Proteome-Based Clustering Approaches Reveal Phylogenetic Insights into Amphistegina

Foraminifera are highly diverse and have a long evolutionary history. As key bioindicators, their phylogenetic schemes are of great importance for paleogeographic applications, but may be hard to recognize correctly. The phylogenetic relationships within the prominent genus Amphistegina are still uncertain. Molecular studies on Amphistegina have so far only focused on genetic diversity within single species and suggested a cryptic diversity that demands for further investigations. Besides molecular sequencing-based approaches, different mass spectrometry-based proteomics approaches are increasingly used to give insights into the relationship between samples and organisms, especially as these do not require reference databases. To better understand the relationship of amphisteginids and test different proteomics-based approaches we applied de novo peptide sequencing and similarity clustering to several populations of Amphistegina lobifera, A. lessonii and A. gibbosa. We also analyzed the dominant photosymbiont community to study their influence on holobiont proteomes. Our analyses indicate that especially de novo peptide sequencing allows to reconstruct the relationship among foraminiferal holobionts, although the detected separation of A. gibbosa from A. lessonii and A. lobifera may be partly influenced by their different photosymbiont types. The resulting dendrograms reflect the separation in two lineages previously suggested and provide a basis for future studies.