Genetic effects of long-term captive breeding on the endangered pygmy hog

Long-term captive populations often accumulate genetic changes that are detrimental to their survival in the wild. Periodic genetic evaluation of captive populations is thus necessary to identify deleterious changes and minimize their impact through planned breeding. Pygmy hog (Porcula salvania) is an endangered species with a small population inhabiting the tall sub-Himalayan grasslands of Assam, India. A conservation breeding program of pygmy hog from six founders has produced a multi-generational captive population destined for reintroduction into the wild. However, the impact of conservation breeding on its genetic diversity remained undocumented. Here, we evaluate temporal genetic changes in 39 pygmy hogs from eight consecutive generations of a captive population using genome-wide SNPs, mitochondrial genomes, and MHC sequences, and explore the relationship between genetic diversity and reproductive success. We find that pygmy hog harbors a very low genome-wide heterozygosity (H) compared to other members of the Suidae family. However, within the captive population we find excess heterozygosity and a significant increase in H from the wild-caught founders to the individuals in subsequent generations due to the selective pairing strategy. The MHC and mitochondrial nucleotide diversities were lower in captive generations compared to the founders with a high prevalence of low-frequency MHC haplotypes and more unique mitochondrial genomes. Further, even though no signs of genetic inbreeding were observed from the estimates of individual inbreeding coefficient F and between individuals (FIS) in each generation, the kinship coefficient showed a slightly increasing trend in the recent generations, due to a relatively smaller non-random sample size compared to the entire captive population. Surprisingly, male pygmy hogs that had higher heterozygosity also showed lower breeding success. We briefly discuss the implications of our findings in the context of breeding management and recommend steps to minimize the genetic effects of long-term captive breeding.

Non-Invasive Reproductive Hormone Monitoring in Endangered Pygmy Hog (Porcula salvania)

The Pygmy hog (Porcula Salvania), till recently, classified as a critically endangered suid, is facing the threat of extinction globally due to habitat degradation. Efforts are being made to protect the pygmy hogs from extinction and breed them in captivity under Pygmy Hog Conservation Pro-gramme (PHCP). However, very little information is available on the reproductive physiology of pygmy hogs. Therefore, the present study aimed to standardize enzyme immunoassays (EIAs) for monitoring pregnancy and reproductive status using progesterone and testosterone metabolites. A total of 785 faecal samples were collected from five females and two males over a period of one year from PHCP Research and Breeding Centre, Guwahati, Assam. High-pressure liquid chro-matography (HPLC) analysis revealed the presence of immunoreactive progesterone and testos-terone metabolites in faeces. Mating was observed in all the five females and four of them gave birth successfully. We were able to detect pregnancy using faecal progesterone metabolites. Based on mating and parturition, the mean gestation period was estimated to be 153.25 days from four females. The breeding centre recorded 172 births between 1996 and 2000 and found strong sea-sonality in births and most of the births were between May and June. Faecal testosterone metabo-lites were significantly higher in the breeding season than the non-breeding season. This is the first study and will help in future breeding programs in other captive breeding centres and reproduc-tive monitoring of reintroduced populations.

Feasibility of reintroducing grassland megaherbivores, the greater one-horned rhinoceros, and swamp buffalo within their historic global range

Reintroduction of endangered species is an effective and increasingly important conservation strategy once threats have been addressed. The greater one-horned rhinoceros and swamp buffalo have declined through historic hunting and habitat loss. We identify and evaluate available habitat across their historic range (India, Nepal, and Bhutan) for reintroducing viable populations. We used Species Distribution Models in Maxent to identify potential habitats and evaluated model-identified sites through field visits, interviews of wildlife managers, literature, and population-habitat viability analysis. We prioritize sites based on size, quality, protection, management effectiveness, biotic pressures, and potential of conflict with communities. Our results suggest that populations greater than 50 for rhinoceros and 100 for buffalo were less susceptible to extinction, and could withstand some poaching, especially if supplemented or managed as a metapopulation. We note some reluctance by managers to reintroduce rhinoceros due to high costs associated with subsequent protection. Our analysis subsequently prioritised Corbett and Valmiki, for rhino reintroduction and transboundary complexes of Chitwan-Parsa-Valmiki and Dudhwa-Pilibhit-Shuklaphanta-Bardia for buffalo reintroductions. Establishing new safety-nets and supplementing existing populations of these megaherbivores would ensure their continued survival and harness their beneficial effect on ecosystems and conspecifics like pygmy hog, hispid hare, swamp deer, hog deer, and Bengal florican.

Genomic analysis on pygmy hog reveals extensive interbreeding during wild boar expansion

Wild boar (Sus scrofa) drastically colonized mainland Eurasia and North Africa, most likely from East Asia during the Plio-Pleistocene (2–1Mya). In recent studies, based on genome-wide information, it was hypothesized that wild boar did not replace the species it encountered, but instead exchanged genetic materials with them through admixture. The highly endangered pygmy hog (Porcula salvania) is the only suid species in mainland Eurasia known to have outlived this expansion, and therefore provides a unique opportunity to test this hybridization hypothesis. Analyses of pygmy hog genomes indicate that despite large phylogenetic divergence (~2 My), wild boar and pygmy hog did indeed interbreed as the former expanded across Eurasia. In addition, we also assess the taxonomic placement of the donor of another introgression, pertaining to a now-extinct species with a deep phylogenetic placement in the Suidae tree. Altogether, our analyses indicate that the rapid spread of wild boar was facilitated by inter-specific/inter-generic admixtures.