Abstract
Our ability to correctly reconstruct a phylogenetic tree is strongly affected by both systematic errors and the amount of phylogenetic signal in the data. Current approaches to tackle tree reconstruction artifacts, such as the use of parameter-rich models, do not translate readily to single-gene alignments. This, coupled with the limited amount of phylogenetic information contained in single-gene alignments, makes gene trees particularly difficult to reconstruct. Opsin phylogeny illustrates this problem clearly. Opsins are G-protein coupled receptors utilized in photoreceptive processes across Metazoa and their protein sequences are roughly 300 amino acids long. A number of incongruent opsin phylogenies have been published and opsin evolution remains poorly understood. Here, we present a novel approach, the canary sequence approach, to investigate and potentially circumvent errors in single-gene phylogenies. First, we demonstrate our approach using two well-understood cases of long-branch attraction in single-gene data sets, and simulations. After that, we apply our approach to a large collection of well-characterized opsins to clarify the relationships of the three main opsin subfamilies.
Highlights
Resolving gene phylogenies is difficult for two reasons
While we investigated the removal of potentially problematic sequences from the dataset, it is clear that such sequences could be retained, and we do not necessarily advocate their exclusion from an analysis
If one was to retain all the sequences from a dataset, the result of the canary pipeline would still be useful, as knowledge of which sequences in the dataset are “potentially problematic”, and which are “canary sequences” would still be useful when interpreting the results of a phylogenetic analysis
Summary
Resolving gene phylogenies is difficult for two reasons. Firstly, single gene alignments are relatively short and might be poor in phylogenetic signal. A general agreement exists that most opsins can be ascribed to one of three “canonical” (i.e. widely recognised – see Ramirez et al 2016) groups: the rhabdomeric opsins, the ciliary opsins , and the group 4 opsins (the peropsins/RGRs, Goopsins and the neuropsins). In addition to these groups, Ramirez et al (2016) defined three more opsin subfamilies: the bathyopsins, the xenopsins and the chaopsins, though the functions of members of these new families are unclear, and their phylogenetic status requires further testing
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