<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Padilla-Gamiño, J. L.</style></author><author><style face="normal" font="default" size="100%">Pochon, X.</style></author><author><style face="normal" font="default" size="100%">Bird, C.</style></author><author><style face="normal" font="default" size="100%">Concepcion, G. T.</style></author><author><style face="normal" font="default" size="100%">Gates, R. D.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">From parent to gamete: vertical transmission of Symbiodinium (Dinophyceae) ITS2 sequence assemblages in the reef building coral Montipora capitata.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS One</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">MCR</style></keyword><keyword><style  face="normal" font="default" size="100%">populations</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">e38440</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Parental effects are ubiquitous in nature and in many organisms play a particularly critical role in the transfer of symbionts across generations; however, their influence and relative importance in the marine environment has rarely been considered. Coral reefs are biologically diverse and productive marine ecosystems, whose success is framed by symbiosis between reef-building corals and unicellular dinoflagellates in the genus Symbiodinium. Many corals produce aposymbiotic larvae that are infected by Symbiodinium from the environment (horizontal transmission), which allows for the acquisition of new endosymbionts (different from their parents) each generation. In the remaining species, Symbiodinium are transmitted directly from parent to offspring via eggs (vertical transmission), a mechanism that perpetuates the relationship between some or all of the Symbiodinium diversity found in the parent through multiple generations. Here we examine vertical transmission in the Hawaiian coral Montipora capitata by comparing the Symbiodinium ITS2 sequence assemblages in parent colonies and the eggs they produce. Parental effects on sequence assemblages in eggs are explored in the context of the coral genotype, colony morphology, and the environment of parent colonies. Our results indicate that ITS2 sequence assemblages in eggs are generally similar to their parents, and patterns in parental assemblages are different, and reflect environmental conditions, but not colony morphology or coral genotype. We conclude that eggs released by parent colonies during mass spawning events are seeded with different ITS2 sequence assemblages, which encompass phylogenetic variability that may have profound implications for the development, settlement and survival of coral offspring.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><accession-num><style face="normal" font="default" size="100%">LTER.2012-93504</style></accession-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Franklin, E. C.</style></author><author><style face="normal" font="default" size="100%">Stat, M.</style></author><author><style face="normal" font="default" size="100%">Pochon, X.</style></author><author><style face="normal" font="default" size="100%">Putnam, H. M.</style></author><author><style face="normal" font="default" size="100%">Gates, R. D.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">GeoSymbio: A hybrid, cloud-based web application of global geospatial bioinformatics and ecoinformatics for Symbiodinium-host symbioses</style></title><secondary-title><style face="normal" font="default" size="100%">Molecular Ecology Resources</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">biogeography</style></keyword><keyword><style  face="normal" font="default" size="100%">bioinformatics</style></keyword><keyword><style  face="normal" font="default" size="100%">ecoinformatics</style></keyword><keyword><style  face="normal" font="default" size="100%">hybrid web application</style></keyword><keyword><style  face="normal" font="default" size="100%">MCR</style></keyword><keyword><style  face="normal" font="default" size="100%">populations</style></keyword><keyword><style  face="normal" font="default" size="100%">symbiodinium</style></keyword><keyword><style  face="normal" font="default" size="100%">symbioses</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">369-373</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The genus Symbiodinium encompasses a group of unicellular, photosynthetic dinoflagellates that are found free living or in hospite with a wide range of marine invertebrate hosts including scleractinian corals. We present GeoSymbio, a hybrid web application that provides an online, easy to use and freely accessible interface for users to discover, explore and utilize global geospatial bioinformatic and ecoinformatic data on Symbiodinium host symbioses. The novelty of this application lies in the combination of a variety of query and visualization tools, including dynamic searchable maps, data tables with filter and grouping functions, and interactive charts that summarize the data. Importantly, this application is hosted remotely or in the cloud using Google Apps, and therefore does not require any specialty GIS, web programming or data programming expertise from the user. The current version of the application utilizes Symbiodinium data based on the ITS2 genetic marker from PCR-based techniques, including denaturing gradient gel electrophoresis, sequencing and cloning of specimens collected during 1982-2010. All data elements of the application are also downloadable as spatial files, tables and nucleic acid sequence files in common formats for desktop analysis. The application provides a unique tool set to facilitate research on the basic biology of Symbiodinium and expedite new insights into their ecology, biogeography and evolution in the face of a changing global climate. GeoSymbio can be accessed at https://sites.google.com/site/geosymbio/.