Phylogenomics and Morphological Reconstruction of Arcellinida Testate Amoebae Highlight Diversity of Microbial Eukaryotes in the Neoproterozoic

Daniel J G Lahr; Anush Kosakyan; Enrique Lara; Edward A D Mitchell; Luana Morais; Alfredo L Porfirio-Sousa; Giulia M Ribeiro; Alexander K Tice; Tomáš Pánek; Seungho Kang; Matthew W Brown

doi:10.1016/j.cub.2019.01.078

Phylogenomics and Morphological Reconstruction of Arcellinida Testate Amoebae Highlight Diversity of Microbial Eukaryotes in the Neoproterozoic

Curr Biol. 2019 Mar 18;29(6):991-1001.e3. doi: 10.1016/j.cub.2019.01.078. Epub 2019 Feb 28.

Authors

Affiliations

¹ Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil. Electronic address: dlahr@ib.usp.br.
² Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 37005, České Budějovice, Czech Republic.
³ Real Jardín Botánico, CSIC, Plaza Murillo 2, ES 28014 Madrid, Spain; Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland.
⁴ Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland; Botanical Garden of Neuchâtel, Pertuis-du-Sault 58, 2000 Neuchâtel, Switzerland.
⁵ Department of Geophysics, Institute of Astronomy, Geophysics and Atmospheric Sciences, University of São Paulo, Brazil.
⁶ Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil.
⁷ Department of Biological Sciences, Mississippi State University, Starkville, MS, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, USA.
⁸ Department of Biological Sciences, Mississippi State University, Starkville, MS, USA; Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic.
⁹ Department of Biological Sciences, Mississippi State University, Starkville, MS, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, USA. Electronic address: mbrown@biology.msstate.edu.

PMID: 30827918
DOI: 10.1016/j.cub.2019.01.078

Abstract

Life was microbial for the majority of Earth's history, but as very few microbial lineages leave a fossil record, the Precambrian evolution of life remains shrouded in mystery. Shelled (testate) amoebae stand out as an exception with rich documented diversity in the Neoproterozoic as vase-shaped microfossils (VSMs). While there is general consensus that most of these can be attributed to the Arcellinida lineage in Amoebozoa, it is still unclear whether they can be used as key fossils for interpretation of early eukaryotic evolution. Here, we present a well-resolved phylogenomic reconstruction based on 250 genes, obtained using single-cell transcriptomic techniques from a representative selection of 19 Arcellinid testate amoeba taxa. The robust phylogenetic framework enables deeper interpretations of evolution in this lineage and demanded an updated classification of the group. Additionally, we performed reconstruction of ancestral morphologies, yielding hypothetical ancestors remarkably similar to existing Neoproterozoic VSMs. We demonstrate that major lineages of testate amoebae were already diversified before the Sturtian glaciation (720 mya), supporting the hypothesis that massive eukaryotic diversification took place in the early Neoproterozoic and congruent with the interpretation that VSM are arcellinid testate amoebae.

Keywords: Arcellinida classification; Neoproterozoic; ancestral state reconstruction; arcellinida; phylogenomics; vase-shaped microfossils.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Fossils / anatomy & histology*
Genes, Protozoan
Lobosea / classification*
Lobosea / genetics*
Phylogeny