Comparative Methods and Phylogenetic Analysis Techniques

9406964马丁斯比较数据被用于生物学的许多领域，以推断表型特征的历史，如行为，生活史或生理学，这些特征的直接证据来自化石记录是罕见的。 当研究人员从动物模型中推断人类的行为和生理学或寻找适用于不同生物群体的一般模式时，也会使用比较数据。 在过去的几年中，一些问题已被指出的比较实验的设计和所得数据的统计分析。 已经提出了一些解决这些问题的办法。 这些解决方案大多来自系统发育（系谱）重建方法，所有涉及的方法，其中系统发育可以纳入比较数据的分析。 这些系统发育分析技术（PAT）在描述如何从活物种中发现的信息推断表型变化方面特别有用。 由于涉及基本的统计问题，PAT在所有比较研究中也很重要，无论是否明确提出历史问题，并最终被研究人员用于几乎所有生物学领域。 然而，由于大多数PAT只是在过去十年中开发的，因此将历史纳入种间研究的许多统计问题尚未得到解决，并且通常很难找到计算机程序来进行分析。 目前的研究建议使用理论，计算机模拟和应用技术相结合，以减轻许多这些问题。 理论方法将被用来开发系统发育技术，将种内变异纳入分析，考虑连续变量和分类变量，包括自然选择可能作用的估计量，并考虑表型性状和观察环境之间的相互作用。 计算机模拟将用于探讨比较研究设计中的问题，例如应对哪些物种进行采样，并就分析分类变量的现有技术的选择提出建议。 在这一过程中，还将制作一个大的计算机程序包，该程序包方便用户使用，可用于所有标准操作系统，并包括详细的手册和联机帮助系统。 这些计划将有助于使系统发育分析技术可供所有比较生物学家使用。

9406964 Martins Comparative data are used in many areas of biology to infer the history of phenotypic characters such as behavior, life histories or physiology for which direct evidence from the fossil record is rare. Comparative data are also used when researchers infer the behavior and physiology of humans from that of animal models or search for general patterns that are true for diverse groups of organisms. In the last few years, a number of problems have been pointed out regarding the design of comparative experiments and the statistical analysis of the resulting data. A number of solutions have been proposed to address those problems. Most of these solutions were derived from phylogenetic (genealogical) reconstruction methods, and all involve ways in which phylogenies can be incorporated into the analysis of comparative data. These phylogenetic analysis techniques (PATs) are particularly useful in describing how to infer phenotypic change from the information found in living species. Because of the basic statistical problems involved, PATs are also important in all comparative studies whether or not explicitly historical questions are being asked and will eventually be used by researchers in almost all areas of biology. As most PATs were only developed during the last decade, however, many of the statistical issues underlying the incorporation of history into interspecific studies have not yet been addressed and it is often difficult to find computer programs to conduct the analyses. The current study proposes to use a combination of theoretical, computer simulation and applied techniques to alleviate many of these problems. Theoretical approaches will be used to develop phylogenetic techniques tthat incorporate within-species variability into the analyses, allow for consideration of both continuous and categorical variables, include estimators for the possible actions of natural selection, and consider the interactions between phenotypic traits and the environments in which th ey are observed. Computer simulation will be used to explore issues in the design of comparative studies such as which species should be sampled, and to make recommendations about the choice of available techniques to analyze categorical variables. During this process, a large package of computer programs will also be produced that is user-friendly, available for all standard operating systems, and includes a detailed manual and on-line help systems. These programs will help to make phylogenetic analysis techniques available and accessible to all comparative biologists.