Did Terrestrial Diversification of Amoebas (Amoebozoa) Occur in Synchrony with Land Plants? (original) (raw)
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Molecular Ecology, 2019
Recent studies show that soil eukaryotic diversity is immense and dominated by micro‐organisms. However, it is unclear to what extent the processes that shape the distribution of diversity in plants and animals also apply to micro‐organisms. Major diversification events in multicellular organisms have often been attributed to long‐term climatic and geological processes, but the impact of such processes on protist diversity has received much less attention as their distribution has often been believed to be largely cosmopolitan. Here, we quantified phylogeographical patterns in Hyalosphenia papilio, a large testate amoeba restricted to Holarctic Sphagnum‐dominated peatlands, to test if the current distribution of its genetic diversity can be explained by historical factors or by the current distribution of suitable habitats. Phylogenetic diversity was higher in Western North America, corresponding to the inferred geographical origin of the H. papilio complex, and was lower in Eurasia...
Multigene phylogeny resolves deep branching of Amoebozoa
Received 17 April 2014 Revised 2 August 2014 Accepted 11 August 2014 Available online 20 August 2014 Amoebozoa is a key phylum for eukaryote phylogeny and evolutionary history, but its phylogenetic validity has been questioned since included species are very diverse: amoebo-flagellate slime-moulds, naked and testate amoebae, and some flagellates. 18S rRNA gene trees have not firmly established its internal topology. To rectify this we sequenced cDNA libraries for seven diverse Amoebozoa and conducted phylogenetic analyses for 109 eukaryotes (17–18 Amoebozoa) using 60–188 genes. We conducted Bayesian inferences with the evolutionarily most realistic site-heterogeneous CAT-GTR-C model and maximum likelihood analyses. These unequivocally establish the monophyly of Amoebozoa, showing a primary dichotomy between the previously contested subphyla Lobosa and Conosa. Lobosa, the entirely non-flagellate lobose amoebae, are robustly partitioned into the monophyletic classes Tubulinea, with predominantly tube-shaped pseudopodia, and Discosea with flattened cells and different locomotion. Within Conosa 60/70-gene trees with very little missing data show a primary dichotomy between the aerobic infraphylum Semiconosia (Mycetozoa and Variosea) and secondarily anaerobic Archamoebae. These phylogenetic features are entirely congruent with the most recent major amoebozoan classification emphasising locomotion modes, pseudopodial morphology, and ultrastructure. However, 188-gene trees where proportionally more taxa have sparser gene-representation weakly place Archamoebae as sister to Macromycetozoa instead, possibly a tree reconstruction artefact of differentially missing data.
Ammonoid Paleobiology: From macroevolution to paleogeography
Topics in Geobiology, 2015
The Topics in Geobiology series covers the broad discipline of geobiology that is devoted to documenting life history of the Earth. A critical theme inherent in addressing this issue and one that is at the heart of the series is the interplay between the history of life and the changing environment. The series aims for high quality, scholarly volumes of original research as well as broad reviews. Geobiology remains a vibrant as well as a rapidly advancing and dynamic field. Given this field's multidiscipline nature, it treats a broad spectrum of geologic, biologic, and geochemical themes all focused on documenting and understanding the fossil record and what it reveals about the evolutionary history of life. The Topics in Geobiology series was initiated to delve into how these numerous facets have influenced and controlled life on Earth. Recent volumes have showcased specific taxonomic groups, major themes in the discipline, as well as approaches to improving our understanding of how life has evolved. Taxonomic volumes focus on the biology and paleobiology of organisms-their ecology and mode of life-and, in addition, the fossil record-their phylogeny and evolutionary patterns-as well as their distribution in time and space. Theme-based volumes, such as predator-prey relationships, biomineralization, paleobiogeography, and approaches to high-resolution stratigraphy, cover specific topics and how important elements are manifested in a wide range of organisms and how those dynamics have changed through the evolutionary history of life. Comments or suggestions for future volumes are welcomed.
Between a pod and a hard test: the deep evolution of amoebae
Molecular biology and evolution, 2017
Amoebozoa is the eukaryotic supergroup sister to Obazoa, the lineage that contains the animals and Fungi, as well as their protistan relatives, and the breviate and apusomonad flagellates. Amoebozoa is extraordinarily diverse, encompassing important model organisms and significant pathogens. Although amoebozoans are integral to global nutrient cycles and present in nearly all environments, they remain vastly understudied. We present a robust phylogeny of Amoebozoa based on broad representative set of taxa in a phylogenomic framework (325 genes). By sampling 61 taxa using culture-based and single-cell transcriptomics, our analyses show two major clades of Amoebozoa, Discosea and Tevosa. This phylogeny refutes previous studies in major respects. Our results support the hypothesis that the last common ancestor of Amoebozoa was sexual and flagellated, it also may have had the ability to disperse propagules from a sporocarp-type fruiting body. Overall, the main macroevolutionary patterns...
Ammonoid paleobiology, Volume II: from macroevolution to paleogeography. Front matter.
The Topics in Geobiology series covers the broad discipline of geobiology that is devoted to documenting life history of the Earth. A critical theme inherent in addressing this issue and one that is at the heart of the series is the interplay between the history of life and the changing environment. The series aims for high quality, scholarly volumes of original research as well as broad reviews.
