/id/dataset/957700
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
2025-04-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Genetic analyses and microsatellite characterization for formal recognition of new species of host-generalist species of dinoflagellate (Cladocopium, Symbiodiniaceae) mutualistic with Indo-Pacific reef corals collected from 2003 through 2015
2025-04-02
publication
2025-04-02
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-04-28
publication
https://doi.org/10.26008/1912/bco-dmo.957700.1
Todd Christopher LaJeunesse
Pennsylvania State University
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: Butler, C. C., Turnham, K. E., LaJeunesse, T. C. (2025) Genetic analyses and microsatellite characterization for formal recognition of new species of host-generalist species of dinoflagellate (Cladocopium, Symbiodiniaceae) mutualistic with Indo-Pacific reef corals collected from 2003 through 2015. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-04-02 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.957700.1 [access date]
Genetic analyses and microsatellite characterization for new species of dinoflagellate Dataset Description: <p>These genetic data were used to justify the formal characterization of new species of ‘ecological generalists’ zooxanthellae, the dinoflagellate symbionts living in the tissues of numerous marine animals including corals.</p>
<p>There are 4 data files: one table of microsatellite data plus three sequence files.</p>
<p><br />
Original paper is Butler, C. C., Turnham, K. E., Lewis, A. M., Nitschke, M. R., Warner, M. E., Kemp, D. W., Hoegh-Guldberg, O., Fitt, W. K., van Oppen, M. J. H. &amp; LaJeunesse, T. C. 2023. Formal recognition of host-generalist species of dinoflagellate (Cladocopium, Symbiodiniaceae) mutualistic with Indo-Pacific reef corals.&nbsp;<em>J Phycol,</em>&nbsp;59<strong>:</strong>698–711.<br />
&nbsp;</p> Methods and Sampling: <p><em><strong>Field collections</strong></em><br />
Samples of Scleractinia from various families were sampled by SCUBA with a hammer and chisel throughout various sites across the Indo-Pacific including the reefs of Palau, the Andaman Sea of western Thailand, Zanzibar of Tanzania, the Phoenix Islands, and the southern Great Barrier Reef (GBR) of Australia, New Caledonia, and Brazil. The samples used were collected from 2002–2018, including some from previously published diversity surveys (Butler et al., 2023). Coral fragments of approximately 1-3 cm<sup>2</sup> were preserved in 20% DMSO buffer or 100% ethanol and stored at -20°C.</p>
<p><em><strong>Genetic analyses</strong></em><br />
A modified Promega Wizard protocol was used to extract genomic DNA from 0.5 cm<sup>2</sup> of each fragment (LaJeunesse et al., 2003). All samples were identified using the PCR-DGGE profiling of the internal transcribed space region 2 (ITS2) rDNA of the ribosomal array (LaJeunesse, 2002; T. C. LaJeunesse et al., 2004). Amplified products were examined with gel electrophoresis with a CB Scientific system with 45–80% denaturing gradient gels. Fingerprints of each sample were visualized using SYBR Green stain and compared to known standards and/or sequenced to confirm the identity of the ITS2 ‘type’ designation. <em>Cladocopium </em>samples typed as C1, C3, C3u, and C40 were investigated by using additional genetic markers, including the large ribosomal subunit (<em>LSU</em>) (Zardoya, Costas, Lopez-Rodas, Garrido-Pertierra, &amp; Bautista, 1995), mitochondrial cytochrome b (<em>cob</em>), mitochondrial cytochrome oxidase 1 (<em>cox 1</em>) (H. Zhang, Bhattacharya, Maranda, &amp; Lin, 2008), partial chloroplast <em>cp23S </em>(Z. Zhang, Green, &amp; Cavalier-Smith, 2000), and the non-coding region of the <em>psbA</em> minicircle (<em>psbA</em><sup>ncr</sup>) (Moore, Ferguson, Loh, Hoegh-Guldberg, &amp; Carter, 2003). These conventional phylogenetic markers (i.e., <em>LSU</em>, <em>cob</em>, <em>cox 1, cp23S</em>) were used to resolve lineages within <em>Cladocopium</em>, and then concatenated together to further differentiate putative species lineages (LaJeunesse <em>et al. </em>2015, Lee <em>et al.</em>&nbsp;2020). For comparison, the <em>psbA<sup>ncr</sup></em> region is a more rapidly evolving locus that provides finer-scale inter-species and intra-species resolution (LaJeunesse &amp; Thornhill, 2011; Moore et al., 2003).</p>
