Genetic Structure and Diversity Among Historic and Modern Populations of the Sumatran Rhinoceros (Dicerorhinus sumatrensis)

Abstract

The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samples. Museum specimens from Laos and Myanmar had divergent mtDNA, consistent with the placement of western mainland rhinos into the distinct subspecies D. s. lasiotis (presumed extinct). Haplotypes from Bornean rhinos were highly diverse, but dissimilar from those of other regions, supporting the distinctiveness of the subspecies D. s. harrissoni. Rhinos from Sumatra and Peninsular Malaysia shared mtDNA haplotypes, consistent with their traditional placement into a single subspecies D. s sumatrensis. Modern samples of D. s. sumatrensis were genotyped at 18 microsatellite loci. Rhinos within Sumatra formed 2 sub-populations, likely separated by the Barisan Mountains, though with only modest genetic differentiation between them. There are so few remaining Sumatran rhinoceros that separate management strategies for subspecies or subpopulations may not be viable, while each surviving rhino pedigree is likely to retain alleles found in no other individuals. Given the low population size and low reproductive potential of Sumatran rhinos, rapid genetic erosion is inevitable, though an under-appreciated concern is the potential for fixation of harmful genetic variants. Both concerns underscore 2 overriding priorities for the species: 1) translocation of wild rhinos to ex situ facilities, and 2) collection and storage of gametes and cell lines from every surviving captive and wild individual.

Shotgun sequencing decades-old lichen specimens to resolve phylogenomic placement of type material

“…Incorporating genetic data from natural history collections representing rare/threatened species and species that are otherwise hard to access into genetic-based analyses can provide critical insights (Heckeberg et al 2016;Hundsdoerfer et al 2017;McGuire et al 2018). For example, genetic data from museum specimens has been used to track temporal and spatial changes in species distributions (Lozier & Cameron 2009), investigate population genetics (Spurgin et al 2014;Schmid et al 2018), and evaluate conservation implications (Anco et al 2018;Brandt et al 2018). Additionally, accessing molecular sequence data from natural history collections may be an invaluable resource for resolving taxonomic questions (Cappellini et al 2014), including generating genetic data from type specimens (Hawksworth 2013;Silva et al 2017;McGuire et al 2018).…”

New Guinea highland wild dogs are the original New Guinea singing dogs

“…In addition, studies of small pockets of wild living dogs will enable the search for the genetic variation that is required for free living, but irrelevant in a captive environment, and vice versa. There is urgency in this exercise, as each new generation of captive NGSD increases the risk for fixation of deleterious alleles, thus compromising subsequent breeding programs (25). This study provides insight into the genetic makeup of an isolated canid population and thus identifies a readily available genetic reservoir for the NGSD, previously thought to be extinct in the wild.…”

An analysis of threats, strategies, and opportunities for African rhinoceros conservation

“…Generally, most of the studies on rhinoceros conservation were explored in isolation without examining how these interventions could be integrated toward the development of holistic rhinoceros conservation management plans (Bending, 2018;Brandt et al, 2018;Harper et al, 2018). In this study, we attempt to fill this gap by providing an analysis of rhinoceros conservation threats, strategies, and opportunities for these species conservation.…”

“…This challenge is exacerbated and more pronounced in cases where fragmentation occurs in combination with illegal harvesting, which magnify the impacts of small, isolated rhinoceros populations. The persistence of the resultant small meta-populations is compromised due to their vulnerability to demographic (Brandt et al, 2018;Hogg et al, 2017), environmental (Child, 2012a(Child, ,2012bFerreira de Souza Dias, 2013;Ndlovu, 2015), and genetic stochastic events (Frankham, 2016;Hübschle, 2017aHübschle, ,2017bMays et al, 2018;Ralls et al, 2018). One critical genetic stochastic process that affects viability of rhinoceros in the wild is inbreeding depression, which results in loss of genetic variation in a metapopulation (Pizzi et al, 2013;Whiteley et al, 2015).…”