Data from: Population structure within an alpine archipelago: strong signature of past climate change in the New Zealand rock wren (Xenicus gilviventris)

Naturally subdivided populations such as those occupying high-altitude habitat patches of the 'alpine archipelago' can provide significant insight into past biogeographical change and serve as useful models for predicting future responses to anthropogenic climate change. Among New Zealand's alpine taxa, phylogenetic studies support two major radiations: the first correlating with geological forces (Pliocene uplift) and the second with climatic processes (Pleistocene glaciations). The rock wren (Xenicus gilviventris) is a threatened alpine passerine belonging to the endemic New Zealand wren family (Acanthisittidae). Rock wren constitute a widespread, naturally fragmented population, occurring in patches of suitable habitat over c. 900 m in altitude throughout the length of the South Island, New Zealand. We investigated the relative role of historical geological versus climatic processes in shaping the genetic structure of rock wren (N = 134) throughout their range. Using microsatellites combined with nuclear and mtDNA sequence data, we identify a deep north–south divergence in rock wren (3.7 ± 0.5% at cytochrome b) consistent with the glacial refugia hypothesis whereby populations were restricted in isolated refugia during the Pleistocene c. 2 Ma. This is the first study of an alpine vertebrate to test and provide strong evidence for the glacial refugia hypothesis as an explanation for the low endemicity central zone known as the biotic 'gap' in the South Island of New Zealand.Allele-level genotype data for 134 Rock wren (Xenicus gilviventris) genotyped at 14 microsatellite lociAllele-level genotype data for 134 Rock wren (Xenicus gilviventris) genotyped at 14 microsatellite loci. Additional sample information includes GPS (NZTM) coordinates for each individual's sampling location.X. gilviventris genotyped individuals.xlsxCytochrome b sequence data for X. gilvivientrisCytochrome b sequence data for twenty X. gilvivientris individuals from throughout their range.X. gilviventris Cyt b sequence data.fastaXenicus gilviventris MtDNA Control Region sequence dataMtDNA Control Region sequence data for 25 Xenicus gilviventris individuals from throughout their range.X.gilviventris Cntrl Reg sequence data.fastaXenicus gilviventris beta fibrinogen intron 7 sequence dataUnphased nuclear beta-fibrinogen intron-7 sequence data for 18 Xenicus giliventris individuals, sampled from throughout their rangeX. gilviventris b-fib int7 sequence data.fastaMatrix of pairwise geographic distances (in kilometres) among eight rock wren (Xenicus gilviventris) populations across the South Island, New Zealand.hic distances (in kilometres) among eight rock wren (Xenicus gilviventris) populations across the South Island, New Zealand. Used to perform Mantel test (Figure S3).X. gilviventris pairwise geographic distances.xlsxMatrix of pairwise geographic distances (kilometres) among three rock wren (Xenicus gilviventris) populations across the northern South Island, New ZealandMatrix of pairwise geographic distances (kilometres) among three rock wren (Xenicus gilviventris) populations across the northern South Island, New Zealand. Used to perform Mantel test (Figure S4a).X. gilviventris pairwise geographic distances_North only.xlsxMatrix of pairwise geographic distances (kilometres) among five rock wren (Xenicus gilviventris) populations across the southern South Island, New Zealand.Matrix of pairwise geographic distances (kilometres) among five rock wren (Xenicus gilviventris) populations across the southern South Island, New Zealand. Used to perform Mantel test (Figure S4b).X. gilviventris pairwise geographic distances_South only.xlsxBayesian cytochrome b phylogenetic tree file for rock wren (Xenicus gilviventris)Bayesian cytochrome b phylogenetic tree file for rock wren (Xenicus gilviventris) using BEASTcytb tree_beast.txtBayesian phylogenetic tree file using control region (1126-bp)Bayesian phylogenetic tree file for rock wren (Xenicus gilviventris) using control region (1126-bp) (Figure S1).Cntrl reg FULL.treBayesian phylogenetic tree file for using control region 1st domainBayesian phylogenetic tree file for rock wren (Xenicus gilviventris) using control region 1st domain (Figure ).Bayes 1stdomain cntl reg.treBayesian phylogenetic tree file - beta fibrinogen intron 7Bayesian phylogenetic tree file for rock wren (Xenicus gilviventris) using beta fibrinogen intron 7 (Figure 5).fig tree bfibphased.treMaximum likelihood β-fibrinogen tree fileMaximum likelihood phylogeny of rock wren (Xenicus gilviventris) using the nuclear β-fibrinogen intron-7.ML beta_ fib.treeMaximum parsimony tree file using nuclear β-fibrinogen intron-7.Maximum parsimony phylogeny of rock wren (Xenicus gilviventris) using the nuclear β-fibrinogen intron-7.MP beta_fib.treeMaximum Likelihood tree file using cytochrome bMaximum likelihood phylogeny of rock wren (Xenicus gilviventris) using cytochrome bML cyt b.treeMaximum parsimony tree file using cytochrome bMaximum parsimony phylogeny of rock wren (Xenicus gilviventris) using cytochrome bMP cyt b.treeMaximum likelihood phylogeny tree file using 1st domain of the control region.Maximum likelihood phylogeny of rock wren (Xenicus gilviventris) using the 1st domain of the control region.ML Cntrl reg 1st dom.treeMaximum parsimony phylogeny tree file using 1st domain of the control region.Maximum parsimony phylogeny of rock wren (Xenicus gilviventris) using the 1st domain of the control region.MP Cntrl reg 1st dom.treeMaximum likelihood phylogeny tree file using the mtDNA control region.Maximum likelihood phylogeny of rock wren (Xenicus gilviventris) using the mtDNA control region.ML cntrl reg.tre