How the microbiome interacts with hosts across evolutionary time is poorly understood. Data sets including many host species are required to conduct comparative analyses. Here, we analyzed 142 intestinal microbiome samples from 92 birds belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene. Using four definitions for microbial taxonomic units (97%OTU, 99%OTU, 99%OTU with singletons removed, ASV), we conducted alpha and beta diversity analyses. We found that raw abundances and diversity varied between the data sets but relative patterns were largely consistent across data sets. Host taxonomy, diet and locality were significantly associated with microbiomes, at generally similar levels using three distance metrics. Phylogenetic comparative methods assessed the evolutionary relationship between the microbiome as a trait of a host species and the underlying bird phylogeny. Using multiple ways of defining "microbiome traits", we found that a neutral Brownian motion model did not explain variation in microbiomes. Instead, we found a White Noise model (indicating little phylogenetic signal), was most likely. There was some support for the Ornstein-Uhlenbeck model (that invokes selection), but the level of support was similar to that of a White Noise simulation, further supporting the White Noise model as the best explanation for the evolution of the microbiome as a trait of avian hosts. Our study demonstrated that both environment and evolution play a role in the gut microbiome and the relationship does not follow a neutral model; these biological results are qualitatively robust to analytical choices.

中文翻译：

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赤道几内亚74种鸟类肠道微生物群中的进化信号。

人们对微生物组在进化过程中如何与宿主相互作用的了解甚少。需要进行包括许多寄主物种的数据集来进行比较分析。在这里，我们使用16S rRNA基因分析了来自赤道几内亚74个物种的92只鸟类的142个肠道微生物组样本。使用微生物分类单位的四个定义（97％OTU，99％OTU，99％OTU去除单例，ASV），我们进行了α和β多样性分析。我们发现数据集之间的原始丰度和多样性有所不同，但相对模式在数据集之间基本保持一致。使用三个距离指标，宿主生物分类，饮食和位置与微生物群落显着相关，处于大致相似的水平。系统发育比较方法评估了微生物组作为宿主物种的性状与潜在鸟类系统发育之间的进化关系。使用多种定义“微生物组特征”的方法，我们发现中性的布朗运动模型不能解释微生物组的变化。相反，我们发现最有可能出现白噪声模型（表明几乎没有系统发生信号）。对Ornstein-Uhlenbeck模型（调用选择）有一些支持，但是支持水平类似于白噪声模拟，进一步支持了白噪声模型作为微生物组特征进化的最佳解释。禽类宿主。我们的研究表明，环境和进化都在肠道微生物组中起作用，并且这种关系不遵循中性模型。