Null Models in Molecular Phylogenetic Systematics

阿奇博士将研究大量生物体中DNA序列的进化模式。通过使用DNA序列数据库中的信息，研究的重点将放在评估DNA序列中累积的随机替换的水平上，并检查这些替换如何影响我们分析序列数据的能力。人们普遍认为，DNA序列包含了生物体进化史的大量信息，可以用来推断物种之间的关系。然而，人们认识到这些序列包含大量的随机信息，因为序列中位点变化的起源的性质，因为每个位点只能采取四种不同的形式。在以前的研究中，生物学家假设在这些序列中存在大量的残留信息，这是生物体进化史的副产品，可以通过结合计算机的现代分析方法来解码。然而，随着随机性水平的增加，分析这些数据的方法失效了，产生的结果也不那么确定。在细胞核内DNA的不同区域之间以及核外的核苷酸序列中，随机性的水平预计会有所不同，并且随着被分析物种之间差异的时间增加，随机性水平预计会增加。由于许多被比较的物种和物种群已经在数百万年、数千万年甚至数亿年的时间里发生了分歧，在许多序列比较中，生物学家期望在序列数据中存在大量关于进化历史的随机信息。该研究计划将分析各种不同生物群体和基因组不同区域的随机序列信息水平。它将依赖于DNA和蛋白质序列数据库中存在的序列信息。由于分子生物学的最新技术进步，这些数据库的规模正在迅速增长。由于随机信息的积累，分析序列数据的各种数值技术的敏感性将被检查。在过去的2-3年里，一些新的分析技术已经被开发出来，并产生了大量的兴趣。然而，无论是这些还是旧的技术都没有从本研究中使用的角度进行检查。这项研究的结果将有助于指出哪些序列和部分序列将有助于推断物种和物种群体之间的关系，通过确定基因组中倾向于以不同速率积累进化有用和随机变化的区域。研究结果还将有助于指出必须检查的序列长度，以便对进化关系做出合理的推断。

Dr. Archie will examine patterns of evolution of DNA sequences in a broad array of organisms. Through the use of information in DNA sequence databases, the emphasis of the research will be on the evaluation of levels of accumulated random substitutions within DNA sequences and an examination of how these substitutions affect our ability to analyze sequence data. It has been generally acknowledged that DNA sequences contain a large amount of information on the evolutionary history of living organisms that can be used to make inferences about relationships among species. However, it is recognized that these sequences contain a large amount of random information because of the nature of the origin of change at sites in the sequences and because each site can take only four different forms. In previous research, biologists have assumed that there is substantial residual information in the sequences, a by- product of the evolutionary history of the organisms, that could be decoded using modern methods of analysis through the incorporation of computers. However, the methods for the analysis of these data break down and produce less certain results as the level of randomness increases. Levels of randomness are expected to vary between different regions of the DNA within the nucleus as well as in nucleotide sequences outside of the nucleus and are expected to increase as the amount of time since divergence between the species being analyzed increases. Since many species and species groups being compared have diverged over millions, tens of millions, or even hundreds of millions of years, in many comparisons of sequences biologists expect substantial amounts of random information about the evolutionary history to be present in the sequence data. The research program will analyze levels of random sequence information for a variety of different groups of organisms and for different areas in the genome. It will rely on sequence information that is present in DNA and protein sequence databases for information. These databases are growing rapidly in size because of recent technological advances in molecular biology. The sensitivity of a variety of numerical techniques for analyzing sequence data due to the accumulation of random information will be examined. Several new analytical techniques have been developed over the last 2-3 years and have generated a substantial amount of interest. However, neither these nor the older techniques have been examined from the perspective to be used in this research. The results from the study will help to indicate which sequences and parts of sequences will be useful for inferring relationships among species and species groups by identifying regions of the genome that tend to accumulate evolutionary useful and random changes at different rates. The results will also help indicate the lengths of sequences that must be examined in order to make reasonable inferences about evolutionary relationships.