DOI: 10.5061/dryad.4b3h7
title: Data from: Geographically contrasting biodiversity reductions in a widespread New Zealand seabird

description: Unravelling prehistoric anthropogenic impacts on biodiversity represents a
 key challenge for biologists and archaeologists. New Zealand's
 endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two
 distinct phylogeographic lineages, currently restricted to the
 country's south and southeast. However, fossil and archaeological
 remains suggest a far more widespread distribution at the time of
 Polynesian settlement ca. 1280 AD, encompassing much of coastal South
 Island. We used modern and ancient DNA, radiocarbon dating, and Bayesian
 modelling, to assess the impacts of human arrival on this taxon. Our
 analyses show that the southeast South Island (Otago) lineage was formerly
 widespread across coastal South Island, but experienced dramatic
 population extinctions, range retraction and lineage loss soon after human
 arrival. By comparison, the southernmost (Foveaux Strait) lineage has
 experienced a relatively stable demographic and biogeographic history
 since human arrival, retaining much of its mitochondrial diversity.
 Archaeological data suggest that these contrasting demographic histories
 (retraction vs. stability) reflect differential human impacts in mainland
 South Island vs. Foveaux Strait, highlighting the importance of testing
 for temporal and spatial variation in human-driven faunal declines.
description: Translation
 TableThis table contains the
 internal laboratory codes used to identify mtDNA control region sequences
 (in the uploaded sequence alignments), and their corresponding GenBank
 numbers. Asterisked (*) sequences indicate exemplar sequences used in the
 33 haplotype dataset.aDNA optomisation
 codeCode for implementing
 the optimisation of ancient-DNA datasets for analysis in
 BayeSSC.SISaDNA1perHap33Nexus file containing one sequence of each haplotype (including out-group sequences) for the 33 haplotype dataset.FoveauxBSPr1BEAST .xml file for the Bayesian Skyline analysis of L. chalconotus Foveaux Strait.OtagoBSPr2BEAST .xml file for Bayesian Skyline analysis of L. chalconotus Otago.BayeSSC par filesBayeSSC .par files for joint (Otago and Foveaux Strait) Models 1-6, and Otago only Models 1-3.Randomisation TestsBEAST .xml files for randomisation tests of estimated substitution rate for L. chalconotus Foveaux Strait (x20) and Otago (x20).BEAST 33 htypeBEAST .xml file for the phylogenetic analysis of the 33 haplotype (including out-group sequences) dataset.Foveaux_var_ratesBEAST .xml files for testing the effect of variable substitution rates on the Bayesian Skyline Plot of L. chalconotus Foveaux Strait including the use of penguin (Lambert et al. 2002) fixed/prior, Otago fixed/prior, and BayesSSC estimates, and the optimised dataset (from BayeSSC).Otago_var_ratesBEAST .xml files for testing the effect of variable substitution rates on the Bayesian Skyline Plot of L. chalconotus Otago including the use of penguin (Lambert et al. 2002) fixed/prior and BayesSSC estimates, and the optimised dataset (from BayeSSC).SIS aDNA Otago alignmentDNA sequence alignment of L. chalconotus Otago.SIS aDNA Foveaux alignmentDNA sequence alignment of L. chalconotus Foveaux Strait.