Genetic structure of captive and free-ranging okapi (Okapia johnstoni) with implications for management

Breeding programs for endangered species increasingly use molecular genetics to inform their management strategies. Molecular approaches can be useful for investigating relatedness, resolving pedigree uncertainties, and for estimating genetic diversity in captive and wild populations. Genetic data can also be used to evaluate the representation of wild population genomes within captive population gene-pools. Maintaining a captive population that is genetically representative of its wild counterpart offers a means of conserving the original evolutionary potential of a species. Okapi, an even-toed ungulate, endemic to the Democratic Republic of Congo, have recently been reclassified as Endangered by the IUCN. We carried out a genetic assessment of the ex-situ okapi (Okapia johnstoni) population, alongside an investigation into the genetic structure of wild populations across their geographic range. We found that while levels of nuclear (12 microsatellite loci) genetic variation in the wild, founder and captive okapi populations were similar, mitochondrial (833 bp of Cyt b, CR, tRNA-Thr and tRNA-Pro) variation within captive okapi was considerably reduced compared to the wild, with 16 % lower haplotype diversity. Further, both nuclear and mitochondrial alleles present in captivity provided only partial representation of those present in the wild. Thirty mitochondrial haplotypes found in the wild were not found in captivity, and two haplotypes found in captivity were not found in the wild, and the patterns of genetic variation at microsatellite loci in our captive samples were considerably different to those of the wild samples. Our study highlights the importance of genetic characterisation of captive populations, even for well-managed ex-situ breeding programs with detailed studbooks. We recommend that the captive US population should be further genetically characterised to guide management of translocations between European and US captive population

Perspectives of genomics for genetic conservation of livestock

Genomics provides new opportunities for conservation genetics. Conservation genetics in livestock is based on estimating diversity by pedigree relatedness and managing diversity by choosing those animals that maximize genetic diversity. Animals can be chosen as parents for the next generation, as donors of material to a gene bank, or as breeds for targeting conservation efforts. Genomics provides opportunities to estimate diversity for specific parts of the genome, such as neutral and adaptive diversity and genetic diversity underlying specific traits. This enables us to choose candidates for conservation based on specific genetic diversity (e.g. diversity of traits or adaptive diversity) or to monitor the loss of diversity without conservation. In wild animals direct genetic management, by choosing candidates for conservation as in livestock, is generally not practiced. With dense marker maps opportunities exist for monitoring relatedness and genetic diversity in wild populations, thus enabling a more active management of diversity

Removing exogenous information using pedigree data

Management of certain populations requires the preservation of its pure genetic background. When, for different reasons, undesired alleles are introduced, the original genetic conformation must be recovered. The present study tested, through computer simulations, the power of recovery (the ability for removing the foreign information) from genealogical data. Simulated scenarios comprised different numbers of exogenous individuals taking partofthe founder population anddifferent numbers of unmanaged generations before the removal program started. Strategies were based on variables arising from classical pedigree analyses such as founders? contribution and partial coancestry. The ef?ciency of the different strategies was measured as the proportion of native genetic information remaining in the population. Consequences on the inbreeding and coancestry levels of the population were also evaluated. Minimisation of the exogenous founders? contributions was the most powerful method, removing the largest amount of genetic information in just one generation.However, as a side effect, it led to the highest values of inbreeding. Scenarios with a large amount of initial exogenous alleles (i.e. high percentage of non native founders), or many generations of mixing became very dif?cult to recover, pointing out the importance of being careful about introgression events in populatio

Pedigree analysis applied to an endangered buffalo population: possible management strategy.

