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González-Miguéns R, Soler-Zamora C, Villar-Depablo M, Todorov M, Lara E. Multiple convergences in the evolutionary history of the testate amoeba family Arcellidae (Amoebozoa: Arcellinida: Sphaerothecina): when the ecology rules the morphology. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Protists are probably the most species-rich eukaryotes, yet their systematics are inaccurate, leading to an underestimation of their actual diversity. Arcellinida (= lobose testate amoebae) are amoebozoans that build a test (a hard shell) whose shape and composition are taxonomically informative. One of the most successful groups is Arcellidae, a family found worldwide in many freshwater and terrestrial environments where they are indicators of environmental quality. However, the systematics of the family is based on works published nearly a century ago. We re-evaluated the systematics based on single-cell barcoding, morphological and ecological data. Overall, test shape appears to be more related to environmental characteristics than to the species’ phylogenetic position. We show several convergences in organisms with similar ecology, some traditionally described species being paraphyletic. Based on conservative traits, we review the synapomorphies of the infraorder Sphaerothecina, compile a list of synonyms and describe a new genus Galeripora, with five new combinations. Seven new species: Arcella guadarramensis sp. nov., Galeripora balari sp. nov., Galeripora bufonipellita sp. nov., Galeripora galeriformis sp. nov., Galeripora naiadis sp. nov., Galeripora sitiens sp. nov. andGaleripora succelli sp. nov. are also described here.
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Affiliation(s)
| | | | - Mar Villar-Depablo
- Real Jardín Botánico (RJB-CSIC), Plaza Murillo 2, Madrid, Spain
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), Serrano 115 bis, Madrid, Spain
| | - Milcho Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Science, Sofia, Bulgaria
| | - Enrique Lara
- Real Jardín Botánico (RJB-CSIC), Plaza Murillo 2, Madrid, Spain
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Strassert JFH, Irisarri I, Williams TA, Burki F. A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids. Nat Commun 2021; 12:1879. [PMID: 33767194 PMCID: PMC7994803 DOI: 10.1038/s41467-021-22044-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 02/25/2021] [Indexed: 01/31/2023] Open
Abstract
In modern oceans, eukaryotic phytoplankton is dominated by lineages with red algal-derived plastids such as diatoms, dinoflagellates, and coccolithophores. Despite the ecological importance of these groups and many others representing a huge diversity of forms and lifestyles, we still lack a comprehensive understanding of their evolution and how they obtained their plastids. New hypotheses have emerged to explain the acquisition of red algal-derived plastids by serial endosymbiosis, but the chronology of these putative independent plastid acquisitions remains untested. Here, we establish a timeframe for the origin of red algal-derived plastids under scenarios of serial endosymbiosis, using Bayesian molecular clock analyses applied on a phylogenomic dataset with broad sampling of eukaryote diversity. We find that the hypotheses of serial endosymbiosis are chronologically possible, as the stem lineages of all red plastid-containing groups overlap in time. This period in the Meso- and Neoproterozoic Eras set the stage for the later expansion to dominance of red algal-derived primary production in the contemporary oceans, which profoundly altered the global geochemical and ecological conditions of the Earth.
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Affiliation(s)
- Jürgen F H Strassert
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden
- Department of Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Iker Irisarri
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, and Campus Institute Data Science (CIDAS), Göttingen, Germany
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, UK
| | - Fabien Burki
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden.
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Abstract
Phagocytosis, or 'cell eating', is a eukaryote-specific process where particulate matter is engulfed via invaginations of the plasma membrane. The origin of phagocytosis has been central to discussions on eukaryogenesis for decades-, where it is argued as being either a prerequisite for, or consequence of, the acquisition of the ancestral mitochondrion. Recently, genomic and cytological evidence has increasingly supported the view that the pre-mitochondrial host cell-a bona fide archaeon branching within the 'Asgard' archaea-was incapable of phagocytosis and used alternative mechanisms to incorporate the alphaproteobacterial ancestor of mitochondria. Indeed, the diversity and variability of proteins associated with phagosomes across the eukaryotic tree suggest that phagocytosis, as seen in a variety of extant eukaryotes, may have evolved independently several times within the eukaryotic crown-group. Since phagocytosis is critical to the functioning of modern marine food webs (without it, there would be no microbial loop or animal life), multiple late origins of phagocytosis could help explain why many of the ecological and evolutionary innovations of the Neoproterozoic Era (e.g. the advent of eukaryotic biomineralization, the 'Rise of Algae' and the origin of animals) happened when they did.