<p>Successful PCR amplicons of each genetic marker were Sanger sequenced using the BigDye Terminator 3.1 Cycle Sequencing Kit (ThermoFisher Scientific, Waltham, MA), with sequences analyzed at the Penn State University Genomics Core Facility on an Applied Biosciences Sequencer. The <em>psbA</em><sup>ncr</sup> region was sequenced in both directions. Sequences were quality checked, assembled, and edited in Geneious v 11.0.5 (Biomatters Ltd, Auckland, NZ).</p>
<p><em><strong>Microsatellite characterization</strong></em><br />
To test for reproductive isolation in the C3-radiation <em>Cladocopium</em> samples, a total of seven microsatellite loci were used to generate multilocus genotypes using the following primers: SgrSpl_22, SgrSpl_24, SgrSpl_25, SgrSpl_78, Spl_1<sup>a</sup>, and Spl_16 were developed in Drew C. Wham, Carmichael, and LaJeunesse (2014), while the remaining locus (C1.05) was described by Bay, Howells, and van Oppen (2009). These loci are unlinked and have sufficient allelic diversity for population genetic analyses (Drew C. Wham et al., 2014). Loci were amplified in reaction volumes of 10 μL according to their respective development studies. Fragment analysis was performed on an ABI 3730 Genetic Analyzer (Applied Biosystems) using a 500-bp standard (LIZ-labeled) at the Penn State University Nucleic Acid Facility. Fragment sizes were scored visually using Geneious (v.2020.2.4). While <em>Cladocopium</em> spp. are haploid organisms, two alleles are often observed in each sample (D. C. Wham &amp; LaJeunesse, 2016). This observation is most likely the result of <em>Cladocopium</em> having a partial or extensively duplicated genome (Chen et al., 2022; Liu et al., 2018). Previous work has shown that <em>psbA</em><sup>ncr</sup><em> </em>sequences are consistent with microsatellite data when differentiating lineages in the C1-radiation (Turnham <em>et al. </em>2021). Microsatellite analyses were only conducted on symbionts from the C3-radiation, which, relative to the C1-radiation, were less differentiated by <em>psbA</em><sup>ncr</sup> sequence divergence (Table S2 in&nbsp;Butler et al., 2023).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1636022 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1636022
Funding provided by NSF Division of Integrative Organismal Systems (NSF IOS) Award Number: IOS-1258058 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1258058
completed
Todd Christopher LaJeunesse
Pennsylvania State University
814-863-2038
208 Mueller Laboratory Department of Biology
University Park
PA
16802
USA
tcl3@psu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_ID
Species
Aphia_ID
Sample_Origin
C1_22
C1_22_2
C1_25
C1_25_2
C1_24
C1_24_2
C1_05
C1_05_2
C1_16
C1_16_2
Z1_Spl_1
Z1_Spl_1_2
z78
z78_2
CB Scientific gel electrophoresis system
Applied Biosciences Sequencer at Penn State University Genomics Core Facility
ABI 3730 Genetic Analyzer (Applied Biosystems)
hammer and chisel
SCUBA
theme
None, User defined
sample identification
species scientific name (binomial)
taxon_code
site
microsatellite
featureType
BCO-DMO Standard Parameters
Agarose Gel Electrophoresis System
Automated DNA Sequencer
Gene Analyzer
Manual Biota Sampler
Self-Contained Underwater Breathing Apparatus
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: Stability, flexibility, and functionality of thermally tolerant coral symbioses
https://osprey.bco-dmo.org/project/708866
Collaborative Research: Stability, flexibility, and functionality of thermally tolerant coral symbioses
<p>NSF abstract:</p>