</style></abstract><accession-num><style face="normal" font="default" size="100%">LTER.2012-86903</style></accession-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Pochon, X.</style></author><author><style face="normal" font="default" size="100%">Putnam, H. M.</style></author><author><style face="normal" font="default" size="100%">Burki, F.</style></author><author><style face="normal" font="default" size="100%">Gates, R. D.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Identifying and characterizing alternative molecular markers for the symbiotic and free-living dinoflagellate genus Symbiodinium.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS One</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">MCR</style></keyword><keyword><style  face="normal" font="default" size="100%">populations</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><edition><style face="normal" font="default" size="100%">4 January 2012</style></edition><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">e29816</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Dinoflagellates in the genus Symbiodinium are best known as endosymbionts of corals and other invertebrate as well as protist hosts, but also exist free-living in coastal environments. Despite their importance in marine ecosystems, less than 10 loci have been used to explore phylogenetic relationships in this group, and only the multi-copy nuclear ribosomal Internal Transcribed Spacer (ITS) regions 1 and 2 have been used to characterize fine-scale genetic diversity within the nine clades (A–I) that comprise the genus. Here, we describe a three-step molecular approach focused on 1) identifying new candidate genes for phylogenetic analysis of Symbiodinium spp., 2) characterizing the phylogenetic relationship of these candidate genes from DNA samples spanning eight Symbiodinium clades (A–H), and 3) conducting in-depth phylogenetic analyses of candidate genes displaying genetic divergences equal or higher than those within the ITS-2 of Symbiodinium clade C. To this end, we used bioinformatics tools and reciprocal comparisons to identify homologous genes from 55,551 cDNA sequences representing two Symbiodinium and six additional dinoflagellate EST libraries. Of the 84 candidate genes identified, 7 Symbiodinium genes (elf2, coI, coIII, cob, calmodulin, rad24, and actin) were characterized by sequencing 23 DNA samples spanning eight Symbiodinium clades (A–H). Four genes displaying higher rates of genetic divergences than ITS-2 within clade C were selected for in-depth phylogenetic analyses, which revealed that calmodulin has limited taxonomic utility but that coI, rad24, and actin behave predictably with respect to Symbiodinium lineage C and are potential candidates as new markers for this group. The approach for targeting candidate genes described here can serve as a model for future studies aimed at identifying and testing new phylogenetically informative genes for taxa where transcriptomic and genomics data are available.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><accession-num><style face="normal" font="default" size="100%">LTER.2012-93505</style></accession-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Stat, M.</style></author><author><style face="normal" font="default" size="100%">Bird, C. E.</style></author><author><style face="normal" font="default" size="100%">Pochon, X.</style></author><author><style face="normal" font="default" size="100%">Chasqui, L.</style></author><author><style face="normal" font="default" size="100%">Chauka, L. J.</style></author><author><style face="normal" font="default" size="100%">Concepcion, G. T.</style></author><author><style face="normal" font="default" size="100%">Logan, D.</style></author><author><style face="normal" font="default" size="100%">Takabayashi, M.</style></author><author><style face="normal" font="default" size="100%">Gates, R. D.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Variation in Symbiodinium ITS2 sequence assemblages among coral colonies.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS One</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">MCR</style></keyword><keyword><style  face="normal" font="default" size="100%">populations</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><edition><style face="normal" font="default" size="100%">2011</style></edition><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">e15854</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Endosymbiotic dinoflagellates in the genus Symbiodinium are fundamentally important to the biology of scleractinian corals, as well as to a variety of other marine organisms. The genus Symbiodinium is genetically and functionally diverse and the taxonomic nature of the union between Symbiodinium and corals is implicated as a key trait determining the environmental tolerance of the