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Affiliation(s)
- Daniel B. Mills
- Department of Geological Sciences, Stanford University, Stanford, CA 94305, USA
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Testate Amoebae in the 407-Million-Year-Old Rhynie Chert. Curr Biol 2019; 29:461-467.e2. [PMID: 30661795 DOI: 10.1016/j.cub.2018.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/09/2018] [Accepted: 12/06/2018] [Indexed: 11/21/2022]
Abstract
The Lower Devonian Rhynie chert is justly famous for the clear glimpse it offers of early terrestrial ecosystems [1]. Seven species of stem- and crown-group vascular plants have been described from Rhynie, many preserved in growth position [2], as well as 14 species of invertebrate animals, all arthropods [3] save for a single nematode population [4]. While these shed welcome light on early tracheophytes and land animals, modern terrestrial ecosystems additionally contain a diversity of microscopic organisms that are key to ecosystem function, including fungi, protists, and bacteria. Fungi ranging from mycorrhizae to saprophytes are well preserved in Rhynie rocks ([5] and references therein), and oomycetes are also present [5]. Both green algae (charophytes) and cyanobacteria have also been documented locally [6, 7, 8]. To date, however, phagotrophic protists have not been observed in Rhynie cherts, even though such organisms contribute importantly to carbon, nitrogen, and silica cycling in modern terrestrial communities [9]. Here, we report a population of organic tests described as Palaeoleptochlamys hassii gen. nov., sp. nov. from a pond along the Rhynie alluvial plain, which we interpret as arcellinid amoebozoans. These fossils expand the ecological dimensions of the Rhynie biota and support the hypothesis that arcellinids transitioned from marine through freshwater environments to colonize soil ecosystems in synchrony with early vascular plants.
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Oliverio AM, Lahr DJG, Grant J, Katz LA. Are microbes fundamentally different than macroorganisms? Convergence and a possible case for neutral phenotypic evolution in testate amoeba (Amoebozoa: Arcellinida). ROYAL SOCIETY OPEN SCIENCE 2015; 2:150414. [PMID: 27019725 PMCID: PMC4807447 DOI: 10.1098/rsos.150414] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
This study reveals extensive phenotypic convergence based on the non-monophyly of genera and morphospecies of testate (shelled) amoebae. Using two independent markers, small subunit ribosomal DNA (ssu-rDNA) and mitochondrial cytochrome oxidase I (COI), we demonstrate discordance between morphology and molecules for 'core Nebela' species (Arcellinida; Amoebozoa). Prior work using just a single locus, ssu-rDNA, also supported the non-monophyly of the genera Hyalosphenia and Nebela as well as for several morphospecies within these genera. Here, we obtained COI gene sequences of 59 specimens from seven morphospecies and ssu-rDNA gene sequences of 50 specimens from six morphospecies of hyalosphenids. Our analyses corroborate the prior ssu-rDNA findings of morphological convergence in test (shell) morphologies, as COI and ssu-rDNA phylogenies are concordant. Further, the monophyly of morphospecies is rejected using approximately unbiased tests. Given that testate amoebae are used as bioindicators in both palaeoecological and contemporary studies of threatened ecosystems such as bogs and fens, understanding the discordance between morphology and genetics in the hyalosphenids is essential for interpretation of indicator species. Further, while convergence is normally considered the result of natural selection, it is possible that neutrality underlies phenotypic evolution in these microorganisms.
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Affiliation(s)
- Angela M. Oliverio
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Daniel J. G. Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
| | - Jessica Grant
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA
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Lahr DJG, Bosak T, Lara E, Mitchell EAD. The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems. PeerJ 2015; 3:e1234. [PMID: 26734499 PMCID: PMC4699787 DOI: 10.7717/peerj.1234] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/19/2015] [Indexed: 11/20/2022] Open
Abstract
The terrestrial cycling of Si is thought to have a large influence on the terrestrial and marine primary production, as well as the coupled biogeochemical cycles of Si and C. Biomineralization of silica is widespread among terrestrial eukaryotes such as plants, soil diatoms, freshwater sponges, silicifying flagellates and testate amoebae. Two major groups of testate (shelled) amoebae, arcellinids and euglyphids, produce their own silica particles to construct shells. The two are unrelated phylogenetically and acquired biomineralizing capabilities independently. Hyalosphenids, a group within arcellinids, are predators of euglyphids. We demonstrate that hyalosphenids can construct shells using silica scales mineralized by the euglyphids. Parsimony analyses of the current hyalosphenid phylogeny indicate that the ability to “steal” euglyphid scales is most likely ancestral in hyalosphenids, implying that euglyphids should be older than hyalosphenids. However, exactly when euglyphids arose is uncertain. Current fossil record contains unambiguous euglyphid fossils that are as old as 50 million years, but older fossils are scarce and difficult to interpret. Poor taxon sampling of euglyphids has also prevented the development of molecular clocks. Here, we present a novel molecular clock reconstruction for arcellinids and consider the uncertainties due to various previously used calibration points. The new molecular clock puts the origin of hyalosphenids in the early Carboniferous (∼370 mya). Notably, this estimate coincides with the widespread colonization of land by Si-accumulating plants, suggesting possible links between the evolution of Arcellinid testate amoebae and the expansion of terrestrial habitats rich in organic matter and bioavailable Si.
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Affiliation(s)
- Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo , Rua do Matão, São Paulo , Brazil
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary Sciences, Massachussetts Institute of Technology , Cambridge, MA , USA
| | - Enrique Lara
- Laboratory of Soil Biology, University of Neuchatel , Neuchatel , Switzerland
| | - Edward A D Mitchell
- Laboratory of Soil Biology, University of Neuchatel, Neuchatel, Switzerland; Jardin Botanique de Neuchâtel, Neuchatel, Switzerland
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Cavalier-Smith T. Mixed heterolobosean and novel gregarine lineage genes from culture ATCC 50646: Long-branch artefacts, not lateral gene transfer, distort α-tubulin phylogeny. Eur J Protistol 2015; 51:121-37. [DOI: 10.1016/j.ejop.2014.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 12/04/2014] [Accepted: 12/09/2014] [Indexed: 12/21/2022]
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