Genome-wide homologies between the tsessebe (Damaliscus lunatus, 2n = 36) and Chinese muntjac (Muntiacus reevesi, 2n = 46) have been established by cross-species painting with Chinese muntjac chromosome paints. Twenty-two autosomal painting probes detected 35 orthologous segments in the tsessebe. Hybridization results confirmed that: (i) D. lunatus carries the (9;14) reciprocal translocation that has been proposed to be a derived chromosomal landmark shared by all species of the Antilopinae; (ii) the karyotype of D. lunatus can be derived almost exclusively from the bovid ancestral karyotype through 12 Robertsonian translocations involving 24 ancestral acrocentric autosomes; (iii) in addition to the Rb fusions, pericentric heterochromatic amplification has shaped the morphology of several of the D. lunatus chromosomes. Integrated analysis of these and published cytogenetic data on pecorans has allowed us to accurately discern the karyotype history of Damaliscus (D. lunatus; D. pygargus, 2n = 38; D. hunteri, 2n = 44). The phylogenomic relationships of 3 species reflected by specific chromosomal rearrangements were consistent with published phylogenies based on morphology, suggesting that chromosomal rearrangements have played an important role in speciation within the Alcelaphini, and that karyotype characters are valuable phylogenetic markers in this group.

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