Phylogeography of Capuchins, Squirrel Monkeys and Owl Monkeys: A Critical Comparative Framework for Studying Evolution, Behavioral Ecology, and Conservation in Neotropical Primates

松鼠猴、猫头鹰猴和卷尾猴，统称为Cebines，人类学家和行为生态学家对它们特别感兴趣，因为它们有不同的社会组织和活动模式，不同的社会学习能力，（在卷尾猴的情况下）与猿类和人类在工具使用、大脑容量和战略思维方面相似。它们也是生物医学研究中最重要的新热带灵长类动物模型，也是我们理解疟疾感染、色视觉、可卡因成瘾和卵巢功能的关键。然而，如果我们了解当前种群之间的进化关系，那么Cebines作为模型系统的效用可以大大增强。事实上，到目前为止，在这些属的种群或物种之间的进化关系方面，还没有得到很好的支持的分子或形态学假设，因此，目前对它们的行为、生理、形态和生活史特征变化的解释缺乏一个进化框架。例如，我们知道一些卷尾猴种群在野外使用工具，而另一些种群则不会，但我们对卷尾猴的系统发育了解不够，无法估计工具使用进化了多少次或多久以前，或者随着工具使用的获得，什么样的身体或生命史特征进化了。该项目的一个重要贡献将是提供一个明确的进化框架，以指导越来越多的研究人员对这些分类群进行生物医学、行为生态学和保护生物学的研究。为此，采用比较方法，本研究项目将首次为Cebines创建详细的分子系统发育和生物地理分析。这些属广泛分布在拉丁美洲的大部分地区。我们将对整个地理范围内的标本进行DNA测序，然后使用统计系统发育方法为每个属生成可靠的系统发育假设。我们将研究线粒体单倍型的模式和分布，以使用历史和古地质框架来测试生物地理学假设。我们的方案是1)从拉丁美洲的Cebine组织中提取，扩增和测序三个线粒体基因；2)利用简约、似然和贝叶斯方法重建每个属内部和跨属的系统发育关系；3)利用化石校准来生成一个Cebines的时间树；4)在这个框架内进行生物地理和比较分析。这项研究将解决体质人类学中长期存在的关于新热带灵长类动物系统发育关系的问题。该项目还将通过我们使用新的实验室方法从降解组织中提取和扩增DNA，在理论和方法上影响生物地理学领域。我们从博物馆组织中提取和扩增DNA的优化方案可以为科学界服务，使这些类型的标本更容易获得，更经济地用于科学探究。本研究中至少有三个领域的数据分析是前沿的，将对从事系统发育和生物地理学研究的人类学家和生物学家产生重大影响。这些包括我们使用新的贝叶斯建模应用程序来估计散度时间；含索引序列比对和系统发育的联合估计我们比较了几种基于事件和基于模型的推断生物地理历史的新技术的有效性。本研究将为本科生和本科生提供国际实地和实验室经验。它还将通过美国和拉丁美洲研究人员之间的强有力的合作研究，提高国际灵长类学社区的分子实验室技术和数据分析技术。本研究的一个重要应用方面是开发一种严格的定量评估工具来衡量目标类群在种群中的生物多样性分布，为广泛分布的类群的保护优先性评估提供依据。

Squirrel monkeys, owl monkeys and capuchin monkeys, collectively called the Cebines, are of particular interest to anthropologists and behavioral ecologists because of diverse social organization and activity patterns, a varied capacity for social learning, and (in the case of capuchin monkeys) parallels to apes and humans in tool use, large brain size, and strategic thinking. They are also the most important model Neotropical primates used in biomedical research, and have been key in our understanding of malarial infection, color vision, cocaine addiction, and ovarian function. However, the utility of the Cebines as model systems could be enhanced greatly if we understood the evolutionary relationships among current populations. In fact, to date, there is no well-supported molecular or morphological hypothesis of evolutionary relationships among populations or species within these genera, and so present interpretations of variation in their behavior, physiology, morphology and life history characteristics lack an evolutionary framework. For example, we know some capuchin populations use tools in the wild and others do not, but we do not know enough about capuchin phylogenetics to estimate how many times or how long ago tool use evolved, or what physical or life history characteristics have evolved in tandem with the acquisition of tool use. One important contribution of this project will be to provide an explicit evolutionary framework to orient the increasing number of researchers in their biomedical, behavioral ecology, and conservation biology studies of these taxa. To this end, using a comparative approach, this research project will create the first detailed molecular phylogenies and biogeographic analyses for the Cebines. These genera are widespread and sympatric across much of Latin America. We will sequence DNA from specimens across the entire geographic range, and then use statistical phylogenetic methods to generate robust phylogenetic hypotheses for each genus. We will examine the pattern and distribution of mitochondrial haplotypes to test biogeography hypotheses using a historical and paleogeological framework. Our protocol is 1) to extract, amplify and sequence three mitochondrial genes from Cebine tissues across Latin America; 2) to reconstruct phylogenetic relationships within and across each genus using parsimony, likelihood and Bayesian approaches; 3) to use fossil calibrations to produce a time tree for Cebines, and 4) to conduct biogeographic and comparative analyses within this framework. This research will resolve long-standing questions in physical anthropology about the phylogenetic relationships of the Neotropical primates. This project will also impact the field of biogeography in both theory and methodology through our use of new laboratory methods for DNA extraction and amplification from degraded tissues. Our optimization of protocols for DNA extraction and amplification from museum tissues can serve the scientific community, by making these types of specimen more accessible and economical for use in scientific inquiry. At least three areas of data analysis in this study are cutting edge and will be of significant influence to both anthropologists and biologists working on phylogenetics and biogeography. These include our use of new Bayesian modeling applications for estimating divergence time; our joint estimation of alignment and phylogeny for sequences containing indels; and our comparison of the efficacy of several new event-based and model-based techniques for inferring biogeographic history. This research will provide international field and laboratory experiences for both undergraduates and undergraduates. It will also enhance molecular lab techniques and data analysis techniques in the international primatology community through strong collaborative research among U.S. and Latin American researchers. An important applied aspect of this research is the development of a rigorous, quantitative assessment tool to measure the distribution of biodiversity of the target taxa across populations, to be used for conservation priority assessment of widely distributed taxa.