A nonparametric estimator of species overlap

For two communities, species overlap has been defined by Smith, Solow, and Preston (1996, Biometrics 52, 1472-1477) as the probability that a randomly selected species is present in both communities given that it is present in at least one community. Species overlap can thus be used to describe the similarity of two communities. In contrast with the parametric estimator of Smith et al., we propose a nonparametric maximum likelihood estimator (NPMLE). We prove that the NPMLE is consistent and asymptotically normally distributed and show that computation of the NPMLE and its standard error is straightforward. We also compare the NPMLE and the estimator of Smith et al. for a variety of situations.     

Highly resistant regression and object matching

In many disciplines, it is of great importance to match objects. Procrustes analysis is a popular method for comparing labeled point configurations based on a least squares criterion. We consider alternative procedures that are highly resistant to outlier points, and we describe an application in electrophoretic gel matching. We consider procedures based on S estimators, least median of squares, and least quartile difference estimators. Practical implementation issues are discussed, including random subset selection and intelligent subset selection (where subsets with small size or near collinear subsets are ignored). The relative performances of the resistant and Procrustes methods are examined in a simulation study.     

Genetic diversity in recent elite faba bean lines using AFLP markers

Amplified fragment length polymorphism (AFLP) markers were used to study the genetic diversity among a large set (n = 79) of inbred lines of recent elite faba bean (Vicia faba L.) cultivars with Asian, European (Northern and Southern) and North African origin. The inbred lines were analyzed using eight selected AFLP primer combinations that produced 477 polymorphic fragments. Errors when scoring repeated lanes of one pre-amplification reaction on one gel were negligible, whereas errors when scoring lanes of two individuals of the same inbred line run on different gels were markedly higher. Scoring across gels should be backed by replicates and several appropriate check entries. Based on clustering with Jaccard's similarity coefficient and Principal Coordinate Analysis, only the Asian lines were distinct as a group, the other lines showed no marked further grouping. Nevertheless, several known pedigree relationships were verified. A priori grouping of inbred lines (geographic origin and seed size) and AFLP data corroborate available information on the history of spread and cultivation of faba bean in the studied regions. Based on the diversity observed, studies especially concerning the relationship between genetic similarity based on AFLP markers and hybrid performance within the European elite germplasm have been launched.Communicated by H.F. Linskens     

Molecular diversity of male sterility inducing and male-fertile cytoplasms in the genus Helianthus

The organisation of mtDNA was investigated for 28 sources of cytoplasmic male sterility (CMS) and a fertile line (normal cytoplasm) of Helianthus annuus by Southern hybridisation. In addition to nine known mitochondrial genes (atp6, atp9, cob, coxI, coxII, coxIII, 18S, 5S and nd5) three probes for the open reading frames in the rearranged area of PET1, orfH522, orfH708 and orfH873, were used. Genetic similarities of the investigat-ed cytoplasms varied between 0.3 and 1. Cluster analyses using the UPGMA method allowed the distinction of ten mitochondrial (mt) types between the 29 investigated cytoplasms. Most mitochondrial types comprise two or more CMS sources, which could not be further separated, like the PET1-like CMS sources (with the exception of ANO1 and PRR1), or ANN1/ANN2/ANN3, ANN4/ ANN5, ARG3/RIG1, BOL1/EXI1/PEF1/PEP1 and GIG1/ PET2. ANL1, ANL2 and the fertile cytoplasms are also regarded as one mitochondrial type. Unique banding patterns were only observed for ANT1 (atp6), MAX1 (atp6, orfH522 and orfH708) and PRR1 (coxII). However, four of the mitochondrial types showed unique hybridisation signals: ANN4/ANN5 had characteristic bands for atp6 and orfH708, PEF1/PEP1/EXI1/BOL1 for atp6 and coxII, and PET2/GIG1 for atp9. The PET1-like cytoplasms all shared the same patterns for orfH522, orfH708 and cob (except ANO1). It could be demonstrated that CMS sources, like, e.g., PET2 and PEF1, are different from PET1 in mtDNA organisation and the CMS mechanism. Therefore, these CMS sources represent interesting candidates for the development of new hybrid breeding systems based on new CMS mechanisms. Received: 20 April 2001 / Accepted: 3 August 2001     

Interactive effects of multiple stressors and restoration priorities in a mined Appalachian watershed

We surveyed benthic macroinvertebrate communities, water chemistry, and thermal regime in the Cheat River, WV, USA in an attempt to quantify the interactive effects of multiple stressors on ecological condition and identify priorities for restoration in this mined Appalachian watershed. We used a novel approach, which combined use of the West Virginia Stream Condition Index (WVSCI) to quantify ecological losses and community similarity analysis to assign specific levels of ecological loss to AMD, thermal effluent, and their interaction. Finally, we developed an ecological currency to quantify the relative benefits of a restoration program that focused either on AMD remediation or heat reduction and to identify spatially explicit restoration priorities. Variation in ecological condition was strongly correlated to variation in water quality when AMD and heat stress occurred in isolation. Acute inputs of AMD or heat caused predictable reductions in condition followed by rapid recovery downstream. However, benthic communities failed to recover from combined inputs of heat and AMD even when these stressors occurred at relatively low levels. Over the course of an entire year, AMD alone was over two times more responsible than heat alone for ecological loss. Consequently, AMD is the dominant factor limiting ecological condition and should be the primary target for restoration. Nevertheless, an AMD × heat interaction also was responsible for extensive ecological loss in lower reaches of the river. Consequently, full restoration of the lower Cheat River mainstem will require an approach that integrates AMD remediation with effective management of thermal effluent. Our results provide some of the first field evidence of the interactive effects of multiple stressors on biological communities in a mined watershed. This approach may be valuable for quantifying impacts from multiple interacting stressors and for prioritizing restoration efforts in other mined watersheds. Handling editor: S. M. Adams     

