Restriction and Recruitment—Gene Duplication and the Origin and Evolution of Snake Venom Toxins

Abstract

Snake venom has been hypothesized to have originated and diversified through a process that involves duplication of genes encoding body proteins with subsequent recruitment of the copy to the venom gland, where natural selection acts to develop or increase toxicity. However, gene duplication is known to be a rare event in vertebrate genomes, and the recruitment of duplicated genes to a novel expression domain (neofunctionalization) is an even rarer process that requires the evolution of novel combinations of transcription factor binding sites in upstream regulatory regions. Therefore, although this hypothesis concerning the evolution of snake venom is very unlikely and should be regarded with caution, it is nonetheless often assumed to be established fact, hindering research into the true origins of snake venom toxins. To critically evaluate this hypothesis, we have generated transcriptomic data for body tissues and salivary and venom glands from five species of venomous and nonvenomous reptiles. Our comparative transcriptomic analysis of these data reveals that snake venom does not evolve through the hypothesized process of duplication and recruitment of genes encoding body proteins. Indeed, our results show that many proposed venom toxins are in fact expressed in a wide variety of body tissues, including the salivary gland of nonvenomous reptiles and that these genes have therefore been restricted to the venom gland following duplication, not recruited. Thus, snake venom evolves through the duplication and subfunctionalization of genes encoding existing salivary proteins. These results highlight the danger of the elegant and intuitive “just-so story” in evolutionary biology.

A Critique of the Toxicoferan Hypothesis

“…Therefore, it is likely that these genes are simply encoding maintenance or "housekeeping" proteins, and are expressed in multiple tissues at low levels. Many of these genes were also found expressed in several other body tissues in Echis coloratus (Hargreaves et al 2014b), adding further support that these are housekeeping genes due to their ubiquitous expression pattern. Several of these genes are also only present as a single copy in the genome of this species, and so there is no evidence of duplication and recruitment of a toxic version to the venom gland (Hargreaves et al 2014a).…”

“…Additionally, it now seems certain that many of the proposed shared venom toxins within the Toxicofera actually result from the confusion of orthologs and paralogs, where non-toxic relatives of toxin genes have been identified (Hargreaves et al 2014a). For example, genes encoding complement c3 and nerve growth factor have been shown to have undergone an Elapid-specific gene duplication (Sunagar et al 2013;Hargreaves et al 2014a, b) to give rise to the putatively toxic "cobra venom factor" and nerve growth factor b (Hargreaves et al 2014b). This mis-identification of physiological orthologs as toxin-encoding paralogs has led to the conclusion that all Toxicoferan reptiles produce toxins in their oral secretions, and are therefore descended from a common venomous ancestor.…”

“…The occurrence of lineage-specific gene duplications (for example complement c3 and nerve growth factor in Elapids (Sunagar et al 2013;Hargreaves et al 2014a;Hargreaves et al 2014b)) would indicate that these genes may confer some preyspecific effects (as seen in the Mangrove catsnake, Boiga dendrophilia (Pawlak et al 2006)), or may have allowed adaptation to a new ecological niche.…”

Toxinology: Taxonomy, Interpretation, and Information Resources

“…This has resulted in claims that a wide array of reptiles are technically venomous, even though such animals do not fit the classic definition as summarized in the MeSH rendition of it and espoused by leading authorities such as Mebs (Mebs 2002). This more recent view of venomousness has been soundly challenged, and emerging research data question its scientific validity (Hargreaves et al 2014;Kardong 2012;Weinstein et al 2013a;Reyes-Velasco et al 2015). It is our view that as more research is pursued, the original and long-standing definition for venomousness will be reinforced (Hargreaves et al 2014).…”

Venom Evolution: Gene Loss Shapes Phenotypic Adaptation

“…However, these families, which include metalloproteinases, phospholipases, serine proteases and three-finger toxins, are multi-locus in nature. They appear to have originated from certain genes that were co-expressed in the ancestral venom gland and other body tissues, followed by their increased expression in the venom gland, and in some cases, the loss of their low-level expression in other tissue types [10][11][12].…”