Problematic character coding methods in morphology and their effects

The effects of different coding practices in morphological phylogenetic analysis are well documented. In many cases, we can determine that certain practices can be regarded as undesirable and should be avoided. Certain coding practices do not correctly translate the expected information to the cladistic algorithm. It may go unnoticed that expressions of character information in character lists, which may be entirely logical to any reader, do not necessarily reflect the mathematics employed by a phylogenetic algorithm. Despite a wealth of literature on coding procedures and documentation of these issues, problematic character coding practices are still common. A review is provided of different coding and character formulation practices, particularly relating to multistate character information that may either: (1) lead to a failure to capture grouping information implied in the character list; (2) cause problematic weighting or spuriously high certainty in particular optimizations; and (3) impose congruence artificially, by linking more than one variable character to a particular state. Each of these is reviewed and presented with a hypothetical example. Recommendations for avoiding these pitfalls are described in light of how parsimony algorithms work with character data. Character lists must be drawn up not only to present character variation logically, but also with consideration for how computer algorithms implement cladistic logic. The widespread use of problematic character coding procedures may account for some of the perceived problems with morphological data. Therefore, an exploration of the effects of these methods and standardization of methods should be a goal for the very near future. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 489–498.     

三种玉米蚜虫种群的生态位分析

对重庆市郊区1998～1999年春玉米上3种蚜虫种群的数量动态、生态位宽度和生态位重叠进行了系统的分析研究．结果表明,发生在春玉米上的玉米蚜(Rhopalosiphum maidis),禾谷缢管蚜(Rhopalosiphum padi)和麦长管蚜(Sitobion avenae)3种蚜虫混合种群的种群数量消长呈现出5月中下旬和6月下旬两个高峰;在生态位宽度上,Livens生态位宽度指数(Bi)分析表明,麦长管蚜表现出时间上的高度分化,玉米蚜表现出空间上的高度聚集特性,而禾谷缢管蚜的分化并不明显;在生态位重叠上,玉米蚜和禾谷缢管蚜的HturlbeIt生态位重叠指数(Lij)最高,玉米蚜和麦长管蚜次之,禾谷缢管蚜和麦长管蚜最小．在春玉米上发生的3种蚜虫中,玉米蚜具有较强的竞争优势．     

温度对玉米蚜种群增长的影响

研究了温度对玉米蚜RhopalosiphummaidisFitch种群存活率、生殖率及内禀增长率的影响 ,同时测定了不同温度条件下玉米蚜种群的净增殖率、周限增长率、种群倍增时间及稳定年龄组配等种群参数。在 1 0℃和 3 5℃条件下 ,玉米蚜若蚜的死亡率较高 ,特别是 4龄若蚜 ;2 5℃最适宜玉米蚜的生长、发育和繁殖 ,其种群增长最快     

基于生态位和水质因子的草鱼两种混养模式的比较

试验通过模拟草鱼2种混养模式(鲮-草模式为草鱼与鲮混养、鲫-草模式为草鱼与鲫鱼混养),引入计算机视觉技术分析了草鱼在2种不同养殖模式下的生态位宽度及生态位重叠,同时测定了水体理化指标及鱼类特定生长率。结果表明:鲮-草模式组草鱼的特定生长率为1.524%.d-1,显著高于鲫-草模式组草鱼的特定生长率(1.346%.d-1);鲮-草模式组水体中的铵态氮、硝酸盐、总氮、总磷、活性磷酸盐浓度高于鲫-草模式组,而pH、DO、亚硝酸盐浓度及叶绿素a含量低于鲫-草模式组;2混养组中草鱼之间的生态位宽度无明显差异;鲮-草模式组草鱼与鲮之间生态位重叠指数为0.5598,鲫-草模式组草鱼与鲫鱼之间的生态位重叠指数为0.6478,二模式组比较,差异显著;鲮与草鱼之间的竞争较鲫鱼与草鱼之间的竞争小;试验组中鲮与草鱼混养要优于鲫鱼与草鱼混养。     

六斑月瓢虫取食不同猎物的生长发育及繁殖特性

六斑月瓢虫是我国农、林、蔬、果生态系统中重要的捕食性天敌之一,能够捕食多种猎物。不同的猎物质量显著影响捕食性天敌昆虫的活力。为评价取食不同猎物对六斑月瓢虫生物学特性的影响,采用实验种群生命表的方法研究了六斑月瓢虫取食烟粉虱、豆蚜和玉米蚜的生长发育和繁殖情况。结果表明,六斑月瓢虫取食烟粉虱的世代发育历期最长、存活率、雌虫寿命和繁殖力最低,分别为(26.15±0.42)d、(52.95±1.98)%、(53.73±2.17)d和(157.67±16.79)粒/雌;而取食玉米蚜的世代发育历期最短、存活率、雌虫寿命和繁殖力最高,分别为(16.40±0.49)d、(77.93±0.76)%、(68.33±4.31)d和(798.77±44.29)粒/雌;取食豆蚜时的各生物学参数介于两者之间。种群生命表参数也反映了类似的结果,取食烟粉虱的净增殖率(R0)、内禀增长率(r_m)和周限增长率(λ)最低分别为71.216、0.092和1.094,世代平均历期(T)最长为47.377d;取食玉米蚜的R_0、r_m和λ最高分别为290.281、0.131和1.143,T最短为42.428d。总体来看,相对于烟粉虱而言,蚜虫更适合六斑月瓢虫的生长发育和繁殖,且玉米蚜优于豆蚜。     

