Ecologically mediated differences in electric organ discharge drive evolution in a sodium channel gene in South American electric fishes

Active electroreception — the ability to detect objects and communicate with conspecifics via the detection and generation of electric organ discharges (EODs) — has evolved convergently in several fish lineages. South American electric fishes (Gymnotiformes) are a highly species-rich group, possibly in part due to evolution of an electric organ (EO) that produces diverse EODs. Neofunctionalization of a voltage-gated sodium channel accompanied the evolution of electrogenic tissue from muscle and resulted in a novel gene (scn4aa) uniquely expressed in the EO. Here, we investigate the link between variation in scn4aa and differences in EOD waveform. We combine gymnotiform scn4aa sequences encoding the C-terminus of the Nav1.4a protein with biogeographic data and EOD recordings. We test whether physiological transitions among EOD types accompany differential selection pressures on scn4aa. We found positive selection on scn4aa coincided with shifts in EOD types. Species that evolved in the a..., This paper investigated the molecular evolution of the Nav1.4a C-terminus (scn4aa gene) from 105 species of electric fishes. Sequences were obtained via Sanger sequencing and aligned via MUSCLE. We used PAML random sites analysis (the M0, M1. M2, M3, M7, M8, and M8a models); and clade model analyses (CMC) compared to a null model (M2a_rel). 
 
PAML analyses are run by combining an alignment file (.txt), phylogenetic tree (.tre) and control file (.ctl) that directs paml what models to run. PAML then outputs a variety of outfiles with parameter estimates about the dataset, including dN/dS (the ratio of nonsynonymous to synonymous nucleotide substitutions (random sites analyses). 
 
Clade Model C (CMC), a different type of PAML analysis, tests whether preselected (Foreground) branches are evolving differently from the remaning (background) branches.
 
 
Analyses
---------------
 
We investigated:
- 105 GYMNOTIFORMES: We tested for positive selection by running random sites models M0-M8. We..., , # Molecular evolution of the Nav1.4a c-terminus in 105 species of South American Electric Fishes

Hauser FE, Xiao D, Van Nynatten A, Brochu-DeLuca KK, Rajakulendran T, Elbassiouny AE, Sivanesan H, Sivananthan P, Crampting WGR, Lovejoy NR. Ecologically mediated differences in electric organce discharge drive evolution in a sodium channel gene in South American electric fishes. In press, Biology Letters

# Reference Information

## Provenance for this README

* File name: README_Hauser_Nav.txt
* Authors: Frances E Hauser
* Other contributors: Dawn Xiao, Alexander Van Nynatten, Kristen K. Brochu-De Luca, Thanara Rajakulendran, Ahmed E. Elbassiouny, Harunya Sivanesan, Pradeega Sivananthan1, William G.R. Crampton, Nathan R. Lovejoy
* Date created: 2024-01-16

## Dataset Attribution and Usage

* Dataset Title: Data for the article \"Ecologically mediated differences in electric organce discharge drive evolution in a sodium channel gene in South American electric fishes\"

* Persiste...