title: Phylogenomics of 'Discosea': A new molecular phylogenetic perspective on Amoebozoa with flat body forms.
abstract: The majority of amoeboid lineages with flattened body forms are placed under a taxonomic hypothetical class 'Discosea' sensu Smirnov et al. (2011), which encompasses some of the most diverse morphs within Amoebozoa. However, its taxonomy and phylogeny is poorly understood. This is partly due to lack of support in studies that are based on limited gene sampling. In this study we use a phylogenomic approach including newly-generated RNA-Seq data and comprehensive taxon sampling to resolve the phylogeny of 'Discosea'. Our analysis included representatives from all orders of 'Discosea' and up to 550 genes, the largest gene sampling in Amoebozoa to date. We conducted extensive analyses to assess the robustness of our resulting phylogenies to effects of missing data and outgroup choice using probabilistic methods. All of our analyses, which explore the impact of varying amounts of missing data, consistently recover well-resolved and supported groups of Amoebozoa. Our results neither support the monophyly nor dichotomy of 'Discosea' as defined by Smirnov et al. (2011). Rather, we recover a robust well-resolved clade referred to as Eudiscosea encompassing the majority of discosean orders (seven of the nine studied here), while the Dactylopodida, Thecamoebida and Himatismenida, previously included in 'Discosea,' are non-monophyletic. We also recover novel relationships within the Eudiscosea that are largely congruent with morphology. Our analyses enabled us to place some incertae sedis lineages and previously unstable lineages such as Vermistella, Mayorella, Gocevia, and Stereomyxa. We recommend some phylogeny-based taxonomic amendments highlighting the new findings of this study and discuss the evolution of the group based on our current understanding.
authors.affiliation: Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA. Electronic address: ytekle@spelman.edu.
authors.forename: Yonas I
authors.initials: YI
authors.lastname: Tekle
authors.affiliation: Biology, Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY, USA.
authors.forename: O Roger
authors.initials: OR
authors.lastname: Anderson
authors.affiliation: Department of Biological Sciences, Smith College, Northampton, MA, USA; Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA, USA.
authors.forename: Laura A
authors.initials: LA
authors.lastname: Katz
authors.affiliation: Department of Biological Sciences, Smith College, Northampton, MA, USA; Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA, USA.
authors.forename: Xyrus X
authors.initials: XX
authors.lastname: Maurer-Alcalá
authors.affiliation: Department of Biological Sciences, Smith College, Northampton, MA, USA; Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA, USA.
authors.forename: Mario Alberto Cerón
authors.initials: MAC
authors.lastname: Romero
authors.affiliation: American Type Culture Collection, Manassas, VA, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Molestina
mesh_terms: D056894:Amoebozoa / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D012313:RNA / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D012313:RNA
keywords: Amoeba; Flabellinea; Lobosea; RNA-Seq; Transcriptome; Tubulinea