Contrasting results from molecular and pedigree-based population diversity measures in captive zebra highlight challenges facing genetic management of zoo populations

Evaluation of the Impact of Population Management on the Genetic Parameters of Selected Spiral-Horned Antelopes

The rapid loss of biodiversity and the associated reduction and fragmentation of habitats means that ex situ populations have become an important part of species conservation. These populations, which are often established from a small number of founders, require careful management to avoid the negative effects of genetic drift and inbreeding. Although the inclusion of molecular data is recommended, their availability for captive breeding management remains limited. The aim of this study was to evaluate the relationship between the levels of genetic diversity in six spiral-horned antelope taxa bred under human care and their respective management strategies, conservation status, demography, and geographic origin, using 10 nuclear DNA microsatellite loci and mitochondrial control region DNA sequences. Our findings include associations between genetic diversity and management intensity but also with the diversity and contribution of wild populations to captive founders, with some populations apparently composed of animals from divergent wild lineages elevating captive genetic diversity. When population sizes are large, the potential advantages of maximizing genetic diversity in widely outcrossed populations may need careful consideration with respect to the potential disruption of adaptive diversity. Genetic data serve as a robust tool for managing captive populations, yet their interpretation necessitates a comprehensive understanding of species biology and history.

Comparison of the Genetic Diversity of the Captive and Wild Populations of the Tsushima Leopard Cat Using a GRAS-Di Analysis

Simple Summary

The Tsushima leopard cat (Prionailurus bengalensis euptilurus) is exclusively found on the Tsushima Island in Japan; however, its population has been declining in recent years and is in danger of extinction. Hence, effort is underway for both in situ and ex situ conservation. Genetic management is also important in the management of captive populations, and various studies are being conducted regarding the same. In our previous study, we developed a reference genome of the Tsushima leopard cat and used GRAS-Di analysis, a genome-wide analysis, to genetically evaluate the wild populations. In this study, we attempted to improve the Tsushima leopard cat reference genome and compared the captive and wild populations by GRAS-di analysis. The results showed that the captive population had almost the same genetic diversity as the wild population and managed to remain in good condition.

Abstract

The Tsushima leopard cat (Prionailurus bengalensis euptilurus) (TLC) is a regional population of the Amur leopard cat (P. bengalensis euptilurus) that lives only on the Tsushima Island in Japan and is threatened with extinction. Because the TLC population is small, genetic management is important. In this study, we obtained the draft genome of the TLC and identified single-nucleotide polymorphism (SNP) markers using a genotyping by random amplicon sequencing-direct (GRAS-Di) analysis. We genotyped 31 captive individuals and 50 wild individuals, of which 48 were from a previous study. The identified SNPs were used to clarify the genetic diversity and genetic structure of the wild and captive populations of the TLC. The size of the genome was estimated to be about 2.42 Gb. The number of SNP markers developed was 139, and although PID and probability of exclusion obtained using these SNP markers were not as high as those reported in the studies of other wild species, these SNP markers could be used to identify individuals and parentage. Moreover, the genetic diversity indices of the captive population were similar to those of the wild population. These SNP markers will be useful for understanding the ecology of the TLC and planning conservation strategies.

Genetic Diversity and Relatedness among Captive African Painted Dogs in North America

African painted dogs (Lycaon pictus, APD) are highly endangered, with fewer than 7000 remaining in nature. Captive breeding programs can preserve a genetically diverse population and provide a source of individuals for reintroductions. However, most programs are initiated from few founders and suffer from low genetic diversity and inbreeding. The aims of this study were to use molecular markers to assess genetic variation, inbreeding, and relatedness among APDs in the North American captive population, to use these data to realign studbook records, and to compare these data to wild populations and to the European captive population to facilitate the development of a global management plan. We sequenced mitochondrial and major histocompatibility (MHC) class II loci and genotyped 14 microsatellite loci from 109 APDs from 34 institutions in North America. We identified three likely studbook errors and resolved ten cases of uncertain paternity. Overall, microsatellite heterozygosity was higher than reported in Europe, but effective population size estimates were lower. Mitochondrial sequence variation was extremely limited, and there were fewer MHC haplotypes than in Europe or the wild. Although the population did not show evidence of significant inbreeding overall, several individuals shared high relatedness values, which should be incorporated into future breeding programs.

