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 (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.
Highlights
Captive breeding has become a major conservation tool for safeguarding criticallyendangered species from extinction and restoring declining populations in the wild
Further we recorded a significant increase of H in captive-born individuals from all generations (Gen2 to Gen6) relative to the founders (Table 1; Fig. 1A)
Higher success rate in species recovery programs following genetic enrichment was observed in black-footed ferrets where individuals and their offspring produced through artificial insemination using long cryopreserved spermatozoa were integrated into their captive population (Howard et al, 2016)
Summary
Captive breeding has become a major conservation tool for safeguarding criticallyendangered species from extinction and restoring declining populations in the wild. Factors attributed to reduced performances could be (1) inbreeding within a population with a small number of founders, (2) relaxed natural selection in captive conditions, (3) accumulation of mildly deleterious mutations and (4) adaptation to captivity (Frankham, 2008). Identifying these factors in a captive population is extremely difficult owing to their subtle differences in manifest effects (Snyder et al, 1997); it is essential to identify these factors in order to provide customized management solutions for an effective breeding and reintroduction program. There is a growing incidence of usage of both SNPs and functional markers in population genetic studies to gain complete insight into different underlying mechanisms shaping the genetic diversity in a population (Lenz et al, 2013; Yıldırım, Tolun & Tüysüz, 2011)
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