Between a Pod and a Hard Test: The Deep Evolution of Amoebae.
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Cites background from "Between a Pod and a Hard Test: The ..."
...Large numbers of cells can be isolated en masse from the environment then screened using molecular techniques to identify important organisms for further study [78–83]; alternatively, target cells can be identified by microscopy and selected individually [40,41,61,75]....
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381 citations
Cites background or methods from "Between a Pod and a Hard Test: The ..."
...To preserve this widely used name, Kang et al. (2017) proposed including in the Eumycetozoa only one group of protostelids, the Protosporangiida, which forms a monophyletic unit with myxomycetes and dictyostelids....
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...To preserve this widely used name, Kang et al. (2017) proposed including in the Eumycetozoa only one group of protostelids, the Protosporangiida, which forms a monophyletic unit with myxomycetes and dictyostelids. In terms of botanical nomenclature, the Protosporangiida may be considered as the class Ceratiomyxomycota (Leontyev et al. 2019). Therefore, in the classification given below, we recognize three classes within the Eumycetozoa. These are the Dictyosteliomycetes, Ceratiomyxomycetes and Myxomycetes, as outlined by Leontyev et al. (2019)....
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...This group was initially described under the zoological name Protosporangiida (Kang et al. 2017). The botanical name Ceratiomyxomycetes was proposed by Hawksworth et al. (1983) as nom....
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...This group was initially described under the zoological name Protosporangiida (Kang et al. 2017). The botanical name Ceratiomyxomycetes was proposed by Hawksworth et al. (1983) as nom. inval. (ICN, Art. 39.1), and later validated by Leontyev et al. (2019)....
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...All available phylogenies support the placement of these organisms in the supergroup Amoebozoa (Shadwick et al. 2009, Tice et al. 2016, Kang et al. 2017) (Table 2)....
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297 citations
Cites background from "Between a Pod and a Hard Test: The ..."
...Sporocarps, where a single cell develops into a stalked spore-bearing structure, are unique to Amoebozoa (Kang et al. 2017; Spiegel et al. 2017)....
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...All sporocarpic and some sorocarpic species are found within the Amoebozoa (Fiore-Donno et al. 2010; Kang et al. 2017; Spiegel et al. 2017), whereas the remainder of the sorocarpic forms are found throughout the whole eukaryotic tree (Brown and Silberman 2013)....
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...Protosteloid amoebae occur separately in several clades of Amoebozoa suggesting that spore formation might be a synapomorphic character for the entire supergroup Amoebozoa (Kang et al. 2017; Spiegel et al. 2017)....
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...…Legionella spp. legionnaires’ disease, opportunistic infections Rowbotham 1980 Vibrio cholerae cholera Thom et al. 1992 Dictyostelia and Copromyxa (Kang et al. 2017), but also in several taxa in diverse supergroups such as in one ciliate (Olive and Blanton 1980), Heterolobosea (Brown, Silberman…...
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...Naegleria Legionella spp. legionnaires’ disease, opportunistic infections Rowbotham 1980 Vibrio cholerae cholera Thom et al. 1992 Dictyostelia and Copromyxa (Kang et al. 2017), but also in several taxa in diverse supergroups such as in one ciliate (Olive and Blanton 1980), Heterolobosea (Brown, Silberman and Spiegel 2010), Opisthokonts (Brown, Spiegel and Silberman 2009), Rhizaria (Brown et al. 2012), and Stramenopiles (Tice et al. 2016)....
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92 citations
Cites background from "Between a Pod and a Hard Test: The ..."
...There is considerable debate over the position of the root, however (Cavalier-Smith 2010; Katz et al. 2012; He et al. 2014)....
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References
13,668 citations
"Between a Pod and a Hard Test: The ..." refers methods in this paper
...…LGþC4þ FþC60þ PMSF model that similarly estimates site-specific amino acid (AA) Deep Evolution of Amoebae . doi:10.1093/molbev/msx162 MBE profiles for phylogenomic analyses based on the C60 empirical frequency profiles (Le and Gascuel 2008) was used for ML analyses in IQ-Tree (Nguyen et al. 2014)....
