Parentage analysis in a free-ranging, closed population of southern white rhinoceros : genetics, pedigrees and management

Abstract

Small populations of animals are vulnerable to the consequences of breeding within a closed group – inbreeding depression and genetic drift lead to reductions in genetic variability, which in turn can give rise to the amplification of deleterious traits. Traditionally, managers attempt to minimise these effects by controlling the genetic structure via a manipulation of the paternal line, in the case of rhinos usually by translocation of breeding and sub-adult bulls. This strategy depends on having access to detailed pedigree data, and, in particular, some knowledge of the parentage of the offspring within the population. This information is particularly difficult to obtain in long-lived, free-ranging populations (particularly for rare and endangered species) where the identity of the father must be inferred from behavioural observations, and often the identity of the mother cannot be determined once juveniles have dispersed. In this thesis I present the results of a study to determine the parentage within a free-ranging, enclosed population of southern white rhinoceros (Ceratotherium simum simum) located on Ongava Game Reserve (OGR) in the north of Namibia. I used genetic techniques to obtain a genotype for each animal in the population, and then used detailed reserve management records from the period 1993-2009 to constrain the statistical process of parentage assignment. Using these different methods, I was able to assign both parents for 22 of 23 offspring with 80% confidence (16 of 23 at 95% confidence, mother only in 1 of 23), making this study the first to successfully complete a comprehensive parentage analysis in a free-ranging population of southern white rhinoceros. The key to the success of this study was a combination of accurate pedigree data and a complete set of genotype data. The parentage assignments allowed me to construct a complete lineage diagram for each of the founder matrilines, and further analyse the status and reproductive success of the population. OGR’s southern white rhinoceros population is expanding at close to 14%, well over the expected maximum growth rate for rhinoceros metapopulations (9%). The mean inter-calf interval is about 2.2 years and average age at first parturition is 6 years, indicating good fecundity. Conception is strongly seasonal, occurring mainly (89%) during the rainy season. The current management practice is to replace dominant bulls after their breeding tenure, and also to remove all young bulls from the population before they reach breeding age (with the aim to restrict potential inbreeding). Only one calf of seven in the F2 generation is inbred. My analysis indicates that, at least in the 2006 cohort of eight calves, founder females bred only with the founder male, while offspring females (F1 generation) bred only with introduced males. This suggests some form of mate selection leading to inbreeding avoidance within the population. Finally, there is some evidence that certain matrilines exhibit/experience different reproductive potential (daughters in one matriline exhibit longer inter-calving intervals and male bias in calf birth sex ratios). These details indicate that genetic data provide valuable information for management. When reviewing management decisions to date, I found that one of the founder bulls was the more successful in terms of calves sired (10 of 13). Management had, however, selected the other founder bull for removal by sale based on the assumption that he was behaviourally dominant and territorial and therefore likely to have been more successful at breeding. I also found that introduced bulls were breeding successfully before they appeared to have established territories. Thus these findings challenge the assumption that male white rhinoceros reproductive success is related to dominant, territorial behaviour. I conclude that in order to optimally manage small, free-ranging enclosed populations of southern white rhinoceros it is essential to have reliable and accurate pedigree data (this includes a methodology for identifying individual rhino), as well as genetic data for the entire population. I recommend that conservation management programmes for rhinoceros populations incorporate both genetic and demographic data. This will allow for the development of white rhinoceros population management strategies that attempt to optimize genetic diversity and population health, and benefit the establishment of new, robust populations. Translocations of animals are an important aspect of meta-population management of rhinoceros and data which provides accurate insight into the true mating system and reproductive success within a population allows for the correct selection of individuals for this process. Copyright