Collaborative Research: Integrating the geological and genomic records: time-calibrating Earth's dynamic biogeochemical history

这项研究将通过开发一个更准确和精确的时间校准生命树（ToL），将生物和行星变化整合到地质时间尺度上，即，基于微生物进化年代测定新方法的生命年表。长期以来，地质记录一直是我们了解行星历史的唯一来源。相比之下，保存在基因组中的深层时间记录直到最近才被发现，并且仍然缺乏特征。当通过系统发育分析、分子钟和强大的校准解锁时，这一基因组记录将为地球历史上的地球化学、大气和气候过程提供独特的见解。许多与生命和地球共同进化有关的事件发生的时间仍然不确定。对于地球历史上非常早期的事件来说尤其如此，那里的化石和地球化学记录通常是稀疏的，模糊的，或者完全不存在。 事实上，在古希腊（也可能是古冥古宙）的大部分时间里，唯一剩下的记录可能是保存在基因组中的记录。为了揭示这一记录，该研究有三个主要目标：（1）通过使用HGT来确定整个ToL中基因组进化的古代时间校准（2）通过对古动物谱系的共同进化的微生物组进行测序，将化石记录与微生物历史联系起来;以及（3）开发新的生物信息学方法来整合这些限制，生成早期生命进化和行星历史的准确可靠的年表，直接检验与地球深层地球化学历史有关的几个假设。生命进化与地球之间深刻的、交织的关系具有根本的重要性。虽然许多以前的研究已经提出了将早期微生物进化中的事件与保存的生物地球化学记录联系起来的方案，但为了实际测试这些不同的共同进化假设，需要独立的方法来校准微生物进化本身。为此，这项工作的关键智力贡献是使用水平基因转移（HGT）作为确定早期地球事件发生时间的强大新工具。跨越ToL的基因流动限制了远亲谱系的相对分歧时间。HGT的这种解释允许基因组地层学，其中时间校准可用于ToL内的一些组（即，通过生物标志物和/或化石记录）可以传播到其他群体。这种方法类似于生物地层学，生物地层学使用不同化石的存在或不存在来确定沉积岩地层的年代。同样，化石校准的日期可以通过共同物种形成事件在整个ToL中传播，正如在微生物共生体及其动物宿主之间经常观察到的那样。将这种技术扩展到以前未采样的最古老的节肢动物谱系的微生物组将大大扩展这种方法的时间范围。这项工作将允许直接评估地球早期生物圈、地圈和大气演化中的主要问题，包括有氧和无氧光合作用的出现，通过甲烷生成产生甲烷，以及微生物氮、碳、硫和氧循环的建立

This research will integrate biological and planetary change across geological timescales by developing a more accurate and precise time-calibrated Tree of Life (ToL), i.e., a Chronogram of Life (CoL) based on novel methods for dating microbial evolution. The geological record has long been our sole source of information about planetary history. In contrast, the deep time record preserved within genomes has only been recently discovered, and remains poorly characterized. When unlocked through phylogenetic analysis, molecular clocks, and robust calibration, this genomic record will provide unique insights into geochemical, atmospheric, and climate processes across Earth's history. The timing of many events linking the co-evolution of life and the planet remain uncertain. This is especially true for very early events in Earth's history, where the fossil and geochemical record is often sparse, ambiguous, or entirely absent. In fact, across much of the Archaean (and possibly Hadean) Eons, the only remaining record may be the one preserved within genomes. To reveal this record, the research has three major aims: (1) identifying ancient time calibrations in genome evolution across the ToL by using HGT (Horizontal Gene Transfer) events via genome stratigraphy; (2) linking the fossil record to microbial history via sequencing co-evolving microbiomes of ancient animal lineages; and (3) developing new bioinformatics approaches to integrate these constraints, generating an accurate and reliable chronology of early life evolution and planetary history, directly testing several hypotheses related to the deep biogeochemical history of the Earth.The deep, intertwined relationship between the evolution of life and the planet is of fundamental importance. While many previous investigations have proposed scenarios linking events in early microbial evolution to the preserved biogeochemical record, in order to actually test these different co-evolutionary hypotheses, independent methods are required to time-calibrate microbial evolution itself. To this end, the key intellectual contribution of this work is using horizontal gene transfer (HGT) as a powerful new tool for determining the timing of events on the early Earth. Flows of genes across the ToL constrain the relative divergence times of distantly related lineages. This interpretation of HGT permits genomic stratigraphy, wherein time calibrations available for some groups within the ToL (i.e., via biomarker and/or fossil records) can be propagated to other groups. This approach is analogous to biostratigraphy, which uses the presence or absence of different fossils to date strata of sedimentary rocks. Similarly, dates from fossil calibrations can be propagated across the ToL through co-speciation events, as are often observed between microbial symbionts and their animal hosts. Expanding this technique to previously unsampled microbiomes of the most ancient arthropod lineages will greatly extend the temporal reach of this method. Together, these novel stratigraphic uses for genomic information will translate the ToL into an accurate CoL. This work will permit direct evaluation of major questions in the evolution of Earth's early biosphere, geosphere and atmosphere, including the emergence of oxygenic and anoxygenic photosynthesis, methane production via methanogenesis, and the establishment of microbial nitrogen, carbon, sulfur,and oxygen cycles