Assessing the evolutionary history of the class Synurophyceae (Heterokonta) using molecular, morphometric, and paleobiological approaches

Siver, Peter A.; Jo, Bok Yeon; Kim, Jong Im; Shin, Woongghi; Lott, Anne Marie; Wolfe, Alexander P.

doi:10.3732/ajb.1500004

Cited by 60 publications

(126 citation statements)

References 44 publications

(78 reference statements)

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“…The period of origin and the divergence estimations made by Siver et al. () were slightly younger, dated in the Early Cretaceous, at ~135 and 113 Ma, respectively. According to Siver et al.…”

mentioning

confidence: 72%

“…The silica scales can be preserved in sediment for millions of years (Siver et al. ). Currently, there are two major localities with massive assemblages of fossil Mallomonas siliceous structures, Wombat and Giraffe, dating back to Paleocene and Middle Eocene, respectively.…”

mentioning

confidence: 99%

“…() were the first who suggested that two Mallomonas subclades (described later as A1 and A2 by Siver et al. ) can be distinguished by the presence or absence of the V‐rib. In addition, Jo et al.…”

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confidence: 99%

“…According to Siver et al. (), the earliest‐diverging taxa are M. insignis within A1 subclade and three closely related species, M. bangladeshica , M. peronoides , and M. ceylanica within A2 subclade. All these taxa have very complex scales with reticulation, papillae, or a U‐shaped ridge, which contradicts an early assumption that scales with basal morphology lacking any additional structures are the most ancient ones (Asmund and Kristiansen , Kristiansen ).…”

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confidence: 99%

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Molecular phylogeny and evolution of phenotype in silica‐scaled chrysophyte genus Mallomonas

Čertnerová

Čertner

Škaloud

2019

Journal of Phycology

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The evolution of phenotypes is highly understudied in protists, due to the dearth of morphological characters, missing fossil record, and/or unresolved phylogeny in the majority of taxa. The chrysophyte genus Mallomonas (Stramenopiles) forms species‐specific silica scales with extraordinary diversity of their ornamentation. In this paper, we molecularly characterized three additional species to provide an updated phylogeny of 43 species, and combined this with evaluations of 24 morphological traits. Using phylogenetic comparative methods, we evaluated phylogenetic signal in traits, reconstructed the trait evolution, and compared the overall phylogenetic and morphological diversity. The majority of traits showed strong phylogenetic signal and mostly dynamic evolution. Phylogenetic relatedness was often reflected by the phenotypic similarity. Both V‐rib and dome are very conservative structures that are presumably involved in precise scale overlap and bristle attachment, respectively. Based on modern species, it seems the dome firstly appeared on apical and/or caudal scales, and only later emerged on body scales. Bristle was presumably present in the common ancestor and gradually elongated ever since. However, most other morphological traits readily changed during the evolution of Mallomonas.

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confidence: 72%

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confidence: 99%

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confidence: 99%

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confidence: 99%

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Molecular phylogeny and evolution of phenotype in silica‐scaled chrysophyte genus Mallomonas

Čertnerová

Čertner

Škaloud

2019

Journal of Phycology

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“…However, the precise branching order of the major chrysomonad clades varies with algorithm and taxon sampling (Scoble & Cavalier-Smith, 2014; Grossmann et al, 2016; Bock et al, 2014). Current molecular phylogenetic analyses concentrate on few chrysophyte taxa such as the phototrophic genera Synura and Mallomonas (Škaloud, Kristiansen & Škaloudová, 2013; Siver et al, 2015) and the mixotrophic genus Dinobryon (Bock et al, 2014), as well as on mixotrophic and colourless single-celled taxa originally lumped into the genera Paraphysomonas (Scoble & Cavalier-Smith, 2014), Spumella (Grossmann et al, 2016) and Ochromonas (Andersen (2007) and RA Andersen, pers. comm., 2007).…”

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confidence: 99%

Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes

Beißer

Graupner

Böck

et al. 2017

PeerJ

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BackgroundChrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms. Recent phylogenies and megasystematics demonstrate an immense complexity of eukaryotic diversity with numerous transitions between phototrophic and heterotrophic organisms. The question we aim to answer is how the diverse nutritional strategies, accompanied or brought about by a reduction of the plasmid and size reduction in heterotrophic strains, affect physiology and molecular processes.ResultsWe sequenced the mRNA of 18 chrysophyte strains on the Illumina HiSeq platform and analysed the transcriptomes to determine relations between the trophic mode (mixotrophic vs. heterotrophic) and gene expression. We observed an enrichment of genes for photosynthesis, porphyrin and chlorophyll metabolism for phototrophic and mixotrophic strains that can perform photosynthesis. Genes involved in nutrient absorption, environmental information processing and various transporters (e.g., monosaccharide, peptide, lipid transporters) were present or highly expressed only in heterotrophic strains that have to sense, digest and absorb bacterial food. We furthermore present a transcriptome-based alignment-free phylogeny construction approach using transcripts assembled from short reads to determine the evolutionary relationships between the strains and the possible influence of nutritional strategies on the reconstructed phylogeny. We discuss the resulting phylogenies in comparison to those from established approaches based on ribosomal RNA and orthologous genes. Finally, we make functionally annotated reference transcriptomes of each strain available to the community, significantly enhancing publicly available data on Chrysophyceae.ConclusionsOur study is the first comprehensive transcriptomic characterisation of a diverse set of Chrysophyceaen strains. In addition, we showcase the possibility of inferring phylogenies from assembled transcriptomes using an alignment-free approach. The raw and functionally annotated data we provide will prove beneficial for further examination of the diversity within this taxon. Our molecular characterisation of different trophic modes presents a first such example.

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Chrysophyta

Kristiansen

Škaloud

2017

Handbook of the Protists

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Assessing the evolutionary history of the class Synurophyceae (Heterokonta) using molecular, morphometric, and paleobiological approaches

Cited by 60 publications

References 44 publications

Molecular phylogeny and evolution of phenotype in silica‐scaled chrysophyte genus Mallomonas

Molecular phylogeny and evolution of phenotype in silica‐scaled chrysophyte genus Mallomonas

Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes

Chrysophyta

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