Multi-gene analysis of the symbiotic and free-living dinoflagellate genus Symbiodinium
- Subject Areas
- Ecology, Evolutionary Studies, Marine Biology, Molecular Biology
- symbiosis, chloroplast, rarity, evolutionary rates, mitochondria, nuclear, dinoflagellate., Symbiodinium, Multi-gene analysis, rarity
- © 2014 Pochon et al.
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2014. Multi-gene analysis of the symbiotic and free-living dinoflagellate genus Symbiodinium. PeerJ PrePrints 2:e267v1 https://doi.org/10.7287/peerj.preprints.267v1
Symbiodinium, a large group of dinoflagellates, live in symbiosis with marine protists, invertebrate metazoans, and free-living in the environment. Symbiodinium are functionally variable and play critical energetic roles in symbiosis. Our knowledge of Symbiodinium has been historically constrained by the limited number of molecular markers available to study evolution in the genus. Here we compare six functional genes, representing three cellular compartments, in the nine known Symbiodinium lineages. Despite striking similarities among the single gene phylogenies from distinct organelles, none were evolutionarily identical. A fully concatenated reconstruction, however, yielded a well-resolved topology identical to the current benchmark nr28S gene. Evolutionary rates differed among cellular compartments and clades, a pattern largely driven by higher rates of evolution in the chloroplast genes of Symbiodinium clades D2 and I. The rapid rates of evolution observed amongst these relatively uncommon Symbiodinium lineages in the functionally critical chloroplast may translate into potential innovation for the symbiosis. The multi-gene analysis highlights the potential power of assessing genome-wide evolutionary patterns using recent advances in sequencing technology and emphasizes the importance of integrating ecological data with more comprehensive sampling of free-living and symbiotic Symbiodinium in assessing the evolutionary adaptation of this enigmatic dinoflagellate.
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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.
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.
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.
Description of Symbiodinium samples, host origin, and GenBank accession numbers of all DNAs used in this study.
Selected model of evolution and corresponding parameters for each DNA alignment used in this study.
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.