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Aggregative Multicellularity Evolved Independently in the Eukaryotic Supergroup Rhizaria

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Aggregative Multicellularity Evolved Independently in the Eukaryotic Supergroup Rhizaria Current Biology 22, 1123–1127, June 19, 2012 ª2012 Elsevier Ltd All rights reserved DOI 10.1016/j.cub.2012.04.021 Report Aggregative Multicellularity Evolved Independently in the Eukaryotic Supergroup Rhizaria Matthew W. Brown,1,* Martin Kolisko,1,2 called a sorocarp (Figure 1A). Their life cycles are socially Jeffrey D. Silberman,3 and Andrew J. Roger1,* intricate because each cell retains its individuality yet works 1Centre for Comparative Genomics and Evolutionary with other like-cells to form a variably complex multicellular Bioinformatics, Department of Biochemistry sorocarp. The ‘‘patchy’’ phylogenetic distribution of soro- and Molecular Biology carpic protists across the tree of eukaryotes suggests that 2Centre for Comparative Genomics and Evolutionary they have independently converged upon this analogous Bioinformatics, Department of Biology mode of propagule dispersal, which is also similar to that of Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada the analogous life cycle in myxobacteria [9]. Here we conclu- 3Department of Biological Sciences, University of Arkansas, sively determine the evolutionary position of Guttulinopsis Fayetteville, AR, 72701, USA vulgaris, a ubiquitous but under-studied sorocarpic amoeba, using a phylogenomic approach with one of the largest protein supermatrices assembled to date that encompasses all major Summary groups of eukaryotes. The genus Guttulinopsis, composed of four species, was Multicellular forms of life have evolved many times, indepen- described over a century ago [10] and has been variously dently giving rise to a diversity of organisms such as classified [11, 12]. Guttulinopsis vulgaris is the most common animals, plants, and fungi that together comprise the visible species and can be found globally on the dung of various biosphere. Yet multicellular life is far more widespread herbivores [11, 13–15]. Despite morphological and ultrastruc- among eukaryotes than just these three lineages. A particu- tural studies [11, 12, 14, 16] of sorocarps (Figures 1A–1C) larly common form of multicellularity is a social aggregative and trophozoites (Figures 1D and 1E), the phylogenetic fruiting lifestyle whereby individual cells associate to form position of Guttulinopsis has remained unclear. The lobose a ‘‘fungus-like’’ sorocarp. This complex developmental pro- morphology of the amoebae suggests an affinity to either cess that requires the interaction of thousands of cells the supergroup Amoebozoa or the Excavata phylum Heterolo- working in concert was made famous by the ‘‘cellular slime bosea (Figures 1D and 1E). The mitochondria of G. vulgaris mold’’ Dictyostelium discoideum, which became an impor- have flattened discoid cristae [2, 16] and the cells lack a tant model organism [1]. Although sorocarpic protistan discrete Golgi apparatus [17], both characteristics of Heterolo- lineages have been identified in five of the major eukaryote bosea [2, 18]. On the other hand, G. vulgaris lacks rough endo- groups [2–8], the ubiquitous and globally distributed plasmic reticulum surrounding its mitochondria, a character species Guttulinopsis vulgaris has eluded proper classifica- present in most heteroloboseans [16, 18]. The balance of tion. Here we demonstrate, by phylogenomic analyses of morphological data hinted that G. vulgaris might be related a 159-protein data set, that G. vulgaris is a member of Rhiza- to the putative heterolobosean amoeba genus, Rosculus, ria and is thus the first member of this eukaryote supergroup which shares all of the above morphological characteristics known to be capable of aggregative multicellularity. [2, 19, 20] but does not form sorocarps. However, to date, no sequence data from Guttulinopsis was available to test Results and Discussion these hypotheses, and the only sequence currently available from Rosculus spp. is a nuclear encoded mitochondrial The origins of multicellular life forms from unicellular ancestors single-subunit RNA polymerase gene (mtSNAP) (GenBank are among the most profound innovations in the history of life. DQ388527) that, to our knowledge, has not been phylogeneti- Although multicellularity has originated multiple times in a cally analyzed. great diversity of eukaryotic lineages and, more controver- The standard approach to investigate phylogenetic affinity sially, in some prokaryote lineages [9], many of these indepen- of protistan taxa is to utilize an 18S ribosomal RNA gene dent evolutionary transitions have been overlooked. Molecular phylogeny. However, attempts to amplify G. vulgaris 18S phylogenetic data have recently revealed that the sorocarpic rDNA were unsuccessful when employing a comprehensive