Dating phototrophic microbial lineages with reticulate gene histories.
Dating phototrophic microbial lineages with reticulate gene histories.
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DOI：
10.1111/gbi.12273
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发表时间：
2018-03
期刊：
影响因子：
3.7
通讯作者：
Fournier GP
中科院分区：
文献类型：
--
作者：
Magnabosco C;Moore KR;Wolfe JM;Fournier GP
光养细菌是地球上最具生物地球化学意义的生物之一，通过使用反应中心收集光子进行能量代谢而在生理上相互关联。然而，主要的光养谱系是不是密切相关的另一个在细菌的光合作用，其各自的光合机制的起源仍然模糊的时间和低序列相似性。为了更好地了解蓝藻和其他古老的无氧光合谱系在地质时期的共同进化，我们设计并实现了各种分子钟，这些分子钟使用水平基因转移（HGT）作为额外的相对约束。这些HGT限制提高了光合细菌分歧日期估计的精度，并表明茎绿色非硫细菌可能是最古老的光合细菌谱系。与此同时，冠蓝细菌的年龄估计范围从2.2 Ga到2.7 Ga，茎蓝细菌发散~2.8 Ga。这些估计提供了一个几百Ma的窗口，氧光合作用演化之前的大氧化事件（GOE）~2.3 Ga。在所有的模型中，冠绿色硫细菌多样化后，从沉积记录（~1.8 Ga）的带状铁地层的损失，并可能表明扩展到一个新的生态位后的GOE谱系。我们的日期估计还提供了一个时间轴，以调查不同的光系统HGT事件之间的光养谱系的时间可行性。使用这种方法，我们推断茎蓝细菌不太可能是来自绿色硫细菌的光系统I蛋白的HGT的受体，但在GOE之前，仍然可能是HGT供体或光系统II蛋白与绿色非硫细菌的受体。总之，这些结果表明，HGT约束的分子钟是有用的工具，用于评估各种地质和进化假说，使用基因和有机体谱系的进化历史。
Phototrophic bacteria are among the most biogeochemically significant organisms on Earth and are physiologically related through the use of reaction centers to collect photons for energy metabolism. However, the major phototrophic lineages are not closely related to one another in bacterial phylogeny, and the origins of their respective photosynthetic machinery remain obscured by time and low sequence similarity. To better understand the co‐evolution of Cyanobacteria and other ancient anoxygenic phototrophic lineages with respect to geologic time, we designed and implemented a variety of molecular clocks that use horizontal gene transfer (HGT) as additional, relative constraints. These HGT constraints improve the precision of phototroph divergence date estimates and indicate that stem green non‐sulfur bacteria are likely the oldest phototrophic lineage. Concurrently, crown Cyanobacteria age estimates ranged from 2.2 Ga to 2.7 Ga, with stem Cyanobacteria diverging ~2.8 Ga. These estimates provide a several hundred Ma window for oxygenic photosynthesis to evolve prior to the Great Oxidation Event (GOE) ~2.3 Ga. In all models, crown green sulfur bacteria diversify after the loss of the banded iron formations from the sedimentary record (~1.8 Ga) and may indicate the expansion of the lineage into a new ecological niche following the GOE. Our date estimates also provide a timeline to investigate the temporal feasibility of different photosystem HGT events between phototrophic lineages. Using this approach, we infer that stem Cyanobacteria are unlikely to be the recipient of an HGT of photosystem I proteins from green sulfur bacteria but could still have been either the HGT donor or the recipient of photosystem II proteins with green non‐sulfur bacteria, prior to the GOE. Together, these results indicate that HGT‐constrained molecular clocks are useful tools for the evaluation of various geological and evolutionary hypotheses, using the evolutionary histories of both genes and organismal lineages.
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