Sex linkage of the skeletal muscle sodium channel gene (SCN4A) explains apparent deviations from Hardy–Weinberg equilibrium of tetrodotoxin-resistance alleles in garter snakes (Thamnophis sirtalis)

Abstract

The arms race between tetrodotoxin-bearing Pacific newts (Taricha) and their garter snake predators (Thamnophis) in western North America has become a classic example of coevolution, shedding light on predator-prey dynamics, the molecular basis of adaptation, and patterns of convergent evolution. Newts are defended by tetrodotoxin (TTX), a neurotoxin that binds to voltage-gated sodium channels (Nav proteins), arresting electrical activity in nerves and muscles and paralyzing would-be predators. However, populations of the common garter snake (T. sirtalis) have overcome this defense, largely through polymorphism at the locus SCN4A, which renders the encoded protein (Nav1.4) less vulnerable to TTX. Previous work suggests that SCN4A commonly shows extreme deviations from Hardy–Weinberg equilibrium (HWE) in these populations, which has been interpreted as the result of intense selection imposed by newts. Here we show that much of this apparent deviation can be attributed to sex linkage of SCN4A. Using genomic data and quantitative PCR, we show that SCN4A is on the Z chromosome in Thamnophis and other advanced snakes. Taking Z-linkage into account, we find that most apparent deviations from HWE can be explained by female hemizygosity rather than low heterozygosity. Sex linkage can affect mutation rates, selection, and drift, and our results suggest that Z-linkage of SCN4A may make significant contributions to the overall dynamics of the coevolutionary arms race between newts and snakes.

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Fig. 1: Evidence for sex linkage of four SCNA loci in snakes.
Fig. 2: Evidence for sex-linkage of SCN4A in five T. sirtalis populations.
Fig. 3: Population variation at the SCN4A locus.

Data availability

DNA sequences collected for this study are deposited in the NCBI PopSet database with accession numbers MT043460 - MT043727. qPCR and genotype data can be found at https://doi.org/10.5061/dryad.x95x69pf1.

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Acknowledgements

We thank Drew Schield, Blair Perry, and Todd Castoe for providing an early draft of the C. viridis genome. We are grateful to Caitlin McCaughan and Mercedes Collins for lab assistance and T. St. Pierre for field assistance. We thank the Departments of Fish and Wildlife in Washington, Oregon, and California for scientific collecting permits to MTJH (WA: 18-082, OR: 063-18, and CA: SC-11937) and CRF (CA: SC-000814). We also thank the California Department of Parks and Recreation, Hopland Research and Extension Center, the UC Natural Reserve System, and Sonoma Mountain Ranch. All procedures involving animals were approved by the UNR (protocol 00687) and USU (protocol 1008) IACUCs. This work was supported by a Doctoral Dissertation Improvement Grant from the National Science Foundation to MTJH and EDB III (DEB 1601296), by an RC Lewontin Award from the Society for the Study of Evolution to KLG, and by NSF support to EDB III (DEB 0922251), to CRF (IOS 1355221), and to JWM (DEB 1457463).

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Gendreau, K.L., Hague, M.T.J., Feldman, C.R. et al. Sex linkage of the skeletal muscle sodium channel gene (SCN4A) explains apparent deviations from Hardy–Weinberg equilibrium of tetrodotoxin-resistance alleles in garter snakes (Thamnophis sirtalis). Heredity 124, 647–657 (2020). https://doi.org/10.1038/s41437-020-0300-5

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