Morphology and phylogeny of Bryophryoides ocellatus n. g., n. sp. (Ciliophora, Colpodea) from in situ soil percolates of Idaho, U.S.A.

Bourland, William A.; Wendell, Laura; Hampikian, Greg; Vďačný, Peter

doi:10.1016/j.ejop.2013.09.001

Cited by 10 publications

(7 citation statements)

References 29 publications

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“…In previous work, and in our study, B. pulchra was always the earliest divergent branch of Colpodida in the SSU-rRNA gene tree, which means it has been stable between Colpodida and Cyrtolophosidida (Bourland et al, 2011;Dunthorn et al, 2012;Rajter et al, 2020;Vďačný & Foissner, 2019). But, we established multiple gene trees and they all confirmed the instability of the position of B. pulchra in Colpodida.…”

Section: Bardeliella Pulchra Evolutionary Positionsupporting

confidence: 77%

“…Bromeliothrix has a ciliary and silverline pattern typical for members of the family Colpodidae, and its basic organization of the oral apparatus is also the same as that known from genera of Colpodidae families (Foissner, 2010;Foissner et al, 2002). Foissner pointed out that Bromeliothrix neither belong to the Exocolpodidae nor the Hausmanniellidae due to its complex morphological characteristics, and several phylogenetic analyses based on SSU rRNA gene sequence also indicated that B. discoideus was more closely related to a clade formed by large Colpoda species than with Hausmanniella discoidea, a type of the hausmanniellids (Bourland et al, 2011;Dunthorn et al, 2008).…”

Section: Paracolpoda and Bromeliothrix Phylogenymentioning

confidence: 99%

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Insights into the phylogeny of the ciliate of class Colpodea based on multigene data

Song

Hao

et al. 2022

Ecology and Evolution

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In the class Colpodea, there are many unresolved evolutionary relationships among taxa. Here, we report 30 new sequences including SSU-rRNA, ITS1-5.8S-ITS2 rRNA, and the mitochondrial small subunit ribosomal RNA (mtSSU-rRNA) genes of five colpodeans, and conduct phylogenetic analyses based on each individual gene and a two-gene concatenated dataset. For the first time, multi-genes were used to analyze phylogenetic relationships in the class Colpodea. The main findings are: (1) SSU-rRNA, ITS1-5.8S-ITS2 rRNA, and mtSSU-rRNA gene sequences of C. reniformis and C. grandis are provided for the first time, and these two species group into the clade including C. inflata, C. lucida, C. cucullus, and C. henneguyi; (2) clustering pattern and morphological similarity indicate that Bresslauides discoideus has a close relation with Colpodidae spp.; (3) Emarginatophrya genus diagnosis is improved to be 'Hausmanniellidae with sharply shortened and isometric leftmost 1-4 ciliary rows' and Colpoda elliotti is transferred to Emarginatophrya; (4) the genus Colpoda is still non-monophyletic with the addition of 10 populations from five Colpoda species sequences, but there are only two Colpoda groups left based on the present work: Group I comprises C. inflata, C. lucida, C. cucullus, C. henneguyi, C. reniformis, and C. grandis, Group II comprises C. maupasi and C. ecaudata, and the presence of diagonal grooves and the way the vestibular opens might be the two key features that differentiates Colpoda species groups;(5) a close molecular relationship, and highly similar merotelokinetal mode, somatic ciliary pattern, and basic organization of the oral apparatus with P. steinii suggests Bromeliothrix metopoides should be temporarily assigned to Colpodidae.

