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

这项研究将通过开发更准确和精确的时间校准的生命树(TOL)，即基于新的微生物进化测年方法的生命计时表(COL)，将跨地质时间尺度的生物和行星变化整合在一起。长期以来，地质记录一直是我们关于行星历史的唯一信息来源。相比之下，保存在基因组中的深层时间记录只是最近才被发现，而且仍然缺乏特征。当通过系统发育分析、分子时钟和可靠的校准解锁时，这些基因组记录将提供对地球历史上的地球化学、大气和气候过程的独特见解。许多将生命和地球的共同进化联系在一起的事件的时间仍然不确定。对于地球历史上非常早期的事件尤其如此，在这些事件中，化石和地球化学记录往往稀少、模棱两可或完全不存在。事实上，在太古代(可能还有太古代)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，这项研究有三个主要目标：(1)通过基因组地层学，利用HGT(水平基因转移)事件，确定整个TOL地区基因组进化的古代时间校准；(2)通过对古代动物谱系的共同进化微生物群进行测序，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，生成准确可靠的早期生命进化和行星历史的年表，直接检验与地球深刻的生物地球化学史相关的几个假说。生命进化和地球之间的深层次、相互交织的关系是至关重要的。虽然以前的许多研究都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情景，但为了实际检验这些不同的共同进化假说，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)作为一种强大的新工具来确定地球早期事件的时间。跨TOL的基因流动限制了远亲血统的相对分化时间。这种对HGT的解释允许基因组地层学，其中TOL内某些群体可用的时间校准(即，通过生物标记物和/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，它使用不同化石的存在或不存在来确定沉积岩的年代。同样，来自化石校准的数据可以通过共物种形成事件传播到TOL，就像在微生物共生体和它们的动物宿主之间经常观察到的那样。将这项技术扩展到以前未采样的最古老节肢动物谱系的微生物群，将极大地扩展该方法的时间范围。总而言之，这些基因组信息的新地层学用途将把TOL转化为准确的COL。这项工作将能够直接评估地球早期生物圈、地圈和大气演化中的主要问题，包括产氧和产氧光合作用的出现，通过产甲烷产生甲烷，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