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

Deepanwita Purohit; Shivakumara Manu; Muthuvarmadam Subramanian Ram; Shradha Sharma; Harika Chinchilam Patnaik; Parag Jyoti Deka; Goutam Narayan; Govindhaswamy Umapathy

doi:10.7717/peerj.12212

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

PeerJ. 2021 Oct 8:9:e12212. doi: 10.7717/peerj.12212. eCollection 2021.

Authors

Deepanwita Purohit¹, Shivakumara Manu¹, Muthuvarmadam Subramanian Ram^{1

2}, Shradha Sharma¹, Harika Chinchilam Patnaik¹, Parag Jyoti Deka^{3

4}, Goutam Narayan⁵, Govindhaswamy Umapathy¹

Affiliations

¹ CSIR- Centre for Cellular and Molecular Biology, Hyderabad, India.
² CES, Indian Institute of Science, Bangalore, India.
³ Aaranyak, Threatened Species Recovery Programme,, Beltola, Guwahati, India.
⁴ Durrell Wildlife Conservation Trust - Pygmy Hog Conservation Programme, Indira Nagar, Basistha, Guwahati, Assam, India.
⁵ EcoSystems-India, Rare & Endangered Species Conservation Unit, Beltola, Guwahati, India.

Abstract

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 (F_IS) 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.

Keywords: Captive breeding; Genetic diversity; MHC; Pygmy hog; ezRAD sequencing.

Grants and funding

The study was funded by a Nehru Postdoctoral Fellowship (Deepanwita Purohit) from the Extramural Research Division, Council of Scientific and Industrial Research (CSIR), Govt. of India. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.