Animals and fungi independently evolved from the protozoan phylum Choanozoa, these three groups constituting a major branch of the eukaryotic evolutionary tree known as opisthokonts. Opisthokonts and the protozoan phylum Amoebozoa (amoebae plus slime moulds) were previously argued to have evolved independently from the little-studied, largely flagellate, protozoan phylum, Sulcozoa. Sulcozoa are a likely evolutionary link between opisthokonts and the more primitive excavate flagellates that have ventral feeding grooves and the most primitive known mitochondria. To extend earlier sparse evidence for the ancestral (paraphyletic) nature of Sulcozoa, we sequenced transcriptomes from six gliding flagellates (two apusomonads; three planomonads; Mantamonas). Phylogenetic analyses of 173–192 genes and 73–122 eukaryote-wide taxa show Sulcozoa as deeply paraphyletic, confirming that opisthokonts and Amoebozoa independently evolved from sulcozoans by losing their ancestral ventral groove and dorsal pellicle: Apusozoa (apusomonads plus anaerobic breviate amoebae) are robustly sisters to opisthokonts and probably paraphyletic, breviates diverging before apusomonads; Varisulca (planomonads, Mantamonas, and non-gliding flagellate Collodictyon) are sisters to opisthokonts plus Apusozoa and Amoebozoa, and possibly holophyletic; Glissodiscea (planomonads, Mantamonas) may be holophyletic, but Mantamonas sometimes groups with Collodictyon instead. Taxon and gene sampling slightly affects tree topology; for the closest branches in Sulcozoa and opisthokonts, proportionally reducing missing data eliminates conflicts between homogeneous-model maximum-likelihood trees and evolutionarily more realistic site-heterogeneous trees. Sulcozoa, opisthokonts, and Amoebozoa constitute an often-pseudopodial ‘podiate’ clade, one of only three eukaryotic ’supergroups’. Our trees indicate that evolution of sulcozoan dorsal pellicle, ventral pseudopodia, and ciliary gliding (probably simultaneously) generated podiate eukaryotes from Malawimonas-like excavate flagellates.
Molecular Phylogenetics and Evolution, 2008
Placing amoeboid lineages on the eukaryotic tree of life is difficult due to the paucity of comparable morphological characters and the limited molecular data available for many groups. This situation has led to the lumping of distantly related lineages into large inclusive groups, such as Sarcodina, that do not reflect evolutionary relationships. Previous analyses of molecular markers with limited taxon sampling reveal members of Sarcodina are scattered in five of the six proposed supergroups. We have used multigene analyses to place seven diverse amoeboid lineages-two Nolandella spp., Rhizamoeba sp., Pessonella sp., Arcella hemisphaerica, Arachnula sp. and Trichosphaerium sp.-on the eukaryotic tree of life. Bayesian analysis of the concatenated data of the four genes sequenced (SSU-rDNA, actin, alpha-tubulin and beta-tubulin), including diverse representatives of eukaryotes, indicates that all seven taxa group within the 'Amoebozoa' supergroup. We further performed separate analyses of the well-sampled SSU-rDNA and actin genes using Bayesian and Maximum Likelihood analyses to assess the positions of our newly characterized taxa. In the case of SSU-rDNA, we performed extensive analyses with removal of the fastest rates classes to evaluate the stability and resolution of various taxonomic hypotheses within 'Amoebozoa'. Five of our seven amoeboid lineages fall within well-supported clades that are corroborated by morphology. In contrast, the positions of Arachnula sp. and Trichosphaerium sp. in the SSU-rDNA gene trees are unstable and vary by analyses. Placement of these taxa will require additional data from slowly evolving genes combined with taxon-rich phylogenetic analyses. Finally, the analyses without the fastest rate classes demonstrate that SSU-rDNA has a limited signal for deep relationships within the 'Amoebozoa'.
Plasmodial slime molds (Myxogastria or Myxomycetes) are common and widespread unicellular organisms that are commonly assumed to have a sexual life cycle culminating with the formation of often macroscopic fruiting bodies that efficiently disseminate spores. However, laboratory studies based on mating compatibility revealed the coexistence of asexual as well as sexual strains. To test this hypothesis in natural populations, we investigated the genetic variability of two species of the genus Lamproderma. Detailed ecological releve´s were carried out in 2007 and 2009 in several deep ravines in the Elbsandsteingebirge (Saxony, south-eastern Germany). Morphological characters of 93 specimens of Lamproderma were recorded and genetic analyses, based on the small subunit ribosomal gene, the internal transcribed spacer 1 and partial elongation factor 1a sequences were carried out for 52 specimens. Genetic analyses showed the existence of two major clades, each composed of several discrete lineages. Most of these lineages were composed of several identical sequences (SSU, ITS 1 and EF-1a) which is explained best by an asexual mode of reproduction. Detrended Correspondence Analysis of morphological characters revealed two morphospecies that corresponded to the two major clades, except for one genotype (Lc6), thus challenging the morphospecies concept. Genetic patterns were not related to the geographical distribution: specimens belonging to the same genotype were found in distinct ravines, suggesting effective long-distance dispersal via spores, except for the Lc6 genotype which was found only in one ravine. Implications for the morphological and biological species concept are discussed.
Phylogenetic position of Multicilia marina and the evolution of Amoebozoa
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2006
Recent molecular phylogenetic studies have led to the erection of the phylum Amoebozoa, uniting naked and testate lobose amoebae, the mycetozoan slime moulds and amitochondriate amoeboid protists (Archamoebae). Molecular data together with ultrastructural evidence have suggested a close relationship between Mycetozoa and Archamoebae, classified together in the Conosea, which was named after the cone of microtubules that, when present, is characteristic of their kinetids. However, the relationships of conoseans to other amoebozoans remain unclear. Here, we obtained the complete small-subunit (SSU) rRNA gene sequence (2746 bp) of the enigmatic, multiflagellated protist Multicilia marina, which has formerly been classified either in a distinct phylum, Multiflagellata, or among lobose amoebae. Our study clearly shows that Multicilia marina belongs to the Amoebozoa. Phylogenetic analyses including 60 amoebozoan SSU rRNA gene sequences revealed that Multicilia marina branches at the base ...