Comparative Methods and Phylogenetic Analysis Techniques

9406964马丁斯：比较数据在生物学的许多领域被用来推断表型特征的历史，如行为、生活史或生理学，而化石记录的直接证据是很少的。当研究人员从动物模型中推断人类的行为和生理，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。在过去的几年里，关于比较实验的设计和结果数据的统计分析，已经指出了一些问题。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生（系谱）重建方法，并且都涉及系统发生可以纳入比较数据分析的方法。这些系统发育分析技术（PATs）在描述如何从现存物种中发现的信息推断表型变化方面特别有用。由于涉及到基本的统计问题，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，并最终将被几乎所有生物学领域的研究人员使用。然而，由于大多数pat是在最近十年才发展起来的，因此将历史纳入种间研究的许多统计问题尚未得到解决，而且通常很难找到计算机程序来进行分析。目前的研究建议采用理论、计算机模拟和应用技术相结合的方法来缓解这些问题。理论方法将用于发展系统发育技术，将种内变异性纳入分析，允许考虑连续变量和分类变量，包括自然选择可能行为的估计，并考虑表型性状与观察环境之间的相互作用。计算机模拟将用于探索比较研究设计中的问题，例如应该对哪些物种进行抽样，并就选择可用的技术来分析分类变量提出建议。在这个过程中，还将产生一个大型的计算机程序包，它是用户友好的，可用于所有标准操作系统，并包括详细的手册和在线帮助系统。这些程序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.