多核变形虫缺乏线粒体和一些真核细胞的其他细胞器(如过氧化物酶体和高尔基体)。同时,由于没有鞭毛,多核变形虫也无法进行有丝分裂。多核变形虫作为有核细胞却缺乏其他真核生物所拥有的细胞器[11],一时间多核变形虫被认为是真核生物原始的样子,它们处于细菌和真核生物之间的过渡。[12]1973年,有人提出在沼泽多核变形虫的祖先在其进化演变之前,真核生物已经开始出现线粒体。[13]在1976年,Jean M. Whatley写道沼泽多核变形虫可能是目前最原始的真核生物。[14]因此,多核变形虫可能是现代真核生物的雏形。而根据共生体学说,共生的内部细菌,可能在后来演变为现代真核细胞的线粒体。这些共生细菌的功能目前仍不清楚,Whatley认为它们可能会提供一个进化的范例,来说明细菌到线粒体这种转变方式。[14]
在1988年,多核变形虫的原始形态又再一次被怀疑,Joe I. Griffin的研究表明沼泽多核变形虫确实拥有不成熟的基础鞭毛,它可以进行简单的有丝分裂,Griffin表明多核变形虫既不是真核细胞生物的原始形态,也没有和其他变形虫类存在很大的不同,它仅仅是一种变形体鞭毛虫。[16]1995年,反对多核变形虫属于原始形态的呼声越来越高,分子分析表明沼泽多核变形虫的祖先很可能拥有线粒体。[17]几年过后,很明显,所有变形虫纲的生物都被确认它们的线粒体已经消失。换句话说,多核变形虫并不是处于早期的原始真核生物,而是已经退化并失去了它们祖先的细胞器的原生生物。[18]
Chistyakova, L. V., and A. O. Frolov. "Light and electron microscopic study of Pelomyxa stagnalis sp. n.(Archamoebae, pelobiontida)." Cell and Tissue Biology 5.1 (2011): 90-97.
Brugerolle G. and Patterson D. 2000. Order Pelobiontida Page 1976. In: An illustrated guide to the protozoa, second edition (Eds. Lee J., Leedale G. and Bradbury P.). Allen press inc., Lawrence, USA. pp. 1097-1103.
Frolov, Alexander O., Ludmila V. Chystjakova, and Andrew V. Goodkov. "A new pelobiont protist Pelomyxa corona sp. n.(Peloflagellatea, Pelobiontida)." Protistology 3 (2004): 233-241.
Frolov, Alexander O., Ludmila V. Chystjakova, and Andrew V. Goodkov. "Light and electron microscopic study of Pelomyxa binucleata (Gruber, 1884)(Peloflagellatea, Pelo biontida)." Protistology 4 (2005): 57-73.
Frolov, A. O., et al. "Light and electron microscopic investigation of Pelomyxa prima (Gruber, 1884)(Peloflagellatea, Pelobiontida)." Tsitologiia 47.1 (2005): 89-98.
Frolov, A. O., L. V. Chistiakova, and M. N. Malysheva. "Light-and electron-microscopical study of Pelomyxa flava sp. n.(archamoebae, pelobiontida)]." Tsitologiia 52.9 (2010): 776.
Whatley, Jean M. et al. (April 1979). "From Extracellular to intracellular: the establishment of mitochondria and chloroplasts." Proceedings of the Royal Society of London. Series B, Biological Sciences. 204(155):51)
Bovee, E. C., and T. L. Jahn. 1973. "Taxonomy and phylogeny." Pages 38–76 in K. W. Jeon, ed. The biology of amoeba. Academic Press, New York; cited in Roger, Andrew J. (1999) "Reconstructing Early events in Eukaryotic Evolution." The American Naturalist. 154(S4):S147
Whatley, Jean M. Bacteria and Nuclei in Pelomyxa Palustris: Comments on the Theory of Serial Endosymbiosis. New Phytologist. January 1976, 76 (1): 111–120. JSTOR 2431427. doi:10.1111/j.1469-8137.1976.tb01443.x.
Cavalier-Smith, T. 1983. "A 6-kingdom classification and a unified phylogeny." In W. Schwemmler and H. E. A. Schenk (ed.), Endocytobiology II. de Gruyter, Berlin. pp. 1027-1034.
Morin, L., and J.-P. Mignot. 1995. Are Archamoebae true Archezoa? the phylogenetic position of Pelomyxa sp. as inferred from large subunit ribosomal RNA sequencing.
European Journal of Protistology 31:402.