Heterotachy Processes in Rhodophyte-Derived Secondhand Plastid Genes: Implications for Addressing the Origin and Evolution of Dinoflagellate Plastids

Heterotachy Processes in Rhodophyte-Derived Secondhand Plastid Genes: Implications for Addressing the Origin and Evolution of Dinoflagellate Plastids Kamran Shalchian-Tabrizi,* Marianne Skånseng,* Fredrik Ronquist, 1 Dag Klaveness,à Tsvetan R. Bachvaroff,§2 Charles F. Delwiche,§ Andreas Botnen,k Torstein Tengs,*3 and Kjetill S. Jakobsen* *Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway; Evolutionary Biology Centre, Department of Systematic Zoology, Uppsala University, Uppsala, Sweden; àProgram for Plankton Biology, Department of Biology, University of Oslo, Oslo, Norway; §Cell Biology and Molecular Genetics, University of Maryland, College Park; and kScientific Computer Group, Center for Information Technology Services, University of Oslo, Oslo, Norway Introduction It is widely accepted that rhodophytes, glaucophytes, and virideplantae obtained their plastids from an association with endosymbiontic cyanobacteria (Goksøyr 1967). The plastids of these algae are therefore termed primary. All other algae have probably obtained their plastids secondarily by engulfing eukaryotic algae (Delwiche 1999; Palmer 2003). In this manner, rhodophyte plastids have become incorporated into cryptophytes, heterokonts, haptophytes (defined as the chromists; Cavalier-Smith 1999) as well as into dinoflagellates and apicomplexa (CavalierSmith 1999; Fast et al. 2001; Patron et al. 2004). About half of the dinoflagellates are photosynthetic, harboring endosymbionts and plastids from several eukaryotic phyla (Watanabe et al. 1990; Chesnick et al. 1997; Tengs et al. 2000; Takishita et al. 2002). The vast majority of the dinoflagellate plastids use chlorophyll c and the pigment peri1 Florida State University, Department of Biological Science. Center of Marine Biotechnology, Baltimore, Maryland. 3 National Veterinary Institute, Department of Microbiology, Ullevålsveien 68, Oslo, Norway. 2 Key words: chromalveolates, chromists, covarion, dinoflagellates, heterotachy, plastid evolution. E-mail: . Mol. Biol. Evol. 23(8):1504–1515. 2006 doi:10.1093/molbev/msl011 Advance Access publication May 15, 2006 Ó The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: dinin, usually regarded as the ancestral plastid form (Hoek et al. 1995; Saunders et al. 1997; Saldarriaga et al. 2001). The other small groups of dinoflagellates with aberrant pigmentation have until recently been regarded as representatives of newer plastid lineages that replaced the peridinincontaining plastid during the radiation of dinoflagellates (Saldarriaga et al. 2001; Cavalier-Smith 2003; Patron et al. 2006). One of these replacement events involved a tertiary endosymbiosis of a haptophyte, resulting in dinoflagellates with 19#-hexanoyloxyfucoxanthin, the characteristic carotenoid of haptophytes (hereafter 19#-HNOF; Tengs et al. 2000). This evolutionary scenario for the plastids among dinoflagellates would imply several independent plastid acquisitions, but phylogenetic inference by Yoon et al. (2002) indicated a single origin for the peridininand 19#-HNOF–containing plastids involving engulfment of a haptophyte alga. In contrast to this study, subsequent analysis of protein characters applying 5 plastidencoding genes divided the 2 dinoflagellate plastid groups (Yoon et al. 2005) and placed the peridinin plastids weakly within the heterokonts. Using 9 (and 10) plastid genes, Bachvaroff et al. (2005) showed the peridinin plastid and the haptophytes as sister groups with moderate to weak to support. Thus, the inferences of the dinoflagellate plastids have so far generated incongruent results. When plastids are transferred from one algal host to another, one might expect significant effects on the nature Serial transfer of plastids from one eukaryotic host to another is the key process involved in evolution of secondhand plastids. Such transfers drastically change the environment of the plastids and hence the selection regimes, presumably leading to changes over time in the characteristics of plastid gene evolution and to misleading phylogenetic inferences. About half of the dinoflagellate protists species are photosynthetic and unique in harboring a diversity of plastids acquired from a wide range of eukaryotic algae. They are therefore ideal for studying evolutionary processes of plastids gained through secondary and tertiary endosymbioses. In the light of these processes, we have evaluated the origin of 2 types of dinoflagellate plastids, containing the peridinin or 19#-hexanoyloxyfucoxanthin (19#-HNOF) pigments, by inferring the phylogeny using ‘‘covarion’’ evolutionary models allowing the pattern of among-site rate variation to change over time. Our investigations of genes from secondary and tertiary plastids derived from the rhodophyte plastid lineage clearly reveal ‘‘heterotachy’’ processes characterized as stationary covarion substitution patterns and changes in proportion of variable sites across sequences. Failure to accommodate covarion-like substitution patterns can have strong effects on the plastid tree topology. Importantly, multigene analyses performed with probabilistic methods using among-site rate and covarion models of evolution conflict with proposed single origin of the peridinin- and 19#-HNOF–containing plastids, suggesting that analysis of secondhand plastids can be hampered by convergence in the evolutionary signature of the plastid DNA sequences. Another type of sequence convergence was detected at protein level involving the psaA gene. Excluding the psaA sequence from a concatenated protein alignment grouped the peridinin plastid with haptophytes, congruent with all DNA trees. Altogether, taking account of complex processes involved in the evolution of dinoflagellate plastid sequences (both at the DNA and amino acid level), we demonstrate the difficulty of excluding independent, tertiary origin for both the peridinin and 19#-HNOF plastids involving engulfment of haptophyte-like algae. In addition, the refined topologies suggest the red algal order, Porphyridales, as the endosymbiont ancestor of the secondary plastids in cryptophytes, haptophytes, and heterokonts. Dinoflagellate Plastid Evolution 1505 occur in the majority of sites that are free to vary. The characteristic codon usage in the fast-evolving dinoflagellate plastid genes could explain the conflicting DNA and protein phylogenies of these plastids (Yoon et al. 2002; Inagaki, Simpson et al. 2004; Yoon et al. 2005). Here, we investigate the discrepancies between DNA and protein tree topologies, and reevaluate recent DNA and protein trees taking into account covarion-like substitution patterns, which has been shown for the green algal/plant plastid lineage but to a lesser extent been investigated for the rhodophyte-derived plastid lineages (Lockhart et al. 1998; Ané et al. 2 (...truncated)