Data from: Geographically contrasting biodiversity reductions in a widespread New Zealand seabird

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.,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.,