Unrevealing Conservation Statue of The Endangered Pygmy Hog (Procula salvania ) Using Genomic Information

Conservation breeding is becoming an increasingly important tool to prevent extinction. This by providing organisms for reintroduction to either re-establish or wild populations in their natural environment, or for assisted colonization outside of historical natural ranges by species translocation. The pygmy hog (Procula salvania) is the smallest and the rarest wild suid in the world. Once thought extinct, it has been classified as a critically endangered species according to the International Union of Conservation of Nature (IUCN) since 2008 with only a few hundred living in wild. However, little is known of the population structure of pygmy hog. Even the most fundamental aspects of population ecology, such as the effective population size, are unknown. Here, we analyzed the whole genome sequencing data of six individual pygmy hogs: three from the wild and three from a captive population to access the current and past population history of pygmy hog. First, we show that pygmy hog has remained at small population sizes with low genetic diversity since ~1 Mya. Surprisingly, mitochondrial haplotype analysis indicated that the existing populations from both wild and captivity are coming from the same maternal linage. Second, to determine the degree of inbreeding we searched the genomes for regions of homozygosity (ROHs). The ROH analysis suggests that pygmy hog has gone through past and not recent inbreeding which is in line with results from other small and inbred populations.