DOI: 10.5061/dryad.mg363
title: Data from: Symbiodinium glynnii sp. nov., a species of stress-tolerant symbiotic dinoflagellates from pocilloporid and montiporid corals in the Pacific Ocean

description: A formal Symbiodinium species taxonomy enhances understanding of the
 physiology and ecology of coral–dinoflagellate symbioses. Here we formally
 define a new species of stress tolerant Symbiodinium in Clade D,
 Symbiodinium glynnii sp. nov. This species exhibits high host specificity
 for members of the stony coral genus Pocillopora in the Pacific Ocean and
 can also be found in symbiosis with the coral genera Seriatopora and
 Montipora. Symbiodinium glynnii is especially common in the Eastern
 Tropical and subtropical Pacific, where Pocillopora is abundant and
 ecologically important. While S. glynnii is evolutionarily closely related
 to Symbiodinium trenchii, a combination of multilocus genetic data
 including rDNA, chloroplast (psbA), and single copy nuclear
 microsatellites, as well as differences in ecology (host associations),
 morphology (cell size), and ultrastructure (chromosome size), identify S.
 glynnii as distinct from S. trenchii and other Clade D species. Finally we
 use these data to parameterize a provisional classification and regression
 model to show how closely related species are recognized by integrating
 multiple sources of evidence.
description: Pyrenoid_S.glynnii_example13-D movie reconstruction of pyrenoid ultrastructure showing connections (stalks) to the cell cytoplasm and chloroplast lobes. Data were obtained from serial block face scanning electron microscopy on preserved cells of Symbiodinium glynnii sp. nov. Detailed protocol concerning the chemical fixation and preparation of specimens for serial block face scanning electron microscopy available at Deerinck TJ, Bushong EA, Thor A, and Ellisman EH (2010). NCMIR Methods for 3D EM: A New Protocol for Preparation of Biological Specimens for Serial Blockface Scanning Electron Microscopy. SBEM Protocol version 7_01_10. Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA. https://ncmir.ucsd.edu/sbem-protocolPyrenoid_S.glynnii_example23-D movie reconstruction of pyrenoid ultrastructure showing connections (stalks) to the cell cytoplasm and chloroplast lobes. Data were obtained from serial block face scanning electron microscopy on preserved cells of Symbiodinium glynnii sp. nov. Detailed protocol concerning the chemical fixation and preparation of specimens for serial block face scanning electron microscopy available at Deerinck TJ, Bushong EA, Thor A, and Ellisman EH (2010). NCMIR Methods for 3D EM: A New Protocol for Preparation of Biological Specimens for Serial Blockface Scanning Electron Microscopy. SBEM Protocol version 7_01_10. Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA. https://ncmir.ucsd.edu/sbem-protocolPyrenoid_S.glynnii_example33-D movie reconstruction of pyrenoid ultrastructure showing connections (stalks) to the cell cytoplasm and chloroplast lobes. Data were obtained from serial block face scanning electron microscopy on preserved cells of Symbiodinium glynnii sp. nov. Detailed protocol concerning the chemical fixation and preparation of specimens for serial block face scanning electron microscopy available at Deerinck TJ, Bushong EA, Thor A, and Ellisman EH (2010). NCMIR Methods for 3D EM: A New Protocol for Preparation of Biological Specimens for Serial Blockface Scanning Electron Microscopy. SBEM Protocol version 7_01_10. Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA. https://ncmir.ucsd.edu/sbem-protocolPyrenoid_S.glynnii_example43-D movie reconstruction of pyrenoid ultrastructure showing connections (stalks) to the cell cytoplasm and chloroplast lobes. Data were obtained from serial block face scanning electron microscopy on preserved cells of Symbiodinium glynnii sp. nov. Detailed protocol concerning the chemical fixation and preparation of specimens for serial block face scanning electron microscopy available at Deerinck TJ, Bushong EA, Thor A, and Ellisman EH (2010). NCMIR Methods for 3D EM: A New Protocol for Preparation of Biological Specimens for Serial Blockface Scanning Electron Microscopy. SBEM Protocol version 7_01_10. Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA. https://ncmir.ucsd.edu/sbem-protocolPyrenoid_S.glynnii_example53-D movie reconstruction of pyrenoid ultrastructure showing connections (stalks) to the cell cytoplasm and chloroplast lobes. Data were obtained from serial block face scanning electron microscopy on preserved cells of Symbiodinium glynnii sp. nov. Detailed protocol concerning the chemical fixation and preparation of specimens for serial block face scanning electron microscopy available at Deerinck TJ, Bushong EA, Thor A, and Ellisman EH (2010). NCMIR Methods for 3D EM: A New Protocol for Preparation of Biological Specimens for Serial Blockface Scanning Electron Microscopy. SBEM Protocol version 7_01_10. Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA. https://ncmir.ucsd.edu/sbem-protocolPyrenoid_S.glynnii_example63-D movie reconstruction of pyrenoid ultrastructure showing connections (stalks) to the cell cytoplasm and chloroplast lobes. Data were obtained from serial block face scanning electron microscopy on preserved cells of Symbiodinium glynnii sp. nov. Detailed protocol concerning the chemical fixation and preparation of specimens for serial block face scanning electron microscopy available at Deerinck TJ, Bushong EA, Thor A, and Ellisman EH (2010). NCMIR Methods for 3D EM: A New Protocol for Preparation of Biological Specimens for Serial Blockface Scanning Electron Microscopy. SBEM Protocol version 7_01_10. Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA. https://ncmir.ucsd.edu/sbem-protocolPyrenoid_S.glynnii_example73-D movie reconstruction of pyrenoid ultrastructure showing connections (stalks) to the cell cytoplasm and chloroplast lobes. Data were obtained from serial block face scanning electron microscopy on preserved cells of Symbiodinium glynnii sp. nov. Detailed protocol concerning the chemical fixation and preparation of specimens for serial block face scanning electron microscopy available at Deerinck TJ, Bushong EA, Thor A, and Ellisman EH (2010). NCMIR Methods for 3D EM: A New Protocol for Preparation of Biological Specimens for Serial Blockface Scanning Electron Microscopy. SBEM Protocol version 7_01_10. Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA. https://ncmir.ucsd.edu/sbem-protocolpsbA coding and non-coding region (partial sequences)Sequence alignments of partial psbA coding and non-coding region haplotypes of Symbiodinium glynnii sp. nov. from the western, central and eastern Pacific Ocean.PsbA_trenchii_vs_glynni_DryadFileCell1_Pal16_1_ROI_02.1aSerial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.Cell1_Pal16_1_ROI_02.1bSerial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.Cell1_Pal16_1_ROI_02.1cSerial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.Cell2_Pal16_1-2_sept19bSerial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.Cell2_Pal16-1-2_Sept19aSerial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.Cell3_Chromosome_counts_S.glynniiSerial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.Cell4_Pal16-1-2-sept19-cell3Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.Cell5_Pal16_1_glynnii_ROI_01aSerial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.Cell5_Pal16_1_glynnii_ROI_01bSerial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.Cell5_Pal16_1_glynnii_ROI_01cSerial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.Cell5_Pal16_1_glynnii_ROI_01dSerial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.SymbXGb.rThis script creates a classification/regression model then validates the model using a subset of samples where data is complete for all character traits.Master microsatellite DatasetMaster file of microsatellite data, including host identity and location information, Symbiodinium species, ITS2 genotypemakeTrainTestR script that reads in all data sources, merges them into a single master data table, and then divides the data into a training and test set