Testing the rogue taxa hypothesis for clustering instability

Saunders, Amanda; Ashlock, Daniel; Graether, Steffen P.

doi:10.1016/j.jtbi.2019.04.002

Cited by 1 publication

(2 citation statements)

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“…Rogue sequences introduce instability to a phylogeny by jumping around from one place to another and may change the relationships and branch supports within the phylogeny unpredictably [ 47 , 48 ]. To remove such rogue sequences as well as long branches, we split the dataset randomly into subsets of about 900 sequences, aligned each subset with PASTA and built a phylogenetic tree and bootstrap trees with IQ-Tree 2.…”

Section: Methodsmentioning

confidence: 99%

“…The rogue sequences and the sequences of the long branches were removed from the main dataset with SeqKit. However, since what a rogue sequence is, depends also on the other sequences in the dataset [ 48 ], we repeated this splitting and removal procedure for 20 iterations. Once the 20 iterations were complete, we used iteration 10 as a base and built from there trees containing all sequences up to iteration 20.…”

Section: Methodsmentioning

confidence: 99%

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The Gluopsins: Opsins without the Retinal Binding Lysine

Gühmann

Porter

Bok

2022

Cells

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Opsins allow us to see. They are G-protein-coupled receptors and bind as ligand retinal, which is bound covalently to a lysine in the seventh transmembrane domain. This makes opsins light-sensitive. The lysine is so conserved that it is used to define a sequence as an opsin and thus phylogenetic opsin reconstructions discard any sequence without it. However, recently, opsins were found that function not only as photoreceptors but also as chemoreceptors. For chemoreception, the lysine is not needed. Therefore, we wondered: Do opsins exists that have lost this lysine during evolution? To find such opsins, we built an automatic pipeline for reconstructing a large-scale opsin phylogeny. The pipeline compiles and aligns sequences from public sources, reconstructs the phylogeny, prunes rogue sequences, and visualizes the resulting tree. Our final opsin phylogeny is the largest to date with 4956 opsins. Among them is a clade of 33 opsins that have the lysine replaced by glutamic acid. Thus, we call them gluopsins. The gluopsins are mainly dragonfly and butterfly opsins, closely related to the RGR-opsins and the retinochromes. Like those, they have a derived NPxxY motif. However, what their particular function is, remains to be seen.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%