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<p>Reintroduction programs for endangered species depend not only on population numbers but also on the genetic health of captive stocks; immune-related genes, in particular, help animals resist disease and adapt to local environmental pressures, yet how these genes fare under long-term captivity remains poorly understood. The Persian fallow deer (<i>Dama mesopotamica</i>), managed in Iran within captive-breeding centers since the 1960s, descends from an extremely small founder population and faces ongoing inbreeding risk. It remains unclear whether functional MHC diversity has been retained, lost, or reshaped across captive-bred populations relative to the founders. We sampled 43 individuals from eight Iranian breeding centers and three historical founder specimens and characterized polymorphism at two MHC class II loci (MHC-DRB IIA and MHC-DOB IIB) using PCR, SSCP, and DNA sequencing. MHC-DOB IIB was monomorphic across all samples, consistent with strong purifying selection, whereas MHC-DRB IIA showed nine haplotypes, consistent with balancing selection. Diversity at MHC-DRB IIA was characterized by moderate heterozygosity (Hₒ = 0.15, Hₑ = 0.23) and a locus-specific inbreeding coefficient of F ≈ 0.35. Sequencing of the mitochondrial D-loop, a neutral marker, revealed a single haplotype shared by all 43 individuals, indicating that — unlike MHC-DRB IIA — neutral genetic diversity has been essentially lost, consistent with previously reported low neutral diversity in this species. DAPC identified four genetic clusters among contemporary populations; the higher MHC-DRB IIA polymorphism observed in contemporary breeding centers relative to the three founder specimens most likely reflects the much smaller founder sample size rather than rapid adaptive diversification, and we interpret this contrast cautiously. These results suggest that, despite a severe historical bottleneck and continued loss of neutral genetic variation, functional diversity at MHC-DRB IIA has been at least partly retained, while MHC-DOB IIB shows no variation at all. Conservation strategies should prioritize monitoring MHC-DRB IIA diversity, enhancing connectivity between populations to counter ongoing inbreeding, and using genetically informed breeding to preserve rare alleles.</p>

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MHC diversity and conservation genetics in endangered Persian fallow deer after over six decades of captive breeding

  • 期刊论文

  • 发表日期：

    2026年7月13日

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  • Hossein Yazdandad,
  • Hamid Reza Rezaei,
  • Mansour Aliabadian,
  • Mahmood Soofi,
  • Seyed Mahmoud Ghasempouri

摘要

Reintroduction programs for endangered species depend not only on population numbers but also on the genetic health of captive stocks; immune-related genes, in particular, help animals resist disease and adapt to local environmental pressures, yet how these genes fare under long-term captivity remains poorly understood. The Persian fallow deer (Dama mesopotamica), managed in Iran within captive-breeding centers since the 1960s, descends from an extremely small founder population and faces ongoing inbreeding risk. It remains unclear whether functional MHC diversity has been retained, lost, or reshaped across captive-bred populations relative to the founders. We sampled 43 individuals from eight Iranian breeding centers and three historical founder specimens and characterized polymorphism at two MHC class II loci (MHC-DRB IIA and MHC-DOB IIB) using PCR, SSCP, and DNA sequencing. MHC-DOB IIB was monomorphic across all samples, consistent with strong purifying selection, whereas MHC-DRB IIA showed nine haplotypes, consistent with balancing selection. Diversity at MHC-DRB IIA was characterized by moderate heterozygosity (Hₒ = 0.15, Hₑ = 0.23) and a locus-specific inbreeding coefficient of F ≈ 0.35. Sequencing of the mitochondrial D-loop, a neutral marker, revealed a single haplotype shared by all 43 individuals, indicating that — unlike MHC-DRB IIA — neutral genetic diversity has been essentially lost, consistent with previously reported low neutral diversity in this species. DAPC identified four genetic clusters among contemporary populations; the higher MHC-DRB IIA polymorphism observed in contemporary breeding centers relative to the three founder specimens most likely reflects the much smaller founder sample size rather than rapid adaptive diversification, and we interpret this contrast cautiously. These results suggest that, despite a severe historical bottleneck and continued loss of neutral genetic variation, functional diversity at MHC-DRB IIA has been at least partly retained, while MHC-DOB IIB shows no variation at all. Conservation strategies should prioritize monitoring MHC-DRB IIA diversity, enhancing connectivity between populations to counter ongoing inbreeding, and using genetically informed breeding to preserve rare alleles.