Convergent_nAChR venom resistance Mammals 2022
Data files
Dec 05, 2025 version files 81.85 KB
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codeml_BS_Alt_A.ctl
760 B
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codeml_BS_Alt.ctl
752 B
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codeml_BS_Null.ctl
750 B
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codeml_BSNull_A.ctl
758 B
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DROPOUT_Tree.tre
3.57 KB
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DropoutSitecodeml.ctl
763 B
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Dropped_Alignment.phy
18.96 KB
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FINAL_MamTree.tre
4.22 KB
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GeneTree_SiteModel_M8.tre
8.35 KB
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M8_Ancestors.fasta
9.26 KB
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Mammal_Full.phy
22.25 KB
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README.md
9.49 KB
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README.txt
1.24 KB
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Sitecodeml.ctl
745 B
Abstract
Convergent evolution is central to the study of adaptation and has been used to understand both the limits of evolution and the diverse patterns and processes which result in adaptive change. Resistance to snake venom α-neurotoxins (αNTXs) is a case of widespread convergence having evolved several times in snakes, lizards, and mammals. Despite extreme toxicity of αNTXs, substitutions in its target, the nicotinic acetylcholine receptor (nAChR), prevent αNTX binding and render species resistant. Recently, the published meerkat (Herpestidae) genome revealed that meerkats have the same substitutions in nAChR as the venom-resistant Egyptian mongoose (Herpestidae), suggesting that venom-resistant nAChRs may be ancestral to herpestids. Like the mongoose, many other species of feliform carnivores prey on venomous snakes, though their venom resistance has never been explored. To evaluate the prevalence and ancestry of αNTX resistance in mammals, we generate a dataset of mammalian nAChR utilizing museum specimens and public datasets. We find five instances of convergent evolution within feliform carnivores, and an additional eight instances across all mammals sampled. Tests of selection show that these substitutions are evolving under positive selection. Repeated convergence suggests that this adaptation played an important role in the evolution of mammalian physiology and potentially venom evolution.
Dataset DOI: 10.5061/dryad.jh9w0vtf8
Author: Dr. Danielle H. Drabeck
Affiliation: University of Minnesota
Date of data collection: 2022
Date of publication: 2025
1. OVERVIEW
This dataset accompanies the manuscript “Convergent evolution of α-neurotoxin resistance in mammalian nicotinic acetylcholine receptors (nAChR).” It contains sequence alignments, phylogenetic trees, and codeml control files used to test for positive selection on the nAChR α-subunit across mammals. The dataset enables replication of analyses showing repeated, independent amino acid substitutions conferring snake venom α-neurotoxin resistance in multiple mammalian lineages.
2. PURPOSE OF THE DATASET
The purpose of this dataset is to:
- Document convergence in the nAChR α-subunit gene among mammals.
- Evaluate molecular evidence for α-neurotoxin resistance via convergent amino acid substitutions.
- Provide data used in codon-based models (PAML codeml) for positive selection and ancestral state reconstruction.
- Facilitate reuse by researchers studying coevolution, convergence, or toxin resistance.
3. DESCRIPTION OF FILES
Mammal_Full.phy – Full codon alignment of mammalian nAChR α-subunit sequences used in PAML analyses.
Dropped_Alignment.phy – Reduced alignment excluding low-quality sequences.
FINAL_MamTree.tre – Mammalian species tree used for all selection analyses.
DROPOUT_Tree.tre – Pruned version of the tree matching Dropped_Alignment.phy.
GeneTree_SiteModel_M8.tre – Gene tree estimated under the M8 site model.
M8_Ancestors.fasta – Reconstructed ancestral sequences under the M8 model.
codeml_BS_Alt.ctl / codeml_BS_Alt_A.ctl – PAML control files for branch-site model alternative hypotheses.
codeml_BS_Null.ctl / codeml_BSNull_A.ctl – PAML control files for branch-site null models.
Sitecodeml.ctl / DropoutSitecodeml.ctl – PAML control files for site-model analyses.
README.txt – Metadata summary included in the dataset.
4. METHODS SUMMARY
Sequence acquisition: nAChR α-subunit coding sequences were obtained from public databases (NCBI GenBank, Ensembl) and museum-derived genomic extracts.
Alignment: Sequences were aligned at the codon level using MACSE v2 to preserve reading-frame integrity.
Phylogenetic analysis: Species trees were curated from TimeTree and reconciled with taxonomic references.
Selection tests: Positive selection was tested using codeml (PAML v4.9) under site and branch-site models (M7 vs. M8, Null vs. Alt). Likelihood ratio tests were used to detect sites or branches under selection.
Ancestral reconstruction: Posterior probabilities of ancestral states were estimated under the M8 model to infer substitution histories across mammalian lineages.
5. KEY FINDINGS SUPPORTED BY THESE DATA
- Independent amino acid substitutions at α-neurotoxin binding sites evolved multiple times in mammals.
- Venom resistance occurs in several feliform carnivore lineages and at least eight other mammalian groups.
- Branch-site models support positive selection acting on binding-site residues.
6. FILE USE AND REPRODUCIBILITY
PAML control files (*.ctl) can be used directly with the provided alignments and trees.
File paths may need adjustment for local directories. Analyses were run using PAML v4.9 on Linux with parameters described within each control file.
7. FUNDING AND ACKNOWLEDGMENTS
This dataset was supported by the National Institute of General Medical Sciences (K12GM119955) and the University of Minnesota.
Museum specimens and genomic resources were provided by collaborating institutions listed in the associated publication.
