Authors: Chrzanová Pečnerová, Patrícia; Ishida, Yasuko;Meisner, Jonas;Hanghoej, Kristian;Dalen, Love;Heller, Rasmus;Roca, Alfred;Siegismund, Hans;

Genome-wide data is becoming an integral resource for conservation of species. In African elephants, a handful of genomes has been used to strengthen the case of recognizing savanna and forest elephants as two separate species. Here, we generate and analyse 165 genomes from African savanna and forest elephants in 13 countries, covering most of their current range. Compared to the previously-used traditional genetic markers like microsatellites and mitochondrial DNA, this genome-wide data allows us to infer: 1) a finer-scale population structure and the main trajectories of gene flow, 2) differences in genetic make-up of elephant populations in the different parts of the continent, and 3) demographic processes which resulted in the present-day patterns of genetic diversity. Besides providing essential insights for conservation genetics, this data serves as a valuable resource for conservation management. We identify and optimize a set of standardized genetic markers that will be implemented in genetic monitoring of wild elephant populations, thus, providing an example of genetics can be incorporated in future research and conservation.