Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia.
Department of Integrative Biology, University of South Florida, Tampa, Florida.
Mol Ecol. 2019 Feb;28(3):568-583. doi: 10.1111/mec.14891. Epub 2018 Nov 22.
Adaptation in nature is ubiquitous, yet characterizing its genomic basis is difficult because population demographics cause correlations with nonadaptive loci. Introduction events provide opportunities to observe adaptation over known spatial and temporal scales, facilitating the identification of genes involved in adaptation. The pathogen causing avian malaria, Plasmodium relictum, was introduced to Hawai'i in the 1930s and elicited extinctions and precipitous population declines in native honeycreepers. After a sharp initial population decline, the Hawai'i 'amakihi (Chlorodrepanis virens) has evolved tolerance to the parasite at low elevations where P. relictum exists, and can sustain infection without major fitness consequences. High-elevation, unexposed populations of 'amakihi display little to no tolerance. To explore the genomic basis of adaptation to P. relictum in low-elevation 'amakihi, we genotyped 125 'amakihi from the island of Hawai'i via hybridization capture to 40,000 oligonucleotide baits containing SNPs and used the reference 'amakihi genome to identify genes potentially under selection from malaria. We tested for outlier loci between low- and high-elevation population pairs and identified loci with signatures of selection within low-elevation populations. In some cases, genes commonly involved in the immune response (e.g., major histocompatibility complex) were associated with malaria presence in the population. We also detected several novel candidate loci that may be implicated in surviving malaria infection (e.g., beta-defensin, glycoproteins and interleukin-related genes). Our results suggest that rapid adaptation to pathogens may occur through changes in different immune genes, but in the same classes of genes, across populations.
自然界中的适应现象无处不在，但要描述其基因组基础却很困难，因为种群动态会导致与非适应性基因座产生关联。引入事件为观察已知时空尺度上的适应提供了机会，有助于识别参与适应的基因。导致鸟类疟疾的病原体 Plasmodium relictum 于 20 世纪 30 年代传入夏威夷，并导致当地的花蜜鸟灭绝和数量急剧下降。在最初的种群急剧下降之后，夏威夷吸蜜鸟（Chlorodrepanis virens）在低海拔地区对寄生虫产生了耐受性，在那里存在 P. relictum，并且可以在没有重大适应代价的情况下维持感染。而在高海拔、未暴露的吸蜜鸟种群中，这种耐受性则很小或不存在。为了探索低海拔吸蜜鸟对 P. relictum 适应的基因组基础，我们通过杂交捕获对来自夏威夷岛的 125 只吸蜜鸟进行了基因分型，使用参考吸蜜鸟基因组鉴定了来自疟疾的潜在选择基因。我们在低海拔和高海拔种群对之间测试了外显子基因座，并在低海拔种群中鉴定了具有选择信号的基因座。在某些情况下，与免疫反应相关的常见基因（例如主要组织相容性复合体）与种群中疟疾的存在有关。我们还检测到了几个可能与抗疟疾感染有关的新候选基因座（例如，β-防御素、糖蛋白和白细胞介素相关基因）。我们的研究结果表明，通过不同免疫基因的改变，同一类基因在不同种群中可能快速适应病原体。
