Spectral analysis of phylogenetic data

The spectral analysis of sequence and distance data is a new approach to phylogenetic analysis. For two-state character sequences, the character values at a given site split the set of taxa into two subsets, a bipartition of the taxa set. The vector which counts the relative numbers of each of these bipartitions over all sites is called a sequence spectrum. Applying a transformation called a Hadamard conjugation, the sequence spectrum is transformed to the conjugate spectrum. This conjugation corrects for unobserved changes in the data, independently from the choice of phylogenetic tree. For any given phylogenetic tree with edge weights (probabilities of state change), we define a corresponding tree spectrum. The selection of a weighted phylogenetic tree from the given sequence data is made by matching the conjugate spectrum with a tree spectrum. We develop an optimality selection procedure using a least squares best fit, to find the phylogenetic tree whose tree spectrum most closely matches the conjugate spectrum. An inferred sequence spectrum can be derived from the selected tree spectrum using the inverse Hadamard conjugation to allow a comparison with the original sequence spectrum. A possible adaptation for the analysis of four-state character sequences with unequal frequencies is considered. A corresponding spectral analysis for distance data is also introduced. These analyses are illustrated with biological examples for both distance and sequence data. Spectral analysis using the Fast Hadamard transform allows optimal trees to be found for at least 20 taxa and perhaps for up to 30 taxa. The development presented here is self contained, although some mathematical proofs available elsewhere have been omitted. The analysis of sequence data is based on methods reported earlier, but the terminology and the application to distance data are new.     

徐州市奎河水质遗传毒理学分析

用蚕豆根尖细胞微核这一遗传毒理学技术,测定分析了市区奎河段水质的遗传学毒性,反映其污染情况。实验结果显示市区奎河段水质处于重度污染水平,部分水域的水质遗传毒理学指标很高,提示其中含有较多的污染物,对居民构成潜在的遗传毒性威胁。此外,对造成上述水域污染的原因进行了初步分析。     

基于遗传算法的ATM网络中VCC路由选择方法

针对遗传算法强大的全局寻优和并行处理能力 ,提出了一种改进的遗传算法调度ATM网络动态路由的新算法。综述了使用遗传算法进行通信网络节点选择的问题 ,指出了原有算法进行遗传算法优化时存在的不足 ,并提出一种新的基于动态惩罚的解决策略 ,其思想是在进化的过程中 ,逐渐减小对可行解惩罚的力度 ,使网络向可行解逼近。通过简单模型的仿真 ,验证了动态惩罚策略的可行性和有效性。     

外来入侵种空心莲子草的RAPD遗传多样性分析

基于随机扩增多态DNA(RAPD)方法,对8个居群空心莲子草Agasicles hygrophila的遗传多样性及分化程度进行分析。10条随机引物扩增出99个可分析位点,多态位点百分比为36．3％。POPOGENE分析发现,空心莲子草居群平均水平的多态位点百分比为26．2％,Nei’s基因多样度为0．0906,Shannon信息指数为0．1609,具有较高的遗传多样性;居群间遗传分化比例为30．88％,居群内遗传分化占69．12％;居群间基因流为1．1189。结合居群遗传多样性及UPGMA聚类分析表明,镇江及南京地区是空心莲子草遗传变异程度最高的中心区,应该作为外来种空心莲子草防治及根除的重点地带,防治的最有效措施是加强对其无性繁殖体临近传播、蔓延和扩散途径的阻断。     

What was classical genetics?

I present an account of classical genetics to challenge theory-biased approaches in the philosophy of science. Philosophers typically assume that scientific knowledge is ultimately structured by explanatory reasoning and that research programs in well-established sciences are organized around efforts to fill out a central theory and extend its explanatory range. In the case of classical genetics, philosophers assume that the knowledge was structured by T. H. Morgan’s theory of transmission and that research throughout the later 1920s, 30s, and 40s was organized around efforts to further validate, develop, and extend this theory. I show that classical genetics was structured by an integration of explanatory reasoning (associated with the transmission theory) and investigative strategies (such as the ‘genetic approach’). The investigative strategies, which have been overlooked in historical and philosophical accounts, were as important as the so-called laws of Mendelian genetics. By the later 1920s, geneticists of the Morgan school were no longer organizing research around the goal of explaining inheritance patterns; rather, they were using genetics to investigate a range of biological phenomena that extended well beyond the explanatory domain of transmission theories. Theory-biased approaches in history and philosophy of science fail to reveal the overall structure of scientific knowledge and obscure the way it functions.     

改进组合遗传算法的信道分配研究

介绍了信道分配问题中的干扰约束模型并在组合遗传算法的信道分配基础上结合难度分配小区优先分配的概念提出了改进组合遗传算法以及算法的实施方法,改善了"热点"地区信道分配难的问题,提高了最优分配方案的收敛率。     

杨树不同杂交组合苗期性状遗传变异

对T120×S3107等8个杂交组合及各组合内无性系间的苗高、胸径、分枝情况等性状变异进行了研究。结果表明,组合间和无性系间在各性状上存在着显著的变异,苗高、胸径、侧枝的广义遗传力分别为77.75%,52.64%,56.96%。各杂交组合苗高和胸径平均值均超过对照T120和I 69。I 69×S3244,I 69×I 63组合的苗高和胸径性状表现都较好。因此,从这批材料中选出优良无性系是有可能的。     

用混合遗传算法求解N皇后问题

N皇后问题是NP难题,一般求解的方法为回溯法.当问题规模较小时用回溯法能有效求解,但当问题规模较大时其求解时间耗费非常巨大.该文提出用局部搜索与简单遗传算法(SGA)相结合的混合遗传算法(HGA)来求解N皇后问题,用N皇后的约束条件作为遗传算法的适应值函数.设计了高效的染色体编码、初始化种群方法、遗传算子以及局部搜索算子,使它们符合求解问题的需要.通过与回溯法和相关的遗传算法比较,实验证实了用混合遗传算法求解N皇后的有效性.     

用多目标遗传算法优化设计水库分期汛限水位

水库分期汛限水位利用洪水的季节性规律,可在不降低水库防洪标准的前提下,显著提高水库兴利效益.论述了优化设计分期汛限水位的必要性、基于模拟调度优化设计分期汛限水位的可行性.以防洪、发电、航运等多目标来评价分期汛限水位方案,以不降低水库防洪能力为约束条件,建立了优化设计模型.对简单遗传算法进行了多目标评价、引入共享函数、线性变换适应度函数、优解保持策略、重新洗牌等改进,建立了一种改进的多目标遗传算法,用以优化设计分期汛限水位方案.以三峡水库为研究背景,采用混合编码方法描述分期汛限水位方案,利用1882~2003年宜昌站汛期的实测日流量资料进行模拟优化,得出了较优的分期汛限水位方案.计算结果表明,分期汛限水位优化设计能权衡防洪与兴利之间的关系,在满足防洪要求的前提下,显著提高水库兴利效益.     

基于JMF实时传输的远程授课系统的设计与实现

在简要介绍多媒体实时传输关键技术的基础上,对在JMF平台上实现音视频数据实时处理传输技术的远程授课系统的硬件结构和软件层次结构设计以及RTP流的发送和接收作了详细阐述,提出了一套从硬件到软件的完整设计和实现方案。为保证系统高度的实时性,采用了对音频和视频建立不同的虚拟信道,以负责不同媒体信息的传输,每个信道根据其媒体信息特点,赋予相应的服务质量参数,保证了信息的高效传输。