The Carabao breed (Bubalus bubalis kerebao) in Brazil may be endangered and at risk of losing specific qualities. This makes preservation and population studies extremely important. In this pedigree analysis on a Brazilian herd, low values for populational parameters and high mean endogamy were found. Mating optimization based on bulls of lesser kinship improves populational parameters and reduces inbreeding rates. Use of this tool, in addition to conservation programs, will help to mitigate genetic variability losses in the Brazilian Carabao herd, thus allowing its future enrollment in genetic improvement programs

Evaluating genetic diversity in the critically endangered orange-bellied parrot: informing species management

The orange-bellied parrot (Neophema chrysogaster) is a critically endangered small Australian parrot. It was the first species in Australia to have a single species Recovery Plan developed, and efforts to conserve the species have been active for over 35 years. Despite this, the wild population has declined to fewer than 20 individuals. Approximately 450 birds are maintained in a captive insurance population. This thesis investigated genetic diversity across both wild and captive populations of the OBP between 2010 and 2018. Relatively low genome-wide diversity was found across the species, as measured with 7768 SNP markers. Low functional diversity was also found at immune genes the Toll-like receptors, consistent with other studies of critically endangered birds. Although genetic diversity in the wild population decreased following removal of 21 fledglings in 2010/11 to supplement the captive population, annual releases of captive birds since 2013, and their successful breeding post-release, have improved wild diversity levels. Wild and captive populations were not found to be genetically distinct. Inbreeding depression was investigated by modelling correlations between genetic diversity and 1) differential responses to infectious disease agents, and 2) reproductive success. No evidence of inbreeding depression was found, but a relationship between younger age and greater reproductive success was identified. Finally, a preliminary phylogeny of the genus Neophema was produced using two mitochondrial markers, and was found to support some of the current structure within the genus, but was ultimately inconclusive as to placement of the OBP. This work has explored genetic diversity in the OBP to a greater extent than ever previously. It has helped inform management of the species and will act as a foundation for future studies

Subspecies hybridization as a potential conservation tool in species reintroductions

Reintroductions are a powerful tool for the recovery of endangered species. However, their long‐term success is strongly influenced by the genetic diversity of the reintroduced population. The chances of population persistence can be improved by enhancing the population's adaptive ability through the mixing of individuals from different sources. However, where source populations are too diverse the reintroduced population could also suffer from outbreeding depression or unsuccessful admixture due to behavioural or genetic barriers. For the reintroduction of Asiatic wild ass Equus hemionus ssp. in Israel, a breeding core was created from individuals of two different subspecies (E. h. onager & E. h. kulan). Today the population comprises approximately 300 individuals and displays no signs of outbreeding depression. The aim of this study was a population genomic evaluation of this conservation reintroduction protocol. We used maximum likelihood methods and genetic clustering analyses to investigate subspecies admixture and test for spatial autocorrelation based on subspecies ancestry. Further, we analysed heterozygosity and effective population sizes in the breeding core prior to release and the current wild population. We discovered high levels of subspecies admixture in the breeding core and wild population, consistent with a significant heterozygote excess in the breeding core. Furthermore, we found no signs of spatial autocorrelation associated with subspecies ancestry in the wild population. Inbreeding and variance effective population size estimates were low. Our results indicate no genetic or behavioural barriers to admixture between the subspecies and suggest that their hybridization has led to greater genetic diversity in the reintroduced population. The study provides rare empirical evidence of the successful application of subspecies hybridization in a reintroduction. It supports use of intraspecific hybridization as a tool to increase genetic diversity in conservation translocations

Using model systems to investigate the effects of captivity on phenotypic variation: implications for captive breeding programmes

Captive breeding programmes (CBPs) offer a method for preventing the extinction of threatened species by assisting with species recovery, primarily by generating animals for reintroduction and supplementing wild populations. However, CBPs often have difficulty establishing self-sustaining populations, unable to maintain consistent reproduction and survivorship in captivity for reintroducing animals back into the wild. A contributing factor leading to this issue may be captive conditions producing phenotypes that differ from wild phenotypes. These phenotypic changes may lead to captive individuals having reduced survivorship, as well as reduced reproductive success, both in captivity and following reintroduction. Ultimately, a range of factors will determine the success of reintroductions; however, the phenotypic changes occurring in captivity, and how this may impact reintroduction success remains largely unknown. In this thesis, I outline how an animal’s phenotype may contribute to the success or failure of CBPs, and in turn, reintroduction success. I used a mammalian and an amphibian species as models to examine phenotypic changes in captivity and specifically looked at developmental, morphological and behavioural phenotypes