<p>All reef-building corals require large numbers of internal symbiotic microalgae (called Symbiodinium) for their survival and growth. These mutualisms have shown considerable sensitivity to changes in the environment in recent decades, especially due to global increases in ocean temperatures. When exposed to severe thermal stress, corals loose their symbionts and often die. However, recent experiments show that some symbionts may be more stress-tolerant. Corals with these heat-resistant symbionts continue to receive high amounts of algal derived nutrients and grow under elevated temperatures. If the global trend in seawater warming continues to increase, these heat-resistant symbioses may become more ecologically prevalent on reef systems around the world and could play a critical role in maintaining healthy and productive coral communities. This project will examine the ecological and physiological attributes of stress-tolerant symbioses from the Indo Pacific where coral communities are the largest, most diverse, and productive in the world. The researchers will conduct a series of experiments to (1) evaluate host and symbiont attributes that contribute to thermal tolerance and (2) characterize the relative flexibility and functionality of various corals and symbionts exposed to typical ambient and stressful temperatures. Broader impacts of the project include the training of several Ph.D. students, undergraduates, and high school students in the disciplines of physiology and ecology. The researchers will partner with Global Ocean Exploration, Inc. to communicate this research to the general public through short documentary videos, editorials, and podcasts. An interactive K-5 program, "Invertebrates on the Road," will introduce elementary students in Pennsylvania to marine invertebrate diversity. Research results will also be disseminated to the public at the University of Delaware via educational seminars, as well as through hands-on research displays and demonstrations presented at the annual open house "Coast Day" festival in each year of the project.</p>
<p>This project will examine several attributes important to the functional ecology of coral-dinoflagellate symbioses. Specifically, the research team seeks to understand the interplay between coral and symbiont physiologies under different environmental conditions and determine the relative influence of biotic factors crucial to the performance of stress tolerant symbioses. Results from recent experiments on Indo-west Pacific corals found that Clade D (S. trenchii) symbionts are stress-tolerant. These symbionts are able to maintain function and provide nutrients to their hosts under high temperatures that typically elicit the breakdown of symbioses involving many other species of symbiont. A number of questions arise about how enhanced thermal tolerance symbioses may be aided by a combination of factors; for example: Are symbionts physiologically hardier in corals that are routinely feeding? Do host genotypes that are adapted to high temperatures affect the physiology of their symbionts in ways that make the partnership more stress-tolerant? A series of experiments over three years will examine the functionality of different coral-symbiont pairings exposed to ambient and high temperatures. Reciprocal transplants between inshore (stress-tolerant) and offshore (stress-susceptible) reef sites will be used to produce specific host-symbiont parings. Controlled experiments will test the relative importance of coral trophic status (nutrient content) while holding symbiont type constant and how changes in both coral trophic status and symbiont species identity of the resident affect thermal tolerance. Tank experiments on shore will track rates of photosynthesis as well as carbon translocation and assimilation from symbiont to host tissues and skeletons. Long-term growth rates via skeletal density, linear extension, and biomass gain will also be measured. This project will help elucidate how biochemical, physiological and ecological differences among host-symbiont pairings may respond to rising ocean temperatures and enhance the future viability of coral reefs.</p>
