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、海豚和江豚)的进化起源于5000万年前的始新世，是有最好记录的宏观进化转变之一。对于非科学家来说，从陆地栖息地转变为固定的水生生活方式似乎是不太可能的，但这种转变所需的解剖学上的大规模变化记录在化石记录中。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进化起源中改变的特征的遗传基础，并追踪产生现代鲸鱼的分子变化。在这个项目中，研究人员将在少数族裔服务机构加州大学河滨分校培训一名博士后学者、研究生和多名本科生实习生。加州大学河滨分校的种族多元化构成为那些在科学领域历来代表性不足的学生提供了一个机会，将尖端研究带给他们。这项研究的结果也将被纳入课程作业，并为侧重于进化原理的博物馆展示提供内容。获奖者，包括学生，将与圣地亚哥自然历史博物馆的工作人员合作，通过双语教学模块讲述一个重新焕发活力的“化石之谜”展览中令人兴奋的研究突破。对于鲸目动物，对化石和分子数据的标准系统发育分析已被用于重建该组中的主要表型转变，化石提供了与地球历史相关的关键进化创新的路标。然而，尽管正在进行基于大型数据集的系统发育研究，但完全解决鲸目动物进化的重建一直是难以捉摸的。研究人员提出了一种三管齐下的方法来加强鲸目动物进化史的研究，该方法将利用500个基因：1)使用稳健的遗传数据样本比较重建物种树的替代方法；2)解决Delphinidae(海洋海豚)、Phocoenenidae(江豚)和Balaenopteroidae(江豚和灰鲸)之间有问题的系统关系；3)合成现代鲸目动物的系统基因组蓝图。外显子捕获和下一代测序方法将被用来快速表征代表预测经历了适应性或退化变化的基因的候选基因座。研究人员将针对对该群体高度衍生的行为和解剖学特征至关重要的基因，包括与视觉、听力、嗅觉、深潜、衰老、牙齿发育、须毛形成和大脑大小有关的基因。最终结果将是一个重大的宏观进化转变的第一个详细的基因组特征，这一转变也被广泛的化石证据所证明。

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.