Department of Biology, University of Oregon, Eugene, OR, USA.
Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA.
ISME J. 2022 Jan;16(1):159-167. doi: 10.1038/s41396-021-01069-8. Epub 2021 Jul 19.
The phylogenetic resolution at which microorganisms display geographic endemism, the rates at which they disperse at global scales, and the role of humans on global microbial dispersal are largely unknown. Answering these questions is necessary for interpreting microbial biogeography, ecology, and macroevolution and for predicting the spread of emerging pathogenic strains. To resolve these questions, I analyzed the geographic and evolutionary relationships between 36,795 bacterial and archaeal ("prokaryotic") genomes from ∼7000 locations around the world. I find clear signs of continental-scale endemism, including strong correlations between phylogenetic divergence and geographic distance. However, the phylogenetic scale at which endemism generally occurs is extremely small, and most "species" (defined by an average nucleotide identity ≥ 95%) and even closely related strains (average nucleotide identity ≥ 99.9%) are globally distributed. Human-associated lineages display faster dispersal rates than other terrestrial lineages; the average net distance between any two human-associated cell lineages diverging 50 years ago is roughly 580 km. These results suggest that many previously reported global-scale microbial biogeographical patterns are likely the result of recent or current environmental filtering rather than geographic endemism. For human-associated lineages, estimated transition rates between Europe and North America are particularly high, and much higher than for non-human associated terrestrial lineages, highlighting the role that human movement plays in global microbial dispersal. Dispersal was slowest for hot spring- and terrestrial subsurface-associated lineages, indicating that these environments may act as "isolated islands" of microbial evolution.
微生物在何种系统发育分辨率上表现出地理特有性、它们在全球尺度上的扩散速度，以及人类在全球微生物扩散中的作用在很大程度上是未知的。回答这些问题对于解释微生物生物地理学、生态学和宏观进化以及预测新兴致病菌株的传播是必要的。为了解决这些问题，我分析了来自全球约 7000 个地点的 36795 个细菌和古菌（“原核”）基因组的地理和进化关系。我发现了明显的大陆尺度特有性的迹象，包括系统发育分歧和地理距离之间的强相关性。然而，特有性通常发生的系统发育尺度极小，大多数“物种”（定义为平均核苷酸同一性≥95%）甚至密切相关的菌株（平均核苷酸同一性≥99.9%）都是全球分布的。与人类相关的谱系比其他陆地谱系具有更快的扩散速度；50 年前分化的任何两个人类相关细胞谱系之间的平均净距离约为 580 公里。这些结果表明，许多先前报道的全球尺度微生物生物地理模式可能是最近或当前环境过滤的结果，而不是地理特有性的结果。对于与人类相关的谱系，估计欧洲和北美的跃迁率特别高，比非人类相关的陆地谱系高得多，突出了人类活动在全球微生物扩散中的作用。温泉和陆地地下相关谱系的扩散速度最慢，这表明这些环境可能是微生物进化的“隔离岛屿”。
