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Supplemental Information

Single-gene phylogenies of Symbiodinium using two genes from three organelles

Best Maximum likelihood (ML) topologies for Symbiodinium clades and sub-clades A to I based on the nuclear genes (A) nr28S and (B) elf2, the chloroplastic genes (C) cp23S and (D) psbA, and the mitochondrial genes (E) coI and (F) cob. Numbers in brackets refer to the Symbiodinium strains detailed in Table 2. Numbers at nodes represent the ML bootstrap pseudoreplicate (BP) values (underlined numbers; 100 BP performed) and Bayesian posterior probabilities (BiPP). Black dots represent nodes with 100% BP and BiPP of 1.0. Nodes without numbers correspond to BP and BiPP lower than 70% and 0.8, respectively. Nodes displaying BP lower than 50% were manually collapsed. The phylograms were rooted using the dinoflagellates Gymnodinium simplex, Pelagodinium beii, and/or Polarella glacialis. GenBank accession numbers are given in Table 2. Note: All clades are represented, except for clade E in the elf2 phylogeny.

DOI: 10.7287/peerj.preprints.267v1/supp-1

Supermatrics topology of Symbiodinium based on six concatenated genes

Best Maximum likelihood (ML) topology for Symbiodinium clades and sub-clades A to I based on fully concatenated DNA alignment (ALL Concat; 4,703 bp) of all six genes investigated in this study. The Symbiodinium strains within each clade/sub-clade are referred using the specific numbers and corresponding ITS2 names in brackets (Table 2; Figure 1). Numbers at nodes represent the ML bootstrap pseudoreplicate (BP) values (underlined numbers; 100 BP performed) and Bayesian posterior probabilities (BiPP). Black dots represent nodes with 100% BP and BiPP of 1.0. The phylograms were rooted using the dinoflagellates Gymnodinium simplex, Pelagodinium beii, and Polarella glacialis.

DOI: 10.7287/peerj.preprints.267v1/supp-2

The nine clades (A-I) and eight sub-clades (D1-D2, F2-F5, and G1-G2) that constitute the genus Symbiodinium, with selected literature highlighting the habitat prevalence/preference of each lineage.

DOI: 10.7287/peerj.preprints.267v1/supp-3

Description of Symbiodinium samples, host origin, and GenBank accession numbers of all DNAs used in this study.

DOI: 10.7287/peerj.preprints.267v1/supp-4

Selected model of evolution and corresponding parameters for each DNA alignment used in this study.

DOI: 10.7287/peerj.preprints.267v1/supp-5

Summary of Approximately Unbiased (AU) topological congruency tests performed between each DNA alignment and best ML topology.

For each comparison, Table A and B shows the log likelihood difference and AU test p-value in brackets. *Accepted topologies display a p-value > 0.05 (highlighted in grey). A) Comparisons of single gene DNA alignments to single gene topologies. Elongation Factor 2 (elf2) is missing from these calculations due to missing data (missing sample #27 and #30). B) Comparisons of single gene and concatenated DNA alignments to the concatenated topologies. elf2 was included in the concatenated alignments, where sample #27 and #30 were coded as missing data.

DOI: 10.7287/peerj.preprints.267v1/supp-6

Additional Information

Competing Interests

The authors have declared that no competing interests exist. Xavier Pochon is an employee of The Cawthron Institute.

Author Contributions

Xavier Pochon conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Hollie M Putnam conceived and designed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Ruth D Gates conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Grant Disclosures

The following grant information was disclosed by the authors:

NSF OCE-0752604

NSF UH EPSCoR EPS-0903833

Swiss NSF PBGEA-115118

US EPA FP917199

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

All sequences have been deposited in GenBank. A detailed table is provided in the manuscript. All sequence accession numbers starting with "JQ" are novel:

JN558040 JN557869 JN557969 JN557844 JN557891 JN557943

JN558045 JN557871 JN557975 JN557846 JN557893 JN557945

JN558048 JN557872 JN557978 JN557847 JN557894 JN557946

JN558042 JN557870 JN557972 JN557845 JN557892 JN557944

JN558051 JN557873 JN557981 JN557848 JN557895 JN557947

JN558053 JN557874 JN557984 JN557849 JN557896 JN557948

JQ247043 JQ277946 JQ247052 JQ277935 JQ277957 JQ277979

JQ247044 JQ277947 JQ247053 JQ277936 JQ277958 JQ277980

JQ247046 JQ277949 JQ247055 JQ277938 JQ277960 JQ277982

JQ247045 JQ277948 JQ247054 JQ277937 JQ277959 JQ277981

JQ247047 JQ277950 JQ247056 JQ277939 JQ277961 JQ277983

JQ247048 JQ277951 JQ247057 JQ277940 JQ277962 JQ277984

JN558063 JN557876 JN557996 JN557851 JN557898 JN557950

JN558069 JN557877 JN558000 JN557852 JN557899 JN557951

JN558066 JN557875 JN557997 JN557850 JN557897 JN557949

JN558072 JN557878 JN558004 JN557853 JN557900 JN557952

JN558057 JN557879 JN557991 JN557854 JN557901 JN557953

JN558060 JN557880 JN557993 JN557855 JN557902 JN557954

JN558055 JN557881 JN557987 JN557856 JN557903 JN557955

FN561559 JQ277955 FN561563 JQ277944 JQ277966 JQ277988

FN561560 JQ277956 FN561564 JQ277945 JQ277967 JQ277989

JN558075 JN557882 JN558007 JN557857 JN557904 JN557956

JN558078 JN557883 JN558010 JN557858 JN557905 JN557957

JQ247049 JQ277952 JQ247058 JQ277941 JQ277963 JQ277985

JN558081 JN557884 JN558013 JN557859 JN557906 JN557958

JN558089 JN557885 JN558019 JN557860 JN557907 JN557959

JN558088 JN558017 JN557861 JN557908 JN557960

JQ247050 JQ277953 JQ247059 JQ277942 JQ277964 JQ277986

JQ247051 JQ277954 JQ247060 JQ277943 JQ277965 JQ277987

JN558084 JN558015 JN557862 JN557909 JN557961

JN558097 JN557887 JN558029 JN557864 JN557911 JN557963

JN558100 JN557888 JN558032 JN557865 JN557912 JN557964

JN558091 JN557889 JN558021 JN557866 JN557913 JN557965

JN558094 JN557886 JN558027 JN557863 JN557910 JN557962

JN558103 JN557890 JN558033 JN557867 JN557914 JN557966

JN558106 JN557915 JN557967

JN558108 JN558036 JN557868 JN557916 JN557968

Funding

This research was funded by grants from NSF to RDG (OCE-0752604) and NSF UH EPSCoR (EPS-0903833), and the Swiss National Science Foundation (PBGEA-115118 to XP). HMP was supported by funds from the US EPA (FP917199). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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