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...To examine this conflict, we estimated the rate of evolution at sites in the supermatrix and progressively removed them in a stepwise fashion, plotting bootstrap values for nodes of interest in the tree per site deletion step under the models LGþC4þ F and LGþC4þ FþC60þ PMSF models estimated in IQ-Tree (fig....
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...Although the CAT-GTR model cannot be used in the ML framework, the LGþC4þ FþC60þ PMSF model that similarly estimates site-specific amino acid (AA) Deep Evolution of Amoebae . doi:10.1093/molbev/msx162 MBE profiles for phylogenomic analyses based on the C60 empirical frequency profiles (Le and Gascuel 2008) was used for ML analyses in IQ-Tree (Nguyen et al. 2014)....
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...ML trees were inferred in IQTREE v. 1.5.0 (Nguyen et al. 2014)....
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2,615 citations
"Between a Pod and a Hard Test: The ..." refers methods in this paper
...profiles for phylogenomic analyses based on the C60 empirical frequency profiles (Le and Gascuel 2008) was used...
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...…LGþC4þ FþC60þ PMSF model that similarly estimates site-specific amino acid (AA) Deep Evolution of Amoebae . doi:10.1093/molbev/msx162 MBE profiles for phylogenomic analyses based on the C60 empirical frequency profiles (Le and Gascuel 2008) was used for ML analyses in IQ-Tree (Nguyen et al. 2014)....
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2,452 citations
"Between a Pod and a Hard Test: The ..." refers methods in this paper
...Additionally, constraining the tree with Lobosa (Discoseaþ Tubulinea, with or without Cutosea) can be rejected under approximately unbiased (AU) tests (Shimodaira, 2002) at a confidence interval of 95% using our data set (P-value¼ 0.0059 and 0.0014, respectively, table 1)....
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...Additionally, constraining the tree with Lobosa (Discoseaþ Tubulinea, with or without Cutosea) can be rejected under approximately unbiased (AU) tests (Shimodaira, 2002) at a confidence interval of 95% using our data set (P-value1⁄4 0....
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1,414 citations
"Between a Pod and a Hard Test: The ..." refers background in this paper
...First, Eumycetozoa is the older name such that it even has priority over the entirety of Amoebozoa (see Shadwick et al. 2009; Adl et al. 2012)....
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...Relatively few amoebozoan lineages have a flagellate state, and all confirmed flagellate taxa are found in Evosea (fig. 3, see supplementary table S1, Supplementary Material online; Spiegel 1991; Spiegel et al. 1995; Mikrjukov and Mylnikov 1998; Smirnov et al. 2011; Adl et al. 2012; Ptackova et al. 2013; Berney et al. 2015; Zadrobilkova et al. 2015; P anek et al. 2016)....
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...…each contain some species that are flagellated (usually amoeboflagellates sensu Spiegel 1990), and at least some members of all three groups (Adl et al. 2012) have flagella that contain an electron-dense element in their transition zone, a character not found in any other eukaryotes (see…...
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...Several amoebozoans have life cycles with amoeboid cells that can assume both morphologies at alternate stages (see supplementary table S1, Supplementary Material online), for example, the myxogastrids and some protosteloid amoebae (Olive 1975; Adl et al. 2012)....
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...For instance, it is possible to conclude that LCAA had a flagellate state in its life history (Spiegel 1991, 2011; Spiegel et al. 1995; Lahr et al. 2011b; Adl et al. 2012; Yubuki and Leander 2013) as this character must have been present in the Last Eukaryote Common Ancestor (LECA; Goodenough and Heitman 2014)....
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1,289 citations
"Between a Pod and a Hard Test: The ..." refers background or methods in this paper
...Amoebozoa is morphologically and ecologically very diverse including important pathogens to metazoans (e.g., Entamoeba and Acanthamoeba; Visvesvara et al. 2007) and the model organisms Dictyostelium discoideum and Physarum polycephalum (Eichinger et al. 2005; Schaap et al. 2015)....
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...2007) and the model organisms Dictyostelium discoideum and Physarum polycephalum (Eichinger et al. 2005; Schaap et al. 2015)....
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