White-naped mangabeys' viable insurance population within European Zoo Network

The success and viability of an ex-situ conservation program lie in the establishment and potential maintenance of a demographically and genetically viable insurance population. Such population reserve may support reintroduction and reinforcement activities of wild populations. White-naped mangabeys are endangered restricted-range African primates which have experienced a dramatic population decrease in their natural habitats over the last few decades. Since 2001, some European zoos singularly monitor an ex-situ population aiming to seek the recovery of the current wild population. The aim of the present paper is to evaluate the genetic status and population demographics of European zoo-captive white-naped mangabeys based on pedigree data. The captive population is gradually growing and preserves specific reproductive and demographic parameters linked to the species. The intensive management program that is implemented has brought about the minimization of inbreeding and average relatedness levels, thus maintaining high levels of genetic diversity despite the existence of fragmented populations. This finding suggests white-naped mangabey ex-situ preservation actions may be a good example of multifaceted conservation throughout studbook management which could be used as a model for other ex-situ live-animal populations.

Genetic assessment of a conservation breeding program of the houbara bustard (Chlamydotis undulata undulata) in Morocco, based on pedigree and molecular analyses

Protection and restoration of species in the wild may require conservation breeding programs under genetic management to minimize deleterious effects of genetic changes that occur in captivity, while preserving populations' genetic diversity and evolutionary resilience. Here, through interannual pedigree analyses, we first assessed the efficiency of a 21-year genetic management, including minimization of mean kinship, inbreeding avoidance, and regular addition of founders, of a conservation breeding program targeting on Houbara bustard (Chlamydotis undulata undulata) in Morocco. Secondly, we compared pedigree analyses, the classical way of assessing and managing genetic diversity in captivity, to molecular analyses based on seven microsatellites. Pedigree-based results indicated an efficient maintenance of the genetic diversity (99% of the initial genetic diversity retained) while molecular-based results indicated an increase in allelic richness and an increase in unbiased expected heterozygosity across time. The pedigree-based average inbreeding coefficient F remained low (between 0.0004 and 0.003 in 2017) while the proportion of highly inbred individuals (F > .1) decreased over time and reached 0.2% in 2017. Furthermore, pedigree-based F and molecular-based individual multilocus heterozygosity were weakly negatively correlated, (Pearson's r = -.061 when considering all genotyped individuals), suggesting that they cannot be considered as alternatives, but rather as complementary sources of information. These findings suggest that a strict genetic monitoring and management, based on both pedigree and molecular tools can help mitigate genetic changes and allow to preserve genetic diversity and evolutionary resilience in conservation breeding programs.

Genetic Diversity and Genetic Structure of the Wild Tsushima Leopard Cat from Genome-Wide Analysis

Simple Summary

The Tsushima leopard cat, Prionailurus bengalensis euptilurus, is a small regional population of the Amur leopard cat and is only found on Tsushima Island in Japan. A breeding program will require adequate information on parentage, kinship, and inbreeding for this population. Hence, there is an urgent need to develop this information in order to conserve the population and its genetic diversity. We performed GRAS-Di analysis to investigate the genetic diversity and genetic structure of the Tsushima leopard cat. We identified between 133 and 158 single-nucleotide polymorphism (SNP) markers in three different genotyping methods. These SNP markers can be used in identification of individuals and parentage. In addition, structure analysis using these markers demonstrated the similar genetic composition of the samples from 48 Tsushima leopard cats, and indicated Tsushima leopard cats have no subpopulations. We have provided genetic markers that are useful for conservation of the Tsushima leopard cat, such as individual identification and parentage. Moreover, we have also clarified units for conservation of the Tsushima leopard cat population from structure analysis.

