Genome-wide assessment of genetic diversity has the potential to increase the ability to understand admixture, inbreeding, kinship and erosion of genetic diversity affecting both captive ( ex situ ) and wild ( in situ ) populations of threatened species. The sable antelope ( Hippotragus niger ), native to the savannah woodlands of sub-Saharan Africa, is a species that is being managed ex situ in both public (zoo) and private (ranch) collections in the United States. Our objective was to develop whole genome sequence resources that will serve as a foundation for characterizing the genetic status of ex situ populations of sable antelope relative to populations in the wild. Here we report the draft genome assembly of a male sable antelope, a member of the subfamily Hippotraginae (Bovidae, Cetartiodactyla, Mammalia). The 2.596 Gb draft genome consists of 136,528 contigs with an N50 of 45.5 Kbp and 16,927 scaffolds with an N50 of 4.59 Mbp. De novo annotation identified 18,828 protein-coding genes and repetitive sequences encompassing 46.97% of the genome. The discovery of single nucleotide variants (SNVs) was assisted by the re-sequencing of seven additional captive and wild individuals, representing two different subspecies, leading to the identification of 1,987,710 bi-allelic SNVs. Assembly of the mitochondrial genomes revealed that each individual was defined by a unique haplotype and these data were used to infer the mitochondrial gene tree relative to other hippotragine species. The sable antelope genome constitutes a valuable resource for assessing genome-wide diversity and evolutionary potential, thereby facilitating long-term conservation of this charismatic species.

We developed a biogeographical regionalization of Angolan mammals based on data collected before major declines occurred during the civil war (1975–2002). In terms of its biodiversity, Angola is one of the least known of all African countries. We used 9880 grid records of 140 species (rodents, ungulates and carnivores) collected mainly in 1930–80, at a quarter degree cell resolution. Biogeographical regions were identified by using cluster analysis, based on βsim dissimilarity matrices and a hierarchical classification using Ward's method. An indicator value analysis was used to identify species characterizing each region. Distance‐based redundancy analysis was used to investigate the environmental correlates of mammalian assemblages. Four biogeographical subdivisions emerged from ungulate distributions, while rodent and carnivore data were largely uninformative. In the north, the Zaire‐Lunda‐Cuanza region was mainly characterized by ungulate species associated with Congolian forests. In the south, the Namibe and Cunene‐Cuando Cubango regions were mainly characterized by ungulates widespread in south‐western and southern Africa. In between these regions, the Central Plateau region was mainly characterized by a few widespread ungulate species that are relatively common in dense miombo woodlands. Biogeographical patterns were significantly associated with a dominant north–south gradient of decreasing humidity and increasing temperature, and with a concurrent gradient from dense forests and woodlands to open savannas, grasslands and deserts. The biogeographical regions we identified in Angola were largely consistent with other bioregionalizations developed using various taxonomic groups at larger spatial scales. Biogeographical patterns reflected the southward penetration of Congolian forest species in the north, and the northward penetration of southern African desert/grassland species in the south‐west and of open savanna species in the south. These processes seem to be controlled by the distribution of vegetation types, which in turn are associated with climatic gradients and soil types. The stronger patterns observed for ungulates than for other mammals may reflect the close association of ungulates to specific vegetation types.

Population declines may promote interspecific hybridization due to the shortage of conspecific mates (Hubb’s ‘desperation’ hypothesis), thus greatly increasing the risk of species extinction. Yet, confirming this process in the wild has proved elusive. Here we combine camera-trapping and molecular surveys over seven years to document demographic processes associated with introgressive hybridization between the critically endangered giant sable antelope (Hippotragus niger variani), and the naturally sympatric roan antelope (H. equinus). Hybrids with intermediate phenotypes, including backcrosses with roan, were confirmed in one of the two remnant giant sable populations. Hybridization followed population depletion of both species due to severe wartime poaching. In the absence of mature sable males, a mixed herd of sable females and hybrids formed and grew progressively over time. To prevent further hybridization and recover this small population, all sable females were confined to a large enclosure, to which sables from the other remnant population were translocated. Given the large scale declines in many animal populations, hybridization and introgression associated with the scarcity of conspecific mates may be an increasing cause of biodiversity conservation concern. In these circumstances, the early detection of hybrids should be a priority in the conservation management of small populations.

Secondary sympatry amongst sister lineages is strongly associated with genetic and ecological divergence. This pattern suggests that for closely related species to coexist in secondary sympatry, they must accumulate differences in traits that mediate ecological and/or reproductive isolation. Here, we characterized inter‐ and intraspecific divergence in three giant tree frog species whose distributions stretch across West and Central Africa. Using genome‐wide single‐nucleotide polymorphism data, we demonstrated that species‐level divergence coincides temporally and geographically with a period of large‐scale forest fragmentation during the late Pliocene. Our environmental niche models further supported a dynamic history of climatic suitability and stability, and indicated that all three species occupy distinct environmental niches. We found modest morphological differentiation amongst the species with significant divergence in tympanum diameter and male advertisement call. In addition, we confirmed that two species occur in secondary sympatry in Central Africa but found no evidence of hybridization. These patterns support the hypothesis that cycles of genetic exchange and isolation across West and Central Africa have contributed to globally significant biodiversity. Furthermore, divergence in both ecology and reproductive traits appear to have played important roles in maintaining distinct lineages. At the intraspecific level, we found that climatic refugia, precipitation gradients, marine incursions, and potentially riverine barriers generated phylogeographic structure throughout the Pleistocene and into the Holocene. Further studies examining phenotypic divergence and secondary contact amongst these geographically structured populations may demonstrate how smaller scale and more recent biogeographic barriers contribute to regional diversification.