DOI: 10.5061/dryad.g44c1
title: Data from: Population structure within an alpine archipelago: strong signature of past climate change in the New Zealand rock wren (Xenicus gilviventris)

description: 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.
description: 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.tree