Evaluating the efficacy of the RADseq method for use with historic specimen to explore long-term changes in the population genomics of a butterfly hybrid zone

Background/Question/Methods

Theory predicts that hybrid zones are capable of shifting and that these shifts can have substantial evolutionary impacts. However, empirical examples of hybrid zone movement are rare due to the lack of long-term datasets and difficulties in detection due to inadequate sampling of molecular markers. Consequently, our understanding of the causes and consequences of these shifts has remained limited. Next-generation sequencing (NGS) has the potential overcomes the issue of marker limitation, as many genomic techniques can produce hundreds to thousands of molecular markers. Here we used the Restriction-Site-Associated (RAD) method for producing a genome-wide set of genetic markers from historic samples and evaluated the use of this method to answer population genomics questions in a butterfly hybrid zone that has been sampled extensively over the last 30 years.

Results/Conclusions

After stringent quality control measures the results were promising: contemporary samples produced more (3:1, contemporary:historic; largely due to greater readthrough in the paired end sequences of historic samples) and longer (contemporary: 123bp, historic: 87bp) reads per sample. However, historic samples still performed well beyond expectations given we were able to develop hundreds of genetic markers from most samples. Using custom bioinformatics scripts we identified over 5,000 SNPs with an average coverage per SNP (contemporary samples) of ~ 15X (after conservative quality filters). These results suggest that the RADtag method may be a useful approach for exploring population genomics questions using historic specimens.