The unusually long small subunit ribosomal RNA gene found in amitochondriate amoeboflagellate Pelomyxa palustris : its rRNA predicted secondary structure and phylogenetic implication

Milyutina, Irina A.; Aleshin, Vladimir V.; Mikrjukov, Kirill A.; Kedrova, O. S.; Петров, Н. Б.

doi:10.1016/s0378-1119(01)00556-x

Cited by 41 publications

(22 citation statements)

References 25 publications

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“…A wide range of analyses utilizing different data sets and phylogenetic methods consistently indicated that pelobionts have a recent common evolutionary history with the Entamoebidae (see http://www.mbl.edu/Astrobiology/ PelobiontProject/PelobiontProject.htm for details). Similar suggestions have been made based on analyses that employed fewer taxa (Silberman et al 1999;Milyutina et al 2001). The late branching position of pelobionts in our analyses is consistent with secondary loss of mitochondria or conversion into degenerate organellar forms.…”

supporting

confidence: 89%

“…This result was obtained with the taxon sampling or alignment of Stiller and Hall (1999), or both. The failure of the two pelobionts to cluster together in Stiller and Hall's analysis (1999) may reflect evolutionary history (see also Milyutina et al 2001). A significant difference was found (S-H Test, P Ͻ 0.002) between the topology found in our analysis above and the best tree found under ML criterion with pelobionts constrained as a monophyletic group, further supporting the above result.…”

supporting

confidence: 81%

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Pelobionts are Degenerate Protists: Insights from Molecules and Morphology1

Edgcomb¹,

Simpson²,

Zettler³

et al. 2002

Molecular Biology and Evolution

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Pelobionts (Archamoebae sensu Cavalier-Smith 1991) lack mitochondria and are mostly free-living, heterotrophic, amoeboid, flagellated protists that inhabit organically enriched, microoxic, or anoxic freshwater and marine environments (Schulze 1877;Penard 1921;Brugerolle 1993). Because of their ultrastructural simplicity and the basal position of many amitochondriate parasitic protists in ribosomal RNA phylogenies (Sogin 1997), pelobionts were hypothesized to represent one of the earliest diverging eukaryotic lineages (Margulis 1970;Whatley 1976;Griffin 1979;Cavalier-Smith 1983;Griffin 1988;Whatley and Chapman-Andresen 1990;Cavalier-Smith 1991;Brugerolle 1993;Patterson 1994). However, molecular data support conflicting hypotheses about the monophyly and phylogenetic placement of pelobionts. Early analyses of small subunit rRNAs (SSU rRNA) (Hinkle et al. 1994) and partial sequences of large subunit rRNAs (LSU rRNA) (Morin and Mignot 1995) show that the pelobiont Mastigamoeba balamuthi (ϭPhreatamoeba balamuthi [Simpson et al. 1997]) diverged relatively late among eukaryotes. In contrast, a phylogenetic analysis of DNA-dependent RNA polymerase II (RPB1) genes (Stiller, Duffield, and Hall 1998) placed a sequence from an organism identified as M. invertens as one of the most basal eukaryotes.Discrepancies between inferences from cytology and RPB1 (Stiller, Duffield, and Hall 1998) versus LSU rRNA (Morin and Mignot 1995) and SSU rRNA data (Hinkle et al. 1994) prompted Stiller andHall (1999) to examine the position of M. invertens in SSU rRNA trees. Their initial maximum likelihood (ML)-based analysis did not cluster M. invertens with the other pelobiont sequences, nor were they basal to other eukaryotes. Stiller and Hall hypothesized that long-branch attractions (LBA) or skewed base compositions in rRNAs account for conflicting phylogenies of SSU rRNAs and RNA polymerases. When the rapidly evolving lineages were removed from that analysis, the two pelobionts formed a monophyletic group basal to other eukaryotes, but the GC content of half of the basal branches was not aberrant and was unlikely to impact the analysis.To reexamine the evolutionary position and monophyly of pelobionts, we obtained new pelobiont sequences that were PCR amplified (Sogin 1990) We performed the likelihood analysis shown in figure 1 using PAUP* version 4.0.0b4a (Swofford 1999) with TBR branch swapping and 117 random-addition replicates. Modeltest version 3.0 (Posada and Crandall 1998) revealed that all models more simple than the general time-reversible model of nucleotide substitution, with invariable sites and a gamma distribution of among-site rate variation (GTR ϩ I ϩ ⌫) had a significantly poorer fit to the data. This model was used for both ML and minimum evolution (ME) distance bootstrap analyses with 100 and 1,000 replicates, respectively. Empirical base frequencies were used, the proportion of invariable sites was estimated at 0.173, and the value of the shape parameter for the gamma distribution was 0.615. Under ML we discovered 10 ...

