Commentary on the chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms

Spiegel, Frederick W.

doi:10.1098/rspb.2011.0608

Cited by 18 publications

(15 citation statements)

References 9 publications

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“…However, recent studies (Feng & Schnittler, ; Feng et al., ) concluded that sexual reproduction seems to dominate in natural populations. This is in line with studies showing sexual reproduction as a hallmark of Amoebozoa (Lahr, Parfrey, Mitchell, Katz, & Lara, ; Spiegel, ) and of eukaryotic life in general (Speijer, Lukeš, & Eliáš, ). In case of sexual reproduction, a combination of independent genetic markers can be used to characterize sexually isolated lineages which represent putative biospecies.…”

Section: Introductionsupporting

confidence: 90%

Genetic barcoding of dark‐spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

Dahl

Brejnrod

Unterseher³

et al. 2017

Molecular Ecology Resources

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Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.

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Section: Introductionsupporting

confidence: 90%

Genetic barcoding of dark‐spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

Dahl

Brejnrod

Unterseher³

et al. 2017

Molecular Ecology Resources

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“…That is the loss of complexity in the descendants of more complex common ancestors. Unequivocal examples of such loss of complexity are already documented for Amoebozoa, e.g., multiple losses of sex [56, 59] and flagellate states [13]. …”

Section: Discussionmentioning

confidence: 99%

Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group

Tice¹,

Shadwick²,

Fiore-Donno³

et al. 2016

Biol Direct

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BackgroundAcanthamoebidae is a “family” level amoebozoan group composed of the genera Acanthamoeba, Protacanthamoeba, and very recently Luapeleamoeba. This clade of amoebozoans has received considerable attention from the broader scientific community as Acanthamoeba spp. represent both model organisms and human pathogens. While the classical composition of the group (Acanthamoeba + Protacanthamoeba) has been well accepted due to the morphological and ultrastructural similarities of its members, the Acanthamoebidae has never been highly statistically supported in single gene phylogenetic reconstructions of Amoebozoa either by maximum likelihood (ML) or Bayesian analyses.ResultsHere we show using a phylogenomic approach that the Acanthamoebidae is a fully supported monophyletic group within Amoebozoa with both ML and Bayesian analyses. We also expand the known range of morphological and life cycle diversity found in the Acanthamoebidae by demonstrating that the amoebozoans “Protostelium” arachisporum, Dracoamoeba jormungandri n. g. n. sp., and Vacuolamoeba acanthoformis n.g. n.sp., belong within the group. We also found that “Protostelium” pyriformis is clearly a species of Acanthamoeba making it the first reported sporocarpic member of the genus, that is, an amoeba that individually forms a walled, dormant propagule elevated by a non-cellular stalk. Our phylogenetic analyses recover a fully supported Acanthamoebidae composed of five genera. Two of these genera (Acanthamoeba and Luapeleameoba) have members that are sporocarpic.ConclusionsOur results provide high statistical support for an Acanthamoebidae that is composed of five distinct genera. This study increases the known morphological diversity of this group and shows that species of Acanthamoeba can include spore-bearing stages. This further illustrates the widespread nature of spore-bearing stages across the tree of Amoebozoa.ReviewersThis article was reviewed by Drs. Eugene Koonin, Purificacion Lopez-Garcia and Sandra Baldauf. Sandra Baldauf was nominated by Purificacion Lopez-Garcia, an Editorial Board member.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-016-0171-0) contains supplementary material, which is available to authorized users.

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“…However, the presumed lack of sexual processes correlates directly with the lack of study, i.e., the less studied the group is, more likely it will be considered asexual in the literature. A good example of this is the description of sexual cycles for Myxogastria among “asexual” amoebozoans, which has been attributed to the simple fact that they were more intensively studied when they were still considered to be a group of Fungi . The classification of Myxogastria inside Amoebozoa is fairly recent .…”

Section: Meiosis Toolkit Can Reveal the Nature Of Asexual Scandalsmentioning

confidence: 99%

“…A good example of this is the description of sexual cycles for Myxogastria among "asexual" amoebozoans, which has been attributed to the simple fact that they were more intensively studied when they were still considered to be a group of Fungi. [20] The classification of Myxogastria inside Amoebozoa is fairly recent. [21] Another problem is the heavy bias towards parasites, which represent around 90% of all protist genomes available.…”

Section: Introductionmentioning

confidence: 99%

All Eukaryotes Are Sexual, unless Proven Otherwise

Hofstatter

Lahr

2019

BioEssays

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Here a wide distribution of meiotic machinery is shown, indicating the occurrence of sexual processes in all major eukaryotic groups, without exceptions, including the putative “asexuals.” Meiotic machinery has evolved from archaeal DNA repair machinery by means of ancestral gene duplications. Sex is very conserved and widespread in eukaryotes, even though its evolutionary importance is still a matter of debate. The main processes in sex are plasmogamy, followed by karyogamy and meiosis. Meiosis is fundamentally a chromosomal process, which implies recombination and ploidy reduction. Several eukaryotic lineages are proposed to be asexual because their sexual processes are never observed, but presumed asexuality correlates with lack of study. The authors stress the complete lack of meiotic proteins in nucleomorphs and their almost complete loss in the fungus Malassezia. Inversely, complete sets of meiotic proteins are present in fungal groups Glomeromycotina, Trichophyton, and Cryptococcus. Endosymbiont Perkinsela and endoparasitic Microsporidia also present meiotic proteins.

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Commentary on the chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms

Cited by 18 publications

References 9 publications

Genetic barcoding of dark‐spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

Genetic barcoding of dark‐spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group

All Eukaryotes Are Sexual, unless Proven Otherwise

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