Journal
GENOME BIOLOGY AND EVOLUTION
Volume 12, Issue 2, Pages 3906-3916Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gbe/evaa015
Keywords
opsin; phylogeny; systematic error; nonbilaterian metazoan
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Funding
- NERC-GW4 PhD studentship
- NERC [NE/P013678/1]
- Royal Society University Research Fellowship [UF160226]
- NERC [NE/P013678/1] Funding Source: UKRI
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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.
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