Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics

Abstract

Dinoflagellates are key species in marine environments, but they remain poorly understood in part because of their large, complex genomes, unique molecular biology, and unresolved in-group relationships. We created a taxonomically representative dataset of dinoflagellate transcriptomes and used this to infer a strongly supported phylogeny to map major morphological and molecular transitions in dinoflagellate evolution. Our results show an early-branching position of Noctiluca, monophyly of thecate (plate-bearing) dinoflagellates, and paraphyly of athecate ones. This represents unambiguous phylogenetic evidence for a single origin of the group's cellulosic theca, which we show coincided with a radiation of cellulases implicated in cell division. By integrating dinoflagellate molecular, fossil, and biogeochemical evidence, we propose a revised model for the evolution of thecal tabulations and suggest that the late acquisition of dinosterol in the group is inconsistent with dinoflagellates being the source of this biomarker in pre-Mesozoic strata. Three distantly related, fundamentally nonphotosynthetic dinoflagellates, Noctiluca, Oxyrrhis, and Dinophysis, contain cryptic plastidial metabolisms and lack alternative cytosolic pathways, suggesting that all free-living dinoflagellates are metabolically dependent on plastids. This finding led us to propose general mechanisms of dependency on plastid organelles in eukaryotes that have lost photosynthesis; it also suggests that the evolutionary origin of bioluminescence in nonphotosynthetic dinoflagellates may be linked to plastidic tetrapyrrole biosynthesis. Finally, we use our phylogenetic framework to show that dinoflagellate nuclei have recruited DNA-binding proteins in three distinct evolutionary waves, which included two independent acquisitions of bacterial histone-like proteins.

Keywords: dinoflagellates; dinosterol; phylogeny; plastids; theca.

Fig. 1.

Multiprotein phylogeny of dinoflagellates. (A) Best maximum-likelihood tree (IQ-Tree) of dinoflagellates and relatives based on 101-protein dataset (root 1 matrix, 43 species, 29,400 sites). Branches show ultrafast bootstraps (IQ-Tree)/nonparametric bootstraps (RAxML)/posterior probabilities (PhyloBayes) (dash indicates <50/50/0.5 support; filled circles indicate 100/100/1 support; dt indicates a different topology). Roots of alternative matrices (Perkinsus, root 2, 30,780 sites; and Noctiluca, root 3, 30,988 sites) are shown by arrows. (B) Overview of branch supports for principal findings (taxon and matrix abbreviations as underlined in A) in phylogenies of 12 matrices that differ by their root (R1–R3) and species presence (All, All - Din, All - Pro, All - Din & Pro; SI Appendix, Table S1). (C) Two placements of Dinophysis (Din) relative to Gon, Per, and Sym thecates and a variable position of Prorocentrum (Pro) as identified in phylogenies of the 12 matrices (SI Appendix, Table S3, provides tree topology tests).

Fig. 2.

Thecal evolution and dinoflagellate paleohistory. (A) Phylogeny-driven model of changes between major modern and fossil (crosses) tabulational types. Gymnodinoid tabulation with numerous small, empty amphiesmal vesicles is ancestral and gave rise to the gonyaulacoid–peridinioid tabulation with a few large, cellulose-rich thecal plates. Suessioid and gymnodinioid tabulations in modern Symbiodiniaceae and Borghiellaceae (asterisk) are derived independently of the standard gymnodiniod and Triassic suessioid tabulations (Suessia), and are characterized by decrease or loss of cellulose content. Prorocentroid and dinophysioid tabulations are derived from the gonyaulacoid–peridiniod tabulation (the latter probably via a nannoceratopsioid intermediate). Triassic suessioid and rhaetogonyaulacoid tabulations may represent evolutionary intermediates or independent experiments in thecal plate reduction. (B) Maximum-likelihood phylogeny (IQ-Tree) of 184 eukaryotic GH7 proteins reveals cellulases in athecate dinoflagellates (underlined) and their radiation in the thecate (color-coded). Black rectangles indicate 50% reduction in branch length. Known GH7 cellulases in P. lunula (dCel1) and Lingulodinium polyedrum (dCel2) are shown. Further details are provided in SI Appendix, Fig. S1 and Table S4. (C) Alternative hypotheses (H1 and H2) on the first emergence of triaromatic dinosteranes attributable to dinoflagellates or their direct ancestors (H2 is preferred by our data). Relative species numbers of dinoflagellates (a) and acritarchs (b) and percentage of dinosterane-positive samples (c; see ref. for sample data) from the Proterozoic (green), Paleozoic (red), and Mesozoic (blue) are shown together with the predicted emergence of the last common ancestor (LCA) of modern thecates. Reprinted with permission from refs. , (www.sciencedirect.com/science/journal/14344610), (permission conveyed through Copyright Clearance Center, Inc.), and .

Fig. 3.

Plastid metabolism and dependency in nonphotosyntetic dinoflagellates. (A) Phylogeny-driven reconstruction of plastid and nonplastid variants of core metabolism (isoprenoid, tetrapyrrole, and fatty acid biosynthesis) in genomes (marked as “G”) or transcriptomes (“T”) of dinoflagellates and relatives. Individual enzymes (SI Appendix, Table S5) were classified by protein phylogenies and color-coded as to their presence/absence and origin. The data suggest that Oxyrrhis, Noctiluca, and Dinophysis are metabolically dependent on plastids. Metabolite (Met.) uptake was summarized from the literature. (B) Maximum-likelihood phylogeny (IQ-Tree) reveals IspCs of cyanobacterial origin in nonphotosynthetic dinoflagellates and relatives (bold); ultrafast bootstraps at branches are shown (>50 shown; ≥95 highlighted; filled circles, 100). (C) Three grades in functional organization of core metabolic pathways in nonphotosynthetic plastids in dinoflagellates (blue) and relatives (“P” represents parasites). (D) Model for evolutionary dependency on plastids in dinoflagellates and relatives, which is applicable to other eukaryotes. Ancestral dependency (marked as “d”) on plastid metabolism (loss of cytosolic isoprenoid biosynthesis; later reinforced by the loss of C4 tetrapyrrole biosynthesis in some taxa) led to retention of plastids in all free-living and many parasitic descendants. The dependency can be transferred onto a new plastidial symbiont (Kareniaceae) or host organism (in parasites dependent solely on host-derived metabolites); only the latter leads to an outright loss of the plastid.

Fig. 4.

Evolution of histone-like proteins. Phylogeny of bacterial (HU-like) and dinoflagellate HLPs reveals a dinoflagellate-type histone-like protein, HLP-II, in early-branching core dinoflagellates. HLP-II has a mutually exclusive distribution with HLP-I (e.g., the characterized HCc3 in C. cohnii, in bold). Further details are provided in SI Appendix, Fig. S3 and Table S4.

Fig. 5.

Model for character evolution in dinoflagellates. Ancestral character states (filled circles) of conserved traits are reconstructed on the consensus phylogeny of dinoflagellates and their relatives by parsimony (arrowheads). Dotted branches in the thecate lineages indicate uncertain placement. Gaps indicate missing data, and “not applicable” denotes plastid genome absence or the presence of a different plastid genome type (Kareniaceae). The vertical square bracket indicates an evolutionary range in which traits emerged. Photos of dinoflagellates (by G. S. Gavelis), left to right: Kofoidinium sp. (Noctilucales), Nematodinium sp. (Gymnodiniaceae s.s.), Neoceratium praelongum (Gonyaulacales), Dinophysis miles (Dinophysiales), and Heterocapsa sp. (Peridiniales).