Experimental phylogenies to benchmark ancestral sequence reconstruction

实验古遗传学的概念是在40多年前提出的，作为一种利用分子序列信息来更好地理解现代表型多样性的方法。直到最近，对祖先序列的计算重建才得到了角色状态推理和稳健的系统发育模型的支持。根据这些古老的生物分子的特性，实验室合成的推断基因和蛋白质反过来又指导了关于祖先表型的推断。这一方法旨在通过开发实验系统发育学中的应用程序来提高推断古代基因的准确性。该方法允许研究人员以一种目前不可能的方式将祖先序列重建方法的基因型和表型联系起来。该软件使用理论和计算模拟来对各种模型的性能进行基准测试。这项拟议的研究将扩展和实验验证祖先序列重建的领域，使研究人员对祖先序列重建的能力充满信心，以促进社区对分子适应的了解。研究小组参与旨在培养下一代科学家的教学和服务活动。一方面，这包括教学课程，包括进化合成生物学和天体生物学。另一方面，这包括在大学以外的环境下促进科学思想和培训。例如，已经创建了一个K-12科学推广计划，以促进多样化的学习社区，并增加未被充分代表的群体在进化生物学和分子进化研究中的参与。

The concept of experimental paleogenetics was proposed more than forty years ago as a way to exploit molecular sequence information to gain a better understanding modern phenotypic diversity. Only recently have computational reconstructions of ancestral sequences been supported by models of character state inference and robust phylogenies. Laboratory synthesis of the inferred genes and proteins has, in turn, guided inference regarding ancestral phenotypes based on the properties of these ancient biomolecules. This approach aims to improve the accuracy in inferring ancient genes though the development of an application in experimental phylogenetics. The approach allows researchers to connect genotype and phenotype for ancestral sequence reconstruction methods in a manner currently not possible. The software uses theoretical and computational simulations to benchmark the performances of various models. The proposed research will extend and experimentally validate the field of ancestral sequence reconstruction, allowing researchers to place confidence in the ability of ancestral sequence reconstruction to facilitate the community's understanding of molecular adaptation.The research group participates in teaching and service activities intended to train the next generation of scientists. On one hand, this consists of teaching courses that include Evolutionary Synthetic Biology and Astrobiology. On the other hand, this consists of promoting scientific ideas and training outside of the University setting. For instance, a K-12 science outreach program has been created to promote a diverse learning community and increase the participation of underrepresented groups in evolutionary biology and molecular evolution research.