Patterns of genetic differentiation at MHC class I genes and microsatellites identify conservation units in the giant panda

Abstract

BackgroundEvaluating patterns of genetic variation is important to identify conservation units (i.e., evolutionarily significant units [ESUs], management units [MUs], and adaptive units [AUs]) in endangered species. While neutral markers could be used to infer population history, their application in the estimation of adaptive variation is limited. The capacity to adapt to various environments is vital for the long-term survival of endangered species. Hence, analysis of adaptive loci, such as the major histocompatibility complex (MHC) genes, is critical for conservation genetics studies. Here, we investigated 4 classical MHC class I genes (Aime-C, Aime-F, Aime-I, and Aime-L) and 8 microsatellites to infer patterns of genetic variation in the giant panda (Ailuropoda melanoleuca) and to further define conservation units.ResultsOverall, we identified 24 haplotypes (9 for Aime-C, 1 for Aime-F, 7 for Aime-I, and 7 for Aime-L) from 218 individuals obtained from 6 populations of giant panda. We found that the Xiaoxiangling population had the highest genetic variation at microsatellites among the 6 giant panda populations and higher genetic variation at Aime-MHC class I genes than other larger populations (Qinling, Qionglai, and Minshan populations). Differentiation index (FST)-based phylogenetic and Bayesian clustering analyses for Aime-MHC-I and microsatellite loci both supported that most populations were highly differentiated. The Qinling population was the most genetically differentiated.ConclusionsThe giant panda showed a relatively higher level of genetic diversity at MHC class I genes compared with endangered felids. Using all of the loci, we found that the 6 giant panda populations fell into 2 ESUs: Qinling and non-Qinling populations. We defined 3 MUs based on microsatellites: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. We also recommended 3 possible AUs based on MHC loci: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. Furthermore, we recommend that a captive breeding program be considered for the Qinling panda population.

Spatial patterns of immunogenetic and neutral variation underscore the conservation value of small, isolated American badger populations

“…Although MHC loci capture a fraction of the genetic variation underpinning resistance to pathogens (Acevedo‐Whitehouse & Cunningham, ), evidence from several species have shown that the MHC is useful in examining the adaptive potential of populations in mammalian species (e.g. Aguilar et al., ; de Assunção‐Franco, Hoffmam, Harwood, & Amos, ; Schweizer et al., ; Siddle, Marzec, Cheng, Jones, & Belov, ), and for informing delineation of conservation units in endangered species such as the giant panda ( Ailuropoda melanoleuca, Zhu, Wan, Yu, Ge, & Fang, ) and marbled murrets ( Brachyramphus marmoratus, Vásquez‐Carrillo, Friesen, Hall, & Peery, ). Conservation efforts should ideally focus on maximizing the species evolutionary potential and thus should gather genetic data from multiple functional loci (Grueber, ).…”

Balancing selection and recombination drive genetic variation at MHC class I genes in the giant panda

“…We isolated 21 MHC class I haplotypes from 46 captive giant pandas bred in Wolong population, of which eight were for Aime-C, seven for Aime-I and six for Aime-L (Table S1). Compared with previous 23 haplotypes (nine/seven/seven for Aime-C/I/L) across six extant wild populations [5], Wolong captive population retains a high adaptive variation. Nevertheless, Wolong population lacks the Aime-C*09 and Aime-L*07 haplotypes of wild individuals [5], and its average heterozygosity (0.659) (Table S1) is lower than that of wild populations (0.774) [5], which might be due to a small number of founders and subsequent genetic drift in captive populations [6].…”

“…We characterized haplotype variation at exon 2-intron 2-exon 3 fragments for the Aime-C, Aime-I and Aime-L loci, which have been verified to be classical and polymorphic [5]. We isolated 21 MHC class I haplotypes from 46 captive giant pandas bred in Wolong population, of which eight were for Aime-C, seven for Aime-I and six for Aime-L (Table S1).…”

Microsatellite markers for evaluating the diversity of the natural killer complex and major histocompatibility complex genomic regions in domestic horses

“…Due to the complexity of both genomic regions and their often inaccurate annotation in nonmodel species, the utilization of new high throughput tools, such as NGS, long‐read sequencing and/or SNP chips for individual genotyping and population analyses still has methodological as well as financial limitations. For this reason, MHC microsatellite markers are commonly used for diversity studies not only in horses but also in sheep, platypus, cats, giant pandas, rodents, and even in fish . They allow assessing the extent of polymorphism not only for single loci but they also can be helpful for defining haplotypes .…”