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

“夜蜥蜴”（Xantusiidae）之间的关系已经有超过世纪的问题。由于该群体的古老性，了解其最原始的成员对于了解更大的蜥蜴群体（称为硬舌蜥蜴）的深层进化历史至关重要。 硬舌亚目（Scleroglossa）包括蛇和它们的祖先，在爬行动物（爬行动物、鸟类和哺乳动物）中是独特的，在身体延长和肢体缩短的重复进化中，Xantusiidae是一个“树木变化”的类群，因为它的替代位置可以改变大多数其他硬舌亚目之间的假设关系，但很少有数据可以推断Xantusiidae的确切位置。 因此，该项目将：（1）基于迄今为止最广泛的分类学采样尝试重建Xantusiidae的系统发育;（2）使用该系统发育作为线粒体细胞色素b（cyt-b）基因突变动态和进化的详细研究的框架;（3）使用系统发育推断Xantusiidae在硬舌亚目中的确切位置。本研究将使用分子和形态学数据集。 相关xantusiid物种/种群的分子采样几乎是完整的;大约4500个碱基对（bp）的DNA序列数据将收集约80个个体，代表几个核和线粒体基因（包括整个cyt-b基因）的区域。 将收集广泛的形态学数据，包括通过高分辨率X射线CT（HRCT）扫描显示的所有命名的化石和现存的xantusiids的内部颅骨特征。 高分辨率CT将允许无损收集新的字符从化石仍然嵌入矩阵和至关重要的模式标本太珍贵解剖。 所有字符将被合并，并进行广泛的计算机分析运行在并行集群，以确保详尽的搜索树空间。 线粒体cyt-b序列将映射到系统发育假说的突变动态的统计研究在Xantusiidae的所有水平的分歧。 该项目还将支持大规模测序工作，以解决Xantusiidae在硬舌类中的位置，包括来自6 - 8个核基因的至少8500 bp和一些用于Xantusiidae的相同mtDNA基因区域。 初步数据（高分辨率CT扫描）将收集选定的硬舌类类群的建议，以支持一个免费的形态学研究的放置Xantusiidae硬舌类。 这项研究将提供广泛的形态学和分子数据集，和一个完整的调查cyt-b突变动态，为整个组的蜥蜴（Xantusiidae）。 该小组的规模小，将允许彻底探索的树搜索策略的两个数据集，不同的字符编码方案和假设的字符进化的敏感性分析，并确定该组的基本成员。 这反过来又提供了一个了解的字符状态分布在Xantusiidae，这是关键的硬舌内的位置，因此了解这个更大的群体的演变。 将生成大量数据集，包括新的核基因（优化并可用于其他蜥蜴组的研究）和通过HRCT揭示的新的颅骨特征（并作为在线资源提供）。 这项研究将为本科生培训提供广泛的机会。

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.