Gene Family Evolution: Understanding Selection, Duplications, Losses, and Transposable Elements as Mechanisms Responsible for Toxin Gene Family Expansion

Author

• Ramses Alejandro Rosales Garcia, Clemson UniversityFollow

Date of Award

5-2026

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Biological Sciences

Committee Chair/Advisor

Christopher L. Parkinson

Committee Member

Samantha A. Price

Committee Member

Matthew H. Koski

Committee Member

Jose Jesús Sigala Rodríguez

Committee Member

Norman J. Wickett

Abstract

Snake venom is a complex trait shaped by multiple evolutionary pressures, yet the origins and diversification of venom toxins remain unresolved. Toxin diversity is influenced by selection, drift, and gene expansion and loss, producing distinct venom phenotypes such as neurotoxic venoms dominated by the Crotoxin-like neurotoxin, a heterodimer of two Phospholipases A₂ (PLA₂s). Although similar neurotoxins occur in several New World pitvipers and one Asian species, limited genomic data have prevented robust testing of hypotheses regarding their evolution. I first characterized the venom-gland transcriptomes of the montane pitvipers (Cerrophidion). Their venoms are dominated by snake venom metalloproteases, PLA₂s, and snake venom serine proteases. Cerrophidion petlalcalensis shows little intraspecific variation, whereas C. godmani and C. tzotzilorum differ among populations. Intraspecific variation was driven primarily by expression, and toxins from C. godmani showed little evidence of directional selection, instead displaying patterns of mutation–drift equilibrium. I also discovered the first record of an individual of C. godmani with neurotoxic PLA₂ genes. To investigate the evolutionary origin of crotoxin-like PLA₂s, I generated the most comprehensive New World pitviper genomic dataset to date. The results support a single origin of crotoxin-like subunits in the most recent common ancestor (MRCA) of Gloydius and New World pitvipers, and an independent origin of the acidic subunit in Ophryacus. I also identified an association between a retrotransposon and cis‑regulatory regions within the PLA₂ genomic region, suggesting co-option into venom regulation. Finally, conserved PLA₂–Transposable element arrangements suggest ancient duplications followed by deletions generated the PLA₂haplotypes of rattlesnakes.

Recommended Citation

Rosales Garcia, Ramses Alejandro, "Gene Family Evolution: Understanding Selection, Duplications, Losses, and Transposable Elements as Mechanisms Responsible for Toxin Gene Family Expansion" (2026). All Dissertations. 4231.
https://open.clemson.edu/all_dissertations/4231

Author ORCID Identifier

https://orcid.org/0000-0002-0110-435X