Fleischer Ramona, Risely Alice, Hoeck Paquita E A, Keller Lukas F, Sommer Simone
Institute of Evolutionary Ecology and Conservation Genomics University of Ulm Ulm Germany.
Zoological Museum University of Zurich Zurich Switzerland.
Ecol Evol. 2020 Oct 27;10(23):13345-13354. doi: 10.1002/ece3.6934. eCollection 2020 Dec.
The gut microbiome of animals, which serves important functions but can also contain potential pathogens, is to varying degrees under host genetic control. This can generate signals of phylosymbiosis, whereby gut microbiome composition matches host phylogenetic structure. However, the genetic mechanisms that generate phylosymbiosis and the scale at which they act remain unclear. Two non-mutually exclusive hypotheses are that phylosymbiosis is driven by immunogenetic regions such as the major histocompatibility complex (MHC) controlling microbial composition, or by spatial structuring of neutral host genetic diversity via founder effects, genetic drift, or isolation by distance. Alternatively, associations between microbes and host phylogeny may be generated by their spatial autocorrelation across landscapes, rather than the direct effects of host genetics. In this study, we collected MHC, microsatellite, and gut microbiome data from separate individuals belonging to the Galápagos mockingbird species complex, which consists of four allopatrically distributed species. We applied multiple regression with distance matrices and Bayesian inference to test for correlations between average genetic and microbiome similarity across nine islands for which all three levels of data were available. Clustering of individuals by species was strongest when measured with microsatellite markers and weakest for gut microbiome distributions, with intermediate clustering of MHC allele frequencies. We found that while correlations between island-averaged gut microbiome composition and both microsatellite and MHC dissimilarity existed across species, these relationships were greatly weakened when accounting for geographic distance. Overall, our study finds little support for large-scale control of gut microbiome composition by neutral or adaptive genetic regions across closely related bird phylogenies, although this does not preclude the possibility that host genetics shapes gut microbiome at the individual level.
动物的肠道微生物群具有重要功能，但也可能包含潜在病原体，在不同程度上受宿主基因控制。这可能会产生系统共生信号，即肠道微生物群组成与宿主系统发育结构相匹配。然而，产生系统共生的遗传机制及其作用规模仍不清楚。两个并非相互排斥的假说是，系统共生是由免疫遗传区域（如控制微生物组成的主要组织相容性复合体（MHC））驱动的，或者是由中性宿主遗传多样性通过奠基者效应、遗传漂变或距离隔离进行的空间结构驱动的。另外，微生物与宿主系统发育之间的关联可能是由它们在景观中的空间自相关性产生的，而不是宿主基因的直接影响。在本研究中，我们从加拉帕戈斯模仿鸟物种复合体的不同个体收集了MHC、微卫星和肠道微生物群数据，该复合体由四个异域分布的物种组成。我们应用距离矩阵多元回归和贝叶斯推理来检验在有所有三个数据水平的九个岛屿上平均遗传和微生物群相似性之间的相关性。用微卫星标记测量时，按物种对个体进行聚类最强，而肠道微生物群分布聚类最弱，MHC等位基因频率聚类处于中间。我们发现，虽然跨物种存在岛屿平均肠道微生物群组成与微卫星和MHC差异之间的相关性，但在考虑地理距离时，这些关系会大大减弱。总体而言，我们的研究几乎没有发现支持在密切相关的鸟类系统发育中由中性或适应性遗传区域对肠道微生物群组成进行大规模控制的证据，尽管这并不排除宿主基因在个体水平塑造肠道微生物群的可能性。
