Data from: Specific alleles at immune genes, rather than genome-wide heterozygosity, are related to immunity and survival in the critically endangered Attwater’s prairie-chicken

The negative effects of inbreeding on fitness are serious concerns for populations of endangered species. Reduced fitness has been associated with lower genome-wide heterozygosity and immune gene diversity in the wild; however, it is rare that both types of genetic measures are included in the same study. Thus, it is often unclear whether the variation in fitness is due to the general effects of inbreeding, immunity-related genes, or both. Here, we tested whether genome-wide heterozygosity (20 990 SNPs) or diversity at nine immune genes were better predictors of two measures of fitness (immune response and survival) in the endangered Attwater’s prairie-chicken (Tympanuchus cupido attwatteri). We found that post-release survival of captive-bred birds was related to alleles of the innate (toll-like receptors, TLRs) and adaptive (major histocompatibility complex, MHC) immune systems, but not to genome-wide heterozygosity. Likewise, we found that the immune response at the time of release was related to TLR and MHC alleles, and not to genome-wide heterozygosity. Overall, this study demonstrates that immune genes may serve as important genetic markers when monitoring fitness in inbred populations, and that in some populations specific functional genes may be better predictors of fitness than genome-wide heterozygosity.

近交对适合度的负面影响是濒危物种种群的重大关切问题。野外研究显示，适合度降低与全基因组杂合度（genome-wide heterozygosity）下降及免疫基因多样性降低存在关联，但鲜有研究同时涵盖这两类遗传指标。因此，人们往往难以明确适合度的变异究竟源于近交的一般性效应、免疫相关基因的影响，还是二者共同作用。本研究以濒危物种阿特沃特松鸡（Tympanuchus cupido attwatteri）为研究对象，探究基于20990个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）的全基因组杂合度，与9个免疫基因的多样性，哪一类更能有效预测两项适合度指标——免疫应答与存活能力。研究发现，人工繁育个体的放归后存活率与先天免疫系统的Toll样受体（toll-like receptors, TLRs）及适应性免疫系统的主要组织相容性复合体（major histocompatibility complex, MHC）的等位基因显著相关，而与全基因组杂合度无关。同样，放归时的免疫应答水平也与TLRs和MHC等位基因相关，而非全基因组杂合度。综上，本研究表明，在监测近交种群的适合度时，免疫基因可作为重要的遗传标记；在部分种群中，特定功能基因或许比全基因组杂合度更能有效预测适合度。