Quantifying past and present connectivity illuminates a rapidly changing landscape for the African elephant CLINTON W. EPPS,* SAMUEL K. WASSER, † JONAH L. KEIM, ‡ BENEZETH M. MUTAYOBA § and JUSTIN S. BRASHARES ¶ *Department of Fisheries and Wildlife, Oregon State University, Nash Hall Room 104, Corvallis, OR 97331, USA, †Department of Biology, Center for Conservation Biology, University of Washington, Box 351800, Seattle, WA 98195-1800, USA, ‡Matrix Solutions Inc., #142, 6325 Gateway Boulevard, Edmonton, AB T6H 5H6, Canada, §Department of Veterinary Physiology, Biochemistry, Pharmacology, and Toxicology, Sokoine University of Agriculture, Box 3017, Morogoro, Tanzania, ¶Department of Environmental Science, Policy, and Management, University of California, 137 Mulford Hall 3114, Berkeley, CA 94720-3114, USA Abstract There is widespread concern about impacts of land-use change on connectivity among animal and plant populations, but those impacts are difficult to quantify. Moreover, lack of knowledge regarding ecosystems before fragmentation may obscure appropriate con- servation targets. We use occurrence and population genetic data to contrast connectivity for a long-lived mega-herbivore over historical and contemporary time frames. We test whether (i) historical gene flow is predicted by persistent landscape features rather than human settlement, (ii) contemporary connectivity is most affected by human settlement and (iii) recent gene flow estimates show the effects of both factors. We used 16 microsat- ellite loci to estimate historical and recent gene flow among African elephant (Loxodonta africana) populations in seven protected areas in Tanzania, East Africa. We used histori- cal gene flow (F ST and G’ ST ) to test and optimize models of historical landscape resis- tance to movement. We inferred contemporary landscape resistance from elephant resource selection, assessed via walking surveys across ~15 400 km 2 of protected and unprotected lands. We used assignment-based recent gene flow estimates to optimize and test the contemporary resistance model, and to test a combined historical and con- temporary model. We detected striking changes in connectivity. Historical connectivity among elephant populations was strongly influenced by slope but not human settlement, whereas contemporary connectivity was influenced most by human settlement. Recent gene flow was strongly influenced by slope but was also correlated with contemporary resistance. Inferences across multiple timescales can better inform conservation efforts on large and complex landscapes, while mitigating the fundamental problem of shifting baselines in conservation. Keywords: African elephant, corridor, gene flow, resistance surface, resource selection probability function Received 7 February 2012; revision received 16 November 2012; accepted 5 December 2012 Introduction Habitat fragmentation is a major threat to biodiversity worldwide (Wilcox & Murphy 1985). Widespread rec- ognition of one consequence of habitat fragmentation, loss of connectivity (dispersal and gene flow) among plant and animal populations, has led to growing inter- est in conserving or re-establishing corridors or multi- species linkages (Beier et al. 2008). Conservation efforts aimed at increasing connectivity between isolated popu- lations (e.g. Soule et al. 1979; Newmark 1995, 1996, 2008) assume that such connectivity existed historically but has been reduced by recent and often striking Correspondence: Clinton W. Epps, Fax: 1 541 737 3590; E-mail: Clinton.Epps@oregonstate.edu © 2013 Blackwell Publishing Ltd Molecular Ecology (2013) 22, 1574–1588 doi: 10.1111/mec.12198