%0 Journal Article %A Simon G. Dures %A Chris Carbone %A Andrew J. Loveridge %A Glyn Maude %A Neil Midlane %A Ortwin Aschenborn %A Dada Gottelli %T A century of decline: loss of genetic diversity in a southern African lion-conservation stronghold %D 2018 %R 10.1101/474940 %J bioRxiv %P 474940 %X Aim There is a dearth of evidence that determines the genetic diversity of populations contained within present-day protected areas compared with their historic state prior to large-scale species declines, making inferences about a species’ conservation genetic status difficult to assess. The aim of this paper is to demonstrate the use of historic specimens to assess the change in genetic diversity over a defined spatial area.Location Like other species, African lion populations (Panthera leo) are undergoing dramatic contractions in range and declines in numbers, motivating the identification of a number of lion conservation strongholds across East and southern Africa. We focus on one such stronghold, the Kavango-Zambezi transfrontier conservation area (KAZA) of Botswana, Namibia, Zambia and Zimbabwe.Methods We compare genetic diversity between historical museum specimens, collected during the late 19th and early 20th century, with samples from the modern extant population. We use 16 microsatellite markers and sequence 337 base pairs of the hypervariable control region (HVR1) of the mitochondrial genome. We use bootstrap resampling to allow for comparisons between the historic and modern data.Results We show that the genetic diversity of the modern population was reduced by 12% to 17%, with a reduction in allelic diversity of approximately 15%, compared to historic populations, in addition to having lost a number of mitochondrial haplotypes. We also identify reduced allelic diversity and a number of ‘ghost alleles’ in the historical samples no longer present in the extant population.Main Conclusions We argue a rapid decline in allelic richness after 1895 suggests the erosion of genetic diversity coincides with the rise of a European colonial presence and the outbreak of rinderpest in the region. Our results support the need to improved connectivity between protected areas in order to prevent further loss of genetic diversity in the region.We thank NHM London for access to historic samples; the Botswana Department of Wildlife and National Parks for providing research and collection permits (EWT 8/36/4 XIII [35]); Debbie Peak, Rob Jackson, Kyle burger, Robyn Coetzee, Robert Riggs & Botswana Predator Conservation Trust for contributing samples; the staff at Wilderness Safaris Botswana, Chitabe, and Machaba; Crispin Sanderson, Grant Huskisson, Dane Hawk, Rick Nelson, Erik Verreynne, Alan Wilson, Anna Butterfield & Jaques Van deMerwe of Vision International, Wilton Raats, Dominik Bauer and Kristina Kesch for logistical and veterinary support; Anton van Schalkwyk and Hanri Ehlers for invaluable support and funding; PneuDart for equipment; Wilderness Wildlife Trust for financial support. We also thank Jinliang Wang for helpful comments on previous drafts. All import and export permits were granted. SGD was supported by a BBSRC CASE-studentship (BB/F017324/1). %U https://www.biorxiv.org/content/biorxiv/early/2018/11/21/474940.full.pdf