Barbary macaques (Macaca sylvanus) are critically endangered primates. They are
unique within their genus, as the only African macaque. By the late Miocene, their habitat
extended across Northern Africa and in Southern Europe. Aside from an introduced population
in Gibraltar, their current distribution is reduced to disjointed forests in Algeria and Morocco.
Our knowledge of the phylogeographic history and intra-specific diversity of this highly
endangered species is also fragmented. In this study we aimed to improve our understanding
of the phylogeographic history and genetic diversity of the Barbary macaque by expanding the
genetic data available on the Algerian populations. Moreover, we investigated captive
populations of Barbary macaques for comparison to wild populations. The mtDNA
hypervariable control region I was sequenced using DNA extracts from faecal and hair samples
from wild and captive populations. The newly produced data (N = 157), from both Algerian
and Moroccan populations, were combined with previously published data (N = 212) and used
to characterize genetic variability and reconstruct phylogenetic relationships among wild and
captive populations. We found that Algerian populations exhibit an increased genetic diversity
relative to Moroccan populations. Phylogenetic relationships suggest that the Moroccan
populations diversified after being isolated from the Algerian populations. Captive populations
were found to be not fully representative of the genetic diversity exhibited in the species, but
rather only of Moroccan populations. Findings in this study suggest that the fragmented
Algerian populations should be managed to increase gene flow between them by increasing
habitat connectivity where it is feasible.