DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa.
South African Tuberculosis Bioinformatics Initiative (SATBBI), Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Drive, PO Box 241, Cape Town, 7500, South Africa.
Sci Rep. 2022 Sep 2;12(1):14979. doi: 10.1038/s41598-022-19025-7.
African wild dogs (Lycaon pictus) have undergone severe population reductions and are listed as endangered on the International Union for Conservation of Nature Red List. Small, isolated populations have the potential to suffer from threats to their genetic diversity that may impact species viability and future survival. This study provides the first set of population-wide genomic data to address conservation concerns for this endangered species. Whole genome sequencing data were generated for 71 free-ranging African wild dogs from the Kruger National Park (KNP), South Africa, and used to estimate important population genomic parameters. Genomic diversity metrics revealed that variation levels were low; however, this African wild dog population showed low levels of inbreeding. Very few first- and second-order relationships were observed in this cohort, with most relationships falling into the third-order or distant category. Patterns of homozygosity could have resulted from historical inbreeding or a loss in genome variation due to a population bottleneck. Although the results suggest that this stronghold African wild dog population maintains low levels of inbreeding, likely due to their cooperative breeding system, it may lead to a continuous population decline when a reduced number of suitable mates are available. Consequently, the low genomic variation may influence species viability over time. This study highlights the importance of assessing population genomic parameters to set conservation priorities. Future studies should include the investigation of the potential of this endangered species to adapt to environmental changes considering the low genomic diversity in this population.
非洲野犬（Lycaon pictus）的数量已经大幅减少，被列入国际自然保护联盟濒危物种红色名录。小型、孤立的种群有可能受到威胁，从而影响其遗传多样性，进而影响物种的生存能力和未来的生存。本研究提供了第一组针对这一濒危物种的全种群基因组数据，以解决保护方面的担忧。对来自南非克鲁格国家公园（KNP）的 71 只自由放养的非洲野犬进行了全基因组测序，并利用这些数据来估计重要的种群基因组参数。基因组多样性指标表明，变异水平较低；然而，该非洲野犬种群的近交水平较低。在该队列中观察到的第一和第二阶关系很少，大多数关系属于第三阶或远距离类别。这种同型性模式可能是由于历史上的近亲繁殖或由于种群瓶颈导致基因组变异的丧失。尽管结果表明，由于其合作繁殖系统，这个重要的非洲野犬种群保持着较低的近交水平，但当合适的配偶数量减少时，可能会导致种群持续减少。因此，低基因组变异可能会影响物种的生存能力。本研究强调了评估种群基因组参数以确定保护优先级的重要性。未来的研究应该包括调查这个濒危物种在考虑到该种群低基因组多样性的情况下适应环境变化的潜力。
