The Phylogeny of Xantusiidae, and its Placement with Scleroglossa (Reptilia: Squamata)

一个多世纪以来，“夜蜥蜴”之间的关系一直是个问题。由于这个群体的历史悠久，对其最原始成员的了解对于理解被称为硬舌龙的更大蜥蜴群体的深刻进化史至关重要。硬舌动物包括蛇及其祖先，在羊膜动物(爬行动物、鸟类和哺乳动物)中是独一无二的。在身体伸长和肢体缩小的反复进化中，Xantusiidae是一个“树变”的群体，因为它的替代位置可以改变大多数其他Skeroglossa群体之间的假设关系，但可用来推断Xantusiidae确切位置的数据太少。因此，本项目将：(1)基于迄今尝试的最广泛的分类样本重建苍蝇科的系统发育；(2)将该系统发育作为详细研究线粒体细胞色素-b(Cyt-b)基因突变动力学和进化的框架；以及(3)利用该系统发育树推断苍蝇科在硬舌菌属中的确切位置。这项研究将同时使用分子和形态数据集。相关的苍蝇属物种/种群的分子采样几乎已经完成；将收集大约80个个体的大约4500个碱基对(BP)的DNA序列数据，代表几个核和线粒体基因的区域(包括整个cyt-b基因)。将收集广泛的形态数据，包括通过高分辨率X射线CT(HRCT)扫描所有已命名的化石和现存的珊瑚科动物的内部头骨特征。HRCT将允许从仍然嵌入在基质中的化石和极其重要的类型标本中无损地收集新的特征，这些标本太珍贵而无法解剖。所有字符将被组合在一起，并在并行集群上进行广泛的计算机分析，以确保对树空间进行详尽的搜索。线粒体Cyt-b序列将被映射到由此产生的系统发育假说上，用于统计研究斑腿蝗科所有水平的分歧的突变动力学。该项目还将支持一项大型测序工作，以解决Xantusiidae在Skeroglossa内的位置，包括来自6-8个核基因的至少8500个核苷酸，以及一些与Xantusiidae相同的mtDNA基因区。将收集选定的硬舌科分类群的初步数据(HRCT扫描)，以准备一份提案，以支持对Xantusiidae在硬舌科中的位置进行免费的形态研究。这项研究将提供广泛的形态和分子数据集，以及对整个蜥蜴(斑腿蜥科)的Cyt-b突变动力学的完整调查。该小组的规模较小，将允许对两个数据集的树搜索策略进行彻底探索，对不同字符编码方案和关于字符进化的假设进行敏感性分析，并确定小组的基本成员。这将反过来提供对Xantusiidae内特征状态分布的了解，这是其在Skeroglossa中的位置的关键，因此也是理解这个更大群体的进化的关键。将产生大量的数据集，包括新的核基因(优化后可用于其他蜥蜴类群的研究)和通过HRCT揭示的新的头骨特征(并可作为在线资源获得)。这项研究将为本科生的培养提供广泛的机会。

Relationships among the "night lizards" (Xantusiidae) have been problematic for over a century. Because of the group's antiquity, knowledge of its most primitive members is critical for understanding the deep evolutionary history of the larger group of lizards called scleroglossans. Scleroglossa, which includes snakes and their ancestors, is unique among amniotes (reptiles, birds, and mammals) in the repeated evolution of body elongation and limb reduction, Xantusiidae is a "tree-changing" group in that its alternative placements can alter hypothesized relationships among most other scleroglossan groups, but too few data are available to infer the exact placement of Xantusiidae. Thus, this project will: (1) reconstruct the phylogeny of the Xantusiidae based on the most extensive taxonomic sampling attempted to date; (2) use this phylogeny as a framework for a detailed study of the mutational dynamics and evolution of the mitochondrial cytochrome-b (cyt-b) gene; and (3) use the phylogeny to infer the exact position of Xantusiidae within Scleroglossa. This study will use both molecular and morphological data sets. The molecular sampling of relevant xantusiid species/populations is virtually complete; approximately 4500 base pairs (bp) of DNA sequence data will be collected for about 80 individuals, representing regions of several nuclear and mitochondrial genes (including the entire cyt-b gene). Extensive morphological data will be collected, including internal cranial characters revealed via high-resolution X-ray CT (HRCT) scans of all named fossil and extant xantusiids. HRCT will permit nondestructive collection of novel characters from fossils still embedded in matrix and critically important type specimens too precious to dissect. All characters will be combined and subjected to extensive computer analyses run on parallel clusters to ensure exhaustive searches of tree space. Mitochondrial cyt-b sequences will be mapped onto the resulting phylogenetic hypothesis for statistical studies of mutational dynamics across all levels of divergence in the Xantusiidae. This project will also support a large sequencing effort to address placement of Xantusiidae within Scleroglossa, including at least 8500 bp from 6 - 8 nuclear genes and some of the same mtDNA gene regions used for Xantusiidae. Preliminary data (HRCT scans) will be collected for selected scleroglossan taxa for preparation of a proposal to support a complimentary morphological study of the placement of Xantusiidae within Scleroglossa. This study will provide extensive morphological and molecular data sets, and a complete survey of cyt-b mutational dynamics, for an entire group of lizards (Xantusiidae). The group's small size will permit thorough explorations of tree search strategies for both data sets, sensitivity analyses to different character coding schemes and assumptions about character evolution, and determination of the group's basal members. This will in turn provide an understanding of character state distributions within Xantusiidae, which is key to its placement within Scleroglossa and therefore to understanding the evolution of this larger group. Extensive data sets will be generated including novel nuclear genes (optimized and made available for studies of other lizard groups) and novel cranial characters revealed via HRCT (and made available as an online resource). The study will provide extensive opportunities for undergraduate student training.