Variation in gene regulation is ubiquitous, yet identifying the mechanisms producing such variation, especially for complex traits, is challenging. Snake venoms provide a model system for studying the phenotypic impacts of regulatory variation in complex traits because of their genetic tractability. Here, we sequence the genome of the Tiger Rattlesnake, which possesses the simplest and most toxic venom of any rattlesnake species, to determine whether the simple venom phenotype is the result of a simple genotype through gene loss or a complex genotype mediated through regulatory mechanisms. We generate the most contiguous snake-genome assembly to date and use this genome to show that gene loss, chromatin accessibility, and methylation levels all contribute to the production of the simplest, most toxic rattlesnake venom. We provide the most complete characterization of the venom gene-regulatory network to date and identify key mechanisms mediating phenotypic variation across a polygenic regulatory network.

Novel phenotypes are commonly associated with gene duplications and neofunctionalization, less documented are the cases of phenotypic maintenance through the recruitment of novel genes. Proteolysis is the primary toxic character of many snake venoms, and ADAM metalloproteinases, named Snake Venom Metalloproteinases (SVMPs), are largely recognized as the major effectors of this phenotype. However, by investigating original transcriptomes from 58 species of advanced snakes (Caenophidia) across their phylogeny, we discovered that a different enzyme, matrix metalloproteinase (MMP), is actually the dominant venom component in three tribes (Tachymenini, Xenodontini, and Conophiini) of rear-fanged snakes (Dipsadidae). Proteomic and functional analyses of these venoms further indicate that MMPs are likely playing an ‘SVMP-like’ function in the proteolytic phenotype. A detailed look into the venom-specific sequences revealed a new highly expressed MMP subtype, named snake venom MMP (svMMP), which originated independently on at least three occasions from an endogenous MMP-9. We further show that by losing ancillary non-catalytic domains present in its ancestors, svMMPs followed an evolutionary path toward a simplified structure during their expansion in the genomes, thus paralleling what has been proposed for the evolution of their Viperidae counterparts, the SVMPs. Moreover, we inferred an inverse relationship between the expression of svMMPs and SVMPs along the evolutionary history of Xenodontinae, pointing out that one type of enzyme may be substituting for the other, while the general (metallo)proteolytic phenotype is maintained. These results provide rare evidence on how relevant phenotypic traits can be optimized via natural selection on non-homologous genes, yielding alternate biochemical components.

The migration-selection balance often governs the evolution of lineages, and speciation with gene flow is now considered common across the tree of life. Ecological speciation is a process that can facilitate divergence despite gene flow due to strong selective pressures caused by ecological differences; however, the exact traits under selection are often unknown. The transition from freshwater to saltwater habitats provides strong selection targeting traits with osmoregulatory function. Several lineages of North American watersnakes (Nerodia spp.) are known to occur in saltwater habitat and represent a useful system for studying speciation by providing an opportunity to investigate gene flow and evaluate how species boundaries are maintained or degraded. We use ddRADseq to characterize the migration-selection balance and test for evidence of ecological divergence within the N. fasciata-clarkii complex in Florida. We find evidence of high intraspecific gene flow with a pattern of isolation-by-distance underlying subspecific lineages. However, we identify genetic structure indicative of reduced gene flow between inland and coastal lineages suggesting divergence due to isolation-by-environment. This pattern is consistent with observed environmental differences where the amount of admixture decreases with increased salinity. Furthermore, we identify significantly enriched terms related to osmoregulatory function among a set of candidate loci, including several genes that have been previously implicated in adaptation to salinity-stress. Collectively, our results demonstrate that ecological differences, likely driven by salinity, cause strong divergent selection which promotes divergence in the N. fasciata-clarkii complex despite significant gene flow.

The introduced smooth-billed ani Crotophaga ani has become widespread across the Galápagos archipelago in the past half-century. It is known to predate upon a range of native and endemic species, and is a potential vector for the spread of invasive plants and parasites. Here we report previously undocumented examples of smooth-billed ani predation in Galápagos, including that of an endemic racer snake and a scorpion. We highlight the possibility of smooth-billed anis having a serious impact on the endemic Galápagos carpenter bee, a major pollinator, as well as native and endemic Lepidopterans and other invertebrates. In addition, we report smoothbilled ani predation of other introduced species and note the importance of further research on the widescale impacts of smooth-billed anis in Galápagos and their role within the archipelago's ecological networks. Keywords Invasive species Á Alien bird species Á Island invasions Á Impacts of introduced species Á Endemic species Electronic supplementary material The online version of this article (

The montane pitvipers (Cerrophidion spp.) consist of five recognized species that disjunctly occupy high elevational habitats from southern Mexico to western Panama. However, two of these species were recently delineated, leaving previously published natural history data on Cerrophidionoutdated and in need of a re-examination. To gain more information, we investigated the stomach contents of Cerrophidion specimens housed in the University of Illinois Museum of Natural History Herpetology Collection (UIMNH) and report our findings. We also compiled lists of all known prey items and present a comprehensive dietary synopsis for each species of Cerrophidion according to recent taxonomic changes. These efforts unearthed eleven previously undocumented prey items for three of the species.