Abstract

The Tsushima leopard cat (Prionailurus bengalensis euptilurus) lives on Tsushima Island in Japan and is a regional population of the Amur leopard cat; it is threatened with extinction. Its genetic management is important because of the small population. We used genotyping by random amplicon sequencing-direct (GRAS-Di) to develop a draft genome and explore single-nucleotide polymorphism (SNP) markers. The SNPs were analyzed using three genotyping methods (mapping de novo, to the Tsushima leopard cat draft genome, and to the domestic cat genome). We examined the genetic diversity and genetic structure of the Tsushima leopard cat. The genome size was approximately 2.435 Gb. The number of SNPs identified was 133–158. The power of these markers was sufficient for individual and parentage identifications. These SNPs can provide useful information about the life of the Tsushima leopard cat and the pairings and for the introduction of founders to conserve genetic diversity with ex situ conservation. We identified that there are no subpopulations of the Tsushima leopard cat. The identifying units will allow for a concentration of efforts for conservation. SNPs can be applied to the analysis of the leopard cat in other regions, making them useful for comparisons among populations and conservation in other small populations.

Comparison of divergent breeding management strategies in two species of semi-captive eland in Senegal

Breeding management of small populations may have a critical influence on the development of population characteristics in terms of levels of genetic diversity and inbreeding. Two populations of antelope sister species – Critically Endangered Western Derby eland (Tauroragus derbianus derbianus) and non-native Least Concern Cape eland (Taurotragus oryx oryx) bred under different management strategies were studied in Senegal, Western Africa. The aims of the study were to compare the population genetic parameters of the two species and to test for the presence of interspecific hybrids. In total, blood and tissue samples from 76 Western Derby elands and 26 Cape elands were investigated, using 12 microsatellite markers. No hybrid individuals were detected in the sampled animals within the multispecies enclosure in Bandia Reserve, Senegal. The parameters of genetic polymorphism indicated much lower genetic diversity in Western Derby elands compared to Cape elands. On the other hand, the coefficient of inbreeding was low in both species. It is hypothesized that this could be a positive effect of strict population management of Western Derby elands, which, despite the loss of genetic diversity, minimizes inbreeding.

Studbook and molecular analyses for the endangered black-lion-tamarin; an integrative approach for assessing genetic diversity and driving management in captivity

Breeding strategies based on molecular markers have been adopted by ex-situ conservation programs to assess alternative parameters for the genetic diversity estimates. In this work we evaluated molecular and studbook data for captive populations of black-lion-tamarin (BLT), an endangered primate endemic to Brazil's Atlantic Forest. Pedigree analyses were performed using BLT studbook information collected from 1973 to 2018. We analyzed the whole captive population since its foundation; the current captive population (CCP); and all extant BLTs in the Brazilian captive population (BCP), separately. Microsatellite analyses were implemented on the BCP individuals from the eighth generation (BCP-F8) only to avoid generation overlap. The expected heterozygosity for BCP-F8, using molecular, data was 0.45, and the initial expected heterozygosity was 0.69. Kinship parameters showed high genetic relationships in both pedigree and molecular analyses. The genealogy-based endogamy evidenced a high inbreeding coefficient, while the molecular analyses suggested a non-inbreeding signature. The Mate Suitability Index showed detrimental values for the majority of potential pairs in the CCP. Nevertheless, some individuals evidenced high individual heterozygosity and allele representation, demonstrating good potential to be used as breeders. Thus, we propose the use of molecular data as a complementary parameter to evaluate mating-pairs and to aid management decision-making.

The Tsushima leopard cat exhibits extremely low genetic diversity compared with the Korean Amur leopard cat: Implications for conservation

We examined genetic diversity of the wild Tsushima leopard cat-a regional population of the Amur leopard cat-using microsatellite markers. In addition, we compared genetic diversity of the Tsushima leopard cat with that of the Korean population of Amur leopard cat. Although bias should be considered when applying cross-species amplification, the Tsushima leopard cat showed a lower index of molecular genetic diversity than did the Korean population. These results were consistent with those obtained using other genetic markers, such as mitochondrial DNA and Y chromosome sequences. This low genetic diversity of the wild Tsushima leopard cat may be derived from the founding population. Furthermore, our results suggest that the captive populations held in Japanese zoos may show extremely low genetic diversity, leading to difficulties in genetic management of the Tsushima leopard cat. Moreover, the two regional populations were clearly separated using these marker sets. In the present study, we demonstrated that the genetic diversity of the Tsushima leopard cat is extremely low compared with that of the continental regional population. Importantly, the Japanese captive population for ex situ conservation was derived from a founding population with extremely low genetic diversity; hence, we assume that both the captive and wild populations showed extremely low genetic diversities. Our findings emphasize the need to develop carefully considered management strategies for genetic conservation.