“Phylogenetic reconstruction of Paramoebidae brings into question the validity of the genus Neoparamoeba (7295)”

Phylogenetic reconstruction of Paramoebidae brings into question the validity of the genus Neoparamoeba

Introduction

Throughout the literature, both Paramoeba perurans and Neoparamoeba perurans are accepted names for the causative agent of amoebic gill disease, with no consensus. Historically, the two genera were separated morphologically based on the presence or absence of microscales. However, recent studies have illustrated that morphological characteristics are unreliable, and that members of the Paramoebidae can only truly be distinguished using molecular phylogenetic approaches. Thus, this study aimed to assess the validity of the genera Paramoeba and Neoparamoeba through rigorous phylogenetic reconstruction and examine the utility of established molecular markers, to identify which are most reliable for species delimitation.

Methods

Published sequences for the mitochondrial cytochrome oxidase subunit 1 (cox1) and the nuclear small ribosomal subunit (18S) were retrieved from public databases for species across the Paramoebidae. For direct comparison, phylogenetic reconstructions were performed using both maximum likelihood (ML) and Bayesian (BI) approaches for both genes. Similarly, to verify species interrelationships, concatenated cox1 and 18S sequences were used to perform a detailed assessment of the evolutionary relationships between the Paramoebidae using both the ML and BI approaches. To assess the phylogenetic utility of cox1 and 18S, alignments were subjected to Spart explorer to delimit and compare species partitions. Sequence mutational saturation was also performed using the transition/transversion rates, along with measurements of divergence using pairwise mismatch values within and between species.

Results

ML and BI trees for both cox1 and 18S, and the concatenated genes, show distinct grouping of other Paramoebidae genera with no distinction between the Paramoeba and Neoparamoeba, indicating a single genus of Paramoeba. When assessing the utility of the markers 18S showed a higher rate of transitions compared to transversions, while cox1 showed the reverse, with higher rates of transversions, potentially indicating mutational saturation. Pairwise mismatch values between the species of Paramoeba/Neoparamoeba indicated that these were all distinct species, within a single genus. However, the values within species implied that the sequences for Paramoeba pemaquidensis may have come from separate species. This was supported by the analysis from Spart explorer.

Conclusions

Results indicate that Neoparamoeba and Paramoeba should not be considered two separate genera but should instead revert to the single genus Paramoeba. The concatenated genes show very similar relationships to the single gene markers, despite their different evolutionary signatures. To distinguish these organisms, it is vital to use a phylogenetic approach. To ensure that this is done appropriately, markers must be carefully chosen.

1. DAGEN, SARAH, SRUC, Presenter
2. Lawton, Scott, SRUC, Author
3. Bron, James, University of Stirling, Author
4. Monaghan, Sean, University of Stirling, Author
5. Annette, Boerlage, SRUC, Author