Estimation of divergence times in litostomatean ciliates (Ciliophora: Intramacronucleata), using Bayesian relaxed clock and 18S rRNA gene

Vďačný, Peter

doi:10.1016/j.ejop.2015.06.008

Cited by 26 publications

(16 citation statements)

References 42 publications

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“…Age of the root of the spathidiid tree of life could not be unambiguously calculated in our previous dating analyses (Vďačný ). Moreover, the histogram of posterior ages of the spathidiid root displayed a trimodal distribution, with modes at ca.…”

Section: Methodsmentioning

confidence: 87%

Rapid radiation, gradual extinction and parallel evolution challenge generic classification of spathidiid ciliates (Protista, Ciliophora)

Rajter

Vďačný

2015

Zoologica Scripta

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Rajter, L'., Vd'a cn y, P. (2016). Rapid radiation, gradual extinction and parallel evolution challenge generic classification of spathidiid ciliates (Protista, Ciliophora) -Zoologica Scripta, 45: 200-223. Reconstruction of evolutionary history of the ciliate order Spathidiida has proven elusive. There are weakly statistically supported deeper nodes in 18S rRNA gene phylogenies on one hand, while several statistically strongly supported clusters containing morphologically dissimilar taxa that usually lack any common apomorphies on the other hand. To clarify whether silent aspects of the spathidiid phylogeny are results of methodological problems of tree-building algorithms, we examined informativness of the macronuclear rRNA locus using an increased taxon and marker sampling as well as a complex statistical approach. Likelihood mapping revealed that the macronuclear rRNA locus has enough phylogenetic information to infer spathidiid relationships. However, some noise and conflicts hamper inference of deeper branching events, as documented by short parallelograms in the star-like central part of the split graphs and by low numbers of phylogenetically informative nucleotide homologies supporting deeper nodes of phylogenetic trees. Based on the diversification analyses and the c-statistic, we assembled a body of evidence that the spathidiid phylogeny retains the signature of one or several rapid radiations in the Palaeozoic and a subsequent gradual extinction that has started in the Mesozoic. A combination of these two phenomena along with polyphyly of three large spathidiid genera (Spathidium, Epispathidium and Arcuospathidium) are speculated to be the main reasons for fuzzy phylogenetic picture within the order Spathidiida. Because natural classification of spathidiids cannot be provided at the present state of knowledge, we suggest to keep the existing morphology-based generic classification, but stress that the large spathidiid genera are artificial collective groups.

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Section: Methodsmentioning

confidence: 87%

Rapid radiation, gradual extinction and parallel evolution challenge generic classification of spathidiid ciliates (Protista, Ciliophora)

Rajter

Vďačný

2015

Zoologica Scripta

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“…Evolutionary relationships within the Haptoria based on conventional morphological characters, such as nematodesmata and the dorsal brush, are not confirmed by the molecular data (Foissner & Foissner, ; Lipscomb & Riordan, ). In addition, recent molecular phylogenetic analyses have not corroborated the monophyly of Haptoria, leaving numerous historical problems unresolved (Gao, Warren, et al., ; Pan et al., ; Vďačný, ; Vďačný, Breiner, et al, 2017; Vd'ačný & Rajter ; Zhang, Simpson, & Song, ). For example, three haptorian genera, Cyclotrichium , Paraspathidium and Askenasia , fall into either class Protomatea or Plagiopylea in single and multigene phylogenies (Gao, Warren, et al., ; Zhang et al., ).…”

Section: Introductionmentioning

confidence: 99%

Further insights into the highly derived haptorids (Ciliophora, Litostomatea): Phylogeny based on multigene data

Huang

Zhang

et al. 2018

Zoologica Scripta

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Evolutionary relationships of taxa within the ciliate subclass Haptoria are poorly understood. In this study, we broaden the taxon sampling by adding 14 small subunit ribosomal RNA gene sequences, 13 large subunit ribosomal RNA gene sequences and 13 ITS1‐5.8S‐ITS2 gene sequences of haptorians. This includes the first molecular data from two genera, Pseudotrachelocerca Song, 1990, and Foissnerides Song & Wilbert, 1989. Phylogenies inferred from the three individual genes and concatenated data sets show that: (i) the subclass Haptoria could be a multiphyletic complex with about up to four main clades while “interrupted” by some intermingled with the related subclasses Rhynchostomatia, Trichostomatia and some incertae sedis; (ii) the genus Pseudotrachelocerca Song, 1990, is clearly separated from Litostomatea and clusters within an assemblage comprising the classes Prostomatea, Colpodea and Plagiopylea; (iii) both morphological evidence and molecular evidence indicate that the genus Foissnerides should be transferred from family Trachelophyllidae to Pseudoholophryidae; (iv) the validity of the order Helicoprorodontida Grain, 1994, and its monophyly is strongly supported; (5) the family Chaeneidae does not belong to the order Lacrymarida but represents a distinct clade in the subclass Haptoria.

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“…To reconstruct the evolutionary history of armophorean ciliates and to improve understanding of their phylogenetic relationships, diversification dynamics, and morphological evolution, we utilized the molecular clock theory as well as information contained in the estimated time trees and morphology of extant taxa. Diversification dynamics is only rarely examined in ciliates due to the lack of fossil records (Rajter and Vďačný ; Vďačný ; Vďačný et al. ; Wright and Lynn ).…”

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confidence: 99%

A Proposed Timescale for the Evolution of Armophorean Ciliates: Clevelandellids Diversify More Rapidly Than Metopids

Vďačný

Rajter

Stoeck

et al. 2018

J Eukaryotic Microbiology

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Members of the class Armophorea occur in microaerophilic and anaerobic habitats, including the digestive tract of invertebrates and vertebrates. Phylogenetic kinships of metopid and clevelandellid armophoreans conflict with traditional morphology-based classifications. To reconcile their relationships and understand their morphological evolution and diversification, we utilized the molecular clock theory as well as information contained in the estimated time trees and morphology of extant taxa. The radiation of the last common ancestor of metopids and clevelandellids very likely occurred during the Paleozoic and crown diversification of the endosymbiotic clevelandellids dates back to the Mesozoic. According to diversification analyses, endosymbiotic clevelandellids have higher net diversification rates than predominantly free-living metopids. Their cladogenic success was very likely associated with sharply isolated ecological niches constituted by their hosts. Conflicts between traditional classifications and molecular phylogenies of metopids and clevelandellids very likely come from processes, leading to further diversification without extinction of ancestral lineages as well as from morphological plesiomorphies incorrectly classified as apomorphies. Our study thus suggests that diversification processes and reconstruction of ancestral morphologies improve the understanding of paraphyly which occurs in groups of organisms with an apparently long evolutionary history and when speciation prevails over extinction.

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Estimation of divergence times in litostomatean ciliates (Ciliophora: Intramacronucleata), using Bayesian relaxed clock and 18S rRNA gene

Cited by 26 publications

References 42 publications

Rapid radiation, gradual extinction and parallel evolution challenge generic classification of spathidiid ciliates (Protista, Ciliophora)

Rapid radiation, gradual extinction and parallel evolution challenge generic classification of spathidiid ciliates (Protista, Ciliophora)

Further insights into the highly derived haptorids (Ciliophora, Litostomatea): Phylogeny based on multigene data

A Proposed Timescale for the Evolution of Armophorean Ciliates: Clevelandellids Diversify More Rapidly Than Metopids

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