Genetic structure of the black rhinoceros (Diceros bicornis) in south-eastern Africa

Abstract

Despite an on-going struggle to conserve the endangered black rhinoceros (Diceros bicornis) since the 1980s, huge capital investment and several genetic surveys, the level of genetic structure and connectivity among populations in southern Africa is not well understood. Here, we undertake a major population genetic study of black rhinoceros in the Zimbabwe Lowveld, an area inhabited by over half of that country's original Zambezi descendants plus one large population sourced from the relict KwaZulu stock of South Africa. Using nuclear microsatellite and mitochondrial DNA data, we found much higher levels of genetic diversity in the indigenous Zimbabwean populations, where observed multilocus heterozygosity was 0.54 versus 0.40 in KwaZulu, and maternal haplotype diversity was 0.77 versus 0.03. We show, for the first time, that both gene pools can be differentiated from each other on the basis of nuclear markers. This, along with the discovery of recent gene flow between all Lowveld populations, suggests that Zimbabwean and South African gene pools were prehistorically connected.

Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis)

“…This is why the historic mtDNA sample from South Africa is old (comprising four of the five oldest samples in our historic data set (see Supplementary Table S1 ) and small ( n = 5), because black rhinoceroses were already rare in this country by the mid 1800s when museum collecting became popular. Today, the remnant KwaZulu-Natal population of South Africa comprises over 2,000 individuals, all carrying a single mtDNA haplotype 6 leading to speculation about whether this extreme loss in genetic diversity indicated a loss of historic diversity or rather reflected historically low levels of diversity in the region 20 . Here, even with a small historic sample, we show that while the historic effective population size in South Africa was among the lowest of the five countries, its pre-bottleneck mtDNA diversity contained six haplotypes ( Table 1 ), which includes a specimen shot in the KwaZulu-Natal province in 1913 whose haplotype is not monophyletic with the present day KwaZulu-Natal haplotype.…”

“…This may be credited to the conservation authorities of that country, who recognised the impossibility of protecting the last 300 black rhinoceroses in the Zambezi Valley in the face of unrelenting cross-border poaching from Zambia and Mozambique. These survivors were translocated out of the valley in the 1990s to more defendable areas within Zimbabwe and subsequently underwent high population growth rates 20 , thus moderating the losses of genetic variation due to drift.…”

“…Previous black rhinoceros genetic studies have largely been restricted, either in geographic scale, molecular coverage or sampling 16 17 18 19 20 and therefore have not had the power to comprehensively examine the genetic consequences of population extinctions and declines in order to aid management or define conservation units. Genetic extinction, defined by the irrecoverable loss of genetic diversity, may not occur after local population extinction provided that some of the populations survived.…”

Contrasting evolutionary history, anthropogenic declines and genetic contact in the northern and southern white rhinoceros (Ceratotherium simum)

“…Samples were also amplified for 10 microsatellite loci (electronic supplementary material, table S4). The number of markers used in this study is comparable both with the number and identity of markers used in other publication on rhinoceros [19][20][21]. Markers were selected at random and were developed from a variety of target species (black rhinoceros, SWR and pig).…”

Museum specimens as Noah’s Arc of lost genes. The case of a rhinoceros from Sumatra in the Zoological Museum Hamburg

“…The importance of museum samples for the understanding of historic distribution ranges and the loss of genetic diversity is also highlighted in recent studies on the genetic diversity of the African black rhinoceros (Kotzé et al 2014;Moodley et al 2017) that examined the rangewide genetic structure of historic and modern populations of the species using both mitochondrial and nuclear datasets. Moodley et al (2017) described a staggering loss of 69% of the mitochondrial genetic variation on the basis of recently collected material and historic samples of the black rhinoceros during the 20 th century, including the most ancestral lineages that are now absent from modern populations.…”