doi: 10.1098/rsob.210376. Epub 2022 Apr 13.
The closest lineage of Archaeplastida is revealed by phylogenomics analyses that includeMicroheliella maris
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- PMID:35414259
- PMCID: PMC9006020
- DOI: 10.1098/rsob.210376
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The closest lineage of Archaeplastida is revealed by phylogenomics analyses that includeMicroheliella maris
Euki Yazaki et al. Open Biol.2022 Apr.
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Abstract
By clarifying the phylogenetic positions of 'orphan' protists (unicellular micro-eukaryotes with no affinity to extant lineages), we may uncover the novel affiliation between two (or more) major lineages in eukaryotes.Microheliella maris was an orphan protist, which failed to be placed within the previously described lineages by pioneering phylogenetic analyses. In this study, we analysed a 319-gene alignment and demonstrated thatM. maris represents a basal lineage of one of the major eukaryotic lineages, Cryptista. We here propose a new clade name 'Pancryptista' for Cryptista plusM. maris. The 319-gene analyses also indicated thatM. maris is a key taxon to recover the monophyly of Archaeplastida and the sister relationship between Archaeplastida and Pancryptista, which is collectively called 'CAM clade' here. Significantly, Cryptophyceae tend to be attracted to Rhodophyta depending on the taxon sampling (ex., in the absence ofM. maris and Rhodelphidia) and the particular phylogenetic 'signal' most likely hindered the stable recovery of the monophyly of Archaeplastida in previous studies.
Keywords: Cryptista; Cryptophyceae; Goniomonadea; global eukaryotic phylogeny; phylogenetic artefacts.
Conflict of interest statement
We declare we have no competing interests.
Figures
Phylogenetic position ofMicroheliella maris inferred from the GlobE alignment. The tree topology and branch lengths were inferred from the GlobE alignment (319 genes; 88 592 amino acid positions in total) by the maximum-likelihood (ML) methods. Bayesian analysis recovered principally an identical tree topology (electronic supplementary material, figure S1). For each bipartition, the ML bootstrap support values (MLBPs) and Bayesian posterior probabilities (BPPs; if greater than 0.50) are shown. The bipartitions with dots indicate MLBPs of 100% and BPPs of 1.0. The bar graph for each taxon represents the per cent coverage of the amino acid positions in the GlobE alignment.
Analyses assessing the impact ofMicroheliella maris and Rhodelphidia on the monophyly of Pancryptista, the monophyly of Archaeplastida and CAM clade. We here define CAM clade as the sister relationship between Pancryptista and Archaeplastida on the top of the monophyly of each of both assemblages. If Pancryptista (or Cryptista) is directly grouped with Rhodophyta (the union of Pancryptista–Rhodophyta disrupts the monophyly of Archaeplastida), we do not consider the clade of Pancryptista/Cryptista, Rhodophyta, Chloroplastida, and Glaucophyta as CAM clade. (a) The maximum-likelihood (ML) tree inferred from the Diaph alignment comprising 319 genes (88 592 amino acid positions in total). Clades of closely related taxa are collapsed as triangles. For the detailed ML tree, please refer to electronic supplementary material, figure S2. Bayesian analysis recovered principally an identical tree topology (electronic supplementary material, figure S3). ML bootstrap support values (MLBPs) and Bayesian posterior probabilities (BPPs; if greater than 0.50) are indicated on the bipartitions presented in the figure. (b) Analyses of Diaph alignment processed by fast-evolving position removal (FPR). We repeated ultrafast bootstrap analyses using IQ-TREE 1.6.12 on the Diaph alignment after excluding no position, the top 20, 40, 60 and 80% fastest-evolving positions. The plots in purple, green, blue, and red indicate the ultrafast bootstrap support values (UFBPs) for the monophyly of Pancryptista, the monophyly of Archaeplastida, CAM clade, and the union of Rhodophyta and Pancryptista, respectively. (c–k) Analyses of the alignments generated by random gene sampling (RGS). We sampled 50, 100, 150 and 200 genes randomly from the 319 genes in the Diaph alignment, concatenated into ‘rs50g,’ ‘rs100g,’ ‘rs150g’ and ‘rs200g’ alignments, and subjected to ultrafast bootstrap analyses using IQ-TREE 1.6.12. We presented the UFBPs for CAM clade (i.e. the sister relationship between Pancryptista and Archaeplastida), the monophyly of Archaeplastida, and the monophyly of Pancryptista as box-and-whisker plots (c), (f) and (i), respectively. The above-mentioned analyses were repeated afterRhodelphis spp. orM. maris were excluded from the alignments alternatively. The UFBPs from the analyses excludingRhodelphis spp. and those from the analyses excludingM. maris are presented in (d), (g) and (j), and (e), (h) and (k), respectively. The UFBPs shown in the plots described above are summarized in electronic supplementary material, table S3.
Analyses assessing the phylogenetic affinity of Rhodophyta to Cryptophyceae and/or Goniomonadea. (a–l) Analyses of the alignments generated by random gene sampling (RGS). We excluded bothRhodelphis spp. andMicroheliella maris from the ‘rs50g,’ ‘rs100g,’ ‘rs150g’ and ‘rs200g’ alignments, which were generated from the Diaph alignments (see Methods for the detail) and then subjected to the ultrafast bootstrap analyses using IQ-TREE 1.6.12. The ultrafast support values (UFBPs) for the sister relationship between Archaeplastida and Cryptista, the monophyly of Archaeplastida, and the union of Rhodophyta and Cryptista are presented as box-and-whisker plots (a), (e) and (i), respectively. The ultrafast bootstrap analyses on the rs50g, rs100g, rs150g and rs200g alignments were repeated after further exclusion ofPalpitomonas bilix (b,f andj),P. bilix and Goniomonadea (c,g andk), andP. bilix and Cryptophyceae (d,h andl). The UFBPs shown in the plots described above are summarized in electronic supplementary material, table S4. (m,n) Analyses of the alignments processed by fast-evolving position removal (FPR). We modified the Diaph alignment in two ways, (i) the exclusion ofRhodelphis spp.,M. maris,P. bilix, and Cryptophyceae and (ii) that ofRhodelphis spp.,M. maris,P. bilix and Goniomonadea. The two modified Diaph alignments were processed by FPR and further subjected to ultrafast bootstrap analyses. We plotted the UFBPs for the monophyly of the SAR clade (brown), those for the monophyly of Archaeplastida (green), and those for the uniting of Rhodophyta and Goniomonadea/Cryptophyceae (red).
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