SGER: The Taxonomic Distribution of Middle-Repetitive DNA Families: Homoplasy Free Phylogenetic Data?

在过去的十到十五年中，分子序列数据为研究许多不同生物群体的系统发育关系或谱系关联提供了有力的工具。这些数据通常有助于解决经典形态学数据不足或提出替代和冲突结果的关系。然而，就像形态学数据包括收敛/平行衍生的特征一样，相同的分子序列可以独立出现。这种趋同或平行的特征，被称为同源性，如果它们不被识别，从而无意中用于关联分类群，可能会产生很大的问题。该项目旨在开发一种方法，通过仅从“中间重复序列”中提取来消除分子数据中的同源性，从而有选择地利用罕见的基因组事件。这些可识别的组合（“家族”）对于一个谱系来说是独一无二的，因此“无同源性”的数据将可用于系统发育重建。这一方法将在九种海胆的DNA序列数据上进行开发和测试。如果研究者的假设在这个试验案例中得到证实，那么这项研究的结果可能对许多分子系统学家具有非常广泛的适用性和实用性。该奖项由美国国家科学基金会探索性研究小额资助计划（SGER）提供，该计划旨在资助具有重大发现或对未来研究方向做出贡献的创新、高风险研究。如果这个特殊的项目成功地发展了一种精确的方法来获得信息丰富的分子序列数据，马歇尔博士将为研究新生代辐射生物多样性的系统学家做出潜在的贡献。一种更有效、更可靠的方法得到可靠的分子系统发育，可以大大节省时间和研究经费。

9528964 MARSHALL In the past ten to fifteen years molecular sequence data have provided powerful tools for investigating the phylogenetic relationships or associations of lineages in many diverse groups of organisms. Such data have often helped to resolve relationships where classical morphological data were insufficient or suggested alternative and conflicting results. Yet, just as morphological data includes convergent/parallel derived features, the same molecular sequence can arise independently. Such convergent or parallel features, known as homoplasies, can be very problematic if they are unrecognized and thus unwittingly used to associate taxa. This project seeks to develop a methodology for eliminating homoplasies from molecular data by drawing only from "middle-repetitive sequences", thereby selectively utilizing rare genomic events. Recognizable assemblages of these ("families") will be unique to a lineage and therefore "homoplasy-free" data will be available for phylogenetic reconstruction. This methodology will be developed and tested with DNA sequence data from nine species of sea urchins. If the investigator's suppositions are bore out with this test case, the results of this research may have very broad applicability and utility for numerous molecular systematists. This award is made under NSF's Small Grants for Exploratory Research (SGER) Program, which is designed to fund innovative, high-risk research with the potential, if successful, for major discovery or contribution to future research directions. If successful with this particular project for developing a refined methodology for obtaining informative molecular sequence data, Dr. Marshall will have made a contribution of potential utility to systematists working with a broad diversity of organisms with radiations in the Cenozoic. A more efficient and reliable means of deriving reliable molecular phylogenies can offer great savings in both time and research funds.