Genetic variation within and between species of the New Zealand stick insect genus Clitarchus

Abstract

Recently the New Zealand stick insect genus Clitarchus Stål was revised, formally describing two new species, Clitarchus rakauwhakanekeneke from the Poor Knights Islands and Clitarchus tepaki from Northland, and clarifying the existing Clitarchus hookeri species status from the mainland. The genetic relationship between these three species had only been partially explored. This project aimed to explore the nuclear DNA variation of these species via single nucleotide polymorphisms (SNPs) identified using genotyping-by-sequencing (GBS). A protocol for stick insect DNA extraction appropriate for GBS was developed. Alterations of longer incubation and gentle grinding to the Qiacube Purification of Total DNA from Animal Tissues protocol (Qiagen Blood and Tissue kit) produced high quality and quantity of whole genomic DNA. Analysis of SNPs showed the island endemic C. rakauwhakanekeneke as a single genetic cluster with low genetic variation and heterozygosity. Clitarchus tepaki, which is known to hybridize with C. hookeri, did not form a single genetic cluster and had similarity to C. hookeri populations that were geographically close. There was also a split between C. tepaki from the Te Paki area and from Karikari Peninsula, which supports an earlier study. Clitarchus hookeri showed a pattern of genetic variation which correlates with the pattern of geographic parthenogenesis, with greater variation in the upper North Island sexually reproductive populations than the rest of New Zealand which have largely parthenogenetic reproduction. Examination of the genomic divergence of C. hookeri and C. rakauwhakanekeneke revealed several genomic regions of interest. Genes in these regions were annotated and this will provide a basis for further functional investigation. These analyses provide insight into the amount of gene flow between the Clitarchus species as well as level of reproductive isolation and divergence. This information could have important implications for future conservation of these species.