Euglyphid Testate Amoebae (Rhizaria: Euglyphida) from an Arctic Eocene Waterbody: Evidence of Evolutionary Stasis in Plate Morphology For Over 40 Million Years

Cyphoderia ampulla (Cyphoderiidae: Rhizaria), a tale of freshwater sailors. The causes and consequences of ecological transitions through the salinity barrier in a family of benthic protists

The salinity barrier that separates marine and freshwater biomes is probably the most important division in biodiversity on Earth. Those organisms that successfully performed this transition had access to new ecosystems while undergoing changes in selective pressure, which often led to major shifts in diversification rates. While these transitions have been extensively investigated in animals, the tempo, mode, and outcome of crossing the salinity barrier have been scarcely studied in other eukaryotes. Here, we reconstructed the evolutionary history of the species complex Cyphoderia ampulla (Euglyphida: Cercozoa: Rhizaria) based on DNA sequences from the nuclear SSU rRNA gene and the mitochondrial cytochrome oxidase subunit I gene, obtained from publicly available environmental DNA data (GeneBank, EukBank) and isolated organisms. A tree calibrated with euglyphid fossils showed that four independent transitions towards freshwater systems occurred from the Mid Miocene onwards, coincident with important fluctuations in sea level. Ancestral trait reconstructions indicated that the whole family Cyphoderiidae had a marine origin and suggest that ancestors of the freshwater forms were euryhaline and lived in environments with fluctuating salinity. Diversification rates did not show any obvious increase concomitant with ecological transitions, but morphometric analyses indicated that species increased in size and homogenized their morphology after colonizing the new environments. This suggests adaptation to changes in selective pressure exerted by life in freshwater sediments.

A first account of the heterotrophic eukaryote Rabdiophrys Rainer from the fossil record and description of a new species from an ancient Eocene Arctic freshwater lake

Rotosphaerids are unicellular, heterotrophic, eukayotic protists that have filopodia, an exterior covering consisting of highly ornamented siliceous scales, and are classified in the Rotosphaerida within the opistokont lineage. Given their appearance as relatively large spherical cells with protruding filopodia and a silica scale covering, they are often mistaken for centrohelid heliozoans. Even though these organisms are widely distributed in both marine and freshwater environments, many species are rarely reported, and none have been reported from the fossil record. We report extensive remains of a new species of Rabdiophrys, R. giraffensis, from an ancient waterbody that was situated near the Arctic Circle in northern Canada during the Eocene. The new species has both plate and spine scales that are similar in morphology, but significantly larger than its closest modern congeners, R. monopora and R. anulifera. The waterbody in which the new species grew and thrived is inferred to have been a moderately deep, circumneutral pond, with moderate concentrations of nutrients and dissolved humic material.

Remarkably preserved cysts of the extinct synurophyte, Mallomonas ampla, uncovered from a 48 Ma freshwater Eocene lake

Chrysophyte algae produce a siliceous stage in their life cycle, through either asexual or sexual reproduction, known as a cyst. Cysts form in response to shifts in environmental conditions, population density, or predation pressure, and upon germination provide a seed source for future populations. Cysts are morphologically distinct for each species, and since their remains become part of the sediment or fossil record cysts are valuable tools in ecological and paleolimnological investigations. However, their value as biological indicators is limited because the vast majority of cyst morphotypes have not been linked to specific vegetative species. In the current work, an exquisitely preserved and morphologically complex cyst type is described from a 48 million year old early Eocene fossil site. This finding is remarkable since many of the cysts were still associated with components of the living vegetative cells that produced them, enabling the morphotype to be immediately linked to the synurophyte, Mallomonas ampla. Fusion of identifiable components of the living cell post cyst formation is unknown in modern investigations. The identification of the cyst structure for M. ampla could be valuable in determining cyst morphotypes for other species in the lineage.

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

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.

The sponge genus Ephydatia from the high-latitude middle Eocene: environmental and evolutionary significance

The freshwater sponge species Ephydatia cf. facunda Weltner, 1895 (Spongillida, Spongillidae) is reported for the first time as a fossil from middle Eocene lake sediments of the Giraffe kimberlite maar in northern Canada. The sponge is represented by birotule gemmuloscleres as well as oxea megascleres. Today, E. facunda inhabits warm-water bodies, so its presence in the Giraffe locality provides evidence of a warm climate at high latitudes during the middle Eocene. The morphological similarity of the birotules to modern conspecific forms suggests protracted morphological stasis, comparable to that reported for other siliceous microfossils from the same locality.

How Really Ancient Is Paulinella Chromatophora?

The ancestor of Paulinella chromatophora established a symbiotic relationship with cyanobacteria related to the Prochloroccocus/Synechococcus clade. This event has been described as a second primary endosymbiosis leading to a plastid in the making. Based on the rate of pseudogene disintegration in the endosymbiotic bacteria Buchnera aphidicola, it was suggested that the chromatophore in P. chromatophora has a minimum age of ~60 Myr. Here we revisit this estimation by using a lognormal relaxed molecular clock on the 18S rRNA of P. chromatophora. Our time estimates show that depending on the assumptions made to calibrate the molecular clock, P. chromatophora diverged from heterotrophic Paulinella spp. ~ 90 to 140 Myr ago, thus establishing a maximum date for the origin of the chromatophore.

The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems

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.