Testing the Influence of Habitat Structure and Geographic Distance on the Genetic Differentiation of Mouse Lemurs (Microcebus) in Madagascar Bettina M. Scheel 1 & Johanna Henke-von der Malsburg 2 & Peggy Giertz 2 & S. Jacques Rakotondranary 2,3 & Bernhard Hausdorf 1 & Jörg U. Ganzhorn 2 Received: 26 April 2015 / Accepted: 19 June 2015 / Published online: 27 August 2015 # Springer Science+Business Media New York 2015 Abstract The evolution of the high level of microendemism in Madagascar’ s biota remains poorly understood. Allopatric speciation or adaptations to local conditions along continuous gradients are two mechanisms that could have contributed to the extraordinary radiation of lemurs. Here we tested whether mouse lemurs (Microcebus griseorufus) occurring across three adjacent but distinct vegetation formations (ranging from dry forest to spiny bush) in southwestern Madagascar showed signs of genetic differentiation that could be interpreted as incipient speciation and adaptation to different environmental conditions using analysis of molecular variance and distance- based redundancy analysis. In the context of a mark-recapture study, mouse lemurs were captured with Sherman live traps set eight times for four nights per trapping session in standardized trapping grids in the three vegetation formations between October 2007 and February 2009. For genetic analyses, we used tissue samples from 41 female and 35 male M. griseorufus. Genetic differentiation between demes as estimated by amplified fragment length polymorphism (AFLP) data (as parental Int J Primatol (2015) 36:823–838 DOI 10.1007/s10764-015-9855-z Bettina M. Scheel and Johanna Henke-von der Malsburg contributed equally to this work. Electronic supplementary material The online version of this article (doi:10.1007/s10764-015-9855-z) contains supplementary material, which is available to authorized users. * Jörg U. Ganzhorn ganzhorn@uni-hamburg.de 1 Centre for Natural History, Zoological Museum, 20146 Hamburg, Germany 2 Department of Animal Ecology and Conservation, University of Hamburg, 20146 Hamburg, Germany 3 Département de Paléontologie et d’Anthropologie Biologique, Faculté des Sciences, Université d’Antananarivo, Antananarivo 101, Madagascar