A mother’s story – the phylogenetic relationships in chamois

The chamois, genus Rupicapra, is the most abundant mountain-dwelling ungulate in Europe and the Near East and is currently recognized to be divided into two species: R. rupicapra (Northern chamois) and R. pyrenaica (Southern chamois) further divided into seven and three subspecies, respectively. While neither of the species is of conservation concern, some subspecies are protected at the national level in (part of) their distribution ranges. However, for most subspecies and populations the information necessary to assess the conservation status are lacking and several populations were subject to translocations and reintroductions, further complicating their general taxonomic picture. Here we combine nine newly sequenced mitochondrial genomes (mitogenomes) of four subspecies with previously published mitogenomes of Rupicapra (5) and related (sub)species in the Caprini, Ovibovini and Pantilopini families (39). The Bayesian and maximum likelihood phylogenetic analyses concordantly confirmed the monophyly of the genus Rupicapra and its positioning within the Caprini tribe. Both analyses identified the subdivision of the subspecies into three lineages in accordance with their geographical distributions (Eastern, Central and Western). The Central and Western lineages were more closely related, confirming previously reported results based on partial mitochondrial DNA regions. Within the Eastern lineage, R. r. balcanica was the most differentiated and included all individuals coming from the northern part of the Dinaric Karst mountain range, Mt. Velebit (Croatia), a known human-caused contact zone between R. r. rupicapra and R. r. balcanica, whereas R. r. tatrica and R. r. rupicapra showed a sister group relationship. Overall, our results, while providing an increased resolution, confirmed the phylogeny previously reconstructed using both whole and partial mitochondrial DNA sequences. The discrepancy among nuclear, mitochondrial and Y-chromosome markers in phylogenetic reconstruction of the genus thus remains. Further studies combining multiple markers and possibly including archeological remains are therefore warranted to solve the controversy.