African wild dogs (Lycaon pictus) from the Kruger National Park, South Africa are currently not inbred but have low genomic diversity

Abstract

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.

Homozygosity mapping in the Kazakh national dog breed Tazy

“…In this study, for the first time, we presented an overview of the ROH patterns of the Kazakh national dog breed Tazy from a genome-wide perspective. According to the obtained results, there was strong evidence of distant inbreeding in this breed about 50 generations ago, as most ROH fell into the short (1-2 Mb) category, which allowed ROH decay by recombination over a long period of time 5 . Since the generation length of the Tazy is 1.7-3.1 years, it is likely that the genetic diversity of the Tazy was influenced by the social and climatic disasters in Kazakhstan in 1868-1938.…”

“…Short ROH segments reflect distant or ancient inbreeding, as recombination allows for the breakdown of segments over time. Distant inbreeding can be classified as inbreeding events that occurred between 50 and 12.5 generations ago when ROH lengths range from 1 to 4 Mb, respectively 3 – 5 . The ability of ROH segments to provide information about genetic events in a population makes them a useful tool for studying the breeding process over time.…”

Homozygosity mapping in the Kazakh national dog breed Tazy

“…In this study, for the rst time, we presented an overview of the ROH patterns of the Kazakh national dog breed Tazy from a genome-wide perspective. According to the obtained results, there was strong evidence of distant inbreeding in this breed about 50 generations ago, as most ROH fell into the short (1-2 Mb) category, which allowed ROH decay by recombination over a long period of time [14]. Since the generation length of the Tazy is 1.7-3.1 years, it is likely that the genetic diversity of the Tazy was in uenced by the social and climatic disasters in Kazakhstan in 1868-1938.…”

“…German Shepherd (FROH for lengths > 1MB − 0.119) [13], and the Bulldog (0.151) [12], but did not reach the level of FROH for wild dogs. For example, the FROH for African wild dogs (Lycaon pictus) is much lower (0.0045 ± 0.0012) [5]. These results, combined with the previously shown high diversity of the Tazy breed [1], suggest that the current genetic status of the Tazy dog population is comparable to that of diverse breeds such as the Jack Russell terrier [16].…”

“…Short ROH segments re ect distant or ancient inbreeding, as recombination allows for the breakdown of segments over time. Distant inbreeding can be classi ed as inbreeding events that occurred between 50 and 12.5 generations ago when ROH lengths range from 1 to 8 Mb, respectively [3][4][5]. The ability of ROH segments to provide information about genetic events in a population makes them a useful tool for studying the breeding process over time.…”