Identifying the true number of specimens of the extinct blue antelope (Hippotragus leucophaeus)

Abstract

Native to southern Africa, the blue antelope (Hippotragus leucophaeus) is the only large African mammal species known to have become extinct in historical times. However, it was poorly documented prior to its extinction ~ 1800 AD, and many of the small number of museum specimens attributed to it are taxonomically contentious. This places limitations on our understanding of its morphology, ecology, and the mechanisms responsible for its demise. We retrieved genetic information from ten of the sixteen putative blue antelope museum specimens using both shotgun sequencing and mitochondrial genome target capture in an attempt to resolve the uncertainty surrounding the identification of these specimens. We found that only four of the ten investigated specimens, and not a single skull, represent the blue antelope. This indicates that the true number of historical museum specimens of the blue antelope is even smaller than previously thought, and therefore hardly any reference material is available for morphometric, comparative and genetic studies. Our study highlights how genetics can be used to identify rare species in natural history collections where other methods may fail or when records are scarce. Additionally, we present an improved mitochondrial reference genome for the blue antelope as well as one complete and two partial mitochondrial genomes. A first analysis of these mitochondrial genomes indicates low levels of maternal genetic diversity in the 'museum population', possibly confirming previous results that blue antelope population size was already low at the time of the European colonization of South Africa.

Figure 1

The blue antelope and its historical and potential prehistoric distribution. (a) The only known mounted female specimen of the blue antelope (Hippotragus leucophaeus) (Natural History Museum Vienna, NMW ST 715); the characteristic white patch in front of the eyes is clearly visible (photo credit: Natural History Museum Vienna). (b) Historical and potential prehistoric distribution of the blue antelope (drawn in Inkscape v0.91 (https://inkscape.org) from Kerley et al. and Faith & Thompson; base map: https://www.naturalearthdata.com v2.0.0).

Figure 2

Mapping success to the three Hippotragus references. Comparison of normalized relative mapping success for each sample as base pairs mapping to the mitochondrial genomes of the three Hippotragus species. For each sample the result of the reference it mapped best to was defined as a mapping success of 1 and the results for the other references are given in relation to that. Only four specimens can unambiguously be assigned to the blue antelope (grey), while three are identified as sable (black) and three as roan (white). Photo credits: Glasgow: Photo: E. Hempel, courtesy: the Hunterian, University of Glasgow; Berlin: Photo: E. Hempel, courtesy: Museum für Naturkunde, Berlin, Mammal Collection; Cape Town: Photo: J. T. Faith, courtesy: Terrestrial Vertebrate Collection, Iziko Museums of South Africa; Leiden 1 & 2: Naturalis Biodiversity Center, the Netherlands; St Andrews: University of St Andrews; Stockholm: Swedish Museum of Natural History; Vienna: Natural History Museum Vienna; Paris: Muséum national d’Histoire naturelle, Collections d'Anatomie Comparée; Uppsala: Museum of Evolution.

Figure 3

Clustering of samples in a maximum-likelihood phylogeny. Maximum-likelihood tree based on the mitochondrial genome alignment excluding the control region (15,450 bp in length) using the reference with the highest mapping success for each sample. The tree shows three clades (100% bootstrap support each) in agreement with the three Hippotragus species (black: sable, white: roan, grey: blue antelope), confirming the species assignments from the mapping results. RAxML 8.2.10 with GTR + G was used to generate the phylogeny. Branch values indicate bootstrap support of 100 replicates. Ovis aries musimon (HM236184) was used as outgroup (not shown here). Photo credits: see Fig. 2.

Figure 4

Median joining network of the four blue antelope specimens. The median joining network takes into account only positions of the complete mitochondrial genome (including control region) that are covered in all four specimens, excluding ambiguities (6,300 bp). Dashes and the white circle denote mutational steps and an unsampled haplotype, respectively. The network generated in POPART v1.7 revealed six segregating sites, with the Stockholm and Uppsala specimens being identical in this comparison. Photo credits: Leiden 1: Naturalis Biodiversity Center, the Netherlands; Stockholm: Swedish Museum of Natural History; Vienna: Natural History Museum Vienna; Uppsala: Museum of Evolution.

Figure 5

Mitochondrial diversity comparison. Mitochondrial diversity of the four blue antelope specimens (dashed line) compared to the distribution of 1,000 replicates of the diversity of four randomly drawn sequences of six wild ungulate species based on the alignment of homologous positions of the mitochondrial genome (6,061 bp in length) (shown with bins of 50, generated in RStudio v1.1.423 (https://www.rstudio.com/) using R v3.63 (https://www.R-project.org/)). k represents the average number of substitutions between two individuals.