Comparison of whole mitochondrial genome sequences of northern and southern white rhinoceroses (Ceratotherium simum): the conservation consequences of species definitions

Abstract

The probable extinction of the last confirmed population of northern white rhinoceros (Ceratotherium simum cottoni) in the world has ignited debate regarding its species status compared to the southern white rhinoceros (Ceratotherium simum simum). Previous studies, based on partial mitochondrial sequences, have reported conflicting results regarding the species status of the northern white rhinoceros. We use whole mitochondrial genomes obtained using Next Generation Sequencing of four northern white rhinoceros and three southern white rhinoceros using novel primers in three overlapping fragments. Phylogenetic relationships were constructed, using Maximum Likelihood, and recovered monophyletic clades for northern white rhinoceros and southern white rhinoceros. The divergence time between the two mitochondrial DNA lineages was estimated to be between 0.46 and 0.97 million years ago using Bayesian inferences. Since there are currently only three surviving northern white rhinoceros individuals these results put into sharp focus the ongoing debate regarding the methods of species definition, and in particular the consequences of such definitions in conservation management of endangered species and subspecies. We conclude that the designation of sub-species status is more applicable to northern and southern white rhinoceros.

A potential link between lateral semicircular canal orientation, head posture, and dietary habits in extant rhinos (Perissodactyla, Rhinocerotidae)

“…Harley et al () were able to show a close relationship of black ( D. bicornis ) and white rhinoceros forming a sister group to Indian ( R. unicornis ) and Javan rhinoceros ( R. sondaicus ), with the Sumatran rhinoceros ( D. sumatrensis ) as basal to all extant rhinos. They also report a possible placement of the Sumatran rhino as the sister taxon to the African rhinos (Harley et al, ). Both Sumatran rhino placements as basal or sister to African rhinoceroses are in contrast to Tougard et al () (also depicted in Figure ).…”

“…First appearing in the Eocene and flourishing in the Oligocene (Dinerstein, ), the rhinoceros diversity is reduced to only five species today, two African and three Asiatic (Harley, de Waal, Murray, & O'Ryan, ; IUCN, ). The presence and number of horns is traditionally important for systematics, biological significance, or wildlife protection of rhino populations (Dinerstein, ).…”

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

“…In order to obtain a time frame for the evolutionary history of the species, we reconstructed a species level maternal phylogeny from the seven mitochondrial genomes sequenced by Harley et al [14]. We conducted Bayesian phylogenetic dating using BEAST v. 2.4.3 [30] as this allowed us to parametrize splits in the tree with softbounded priors based on known fossil information, using the same mammalian mtDNA genomes and priors described by Harley et al [14], except that all five calibration times were used simultaneously in a single analysis. We used the Tamura -Nei model for nucleotide substitution with gamma correction, as deduced by JMODELTEST v. 2 [31], placing a relaxed, lognormal prior on the clock rate to account for potential differences in the molecular clock.…”

Poor taxonomy and genetic rescue are possible co-agents of silent extinction and biogeographic homogenization among ungulate mammals

“…Serious problems can result where conservation action plans misconstrue diversity at the population level, especially where distinct species interbreed. For example, the argument by Harley et al (2016) to 'rescue' the Nile rhinoceros Ceratotherium cottoni (Lydekker, 1908) by interbreeding with Ceratotherium simum is misguided, because the subspecies classification of white rhinos had been refuted by the morphological and genetic evidence analysed in a phylogenetic framework . Regrettably, the 'agony of choice' will demand now to save the maximum we can of the genome of the Nile rhinoceros whatever his taxonomic rank actually is (Hildebrandt et al 2018).…”