Accuracy of estimated phylogenetic trees from molecular data

Summary The accuracies and efficiencies of four different methods for constructing phylogenetic trees from molecular data were examined by using computer simulation. The methods examined are UPGMA, Fitch and Margoliash's (1967) (F/M) method, Farris' (1972) method, and the modified Farris method (Tateno, Nei, and Tajima, this paper). In the computer simulation, eight OTUs (32 OTUs in one case) were assumed to evolve according to a given model tree, and the evolutionary change of a sequence of 300 nucleotides was followed. The nucleotide substitution in this sequence was assumed to occur following the Poisson distribution, negative binomial distribution or a model of temporally varying rate. Estimates of nucleotide substitutions (genetic distances) were then computed for all pairs of the nucleotide sequences that were generated at the end of the evolution considered, and from these estimates a phylogenetic tree was reconstructed and compared with the true model tree. The results of this comparison indicate that when the coefficient of variation of branch length is large the Farris and modified Farris methods tend to be better than UPGMA and the F/M method for obtaining a good topology. For estimating the number of nucleotide substitutions for each branch of the tree, however, the modified Farris method shows a better performance than the Farris method. When the coefficient of variation of branch length is small, however, UPGMA shows the best performance among the four methods examined. Nevertheless, any tree-making method is likely to make errors in obtaining the correct topology with a high probability, unless all branch lengths of the true tree are sufficiently long. It is also shown that the agreement between patristic and observed genetic distances is not a good indicator of the goodness of the tree obtained.     

不同玉米品种(系)对玉米蚜生长发育和种群增长的影响

玉米蚜Rhopalosiphum maidis (Fitch)是为害玉米的重要害虫.为评价不同玉米品种(系)对玉米蚜生长发育的适合性,从而为抗性品种(系)的鉴定及其抗性机制分析提供依据,在室内条件下,组建了玉米蚜实验种群在8个玉米品种(系)上的特定时间生命表.结果表明:玉米蚜1龄若虫在供试的4个玉米品种郑单958、浚单20、先玉335和良玉88上的发育历期长于供试的4个自交系87-1、濮改340-1-1、旱21和齐319,其中良玉88和先玉335与4个自交系之间差异显著;成蚜寿命和世代历期在4个自交系上较长;4个供试玉米品种上各虫龄的存活率显著小于4个自交系;成蚜产蚜量在各品种(系)间也存在显著差异,以取食齐319品系时最大,平均产蚜量64.4头,其次是濮改340-1-1,为56.53头,以取食浚单20时最小,只有19.93头.生命表参数表明,玉米蚜在供试的玉米品种(系)上均能繁殖,但与4个玉米自交系相比,玉米蚜在4个玉米品种上的种群净增殖率R0、内禀增长率rm和周限增长率λ均减小或显著减小,而平均世代周期和种群加倍时间则延长,说明供试的4个玉米品种对玉米蚜生长发育和繁殖均有不利影响.     

分子系统发育树构建的简易方法

以系统发育树构建的原有距离方法为基础,吸取了NJ法和FM法中的部分理论,提出了以节点引入为手段的新的简易方法,通过该方法构建了分子系统发育树,结果表明这种方法更加快捷,而且所得结果与FM法完全一致。     

Leaf epidermal character variation and evolution in Gaultherieae (Ericaceae)

The taxonomic value and evolutionary significance of 30 leaf epidermal characters from 238 samples representing 127 species of all seven genera in the tribe Gaultherieae (Ericaceae) and two outgroup genera were investigated by scanning electron microscopy. The character states were coded and optimized onto a maximum‐likelihood tree based on previous molecular data with Fitch parsimony and hierarchical Bayesian analysis to trace the evolution of character states throughout all internodes in the phylogenetic tree for Gaultherieae. Leaf epidermal characters were found to be largely consistent within species, but highly variable at interspecific and higher taxonomic levels. The most recent common ancestral states of 15 characters diagnosed various lineages recovered from prior studies, some with no prior morphological support. Relatively high frequencies of state change occur in the eastern Asian clade Gaultheria series Gymnobotrys + Diplycosia, the American clade G. subsection Dasyphyta p.p., the core East Asian clade and the Australia/New Zealand clade. The characters with the highest frequencies of state change are the outer stomatal ledge ornamentation type, the stomatal apparatus level, stomatal density and area, and the type of abaxial trichomes. These character state change patterns may provide insight into the ecological adaptions of Gaultherieae during their evolutionary history. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 686–710.