Genomics of Hybridisation in New Zealand Stick Insects

Abstract

There are three species in the stick insect genus Clitarchus; Clitatarchus hookeri, Clitarchus tepaki and Clitarchus rakuwhakanekeneke. It has been previously suggested that C. tepaki was isolated on two Pliocene islands in Northland and subsequently formed two independent hybrid zones with C. hookeri following the formation of Karikari and Aupouri peninsulas. It was proposed that a stable hybrid swarm formed on the Aupouri peninsula and genetic swamping occurred on the Karikari peninsula. In these hybrid zones the patterns of divergence and amounts of introgression are unknown. Ecological and evolutionary interactions between lineages which have experienced divergence are able to be analysed using hybrid zones. Investigation of hybridisation was done by analysing population structure, speciation models and patterns of introgression, a large number of single nucleotide polymorphisms (SNPs) were obtained using Genotyping-by-sequencing (GBS) on 273 individuals sampled from 14 populations across the Karikari and Aupouri peninsulas. Before downstream analyses could be done, sequence alignment, genotyping and SNP calling were done using BWA and Stacks to create a SNP dataset required as input. Using population structure analysis, coancestry matrices, and analysing patterns of introgression there is evidence to support the hypothesis that along the Aupouri peninsula there is a stable hybrid zone however on the Karikari peninsula genetic swamping has occurred masking any C. tepaki signal.