Phylogenomics as a tool to infer the Tree of Life and a case study of the environmental footprint of scientific research

生物多样性日益受到各国政府的关注，生物多样性和生态系统服务政府间平台的建立就是明证。然而，我们对与可持续经济相关的大多数方面的理解仍然很差。在这项提议中，我们将通过破译现存生物(真核生物--以核为特征的生物--和原核生物)之间最古老的关系来提高我们对长期进化的认识。为了解决这些难题，我们将开发更强大的推理方法，收集更大的数据集；换句话说，我们将结合基因组学和计算生物学的力量。然而，这种方法依赖资源并产生污染，因此越来越多地导致生物多样性的丧失。这似乎与普遍但往往含蓄的假设相矛盾，即更好地了解生物多样性(如组成、机制、进化)是保护和管理生物多样性的关键。因此，我们将开启一个新的研究方向，通过量化过去和现在的系统发育研究的环境足迹，并研究未来是否有可能减少它，来检验这一知识假说。将在技术一级(即在实验设计方面)和在社会一级(即在选择赠款和出版物方面)寻求不影响科学成果质量的减少足迹的方法。

Biodiversity represents an increasing concern to governments, as demonstrated by the establishment of an Intergovernmental Platform on Biodiversity and Ecosystem Services. Yet, our understanding of most aspects relevant to a sustainable economy remains poor. In this proposal, we will improve our knowledge of evolution over long time periods by deciphering the most ancient relationships among extant organisms (eukaryotes - organisms characterized by a nucleus- and prokaryotes). To resolve these difficult questions, we will develop more powerful inference methods and gather larger datasets; in other words we will combine the power of genomics and computational biology. However, this approach depends on resources and generates pollution, hence increasingly contributes to the loss of biodiversity. This seems to contradict the common, yet often implicit, assumption that a better knowledge of biodiversity (e.g. composition, mechanisms, evolution) is key to its protection and management. Therefore, we will start a new research direction to test this knowledge hypothesis by quantifying the environmental footprint of phylogenetic research in the past and in the present, and by studying whether it would be possible to reduce it in the future. Methods of footprint reduction that will not compromise the quality of the scientific output will be sought at technical level (i.e. in the design of experiments) and at the social level (i.e. in the selection of grants and of publications).