Aim: Repeated cycles of Pleistocene glaciation have influenced phylogeographic structure of taxa on New Zealand’s South Island. Many taxa became restricted to refugia at either end of the island during glaciation, resulting in an area of low endemicity in central South Island. This area of low endemism is typified by the so-called beech (or biotic) gap, where the absence of Nothofagus forest (and many other plant and invertebrate taxa) has been attributed to repeated glaciation. Some taxa, however, appear to have persisted in situ in localized refugia within the biotic gap. We test these alternative hypotheses in a large flightless alpine wētā (grasshopper).

Location: Southern Alps, South Island, New Zealand

Taxon: Hemideina maori Pictet & Saussure, 1891 (Orthoptera: Anostostomatidae)

Methods: We used phylogeographic analysis of mitochondrial cytochrome c oxidase I (cox1) and twenty-five nuclear DNA (nuDNA) markers to test for Pleistocene glacial microrefugia within the current montane South Island range of Hemideina maori.

Results: We identified eight deeply differentiated mtDNA lineages with limited sharing of haplotypes among populations. Genetic differentiation assessed using nuDNA revealed a similar pattern, with three groups broadly corresponding to the deepest mtDNA splits. The central South Island region exhibits substantial endemic mtDNA diversity and a distinctive nuclear lineage.

Main conclusions: These results indicate that H. maori likely persisted in microrefugia within the biotic gap during glaciation. These deep lineages are estimated to have started diverging prior to the initiation of glaciation, up to 3 Ma. These results add to a growing number of Southern Hemisphere examples of deep phyleogeographic differentiation in glaciated regions compared to Europe and North America, probably reflecting less intense glaciation. We suggest that other Southern Alps species showing northern and southern clades alone, are more montane than alpine, and were reliant on warmer habitat to the north and south during glacial eras. Thus, there are species-specific responses to climatic processes, influenced by distinctive habitat requirements and physiological traits.

Wētā (157 in total) were hand-collected from beneath rocks in mostly montane habitats at 32 South Island sites from Oct 2012 to Dec 2014. Antennal clips taken non-destructively from each wētā were preserved in 95% ethanol and stored at -20°C. After DNA extraction, a 925-bp fragment of mitochondrial cytochrome c oxidase (coxI) was amplified and sequenced using Sanger sequencing. COI data was used to make a haplotype network, to perform BEAST divergence dating analysis (attached tree file) and conduct an ancestral area reconstruction.

Nuclear data mostly obtained by Illumina sequencing was used to make an allele network (used phased, concatenated data-set) and analysed using BAPS. BAPS sequence data input file, population name input file, population name index input file and marker file showing marker boundaries in concatenated nuDNA dataset are included here. Nuclear DNA markers were a combination of amplified regions of 3′ untranslated regions (UTR1-25) and nuclear markers derived from transcriptome data and were obtained using Illumina sequencing. Twenty-five markers were used in this analysis.

BAPS missing data in input file indicated by -9. Input file made using only informative sites. Parameters for BEAST analysis and ENM can be found in Methods.