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.
Pyrenoid_S.glynnii_example1
3-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-protocol
Pyrenoid_S.glynnii_example2
3-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-protocol
Pyrenoid_S.glynnii_example3
3-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-protocol
Pyrenoid_S.glynnii_example4
3-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-protocol
Pyrenoid_S.glynnii_example5
3-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-protocol
Pyrenoid_S.glynnii_example6
3-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-protocol
Pyrenoid_S.glynnii_example7
3-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-protocol
psbA 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_DryadFile
Cell1_Pal16_1_ROI_02.1a
Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.
Cell1_Pal16_1_ROI_02.1b
Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.
Cell1_Pal16_1_ROI_02.1c
Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.
Cell2_Pal16_1-2_sept19b
Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.
Cell2_Pal16-1-2_Sept19a
Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.
Cell3_Chromosome_counts_S.glynnii
Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.
Cell4_Pal16-1-2-sept19-cell3
Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.
Cell5_Pal16_1_glynnii_ROI_01a
Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.
Cell5_Pal16_1_glynnii_ROI_01b
Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.
Cell5_Pal16_1_glynnii_ROI_01c
Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.
Cell5_Pal16_1_glynnii_ROI_01d
Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.
SymbXGb.r
This 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 Dataset
Master file of microsatellite data, including host identity and location information, Symbiodinium species, ITS2 genotype
makeTrainTest
R 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