Thermally tolerant coral
largerWorkCitation
project
eng; USA
biota
oceans
39.13373
-171.704
-23.4357
26.22354
2002-01-01
2018-12-31
Coral Reefs of Palau, Micronesia
0
BCO-DMO catalogue of parameters from Genetic analyses and microsatellite characterization for formal recognition of new species of host-generalist species of dinoflagellate (Cladocopium, Symbiodiniaceae) mutualistic with Indo-Pacific reef corals collected from 2003 through 2015
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/957735.rdf
Name: Sample_ID
Units: unitless
Description: <p>Unique identifier for individual samples.</p>
http://lod.bco-dmo.org/id/dataset-parameter/957736.rdf
Name: Species
Units: unitless
Description: <p>The identified evolutionary lineage of the Cladocopium sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/957737.rdf
Name: Aphia_ID
Units: unitless
Description: <p>AphiaID identifier for species ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/957738.rdf
Name: Sample_Origin
Units: unitless
Description: <p>Location of sample origin</p>
http://lod.bco-dmo.org/id/dataset-parameter/957739.rdf
Name: C1_22
Units: base pairs
Description: <p>Microsatellite peak for SgrSpl_22 developed by Wham, Carmichael, and LaJeunesse (2014)</p>
http://lod.bco-dmo.org/id/dataset-parameter/957740.rdf
Name: C1_22_2
Units: base pairs
Description: <p>Second variant microsatellite peak for C1_22</p>
http://lod.bco-dmo.org/id/dataset-parameter/957741.rdf
Name: C1_25
Units: base pairs
Description: <p>Microsatellite peak for SgrSpl_25 developed by Wham, Carmichael, and LaJeunesse (2014)</p>
http://lod.bco-dmo.org/id/dataset-parameter/957742.rdf
Name: C1_25_2
Units: base pairs
Description: <p>Second variant microsatellite peak for C1_25</p>
http://lod.bco-dmo.org/id/dataset-parameter/957743.rdf
Name: C1_24
Units: base pairs
Description: <p>Microsatellite peak for SgrSpl_24 developed by Wham, Carmichael, and LaJeunesse (2014)</p>
http://lod.bco-dmo.org/id/dataset-parameter/957744.rdf
Name: C1_24_2
Units: base pairs
Description: <p>Second variant microsatellite peak for C1_24</p>
http://lod.bco-dmo.org/id/dataset-parameter/957745.rdf
Name: C1_05
Units: base pairs
Description: <p>Microsatellite peak for C1.05 developed by Bay, Howells, and van Oppen (2009).</p>
http://lod.bco-dmo.org/id/dataset-parameter/957746.rdf
Name: C1_05_2
Units: base pairs
Description: <p>Second variant microsatellite peak for C1_05</p>
http://lod.bco-dmo.org/id/dataset-parameter/957747.rdf
Name: C1_16
Units: base pairs
Description: <p>Microsatellite peak for SgrSpl_16 developed by Wham, Carmichael, and LaJeunesse (2014)</p>
http://lod.bco-dmo.org/id/dataset-parameter/957748.rdf
Name: C1_16_2
Units: base pairs
Description: <p>The second variant microsatellite peak for C1_16</p>
http://lod.bco-dmo.org/id/dataset-parameter/957749.rdf
Name: Z1_Spl_1
Units: base pairs
Description: <p>Microsatellite peak for Spl_1a developed by Wham, Carmichael, and LaJeunesse (2014)</p>
http://lod.bco-dmo.org/id/dataset-parameter/957750.rdf
Name: Z1_Spl_1_2
Units: base pairs
Description: <p>The second variant microsatellite peak for Z1_Spl_1</p>
http://lod.bco-dmo.org/id/dataset-parameter/957751.rdf
Name: z78
Units: base pairs
Description: <p>Microsatellite peak for SgrSpl_78 developed by Wham, Carmichael, and LaJeunesse (2014)</p>
http://lod.bco-dmo.org/id/dataset-parameter/957752.rdf
Name: z78_2
Units: base pairs
Description: <p>The second variant microsatellite peak for z78</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
5783
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/6a8b1afd-2a82-4ef6-82f2-135f9fe36682/content
download
https://doi.org/10.26008/1912/bco-dmo.957700.1
download
onLine
dataset
<p><em><strong>Field collections</strong></em><br />
