Genetic Diversity and Differentiation at Structurally Varying MHC Haplotypes and Microsatellites in Bottlenecked Populations of Endangered Crested Ibis.

Lan Lan,Zhou Zhou,Wan Wan,Fang Fang

doi:10.3390/cells8040377

Abstract

Investigating adaptive potential and understanding the relative roles of selection and genetic drift in populations of endangered species are essential in conservation. Major histocompatibility complex (MHC) genes characterized by spectacular polymorphism and fitness association have become valuable adaptive markers. Herein we investigate the variation of all MHC class I and II genes across seven populations of an endangered bird, the crested ibis, of which all current individuals are offspring of only two pairs. We inferred seven multilocus haplotypes from linked alleles in the Core Region and revealed structural variation of the class II region that probably evolved through unequal crossing over. Based on the low polymorphism, structural variation, strong linkage, and extensive shared alleles, we applied the MHC haplotypes in population analysis. The genetic variation and population structure at MHC haplotypes are generally concordant with those expected from microsatellites, underlining the predominant role of genetic drift in shaping MHC variation in the bottlenecked populations. Nonetheless, some populations showed elevated differentiation at MHC, probably due to limited gene flow. The seven populations were significantly differentiated into three groups and some groups exhibited genetic monomorphism, which can be attributed to founder effects. We therefore propose various strategies for future conservation and management.

Highlights

Bottlenecked species are prone to genetic drift and depletion of adaptive variation [1], which may raise the probability of extinction owing to inbreeding depression and reduced adaptability [2].Elucidating the mechanism influencing adaptive genetic variation and differentiation in endangered species is informative for evolutionary processes and critical for conservation biology [3,4].The major histocompatibility complex (MHC), an essential component of the vertebrate immune system, is an ideal fitness-relevant marker [5]
The MHC class I genotyping showed that UAA, UBA, and UCA2 were dimorphic whereas UCA1 and UDA were monomorphic among the crested ibis studied
The Nini-MHC haplotypes are characterized by different copy numbers of IIαβ units

Summary

Introduction

Bottlenecked species are prone to genetic drift and depletion of adaptive variation [1], which may raise the probability of extinction owing to inbreeding depression and reduced adaptability [2].Elucidating the mechanism influencing adaptive genetic variation and differentiation in endangered species is informative for evolutionary processes and critical for conservation biology [3,4].The major histocompatibility complex (MHC), an essential component of the vertebrate immune system, is an ideal fitness-relevant marker [5]. Bottlenecked species are prone to genetic drift and depletion of adaptive variation [1], which may raise the probability of extinction owing to inbreeding depression and reduced adaptability [2]. Elucidating the mechanism influencing adaptive genetic variation and differentiation in endangered species is informative for evolutionary processes and critical for conservation biology [3,4]. The major histocompatibility complex (MHC), an essential component of the vertebrate immune system, is an ideal fitness-relevant marker [5]. This highly polymorphic genetic region contains multigene family members involved in presenting pathogen-derived peptides to T-cells and triggering an adaptive immune reaction [6]. MHC class I molecules, consisting of an α chain and an associated β2-microglobulin, present intracellular antigens to CD8+ T cells, while MHC class II molecules, consisting of α and β chains encoded by separate MHC genes, present extracellular pathogens to CD4+ T cells [6,7].

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