Palpitomonas bilix represents a basal cryptist lineage: insight into the character evolution in Cryptista

Abstract

Phylogenetic position of the marine biflagellate Palpitomonas bilix is intriguing, since several ultrastructural characteristics implied its evolutionary connection to Archaeplastida or Hacrobia. The origin and early evolution of these two eukaryotic assemblages have yet to be fully elucidated, and P. bilix may be a key lineage in tracing those groups' early evolution. In the present study, we analyzed a 'phylogenomic' alignment of 157 genes to clarify the position of P. bilix in eukaryotic phylogeny. In the 157-gene phylogeny, P. bilix was found to be basal to a clade of cryptophytes, goniomonads and kathablepharids, collectively known as Cryptista, which is proposed to be a part of the larger taxonomic assemblage Hacrobia. We here discuss the taxonomic assignment of P. bilix, and character evolution in Cryptista.

Figure 1. Phylogenetic position of Palpitomonas bilix inferred from the maximum-likelihood (ML) analysis of a 157-gene alignment (41,372 amino acid positions).

The 157-protein alignment was analyzed by both maximum-likelihood (ML) and Bayesian methods. As the two methods reconstructed very similar trees, only the ML tree is shown here. Upper and lower values at nodes represent ML bootstrap percentage values (MLBPs) and Bayesian posterior probabilities (BPPs). MLBPs <60% and BPPs <0.95 are omitted from the figure. Dots correspond to MLBP of 100% and BPP of 1.00.

Figure 2. Putative protein components of the ejectisomes.

(a). Tri2/3-1 amino acid sequence alignment. Note that Tri2 and Tri3-1 are indistinguishable based on sequence analyses. Amino acid residues shared among more than 15 out of the 19 homologues are shaded. GenBank accession numbers for the amino acid sequences Pyrenomonas helgolandii Tri2 and Tri3-1 are shown in parentheses. For Tri2/3-1 homologues of Guillaria theta, the protein ids are shown parentheses. For those of R. truncate and those of Goniomonas sp. and Go. avonlea, the Genbank accession numbers and contig numbers of their corresponding nucleotide sequences are shown in parentheses, respectively. (b). Tri3-2 amino acid sequence alignment. Amino acid residues shared among more than 9 out of the 11 homologues are shaded. The numbers in parentheses are shown with the same manner as adopted in Figure 2a.

Figure 3. Character evolution in the Cryptista.

(a). The phylogenetic relationship among cryptophytes, goniomonads, kathablepharids, and Palpitomonas bilix, based on the 157-gene phylogeny (see Fig. 1). The putative morphology and ultrastructural characteristics of the last common ancestor of the Cryptista (LCAC) are schematically illustrated. A, Acquisition of the sheath and the conoid-shaped feeding apparatus, loss of bipartite flagellar hairs, and ‘flat-to-tubular' transformation of the mitochondrial cristae; B, Acquisition of the periplast; C, Acquisition of spines and simplification of flagellar hairs; D, Acquisition of ejectisomes. (b). Alternative scenarios of the evolution of lifestyle in Cryptista. Green and orange lines represent phagotrophic and photosynthetic capacities, respectively. left, LCAC employed both phagocytosis and photosynthesis, as anticipated from the chromalveolata hypothesis; right, LCAC was a non-photosynthetic predator.