DOI: 10.5061/dryad.x95x69pf1
title: 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)

description: 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.
description: <strong>qPCR_all_SCNs.csv</strong>
 qPCR data measured from genomic DNA from 6 <em>Thamnophis
 sirtalis </em>individuals (3 males and 3 females). Here, we compare
 ortholog copy numbers in females versus males for all 9 members of the
 voltage-gated sodium channel (SCN) gene family, known Z-linked gene
 <em>TANC2</em>, as well as the
 gene <em>GH1, </em>which is physically linked
 to <em>SCN4A, </em>using single-copy
 gene <em>EEF1A1 </em>as a normalizer. These data are
 summarized in Figure 1 of the paper.  
 <strong>qPCR_populations.csv</strong>
 qPCR data measured from genomic DNA from 10 <em>Thamnophis
 sirtalis </em>individuals (5 males and 5 females) from different
 populations in the western United States with varying levels of
 tetrodotoxin resistance. Here, we compare ortholog copy numbers in females
 versus males for voltage-gated sodium channel (SCN)
 genes <em>SCN4A </em>and <em>SCN9A </em>and known Z-linked gene <em>TANC2</em>, using single-copy gene <em>EEF1A1 </em>as a normalizer. These data are summarized in Figure 2 of the paper.   <strong>Genotypes.csv</strong> Summary of the sexes and genotypes at the tetrodotoxin binding region (DIV p-loop) of the <em>SCN4A</em> gene obtained from DNA samples of 270 <em>Thamnophis sirtalis </em>individuals from 16 different populations in the western United States. These data are summarized in Figure 3 of the paper. DNA sequences can be found in the NCBI PopSet database (https://www.ncbi.nlm.nih.gov/popset) under accession numbers MT043460 - MT043727.