Samples of Scleractinia from various families were sampled by SCUBA with a hammer and chisel throughout various sites across the Indo-Pacific including the reefs of Palau, the Andaman Sea of western Thailand, Zanzibar of Tanzania, the Phoenix Islands, and the southern Great Barrier Reef (GBR) of Australia, New Caledonia, and Brazil. The samples used were collected from 2002–2018, including some from previously published diversity surveys (Butler et al., 2023). Coral fragments of approximately 1-3 cm<sup>2</sup> were preserved in 20% DMSO buffer or 100% ethanol and stored at -20°C.</p>
<p><em><strong>Genetic analyses</strong></em><br />
A modified Promega Wizard protocol was used to extract genomic DNA from 0.5 cm<sup>2</sup> of each fragment (LaJeunesse et al., 2003). All samples were identified using the PCR-DGGE profiling of the internal transcribed space region 2 (ITS2) rDNA of the ribosomal array (LaJeunesse, 2002; T. C. LaJeunesse et al., 2004). Amplified products were examined with gel electrophoresis with a CB Scientific system with 45–80% denaturing gradient gels. Fingerprints of each sample were visualized using SYBR Green stain and compared to known standards and/or sequenced to confirm the identity of the ITS2 ‘type’ designation. <em>Cladocopium </em>samples typed as C1, C3, C3u, and C40 were investigated by using additional genetic markers, including the large ribosomal subunit (<em>LSU</em>) (Zardoya, Costas, Lopez-Rodas, Garrido-Pertierra, &amp; Bautista, 1995), mitochondrial cytochrome b (<em>cob</em>), mitochondrial cytochrome oxidase 1 (<em>cox 1</em>) (H. Zhang, Bhattacharya, Maranda, &amp; Lin, 2008), partial chloroplast <em>cp23S </em>(Z. Zhang, Green, &amp; Cavalier-Smith, 2000), and the non-coding region of the <em>psbA</em> minicircle (<em>psbA</em><sup>ncr</sup>) (Moore, Ferguson, Loh, Hoegh-Guldberg, &amp; Carter, 2003). These conventional phylogenetic markers (i.e., <em>LSU</em>, <em>cob</em>, <em>cox 1, cp23S</em>) were used to resolve lineages within <em>Cladocopium</em>, and then concatenated together to further differentiate putative species lineages (LaJeunesse <em>et al. </em>2015, Lee <em>et al.</em>&nbsp;2020). For comparison, the <em>psbA<sup>ncr</sup></em> region is a more rapidly evolving locus that provides finer-scale inter-species and intra-species resolution (LaJeunesse &amp; Thornhill, 2011; Moore et al., 2003).</p>
<p>Successful PCR amplicons of each genetic marker were Sanger sequenced using the BigDye Terminator 3.1 Cycle Sequencing Kit (ThermoFisher Scientific, Waltham, MA), with sequences analyzed at the Penn State University Genomics Core Facility on an Applied Biosciences Sequencer. The <em>psbA</em><sup>ncr</sup> region was sequenced in both directions. Sequences were quality checked, assembled, and edited in Geneious v 11.0.5 (Biomatters Ltd, Auckland, NZ).</p>
<p><em><strong>Microsatellite characterization</strong></em><br />
To test for reproductive isolation in the C3-radiation <em>Cladocopium</em> samples, a total of seven microsatellite loci were used to generate multilocus genotypes using the following primers: SgrSpl_22, SgrSpl_24, SgrSpl_25, SgrSpl_78, Spl_1<sup>a</sup>, and Spl_16 were developed in Drew C. Wham, Carmichael, and LaJeunesse (2014), while the remaining locus (C1.05) was described by Bay, Howells, and van Oppen (2009). These loci are unlinked and have sufficient allelic diversity for population genetic analyses (Drew C. Wham et al., 2014). Loci were amplified in reaction volumes of 10 μL according to their respective development studies. Fragment analysis was performed on an ABI 3730 Genetic Analyzer (Applied Biosystems) using a 500-bp standard (LIZ-labeled) at the Penn State University Nucleic Acid Facility. Fragment sizes were scored visually using Geneious (v.2020.2.4). While <em>Cladocopium</em> spp. are haploid organisms, two alleles are often observed in each sample (D. C. Wham &amp; LaJeunesse, 2016). This observation is most likely the result of <em>Cladocopium</em> having a partial or extensively duplicated genome (Chen et al., 2022; Liu et al., 2018). Previous work has shown that <em>psbA</em><sup>ncr</sup><em> </em>sequences are consistent with microsatellite data when differentiating lineages in the C1-radiation (Turnham <em>et al. </em>2021). Microsatellite analyses were only conducted on symbionts from the C3-radiation, which, relative to the C1-radiation, were less differentiated by <em>psbA</em><sup>ncr</sup> sequence divergence (Table S2 in&nbsp;Butler et al., 2023).</p>