symbiosis. Surprisingly, the question of how Symbiodinium diversity partitions within a species across spatial scales of meters to kilometers has received little attention, but is important to understanding the intrinsic biological scope of a given coral population and adaptations to the local environment. Here we address this gap by describing the Symbiodinium ITS2 sequence assemblages recovered from colonies of the reef building coral Montipora capitata sampled across Kaneohe Bay, Hawaii. A total of 52 corals were sampled in a nested design of Coral Colony(Site(Region)) reflecting spatial scales of meters to kilometers. A diversity of Symbiodinium ITS2 sequences was recovered with the majority of variance partitioning at the level of the Coral Colony. To confirm this result, the Symbiodinium ITS2 sequence diversity in six M. capitata colonies were analyzed in much greater depth with 35 to 55 clones per colony. The ITS2 sequences and quantitative composition recovered from these colonies varied significantly, indicating that each coral hosted a different assemblage of Symbiodinium. The diversity of Symbiodinium ITS2 sequence assemblages retrieved from individual colonies of M. capitata here highlights the problems inherent in interpreting multi-copy and intra-genomically variable molecular markers, and serves as a context for discussing the utility and biological relevance of assigning species names based on Symbiodinium ITS2 genotyping.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><accession-num><style face="normal" font="default" size="100%">LTER.2011-86103</style></accession-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Pochon, X.</style></author><author><style face="normal" font="default" size="100%">Stat, M.</style></author><author><style face="normal" font="default" size="100%">Takabayashi, M.</style></author><author><style face="normal" font="default" size="100%">Chasqui, L.</style></author><author><style face="normal" font="default" size="100%">Chauka, L. J.</style></author><author><style face="normal" font="default" size="100%">Logan, D. D. K.</style></author><author><style face="normal" font="default" size="100%">Gates, R. D.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Comparison of endosymbiotic and free-living Symbiodinium (Dinophyceae) diversity in a Hawaiian reef environment</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Phycology</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">MCR</style></keyword><keyword><style  face="normal" font="default" size="100%">populations</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year></dates><volume><style face="normal" font="default" size="100%">46</style></volume><pages><style face="normal" font="default" size="100%">53-65</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Many scleractinian corals must acquire their endosymbiotic dinoflagellates (genus Symbiodinium) anew each generation from environmental pools, and exchange between endosymbiotic and environmental pools of Symbiodinium (reef waters and sediments) has been proposed as a mechanism for optimizing coral physiology in the face of environmental change. Our understanding of the diversity of Symbiodinium spp. in environmental pools is poor by comparison to that engaged in endosymbiosis, which reflects the challenges of visualizing the genus against the backdrop of the complex and diverse micro-eukaryotic communities found free-living in the environment. Here, the molecular diversity of Symbiodinium living in the waters and sediments of a reef near Coconut Island, O'ahu, Hawai'i, sampled at four hourly intervals over a period of 5 d was characterized using a Symbiodinium-specific hypervariable region of the chloroplast 23S. A comparison of Symbiodinium spp. diversity recovered from environmental samples with the endosymbiotic diversity in coral species that dominate the adjacent reef revealed limited overlap between these communities. These data suggest that the potential for infection, exchange, and/or repopulation of corals with Symbiodinium derived from the environment is limited at this location, a finding that is perhaps consistent with the high proportion of coral species in this geographic region that transmit endosymbionts from generation to generation.</style></abstract><accession-num><style face="normal" font="default" size="100%">LTER.2010-83545</style></accession-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Green, D. H.</style></author><author><style face="normal" font="default" size="100%">Edmunds, P.J.</style></author><author><style face="normal" font="default" size="100%">Pochon, X.</style></author><author><style face="normal" font="default" size="100%">Gates, R. D.