Dissertation Research: Surviving the K/Pg Mass Extinction: the genome as a life history character in birds

鸟类是最具魅力和最受欢迎的生物群体之一，但现代鸟类辐射的早期起源仍然笼罩在神秘之中。一个特别令人烦恼的问题与鸟类的年龄有关。基于DNA进化速度的估计表明，现代鸟类大约在1.6亿年前开始进化；然而，化石记录显示，它的年龄不超过6600万年。解释化石记录中大约1亿年的差距严重限制了我们理解现代鸟类多样性何时、如何以及为什么出现的能力。本项目探讨了分子分化时间分析与鸟类化石记录之间的差异，并研究了一个新的假设来解释所观察到的差异。该项目综合了来自古生物学和基因组学数据集的数据以及来自群体遗传理论的预测。这项工作也为研究生命之树其他分支的进化模式铺平了道路。此外，研究了白垩纪-古近纪K/Pg大灭绝的影响，对认识中生代恐龙的灭绝和它们以现代鸟类的形式复活具有重要意义。这项工作可能会揭示地球现代生物多样性是如何以及何时出现的基本线索。最后，研究人员将利用康奈尔鸟类学实验室的各种外展机制，将他们的发现传达给广泛的受众。在该项目的第一部分，研究人员将使用基于系统学研究的各种模拟、经验和理论方法来研究现代鸟类的年龄。研究人员将利用贝叶斯模型的最新发展来验证这样一个假设，即K/Pg大灭绝后身体尺寸的短暂小型化可以解释灭绝后分子速率加速的一段时间。在项目的第二部分，研究人员将研究从现存和灭绝的分类群中重建未知生活史特征的可行性，条件是推断出分子进化的速度。这项工作的一个关键组成部分将是推进分布式高性能计算系统发育方面的专业知识，以及分析与鸟类生活史进化有关的数据。总体而言，该研究将利用基因组进化速率作为生活史变异的重要轴的认识，促进古生活史多样性研究的进步方法，并使历史上不同的信息来源得以整合。该研究将对比较生物学和系统发育学具有潜在的广泛意义，并可能对分化时间分析领域产生短期和长期的影响。

Birds are among the most charismatic and broadly appreciated groups of living organisms, but the early origins of the modern bird radiation remain shrouded in mystery. One particularly vexing problem concerns the age of birds. Estimates based on the rate of DNA evolution suggest modern birds started to evolve about 160 million-years ago; the fossil record however, suggests an age that is scarcely older than 66 million years. Explaining the ~100-million-year gap in the fossil record profoundly limits our ability to understand when, how, and why modern bird diversity came to be. This project examines disagreements between molecular divergence time analyses and the avian fossil record, and studies a new hypothesis to explain the observed discrepancy. The project synthesizes data from paleontological and genomic datasets with predictions from population genetic theory. This work also paves the way for an integrative approach to studying evolutionary patterns across other branches of the tree of life. Moreover, the study investigates the effects of the K/Pg (Cretaceous-Paleogene) mass extinction, with important implications for understanding the decimation of Mesozoic dinosaurs and their resurrection in the form of modern birds. Such work may reveal fundamental clues into how and when Earth's modern biodiversity arose. Finally, the researchers will take advantage of the diverse outreach mechanisms at the Cornell Lab of Ornithology to communicate their findings to a broad audience.In the first part of the project, the researchers will study the age of modern birds using a variety of simulation, empirical and theoretical approaches grounded in the study of systematics. The researchers will use recent developments in Bayesian modeling to test the hypothesis that transient miniaturization of body size in the wake of the K/Pg mass extinction can explain a period of molecular rate acceleration in the extinction's aftermath. In the second part of the project, the researchers will study the feasibility of reconstructing unknown life history traits from extant and extinct taxa, conditioned on inferred rates of molecular evolution. A key component of the work will be to advance expertise in distributed high performance computing for phylogenetics, and in analyzing data related to avian life history evolution. In general, the research will leverage the recognition that rates of genome evolution are an important axis of life history variation to promote a progressive approach to studying paleo-life history diversity, and enable the integration of historically disparate information sources. The research will have potentially broad significance to comparative biology and phylogenetics, and may influence the field of divergence time analysis in both the short and long term.