陕西不同生境核桃内生真菌多样性

【目的】了解核桃内生真菌组成、分布等多样性特性,为活性菌株筛选、作用机理研究等奠定基础。【方法】采用组织分离法对不同季节、不同生境、不同部位的核桃内生真菌进行分离,以形态学和分子生物学相结合的方法进行鉴定,通过定殖率、分离率、分离频率、Shannon-Wiener多样性指数等分析核桃内生真菌的多样性。【结果】共分离获得核桃内生真菌1 450株,隶属于47个属,其中链格孢属Alternaria为优势类群,占菌株总数的20.00%,镰孢属Fusarium和酵母属Saccharomyces相对较多,分别占菌株总数的8.34%和8.14%。核桃不同部位内生真菌的多样性指数(H′)和均匀度指数都以两年生茎的最高,分别为1.15和0.36;不同生境核桃中,山阳的多样性指数(H′)和均匀度最高,分别为1.42和0.42;秋冬两季中,秋季的指标较高,分别为1.92和0.54。【结论】不同部位、不同生境、不同季节核桃都具有丰富的内生真菌且多样性存在差异;相似性系数、均匀度指数反映出,核桃内生真菌在一定程度上相对稳定。     

上海市内不同水质的河道春季浮游细菌群落结构分析

2008年4月采集上海市城郊结合地区的4条河道午潮港、横港、朝阳河和曹杨环浜的水样, 测定水样的相关理化数据, 计算水环境质量综合指数; 提取水样中浮游细菌的总DNA, 进行变性梯度凝胶电泳(DGGE)分析; 并对水体中的可培养浮游细菌的数量进行测定。结果表明, 污染严重的河道浮游细菌的生物量较高, 而多样性明显偏低, 河道不同采样点的微环境影响浮游细菌的组成, 河道中浮游细菌的组成与生物量的变化与水环境质量密切相关。     

Molecular homology and DNA hybridization

Summary We reviewed the concept of homology, which can broadly be defined as a correspondence between characteristics that is caused by continuity of information (Van Valen 1982). The concept applies widely in molecular biology when correspondence is taken to mean a genetic relationship resulting from a unique heritable modification of a feature at some previous point in time. Such correspodence can be established for features within a single organism as well as between organisms, making paralogy a valid form of molecular homology under this definition. Molecular homology can be recognized at a variety of organizational levels, which are intedependent. For example, the recognition of homology at the site level involves a statement of homology at the sequence level, and vice versa. This hierarchy, the potential for nonhomologous identity at the site level, and such processes as sequence transposition combine to yield a molecular equivalent to complex structural homology at the anatomical level. As a result, statements of homology between heritable units can involve a valid sense of percent homology.We analyzed DNA hybridization with respect to the problems of recognizing homology and using it in phylogenetic inference. Under a model requiring continuous divergence among compared sequences, DNA hybridization distances embed evolutionary hierarchy, and groups inferred using pairwise methods of tree reconstruction are based on underlying patterns of apomorphic homology. Thus, symplesiomorphic homology will not confound DNA hybridization phylogenies. However, nonhomologous identities that act like apomorphic homologies can lead to inaccurate reconstructions. The main difference between methods of phylogenetic analysis of DNA sequences is that parsimony methods permit hypotheses of nonhomology, whereas distance methods do not.This article was presented at the C.S.E.O.L. Conference on DNA-DNA Hybridization and Evolution, Lake Arrowhead, California, May 11–14, 1989     

16S rDNA技术研究新生腹泻仔猪粪样细菌区系的多样性变化

用PCR/DGGE技术跟踪一窝5头新生腹泻仔猪自然康复、补饲、断奶过程中粪样细菌区系的演变,构建3头仔猪42日龄粪样的16S rDNA克隆库,分析匹配于DGGE优势谱带23个克隆的16S rDNA序列。结果表明,DGGE图谱由简单(2日龄)到复杂(10日龄),再回复简单(16日龄)到复杂(断奶),最后趋于稳定。2、16日龄DGGE图谱最简单、相似,最优势谱带为大肠杆菌;10日龄(补饲后3天)图谱复杂,大肠杆菌存在但不是最优势谱带,补饲前后图谱的相似性低,补饲导致了粪样细菌区系结构的显著变化;断奶前(27日龄)和后(35、42日龄)图谱复杂,优势谱带、图谱相似性均趋向稳定。序列分析表明,23个克隆中除5个与未知细菌最相似外,其余最相似菌分属于肠球菌(Enterococcus),链球菌(Streptococcus),梭菌(Clostridium),消化链球菌(Peptostreptococcus)和乳酸杆菌(Lactobacillus)。     

基于打分矩阵的多类蛋白质折叠子的预测

依据蛋白质折叠子中氨基酸保守性,以氨基酸、氨基酸的极性、氨基酸的电性以及氨基酸的亲—疏水性为参数,从蛋白质的氨基酸序列出发,采用"一对多"的分类策略,通过构建打分矩阵和选取氨基酸序列模式片断,利用5种相似性打分函数对27类折叠子进行识别,最好的预测精度达到83.46%。结果表明,打分矩阵是预测多类蛋白质折叠子有效的方法。