Specified by the Principal Investigator(s)
<p>Sequences were quality checked, assembled, and edited in Geneious v 11.0.5 (Biomatters Ltd, Auckland, NZ).</p>
<p><em><strong>Phylogenetic Analysis</strong></em></p>
<p><em>LSU, cob,</em>&nbsp;<em>cox 1</em>, and&nbsp;<em>cp23S</em>&nbsp;sequences were aligned using ClustalOmega. PAUP v4.0a169 was used to create an unrooted maximum parsimony phylogeny based on a heuristic search&nbsp;(Swofford, 2014). Independent phylogenies for each marker were compared (not shown). Because each phylogeny was congruent they were concatenated and a phylogenetic tree created with gaps (and insertions) treated as a 5<sup>th</sup>&nbsp;character and scored as one change. Bootstrap values based on 1,000 iterations were evaluated to statistically assess branch support, which was also assessed using Bayesian Inference using MrBayes v.3.2.1 implementing General Time Reversible (where gaps were treated as missing data). Each Markov chain Monte Carlo (MCMC) analysis were run for 10<sup>6</sup>&nbsp;generations total and sampled every 100 generations. The first quarter of trees was discarded as burn-in corresponding with the convergence of chains.</p>
<p>Sequences of the&nbsp;<em>psbA</em><sup>ncr</sup>&nbsp;were then used for finer inter- and intra-species analysis. Sequences were aligned using ClustalOmega followed by manual editing. PAUP v4.0a169 was again used to create an unrooted maximum parsimony phylogeny based on a heuristic search. Gaps and insertions were also treated as a 5<sup>th</sup>&nbsp;character and scored as one change. Bootstrap values based on 1,000 iterations were evaluated to statistically assess node support, which was also assessed using Bayesian Inference using MrBayes v.3.2.1 implementing General Time Reversible. Each MCMC analysis was run for 10<sup>6</sup>&nbsp;generations and sampled every 100 generations. The first quarter of trees was discarded as burn-in corresponding with the convergence of chains.</p>
<p><strong>Microsatellite Analysis</strong></p>
<p>Duplicate (i.e. clone) genotypes and low-quality DNA samples with two or more microsatellites that did not amplify were removed from dataset prior to subsequent analyses. Clonality and basic summary statistics were assessed in GenAlEX v.6.5 (Peakall and Smouse 2012). A genotype accumulation curve was created to assess the resolution of the microsatellites used, and if the microsatellites used are an accurate representation of the population&nbsp;(Arnaud-Haond, Duarte, Alberto, &amp; Serrao, 2007). Next, the hypothesis of reproductive isolation (i.e., the biological species concept) for members of the C3-radiation was tested via an unsupervised Bayesian clustering algorithm employed by Structure&nbsp;with no location prior, assuming no admixture, and uncorrelated allele frequencies (Pritchard et al. 2000). This analysis was conducted using K-values from K=1 to K=5 with ten runs per K-value. The optimum number of clusters was then estimated based on the&nbsp;ΔK statistic procedure through Structure Harvester v0.6.94 (Earl and von Holdt 2012). The average of the ten runs was obtained by CLUMPP to eliminate stochastic differences between Structure&nbsp;runs&nbsp;(Jakobsson &amp; Rosenberg, 2007). Furthermore, a discriminate analysis of principal components (DAPC) was also used to classify samples into clusters of genetically related individuals through the adegenet R package (Jombart et al. 2010).</p>
Specified by the Principal Investigator(s)
- Imported data from source file "SupplementaryTable_S3_Microsat_Data.xlsx" into the BCO-DMO data system.