life style, commonly known as the cellular slime mold habit set of ‘‘universal’’ eukaryotic 18S primers (data not shown). [1], is the most widely distributed form of multicellularity, Instead, we obtained multiple genes for phylogenetic analyses rivaled only by simple colonial pluricellularity. Examples of by conducting massively parallel 454-pyrosequencing (Roche, this form are found in at least five major eukaryote groups Branford, CT, USA) of complementary DNA (cDNA) to sample [2]; these are the dictyostelids and Copromyxa in Amoebozoa, the transcriptome of G. vulgaris and another sorocarpic the acrasids in Excavata, Fonticula alba in Opisthokonta, amoeba, F. alba, that our previous analyses indicate is closely Sorogena in the Alveolata, and Sorodiplophrys in the Strame- related to the fungi [6]. We integrated these protein-coding nopiles [3–8]. The phylogenetic position of Copromyxella has gene sequences into a pre-existing data set united from yet to be confirmed by molecular analyses, and it may two prior phylogenomic studies [21, 22]. The final 67 represent yet another independent derivation of this lifestyle. taxa, 159-protein phylogenomic supermatrix (43,615 amino In all of these organisms, cell aggregates are capable of devel- acid positions), included representatives from each of the oping into a ‘‘fungus-like’’ propagule-bearing fruiting body, proposed eukaryotic supergroups and the stramenopiles, alveolates, haptophytes, and telonemids [2]. Unexpectedly, phylogenetic analyses using both Bayesian inference (BI) and *Correspondence: [email protected] (M.W.B.), [email protected] (A.J.R.) maximum-likelihood (ML) methods revealed that G. vulgaris Current Biology Vol 22 No 12 1124 Figure 1. The Life Stages of Guttulinopsis vulgaris Sorocarps appear as white to pale-yellow stalked ‘‘balls’’ projecting from the surface of 1–7 day old dung. They are macroscopic (200–500 mm in height) and consist of >20,000 cells [1] with a distinct stalk and one to several spore masses (sorus[i]) atop the stalk (Figures 1A–1C). Mature sorocarps consist of distinct cell types, irregu- larly shaped walled spores (Figure 1C) along with stalk compartments containing degenerated, amoeboid, and encysted stalk cells [14]. (A) Multicellular fruiting body with a single sorus fruiting on a piece of cow dung substrate. Scale bar represents 250 mm. (B) Multicellular fruiting body with three sori projecting from a single stalk. Scale bar represents 250 mm. (C) Whole mount of the fruiting body shown in (A). Photo- graphed using differential interference contrast micros- copy. Scale bar represents 50 mm. (D) Typical irregularly shaped spores. Scale bar repre- sents 10 mm. (E) Lobose amoeba and round spore isolated from sorus. Scale bar represents 10 mm. The lobose amoebae (shown in E) of G. vulgaris are very similar to those in the genus Rosculus. The phylogenetic relationship of the two taxa is confirmed through analyses of the mtSNAP gene (Figure S1). robustly groups within the supergroup Rhizaria (1.0/100%, contains organisms such as the taxon-rich Cercozoa [26], BI posterior probability and ML bootstrap, Figure 2). This Foraminifera, testate amoeboid gromiids, and marine plank- affiliation was unanticipated considering the morphological tonic Radiolaria, along with animal and plant parasites (Haplo- and ultrastructural characters of Guttulinopsis, which are not sporidia, Phytomyxea). Despite this diversity, there are two especially similar to any known rhizarian. unifying morphological themes in Rhizaria: possession of The exact position of G. vulgaris within Rhizaria is less tubular mitochondrial cristae and the ability of cells to form definitively resolved. Our phylogenies demonstrate that fine pseudopodia that are either reticulose (network with G. vulgaris consistently branches within Filosea (the ‘‘core- thin thread-like connections) or filose (fine thread-like) [25]. Cercozoa’’) (0.99/99%) (Figure 2), here represented by the However, both of these likely represent symplesiomorphies taxa Limnofila sp., Bigelowiella natans, and Paracercomonas because tubular mitochondrial cristae are common outside marina. Guttulinopsis vulgaris specifically branches sister to of Rhizaria and fine pseudopodia are not restricted to Rhizaria P. marina with moderately high topological support in our (i.e., nucleariid amoebae [Opisthokonta] and diplophoriid ML tree (1.0/94%). Topology tests employing our phyloge- amoebae [stramenopiles]). Guttulinopsis is a very unusual nomic data set reject: (1) the placement of G. vulgaris outside rhizarian, even considering Rhizaria’s extreme morphological but sister to Filosea and (2) as outside but sister to Rhizaria diversity. The amoebae of Guttulinopsis do not produce fine (see Table S1 available online). However, determination of pseudopodia; rather, their pseudopodia are broad-lobose the deep phylogenetic branching patterns within
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