Abstract:
It is human nature to attempt to categorise that which we observe in nature and our environment. By extension, taxonomy, and phylogenetics, are integral to biology. Traditionally, genes known as molecular markers have been used to determine evolutionary relationships between taxa (Patwardhan et al., 2014). However, using only a few markers may cause problems due to incongruence between gene trees (Page et al., 1997) and the species tree, or lack of variation in closely related species. The Lanceocercata are a lineage of stick insects spread throughout the Pacific, in places such as Australia, New Zealand, New Caledonia, and the Mascarene Islands in the Indian Ocean. Previous studies using relatively few markers, have produced conflicting results as to whether the nine New Zealand genera form a monophyletic clade (Buckley et al., 2010; Dunning et al., 2013). A phylogenomic study was undertaken using GBS (Genotyping-By-Sequencing) to discover SNPs from throughout the genome and revisit the relationships among the Lanceocercata. RNA-Seq was also used to investigate the New Zealand genera. These analyses were carried out using various software pipelines and tree construction methods, with the aim to explore not only the phylogenetic relationships, but also the different methodologies commonly used in similar studies, and their effect on the final results. Twelve phylogenies were inferred from the transcriptomic data of 21 samples using concatenated data, as well as via coalescence to investigate the NZ clade. Another 29 phylogenies were produced from the concatenated GBS data, to explore both the New Caledonian, and NZ clades. This study supports the suitability of GBS for phylogenetic studies, and is consistent with previous studies regarding the benefits of including missing data. The results of this study support a monophyletic New Zealand clade, placing Micrarchus as a sister group to a clade consisting of Tectarchus, Asteliaphasma, and N. annulata. Clitarchus and related taxa form a sister group to these two major clades, and Spinotectarchus is the sister group to all of the above. While the placement of Tectarchus may need further investigation, the phylogenies are consistent with each other regarding the New Caledonian genera, and are supported by previous findings.