- Renamed columns/modified parameter names to conform with BCO-DMO naming conventions. The only allowed characters are A-Z,a-z,0-9, and underscores. No spaces, hyphens, commas, parentheses, or Greek letters.
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
CB Scientific gel electrophoresis system
CB Scientific gel electrophoresis system
PI Supplied Instrument Name: CB Scientific gel electrophoresis system PI Supplied Instrument Description:Amplified products were examined with gel electrophoresis with a CB Scientific system with 45–80% denaturing gradient gels. Instrument Name: Agarose Gel Electrophoresis System Instrument Short Name:agarose gel electrophoresis system Instrument Description: A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field.
Applied Biosciences Sequencer at Penn State University Genomics Core Facility
Applied Biosciences Sequencer at Penn State University Genomics Core Facility
PI Supplied Instrument Name: Applied Biosciences Sequencer at Penn State University Genomics Core Facility PI Supplied Instrument Description:Successful PCR amplicons of each genetic marker were Sanger sequenced with sequences analyzed at the Penn State University Genomics Core Facility on an Applied Biosciences Sequencer. (Possibly the Applied Biosystems 3730XL) 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.
ABI 3730 Genetic Analyzer (Applied Biosystems)
ABI 3730 Genetic Analyzer (Applied Biosystems)
PI Supplied Instrument Name: ABI 3730 Genetic Analyzer (Applied Biosystems) PI Supplied Instrument Description:Fragment analysis was performed on an ABI 3730 Genetic Analyzer (Applied Biosystems) using a 500-bp standard (LIZ-labeled) at the Penn State University Nucleic Acid Facility. Instrument Name: Gene Analyzer Instrument Short Name: Instrument Description: An automated analyzer designed for a wide range of sequencing and fragment analysis applications with the ability to perform comparative sequencing, linkage analysis, STR analysis, SNP detection, discovery and validation, mutation detection, and many other applications.
hammer and chisel
hammer and chisel
PI Supplied Instrument Name: hammer and chisel PI Supplied Instrument Description:Samples of Scleractinia from various families were sampled with a hammer and chisel throughout various sites across the Indo-Pacific Instrument Name: Manual Biota Sampler Instrument Short Name:Manual Biota Sampler Instrument Description: "Manual Biota Sampler" indicates that a sample was collected in situ by a person, possibly using a hand-held collection device such as a jar, a net, or their hands. This term could also refer to a simple tool like a hammer, saw, or other hand-held tool. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/90/
SCUBA
SCUBA
PI Supplied Instrument Name: SCUBA PI Supplied Instrument Description:Samples of Scleractinia from various families were sampled by SCUBA with a hammer and chisel throughout various sites across the Indo-Pacific Instrument Name: Self-Contained Underwater Breathing Apparatus Instrument Short Name:SCUBA Instrument Description: The self-contained underwater breathing apparatus or scuba diving system is the result of technological developments and innovations that began almost 300 years ago. Scuba diving is the most extensively used system for breathing underwater by recreational divers throughout the world and in various forms is also widely used to perform underwater work for military, scientific, and commercial purposes.
Reference: https://oceanexplorer.noaa.gov/technology/technical/technical.html