DOI: 10.5061/dryad.31zcrjdhm
title: Persisting in a glaciated landscape: Pleistocene microrefugia evidenced by the tree wētā Hemideina maori in central South Island, New Zealand

description: 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.
description: 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<em style="font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;white-space:normal;"> c </em>oxidase<em style="font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;white-space:normal;"> </em>(<em style="font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;white-space:normal;">coxI</em>) 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 (<i>UTR1-25</i>) and nuclear markers derived from transcriptome data and were obtained using Illumina sequencing. Twenty-five markers were used in this analysis.
description: 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.