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supporting

confidence: 89%

supporting

confidence: 81%

Pelobionts are Degenerate Protists: Insights from Molecules and Morphology1

Edgcomb¹,

Simpson²,

Zettler³

et al. 2002

Molecular Biology and Evolution

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“…2001; Milyutina et al. 2001). It is not possible to design V4 primers that will generate an amplicon of at least 400 bp that can be completely sequenced in all eukaryotic species.…”

Section: Discussionmentioning

confidence: 99%

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?

Brown

Chain

Crease

et al. 2015

Ecology and Evolution

121

136

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DNA metabarcoding is a promising method for describing communities and estimating biodiversity. This approach uses high-throughput sequencing of targeted markers to identify species in a complex sample. By convention, sequences are clustered at a predefined sequence divergence threshold (often 3%) into operational taxonomic units (OTUs) that serve as a proxy for species. However, variable levels of interspecific marker variation across taxonomic groups make clustering sequences from a phylogenetically diverse dataset into OTUs at a uniform threshold problematic. In this study, we use mock zooplankton communities to evaluate the accuracy of species richness estimates when following conventional protocols to cluster hypervariable sequences of the V4 region of the small subunit ribosomal RNA gene (18S) into OTUs. By including individually tagged single specimens and “populations” of various species in our communities, we examine the impact of intra- and interspecific diversity on OTU clustering. Communities consisting of single individuals per species generated a correspondence of 59–84% between OTU number and species richness at a 3% divergence threshold. However, when multiple individuals per species were included, the correspondence between OTU number and species richness dropped to 31–63%. Our results suggest that intraspecific variation in this marker can often exceed 3%, such that a single species does not always correspond to one OTU. We advocate the need to apply group-specific divergence thresholds when analyzing complex and taxonomically diverse communities, but also encourage the development of additional filtering steps that allow identification of artifactual rRNA gene sequences or pseudogenes that may generate spurious OTUs.

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“…For most such organisms no molecular information is available and even rRNA-encoding DNA (rDNA) sequences have been determined for only a few species. Phylogenies based on this molecule with varying species sampling and tree reconstruction methods often suggest paraphyly of different amoeboid genera, with the following order of emergence: Physarum, Entamoeba, Dictyostelium, Mastigamoeba, and Acanthamoeba (4)(5)(6)(7)(8). However, a few genera, for example, Mastigamoeba and Entamoeba (9,10), sometimes group together.…”

mentioning

confidence: 99%

The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium , Entamoeba , and Mastigamoeba

Bapteste

Brinkmann

Lee

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

348

222

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The phylogenetic relationships of amoebae are poorly resolved. To address this difficult question, we have sequenced 1,280 expressed sequence tags from Mastigamoeba balamuthi and assembled a large data set containing 123 genes for representatives of three phenotypically highly divergent major amoeboid lineages: Pelobionta, Entamoebidae, and Mycetozoa. Phylogenetic reconstruction was performed on Ϸ25,000 aa positions for 30 species by using maximum-likelihood approaches. All well-established eukaryotic groups were recovered with high statistical support, validating our approach. Interestingly, the three amoeboid lineages strongly clustered together in agreement with the Conosa hypothesis [as defined by T. Cavalier-Smith (1998) Biol. Rev. Cambridge Philos. Soc. 73, 203-266]. Two amitochondriate amoebae, the free-living Mastigamoeba and the human parasite Entamoeba, formed a significant sister group to the exclusion of the mycetozoan Dictyostelium. This result suggested that a part of the reductive process in the evolution of Entamoeba (e.g., loss of typical mitochondria) occurred in its free-living ancestors. Applying this inexpensive expressed sequence tag approach to many other lineages will surely improve our understanding of eukaryotic evolution.

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The unusually long small subunit ribosomal RNA gene found in amitochondriate amoeboflagellate Pelomyxa palustris : its rRNA predicted secondary structure and phylogenetic implication

Cited by 41 publications

References 25 publications

Pelobionts are Degenerate Protists: Insights from Molecules and Morphology1

Pelobionts are Degenerate Protists: Insights from Molecules and Morphology1

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?

The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium , Entamoeba , and Mastigamoeba

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