What's left of the black rhino's genetic diversity?

With the current poaching epidemic we might lose rhinos before we even have time to get to know them. Luckily, the day has come and thanks to Yoshan Moodley, Mike Bruford and their team we know have a pretty good idea about the genetic diversity of one rhino species, the black rhinoceros.
In ”the largest and most geographically representative sample of black rhinoceroses ever assembled” (as they boldly but appropriately state in the abstract) Moodley et al. compared 19th and 20th century museum specimens with modern samples from universities, zoos, private hunters, and faecal samples collected in the field. Their dataset stretched in time, between 1775 and 2008, as well as in space, covering 20 countries of the black rhino’s historical range. Just so that you know, now we are down to 5 countries.
Probably the most striking result of the study is the 69% loss of mitochondrial diversity, as only 20 out of 64 historical haplotypes were found in present populations.

Fig. 1. Moodley et al. 2017, Sci Reports

Demographic history reconstructed with Bayesian Skyline analysis revealed a collapse in effective population size starting 100-200 years ago and reaching all-time low within the last 50 years. While the onset of rhino’s decline can be clearly associated with the big game hunting in colonial times, the more recent crash is connected to the illegal trade with rhino horn.

“We observed the greatest decreases in both effective population size and genetic diversity in East Africa (Tanzania and Kenya). The onset of these losses can be inferred to 100–150 years ago. Colonial-era British Kenya and German East Africa (Tanzania) represented popular venues for big game hunting, with hunting parties touring the region from the late 19th century. In addition, much land was cleared of game by authorities seeking to establish agriculture in the newly settled colonies. Yet, large numbers of black rhinoceroses were known in East Africa as recently as the early 1960s. Therefore, the major declines in diversity and effective population size are likely to have resulted mainly from poaching episode that began in Kenya and Tanzania in the early 1980s.”

Fig. 5f. Moodley et al. 2017, Sci Reports. Bayesian Skyline plot of effective population sizes.

The loss of haplotypes was mainly caused by local extinctions, but also genetic extinctions in the form of lost private haplotypes. And the rest can be attributed to genetic erosion through genetic drift.
By comparing historical and modern mitochondrial and microsatellite data, Moodley et al. clearly showed the extent of human guilt in the current rhino situation.

“Recently, it has been reported that rhinoceros poaching has reached a critical point, and if the killing continues, rhinoceros deaths would exceed births in 2016–2018. Annual poaching counts have exceeded 1,000 individuals each year since 2013.”

And the reason is well-known. A rhino horn is some seriously luxurious goods for crazy people, mainly in Southeast Asia. Since a marketing genius/lunatic spread the rumour that powder from rhino horn can cure cancer, the price skyrocketed and in 2012 reached $65,000 per kilogram.
If some kind of a miracle stops the poaching, it will be studies like this one helping with conservation and restoration of those bits of genetic diversity that’s left in the last 5000 black rhinos.

Fig. 3. Moodley et al. 2017, Sci Reports. A sad list of the 34 local black rhino populations.

Moodley et al. (2017) Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis). Scientific Reports 7, Article number: 41417. doi:10.1038/srep41417

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