8. DATA LICENSE AND CITATION
All data are released under the Public Domain (CC0 1.0 Universal) license.
Cite as:
Drabeck, D.H. (2025). Convergent evolution of nAChR venom resistance in mammals. Dryad, Dataset. https://doi.org/10.5061/dryad.jh9w0vtf8
Files and variables
File: GeneTree_SiteModel_M8.tre
Description: Gene tree inferred under the PAML site model M8 (beta & ω>1), used to identify codon sites evolving under positive selection across mammals.
File: M8_Ancestors.fasta
Description: FASTA file containing reconstructed ancestral sequences for the nAChR α-subunit, estimated under the M8 model to infer the evolutionary history of toxin-binding site substitutions.
File: Mammal_Full.phy
Description: Full codon alignment of mammalian nAChR α-subunit sequences, including all taxa analyzed for selection and ancestral reconstruction in PAML.
File: DROPOUT_Tree.tre
Description: Pruned phylogenetic tree corresponding to the reduced “Dropped_Alignment.phy,” containing only taxa retained after quality filtering.
File: DropoutSitecodeml.ctl
Description: PAML control file specifying parameters for site-model analyses using the reduced “Dropped_Alignment.phy” dataset and “DROPOUT_Tree.tre.”
File: Dropped_Alignment.phy
Description: Reduced codon alignment excluding sequences with missing data or low alignment quality, used for validation and sensitivity analyses.
File: codeml_BS_Alt.ctl
Description: Branch-site model control file (alternative hypothesis) allowing ω>1 on specified lineages to test for episodic positive selection.
File: codeml_BSNull_A.ctl
Description: Branch-site model control file (null hypothesis, variant A) fixing ω=1 on foreground branches to compare against the alternative model.
File: codeml_BS_Null.ctl
Description: Standard branch-site model control file for null hypothesis tests (ω fixed at 1), paired with “codeml_BS_Alt.ctl” for likelihood ratio testing.
File: codeml_BS_Alt_A.ctl
Description: Alternate branch-site control file using different model initialization parameters to ensure convergence of likelihood optimization.
File: Sitecodeml.ctl
Description: PAML control file for site-model analyses (M7 vs. M8) using the full “Mammal_Full.phy” alignment and “FINAL_MamTree.tre.”
File: FINAL_MamTree.tre
Description: Curated mammalian species tree topology used as the reference phylogeny for all codeml analyses and ancestral reconstructions.
File: README.txt
Description: Metadata file summarizing dataset contents, methods, and usage details for reproducibility and citation.
Variables:
Each alignment file contains codon sequences corresponding to the α-subunit of the nicotinic acetylcholine receptor (nAChR).
Taxon names: standardized mammalian species identifiers.
Codon positions: aligned nucleotide triplets representing protein-coding regions.
Branch labels (in .tre files): indicate species or foreground lineages tested for positive selection.
ω (omega): ratio of nonsynonymous to synonymous substitution rates estimated by PAML.
Posterior probabilities: used to identify sites under positive selection in the M8 model.
Code/software
All analyses were performed using freely available, open-source software. The primary tool used was PAML (Phylogenetic Analysis by Maximum Likelihood), version 4.9, for codon-based models of molecular evolution. The included control files (*.ctl) are formatted for use with the “codeml” program within PAML.
Alignments were prepared using MACSE v2.0 (Ranwez et al., 2018), which maintains reading-frame integrity for protein-coding sequences. Tree visualizations and format conversions were performed using FigTree v1.4.4 and IQ-TREE v2.2 for initial phylogenetic inference.
Workflow summary:
1. Codon alignments were generated in MACSE (v2.0) from nAChR α-subunit nucleotide sequences.
2. Phylogenetic trees were pruned and formatted in FigTree and IQ-TREE to match alignment taxon sets.
3. Selection analyses were performed in PAML v4.9 using the control files provided here:
- Site models (M7 vs. M8) using “Sitecodeml.ctl” and “DropoutSitecodeml.ctl.”
- Branch-site models (Null vs. Alt) using “codeml_BS_Null.ctl,” “codeml_BS_Alt.ctl,” and their variant A counterparts.
4. Ancestral reconstructions were generated under the M8 model, producing “M8_Ancestors.fasta” and “GeneTree_SiteModel_M8.tre.”
No proprietary software was used. All scripts and control files can be run directly with PAML v4.9 or higher on any Unix/Linux system. Results can be viewed or verified with standard text editors or tree-viewing programs (e.g., FigTree, Dendroscope, or ETE3 in Python).
Access information
All data included in this dataset are either newly generated or derived from publicly available genomic resources.
Source data:
- Nucleotide and protein sequences for the nicotinic acetylcholine receptor α-subunit (CHRNA1) were obtained from the National Center for Biotechnology Information (NCBI; https://www.ncbi.nlm.nih.gov) and the Ensembl Genome Browser (https://www.ensembl.org).
- Publicly available genome assemblies and annotations were accessed under their respective open-access licenses (GenBank and Ensembl release terms).
- Museum-derived DNA sequences were generated as part of this study and are deposited here for unrestricted public use under a CC0 1.0 Universal (Public Domain Dedication) license.
No additional access restrictions apply. All files necessary to reproduce analyses are hosted on Dryad and do not require special software beyond those listed in the Code/software section.
- Drabeck, Danielle H.; Holt, Jennifer; McGaugh, Suzanne E. (2022). Widespread convergent evolution of alpha-neurotoxin resistance in African mammals. Biology Letters. https://doi.org/10.1098/rsbl.2022.0361