Cross-specific markers reveal retention of genetic diversity in captive-bred pygmy hog, a critically endangered suid

Purohit, Deepanwita; Ram, Muthuvarmadam Subramanian; Pandey, Virendra Kumar; Pravalika, Satya; Deka, Parag; Narayan, Goutam; Umapathy, Govindhaswamy

doi:10.1007/s12686-019-01091-1

Cited by 4 publications

(5 citation statements)

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“…Therefore, genetic evaluation of captive populations is crucial to understanding the evolutionary impact of captive breeding on the species and to inform conservation breeding and management decisions While our study revealed a low average genome-wide heterozygosity (H ) in pygmy hog (Table 1 & Table S1) compared to other suids, particularly Sus verrucosus and European wild boar (Liu et al, 2020), it was comparable to Amur tiger, African cheetah and vaquita, which have historically maintained a very low population size (Morin et al, 2021;Robinson et al, 2016). The low H underlines previous findings of low observed heterozygosities in pygmy hog using microsatellite markers (Purohit et al, 2020). Moreover, the low standard deviation of individual estimates of H suggests that the paucity of heterozygous sites is evenly distributed in the sequenced regions of the genome.…”

Section: Genetic Variability In Captive Pygmy Hogssupporting

confidence: 78%

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

Purohit

Manu

Ram

et al. 2021

PeerJ

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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.

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Section: Genetic Variability In Captive Pygmy Hogssupporting

confidence: 78%

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

Purohit

Manu

Ram

et al. 2021

PeerJ

Self Cite

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“…Other additional phenotypic traits have not yet been examined within this population, and therefore, it is not known whether the low levels of genetic diversity are impacting population fitness. Considering the recent decline of genetic diversity in captive pygmy hogs (Purohit et al, 2019), genetic defects may become apparent due to the recessive deleterious alleles being homozygous. Recent studies have shown the potential of using genomics information to monitor deleterious mutations in breeding program (Charlier et al, 2016;Derks et al, 2018Derks et al, , 2019.…”

Section: Discussionmentioning

confidence: 99%

“…However, the captive individuals in this study represent the third and fourth generation of the breeding program. The observation that the most recent generation showed a significant decrease in individual heterozygosity indicates that drift effects likely are becoming prominent after more than five generations (Purohit et al., 2019). Since there is no other existing wild population and pygmy hog is the only member in its genus, “genetic rescue” is not feasible for the pygmy hog population.…”

Section: Discussionmentioning

confidence: 99%

Genetic consequences of long‐term small effective population size in the critically endangered pygmy hog

Liu

Bosse

Megens

et al. 2020

Evolutionary Applications

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“…However, the captive individuals in this study represent the third and fourth generation of the breeding programme. The observation that the most recent generation showed a significant decrease in individual heterozygosity indicates that drift effects likely are becoming prominent after more than five generations (Purohit et al, 2019). Since there is no other existing wild population and pygmy hog is the only member in its genus, 'genetic rescue' is not feasible for the pygmy hog population.…”

Section: Discussionmentioning

confidence: 99%

“…Other additional phenotypic traits have not yet been examined within this population and therefore it is not known if the low levels of genetic diversity are impacting population fitness. Considering the recent decline of genetic diversity in captive pygmy hogs (Purohit et al, 2019), genetic defects may become apparent due to the recessive deleterious alleles being homozygous.…”

Section: Discussionmentioning

confidence: 99%

Genome evolution of Suidae: a looking glass of speciation and hybridization

Liu¹

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Liu, L. (2021). Genome evolution of Suidae: a looking glass of speciation and hybridization. PhD thesis, Wageningen University, the Netherlands Understanding the origin of species and biodiversity is one of the fundamental objectives in evolutionary biology. Developments in sequencing technology have revolutionized our understanding of evolutionary biology. In this thesis, with genomics information, I systematically describe the evolutionary history of the Suidae species and examine complex speciation scenarios with hybridization. In Chapter2, utilizing whole-genome sequence data, I show that pygmy hog should be classified into a distinct genus separated from other Suinae species, which initially emerged during the Miocene/Pliocene boundary. In this chapter, admixture analyses reveal at least two independent events of inter-species gene flow during wild boar range expansion across Eurasia. In Chapter3, I provide an in-depth analysis of the formation of the current pygmy hog population and demonstrated consequences of the historical demography. Our demographic analysis reveals that pygmy hog has remained at small population sizes with low genetic diversity since ~1 Mya. The long-term, extremely small population size may have constrained the purifying effect and led to the accumulation of genetic load. In Chapter 4, I present a chromosome level genome assembly of Visayan warty pig. The alignment of the Visayan warty pig assembly and Duroc pig assembly reveal a high degree of collinearity, but also chromosome fission and fusion. The similarity of the chromosome interaction maps may explain the absence of post-zygotic reproductive isolation among Sus species. Moreover, we investigated the evolution of olfactory and gustatory genes and report the genetic basis of species-specific sensation. In Chapter5, I describe a reference-guided assembly approach to generate genome sequences for three other Sus species and the outgroup species pygmy hog. With the near complete phylogenomic framework of Sus species, we were able to perform admixture analyses directly from genome sequences. We provide candidate genes that might have contributed to adaptive radiation and domestication of pigs. Together, thesis findings provide a comprehensive view of the evolutionary history of Suidae, describing species origin and demographic history afterwards. In this work I compared genome scale data from various pig species to refine the understanding of their evolutionary processes and provide new insights on the underlying genetic mechanism. Contents1. General introduction 2. Genomic analysis on pygmy hog (Porcula salvania) reveals multiple interbreeding during wild boar expansion 3. Genetic consequences of long-term small effective population size in the critically endangered pygmy hog 4. Genome assembly of Visayan warty pig (Sus cebifrons) provides insight into genome evolution of Sus during speciation 5. Sus reference-guided genome assemblies provide a high-resolution view of diversification, reticulation and adaptation during pig evolution

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Cross-specific markers reveal retention of genetic diversity in captive-bred pygmy hog, a critically endangered suid

Cited by 4 publications

References 14 publications

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

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

Genetic consequences of long‐term small effective population size in the critically endangered pygmy hog

Genome evolution of Suidae: a looking glass of speciation and hybridization

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