The Phylogeny and Evolution of Cetacea: Resolution of Rapid Radiations and a Molecular Blueprint for Modern Whales, Dolphins, and Porpoises

鲸目动物（鲸鱼、海豚和鼠海豚）的进化起源是在5000万年前的始新世，这是记录最完整的宏观进化转变之一。对于非科学家来说，这种从陆地栖息地到水生生活方式的转变似乎是不可能的，然而这种转变所需的解剖学上的大规模变化在化石记录中得到了记录。随着基因组学的出现，现在有可能在分子水平上研究这种显著的进化变化。在这个项目中，研究人员将记录这些次生水生哺乳动物在进化过程中改变的性状的遗传基础，并追踪产生现代鲸鱼的分子变化。在这个项目中，研究人员将在加州大学河滨分校培养一名博士后学者、研究生和多名本科生实习生，这是一所少数民族服务机构。加州大学河滨分校的种族多元化为那些历史上在科学领域代表性不足的学生提供了一个前沿研究的机会。研究结果也将纳入课程，并为博物馆展示的进化原理提供内容。包括学生在内的资助参与者将与圣地亚哥自然历史博物馆的工作人员合作，在双语教育模块的“化石之谜”展览中讲述令人兴奋的研究突破。对于鲸目动物，化石和分子数据的标准系统发育分析已被用于重建该群体的主要表型转变，化石提供了与地球历史相关的关键进化创新的路标。然而，尽管基于大型数据集的系统发育研究正在进行，但鲸类动物进化的完全解决重建一直难以捉摸。研究人员提出了一个三管齐下的方法来加强对鲸类进化史的研究，将利用500个基因：1)比较使用强大的遗传数据样本重建物种树的替代方法，2)解决在海豚科（海洋海豚），海豚科（鼠海豚）和Balaenopteroidea（长尾鲸和灰鲸）之间存在问题的系统关系，3)合成现代鲸类的系统基因组蓝图。外显子捕获和下一代测序方法将被用于快速表征候选基因座，这些基因座代表预测经历了适应性或退行性变化的基因。研究人员将瞄准对行为和解剖特征至关重要的基因，这些基因在这一群体中高度衍生，包括与视觉、听觉、嗅觉、深潜、衰老、牙齿发育、鲸须形成和大脑大小有关的基因座。最终的结果将是对一个主要的宏观进化转变的第一个详细的基因组特征，这个转变也被大量的化石证据所记录。

The evolutionary origin of Cetacea (whales, dolphins, and porpoises) in the Eocene, 50 million years ago, ranks among the best-documented macroevolutionary transitions. To non-scientists, this move from a terrestrial habitat to a committed aquatic lifestyle might seem improbable, yet the wholesale changes in anatomy required for this transformation are recorded in the fossil record. With the advent of genomics, it is now possible to study this remarkable evolutionary change at the molecular level. In this project, researchers will document the genetic basis of traits that were altered in the evolutionary genesis of these secondarily aquatic mammals and trace the molecular changes that produced a modern whale. In this project, researchers will train a postdoctoral scholar, graduate students, and multiple undergraduate interns at UC Riverside, a minority serving institution. The ethnically diverse makeup of UC Riverside provides an opportunity to bring cutting edge research to students who are historically underrepresented in science. Results from the research also will be incorporated into coursework and provide content for museum displays focused on evolutionary principles. Grant participants, including students, will collaborate with staff at the San Diego Natural History Museum to relate exciting research breakthroughs in a revitalized 'Fossil Mysteries' exhibit with bilingual educational modules.For Cetacea, standard phylogenetic analyses of fossil and molecular data have been used to reconstruct major phenotypic transformations in the group, with fossils providing signposts that place key evolutionary innovations relative to Earth history. Yet, despite ongoing phylogenetic studies based on large datasets, a fully resolved reconstruction of cetacean evolution has been elusive. The researchers propose a three-pronged approach to an enhanced study of cetacean evolutionary history that will utilize 500 genes to: 1) compare alternate approaches to the reconstruction of species trees using a robust sample of genetic data, 2) resolve problematic systematic relationships within Delphinidae (oceanic dolphins), Phocoenidae (porpoises), and Balaenopteroidea (rorquals and gray whale), 3) synthesize a phylogenomic blueprint for modern cetaceans. Exon capture and next generation sequencing methods will be employed to rapidly characterize candidate loci that represent genes predicted to have undergone adaptive or degenerative change. The researchers will target genes that are critical for behavioral and anatomical features that are highly derived in the group, including loci implicated in vision, hearing, olfaction, deep diving, aging, tooth development, baleen formation, and brain size. The end result will be the first, detailed, genomic characterization of a major macroevolutionary transition that is also documented by extensive fossil evidence.