ORIGINAL ARTICLE Crossing barriers in an extremely fragmented system: two case studies in the afro-alpine sky island flora Tigist Wondimu • Abel Gizaw • Felly M. Tusiime • Catherine A. Masao • Ahmed A. Abdi • Galina Gussarova • Magnus Popp • Sileshi Nemomissa • Christian Brochmann Received: 15 March 2013 / Accepted: 7 August 2013 Ó Springer-Verlag Wien 2013 Abstract The flora on the afro-alpine sky islands is renowned for extreme fragmentation, representing a unique natural experiment in biogeography. Here we address the roles of isolation and gene flow, in particular across the narrow Rift Valley (the RV barrier) that cuts through the Ethiopian Highlands (EH), and across the vast low-lying landscape that separates EH from the East African moun- tains (the EH–EA barrier). We inferred the history of two species with different dispersal mechanisms, but with similar geographic ranges and habitats based on Amplified fragment length polymorphisms (AFLPs). Contrary to our predictions, we found that the populations from opposite sides of the RV barrier were less similar than those from opposite sides of the EH–EA barrier, and that only the supposedly short distance-dispersed species (Trifolium cryptopodium) showed a strong signal of secondary gene flow across the RV barrier. In the wind-dispersed Carduus schimperi, we rather found an evidence for the gene flow between differentiated populations inhabiting different EA mountains. Both species harbored little genetic diversity but considerable genetic rarity in several individual mountains, suggesting long-term isolation and bottlenecks during climatically unfavorable periods. Our genetic data corroborate a division of C. schimperi into three subspe- cies, but with new delimitation of their ranges, and of T. cryptopodium into two intraspecific taxa. Our findings support the idea that stochasticity may play a major role in shaping extremely fragmented ecosystems such as the afro- alpine. After initial colonization of different mountains, periods of isolation may alternate with unpredictable epi- sodes of intermountain gene flow. Keywords Afro-alpine flora Á AFLP Á Biogeographic stochasticity Á Carduus schimperi Á Fragmentation Á Phylogeography Á Trifolium cryptopodium Introduction The afro-alpine sky island flora, which occurs above *3,500 m on the tall African mountains, is renowned not only for its peculiarity and inaccessibility, but also for its extreme fragmentation. It thus represents a unique, but still amazingly little explored natural biogeographical T. Wondimu and A. Gizaw should be considered shared first authors. S. Nemomissa and C. Brochmann should be considered shared senior authors. T. Wondimu (&) Á A. Gizaw Á S. Nemomissa Department of Plant Biology and Biodiversity Management, College of Natural Sciences, Addis Ababa University, P.O. Box 3434, Addis Ababa, Ethiopia e-mail: twtigistw@gmail.com T. Wondimu Á A. Gizaw Á F. M. Tusiime Á C. A. Masao Á A. A. Abdi Á G. Gussarova Á M. Popp Á C. Brochmann National Centre for Biosystematics, Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, NO-0318, Oslo, Norway F. M. Tusiime Department of Forestry and Tourism, School of Forestry, Geographical and Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda C. A. Masao Institute of Resource Assessment, University of Dar es Salaam, P.O. Box 35097, Dar es Salaam, Tanzania A. A. Abdi National Museums of Kenya, P.O. Box 40658-00100, Nairobi, Kenya 123 Plant Syst Evol DOI 10.1007/s00606-013-0892-9