Geographically contrasting biodiversity reductions in a widespread New Zealand seabird NICOLAS J. RAWLENCE,* MARTYN KENNEDY,* CHRISTIAN N. K. ANDERSON, † STEFAN PROST, ‡ § CHARLOTTE E. TILL,* ¶ IAN W. G. SMITH,** R. PAUL SCOFIELD, †† ALAN J. D. TENNYSON, ‡‡ JILL HAMEL, §§ CHRIS LALAS, ¶¶ ELIZABETH A. MATISOO-SMITH § and JONATHAN M. WATERS* *Allan Wilson Centre, Department of Zoology, University of Otago, Dunedin, New Zealand, †Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA, ‡Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA, §Allan Wilson Centre, Department of Anatomy, University of Otago, Dunedin, New Zealand, ¶School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA, **Department of Anthropology and Archaeology, University of Otago, Dunedin, New Zealand, ††Canterbury Museum, Christchurch, New Zealand, ‡‡Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand, §§ 42 Ann Street, Dunedin, New Zealand, ¶¶Department of Marine Science, University of Otago, Dunedin, New Zealand Abstract Unravelling prehistoric anthropogenic impacts on biodiversity represents a key chal- lenge 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 settle- ment 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. Keywords: ancient DNA, biodiversity, demography, extinction, human impact, Leucocarbo chalconotus, megafauna, overkill, seabird, Stewart Island Shag Received 2 November 2014; revision received 22 July 2015; accepted 27 July 2015 Introduction A growing body of scientific evidence suggests that pre- historic anthropogenic processes underlie the extinction of numerous vertebrate populations and species in many parts of the world. The ‘overkill’ hypothesis (Martin 1967) was proposed decades ago, and a grow- ing body of more recent studies suggest it accounts for the extinction of numerous species, coincident with human arrival in different parts of the globe (Prideaux et al. 2010; Duncan et al. 2013; Sandom et al. 2014). In contrast, some researchers point to the possible role of nonanthropogenic environmental pressures such as his- toric climate and associated habitat change in driving such extinction events (Dalen et al. 2007; Johnson et al. 2013). In seeking to assess the biodiversity impacts of prehistoric humans, a comparative approach has the potential to be informative. Specifically, by comparing the extent and dynamics of prehistoric faunal declines Correspondence: Nicolas J. Rawlence, Fax: +64 3 479 7584; E-mail: nic.rawlence@otago.ac.nz © 2015 John Wiley & Sons Ltd Molecular Ecology (2015) 24, 4605–4616 doi: 10.1111/mec.13338