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The effects of substratum type on the growth, mortality, and phytophysiology of juvenile corals in St. John, US Virgin Islands</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Experimental Marine Biology and Ecology</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">MCR</style></keyword><keyword><style  face="normal" font="default" size="100%">populations</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year></dates><volume><style face="normal" font="default" size="100%">384</style></volume><pages><style face="normal" font="default" size="100%">18-29</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Coral larvae are selective with regards to the surfaces upon which they settle, but little is known about the outcome of these choices. In this study, we explored the implications for juvenile scleractinians (&lt;40-mm diameter) of growing on igneous versus carbonate rock on the shallow reefs (5-m depth) of St. John, US Virgin Islands. Surveys revealed that juvenile corals occurred at densities of 16 colonies m(-2) and were distributed on igneous and carbonate rocks in proportion to the abundance of these surfaces, suggesting that larvae do not discriminate between rock types at settlement. Repeated surveys demonstrated that all juvenile corals (i.e., pooled among taxa) grew 41% slower on igneous versus carbonate rock between January and August, but not between August and January when the growth was statistically indistinguishable between rock types. Although the growth of the most common juvenile coral, Porites astreoides, was similar on both substrata, the photophysiology of this species was affected by the type of rock. The maximum relative electron transfer rate (rETR, a proxy for photosynthesis) of P. astreoides was down-regulated 30% on igneous compared to carbonate rock. Phylogenetic analyses of the Symbiodinium community sequence profiles within P. astreoides revealed significant differences between substrata, with a greater diversity of co-occurring ITS-2 sequences in corals growing on carbonate compared to igneous rock. While substratum-dependent patterns in the characteristics of juvenile corals suggested there is selective value to the settlement choices made by larvae, these trends did not translate into differences in survival, at least over the time scale investigated. It remains uncertain what features of the rocks affected coral performance, but differences in the temperature of the rock may be an important feature during the warmest period of the year.</style></abstract><accession-num><style face="normal" font="default" size="100%">LTER.2010-83542</style></accession-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Chan, Y. L.</style></author><author><style face="normal" font="default" size="100%">Pochon, X.</style></author><author><style face="normal" font="default" size="100%">Fisher, M. A.</style></author><author><style face="normal" font="default" size="100%">Wagner, D.</style></author><author><style face="normal" font="default" size="100%">Concepcion, G. T.</style></author><author><style face="normal" font="default" size="100%">Kahng, S.</style></author><author><style face="normal" font="default" size="100%">Toonen, R. J.</style></author><author><style face="normal" font="default" size="100%">Gates, R. D.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Generalist dinoflagellate endosymbionts and host genotype diversity detected from mesophotic (67-100 m depths) coral Leptoseris</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Ecology</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">MCR</style></keyword><keyword><style  face="normal" font="default" size="100%">populations</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">21</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><accession-num><style face="normal" font="default" size="100%">LTER.2009-83513</style></accession-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Stat, M.</style></author><author><style face="normal" font="default" size="100%">Pochon, X.</style></author><author><style face="normal" font="default" size="100%">Cowie, R. O. M.</style></author><author><style face="normal" font="default" size="100%">Gates, R. D.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Specificity in communities of Symbiodinium in corals from Johnston Atoll</style></title><secondary-title><style face="normal" font="default" size="100%">Marine Ecology-Progress Series</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">MCR</style></keyword><keyword><style  face="normal" font="default" size="100%">populations</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">&lt;Go to ISI&gt;://000268552500007</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">386</style></volume><pages><style face="normal" font="default" size="100%">83-96</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The diversity of endosymbiotic dinoflagellates (Symbiodinium) in corals at Johnston Atoll in the central Pacific Ocean was assessed using both the internal transcribed spacer 2 (ITS2) region of the nuclear rDNA and chloroplast 23S rDNA. More sequences were recovered from corals using the ITS2 primers than with the chloroplast 23S primers, a finding that reflects both the higher taxonomic resolution and level of intragenomic variation in ITS2 in eukaryotes as compared to chloroplast 23S. Parsimony network analysis, Bray-Curtis coefficient of similarity and 1-way analysis of similarity resolved coral species- and/or genus-specific lineages and/or groupings of Symbiodinium that were generally congruent between the 2 genetic markers. Comparison of coral-Symbiodinium assemblages at Johnston Atoll with those in corals sampled on other reefs in the Pacific reveals differences that include novel host-symbiont unions and a Symbiodinium lineage previously reported to be Caribbean-specific in Acropora from Johnston Atoll.</style></abstract><accession-num><style face="normal" font="default" size="100%">LTER.2009-83532</style></accession-num></record></records></xml>