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Section: Bardeliella Pulchra Evolutionary Positionsupporting

confidence: 77%

Section: Paracolpoda and Bromeliothrix Phylogenymentioning

confidence: 99%

Insights into the phylogeny of the ciliate of class Colpodea based on multigene data

Song

Hao

et al. 2022

Ecology and Evolution

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“…Although the Colpodea are recognized as a taxon based on the presence of the LKm (left kinetodesmal) fiber in the somatic ciliature (Lynn 1976;Small and Lynn 1981;Foissner 1993), molecular support for monophyly from nuclear SSU-rDNA data was lacking in an earlier study when all potentially closely related outgroups were included (Dunthorn et al 2008). Later nuclear and mictochondrial SSU-rDNA analyses did not sample sufficient outgroups to allow for a meaningful test of monophyly (Lynn et al 1999;Lasek-Nesselquist and Katz 2001;Dunthorn et al 2008Dunthorn et al , 2009Foissner and Stoeck 2009;Bourland et al 2011;Dunthorn et al 2011;Foissner et al 2011;Quintela-Alonso et al 2011;Bourland et al 2012;Dunthorn, Katz, et al 2012;Bourland et al 2013;Foissner et al 2013). With the increased taxon sampling here, the Colpodea are inferred to be monophyletic with PairDist, RAxML, and MrBayes; we obtain high bipartition support for this relationship only from PairDist and MrBayes.…”

Section: A Broadly Sampled Ciliate Treementioning

confidence: 99%

Placing Environmental Next-Generation Sequencing Amplicons from Microbial Eukaryotes into a Phylogenetic Context

Dunthorn

Otto

Berger

et al. 2014

Molecular Biology and Evolution

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Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons of these regions are all that are available to answer ecological and evolutionary questions that rely on phylogenetic inferences. With ciliates, we asked how inclusion of the V4 or V9 regions, regardless of alignment quality, affects tree topologies using distinct phylogenetic methods (including PairDist that is introduced here). Results show that the best approach is to place V4 amplicons into an alignment of full-length Sanger SSU-rDNA sequences and to infer the phylogenetic tree with RAxML. A sliding window algorithm as implemented in RAxML shows, though, that not all nucleotide positions in the V4 region are better than V9 at inferring the ciliate tree. With this approach and an ancestral-state reconstruction, we use V4 amplicons from European nearshore sampling sites to infer that rather than being primarily terrestrial and freshwater, colpodean ciliates may have repeatedly transitioned from terrestrial/freshwater to marine environments.

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“…All colpodean species that have been described in enough detail have micronuclei (e.g., Bourland et al, 2013;Dunthorn et al, 2009;Foissner, 1993;Foissner et al, 2014;Quintela-Alonso et al, 2011). As micronuclei are only involved in sex (as far as we know), we propose that this cytological feature would have been lost over evolutionary time if the colpodeans are asexual.…”

Section: Genomic Data Support Secretive Sex In Colpodeansmentioning

confidence: 89%

Meiotic Genes in Colpodean Ciliates Support Secretive Sexuality

Dunthorn

Zufall

Chi

et al. 2017

Preprint

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The putatively asexual Colpodean ciliates potentially pose a problem to macro-organismic theories of evolution. They are extremely ancient (although asexuality is thought to hasten extinction), and yet there is one apparently derived sexual species (implying an unlikely regain of a complex trait). If macro-organismic theories of evolution also broadly apply to microbial eukaryotes, though, then most or all of the colpodean ciliates should merely be secretively sexual. Here we show using de novo genome sequencing, that colpodean ciliates have the meiotic genes required for sex and these genes are under functional constraint. Along with these genomic data, we argue that these ciliates are sexual given the cytological observations of both micronuclei and macronuclei within their cells, and the behavioral observations of brief fusions as if the cells were mating. The challenge that colpodean ciliates pose is therefore not to evolutionary theory, but to our ability to induce microbial eukaryotic sex in the laboratory.

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Morphology and phylogeny of Bryophryoides ocellatus n. g., n. sp. (Ciliophora, Colpodea) from in situ soil percolates of Idaho, U.S.A.

Cited by 10 publications

References 29 publications

Insights into the phylogeny of the ciliate of class Colpodea based on multigene data

Insights into the phylogeny of the ciliate of class Colpodea based on multigene data

Placing Environmental Next-Generation Sequencing Amplicons from Microbial Eukaryotes into a Phylogenetic Context

Meiotic Genes in Colpodean Ciliates Support Secretive Sexuality

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