Parentage analysis in a managed free ranging population of southern white rhinoceros: genetic diversity, pedigrees and management

Abstract

Small populations are vulnerable to the consequences of breeding within closed groups as the loss of genetic variability can lead to inbreeding depression. Here, we use microsatellite genotypes to assess variability and parentage within a small, managed population of southern white rhinoceros in northern Namibia. Tissue samples gathered from either a modified biopsy darting technique or ear notches allowed us to obtain genotypic data for all individuals in the population. As expected for this species, genetic variability in the population was relatively low (overall H obs 0.45). In combination with detailed management records for the period 1993-2009, we were able to assign both parents for all 23 offspring. Only one calf of seven in the F 2 generation arose from father-daughter inbreeding within the population. Our analysis revealed that paternity was initially dominated by a single founder bull siring 10 of 13 calves over nine years; paradoxically, the other founder bull was selected for removal based on observations suggesting he was behaviourally dominant and therefore the likely sire of most calves. We also found that young introduced bulls were breeding successfully within six months of their arrival, well before having established their home ranges. We argue that in order to optimally manage and conserve the southern African rhino metapopulation it is essential to have accurate pedigree information and genetic data for all individuals in the numerous small populations that are key to the survival of the species.(379 words) Keywords Microsatellites, tissue biopsy, biopsy dart method, inbreeding, Ceratotherium simum simumElectronic supplementary material The online version of this article (doi: to come) contains supplementary material, which is available to authorized users.

Combining molecular and incomplete observational data to inform management of southern white rhinoceros (Ceratotherium simum simum)

“…The rates of successful parentage assignment obtained in this study were relatively lower than previous SWR studies. Guerier et al (2012) constructed a complete pedigree of a managed SWR population of 31 individuals by achieving 100% assignment rate of both parents for all 23 offspring using a combination of 11 microsatellite loci sampled from all individuals (H e = 0.450, H o = 0.450, N a = 2.8) and wellmaintained historical records. Labuschagne et al (2017) employed nine microsatellite loci (H e = 0.508, H o = 0.478, N a = 2.8) and 33 SNPs (H e = 0.350, H o = 0.357) to confirm maternity of all 11 dam-offspring pairs known from historical records in a managed SWR population; however, paternity assignment could be obtained with confidence for only six offspring.…”

“…However, the population bottleneck of just over a century ago resulted in inbreeding and loss of genetic diversity, with consequent low number of alleles per locus of microsatellite markers (Florescu et al 2003;Coutts 2009;Guerier et al 2012). The mating system of the species, in which one dominant bull is expected to sire the majority of offspring in a population, results in low effective population size, exacerbating the problem of genetic drift, and generating many surplus bulls (Owen-Smith 1975).…”

Effectiveness of microsatellite and single nucleotide polymorphism markers for parentage analysis in European domestic pigs

“…For instance, Li et al (2010) employed 10 polymorphic microsatellite loci to identify paternity in a plateau pika (Ochotona curzoniae) population, Wang et al (2012) successfully traced all offspring back to sole parent-pairs in the Portunus trituberculatus breeding project by screening 30 published microsatellites, and Guerier et al (2012) also acquired accurate genetic relationship information using microsatellite genotyping.…”

“…Short tandem repeats (STRs, microsatellites) have been the recent and internationally preferred molecular markers to trace studbook information from the species down to the individual level in all types of organisms ranging from lianas (Lacombe et al, 2013) to fish (Liu et al, 2012), insects (Wong et al, 2012), birds (Hadfield et al, 2006;Guerier et al, 2012), and mammals (Cutullé et al, 2010;Stevanovic et al, 2010;Souza et al, 2012). Microsatellites with a high level of heterozygosity are relatively more powerful in assigning relatedness per locus than those with a low level of heterozygosity.…”

Development and testing of a genetic marker‐based pedigree reconstruction system ‘PR‐genie’ incorporating size‐class data

“…On a smaller scale, complete population sampling allowed exact genetic assignment of both parents for 23 southern white rhinoceros ( Ceratotherium simum simum ) in a managed population in northern Namibia (Guerier et al . ). When sampling is more restricted, pedigree reconstruction has been difficult.…”