Intra-Genomic Ribosomal RNA Polymorphism and Morphological Variation in Elphidium macellum Suggests Inter-Specific Hybridization in Foraminifera

Abstract

Elphidium macellum is a benthic foraminifer commonly found in the Patagonian fjords. To test whether its highly variable morphotypes are ecophenotypes or different genotypes, we analysed 70 sequences of the SSU rRNA gene from 25 specimens. Unexpectedly, we identified 11 distinct ribotypes, with up to 5 ribotypes co-occurring within the same specimen. The ribotypes differ by varying blocks of sequence located at the end of stem-loop motifs in the three expansion segments specific to foraminifera. These changes, distinct from typical SNPs and indels, directly affect the structure of the expansion segments. Their mosaic distribution suggests that ribotypes originated by recombination of two or more clusters of ribosomal genes. We propose that this expansion segment polymorphism (ESP) could originate from hybridization of morphologically different populations of Patagonian Elphidium. We speculate that the complex geological history of Patagonia enhanced divergence of coastal foraminiferal species and contributed to increasing genetic and morphological variation.

Rare calcareous microfossils from Middle Miocene strata, Weddell Sea off Antarctic Peninsula

“…According to these authors, in E. pseudoinflatum, septal bridges do not extend the full way across each chamber. This is also the case for our smaller speci− mens (Fig 3.10-11); however, the latest molecular work indicates that recent E. macellum from Patagonian fjords has a strongly variable morphology and some specimens show septal bridges extending only partially across each chamber (Pillet et al 2012, fig. 1D).…”

“…Although E. macellum was reported from Patagonian fossil assemblages since at least Early Miocene (Nanez 1990;Malumian and Scarpa 2005;Malumian and Olivero 2006), comparison of our specimens with well−illustrated modern and fos− sil forms seems to support the Middle Miocene age. Our specimens show interme− diate morphology between modern E. macellum from the Patagonian fjords (Pillet et al 2012) and Elphidium pseudoinflatum known from the Late Eocene to middle Miocene of New Zealand (Hayward et al 1997) (see the taxonomic section for more details).…”

“…3.10-13). In overall shape and ornamentation, this taxon resembles specimens of modern E. macellum from Patagonian fjords (Pillet et al 2012). Our specimens differ by the indications of spinal bases in the keel area in large specimens ( Fig.…”

“…Thus, it resembles Cribroelphidium lene (Cushman et McCul− loch, 1940) but shows more chambers in the final whorl and a distinctively lower apertural face. In this regard, it is a morphological variant of modern Elphidium macellum from Patagonian fjords (Pillet et al 2012, fig. 1F) (see below, the dis− cussion for Elphidium cf.…”

Two new species of Ripella (Amoebozoa, Vannellida) and unusual intragenomic variability in the SSU rRNA gene of this genus

“…The intragenomic variability of ribosomal cluster was also demonstrated in various groups of protists, for example, ciliates (Gong et al 2013), foraminifera (Pillet et al 2012) and dinoflagellates (Gribble and Anderson 2007;Miranda et al 2012). In Amoebozoa some SSU rRNA gene sequence variation between different molecular clones of the same amplicon does occur, and is usually detected by sequencing multiple clones of the PCR product amplified from the genomic DNA.…”