A Fundamental Problem with Amino-Acid-Sequence Characters for Phylogenetic Analyses

Protein-coding genes may be analyzed in phylogenetic analyses using nucleotide-sequence characters and/or amino-acid-sequence characters. Although amino-acid-sequence characters "correct" for saturation (parallelism), amino-acid-sequence characters are subject to convergence and ignore phylogenetically informative variation. When all nucleotide-sequence characters have a consistency index of 1, characters coded using the amino acid sequence may have a consistency index of less than 1. The reason for this is that most amino acids are specified by more than one codon. If two different codons that both code for the same amino acid are derived independent of one another in divergent lineages, nucleotide-sequence characters may not be homoplasious when amino-acid-sequence characters may be homoplasious. Not only may amino-acid-sequence characters support groupings that are not supported by nucleotide-sequence characters, they may support contradictory groupings. Because this convergence is a problem of character delimitation, it affects the results of all tree-construction methods (maximum likelihood, neighbor joining, parsimony, etc.). In effect, coding amino-acid-sequence characters instead of nucleotide-sequence characters putatively corrects for saturation and definitely causes a convergence problem. An empirical example from the Mhc locus is given.     

Artifacts of Coding Amino Acids and Other Composite Characters for Phylogenetic Analysis

A phylogenetic analysis can be no better than the characters on which it is based. Just as it is inappropriate to code character states of individual characters as separate presence/absence characters, it is inappropriate to combine independent characters because not all information in the data is being utilized. Composite characters link otherwise discernible states from different characters together to form new character states. There are two related problems with this coding. First, there is a loss of hierarchic information between the reductive and composite characters when unordered states are used. Second, the linking of separate characters that occurs during the construction of composite character states can create putative synapomorphies that were not present in the separate characters. For amino acid characters, the problem may occur whenever more than one position of a codon is variable among the terminals sampled. Groups that are resolved as paraphyletic with reductive coding may be resolved as monophyletic with composite coding. The artificial character states indicated by the amino acid characters are unlikely to be congruent with the true gene tree.     

The effect of insignificant characters on the multivariate analysis of simple patterns of geographic variation

The multivariate analysis of a set of significant characters portrays a simple geographic cline which is evident even when very few characters are used. The effect of adding insignificant characters to the set of significant characters is studied, as is the effect of replacing significant characters by insignificant characters. The former (addition) causes only a slight decline in congruence between patterns of geographic variation but the latter (replacement) causes a substantial decline in congruence. The congruence between patterns of geographic variation obtained by multivariate analysis of independent character sets is plotted against character number and gives an S-shaped relationship when insignificant or significant plus insignificant characters are used. This is distinct from the convex asymptotic curve obtained when only significant characters are used. In spite of the reduction in congruence caused by the use of insignificant characters, multivariate analysis of insignificant characters consistently revealed the 'same' geographic pattern (i.e. 'cline') as the set of significant characters. However, it required 10 times as many insignificant characters to achieve this.     

THE USEFULNESS OF BEHAVIOR FOR PHYLOGENY ESTIMATION: LEVELS OF HOMOPLASY IN BEHAVIORAL AND MORPHOLOGICAL CHARACTERS

It is widely believed that behavior is more evolutionarily labile and/or more difficult to characterize than morphology, and thus that behavioral characters are not as useful as morphological characters for estimating phylogenetic relationships. To examine the relative utility of behavior and morphology for estimating phylogeny, we compared levels of homoplasy for morphological and behavioral characters that have been used in systematic studies. In an analysis of 22 data sets that contained both morphological and behavioral characters we found no significant difference between mean consistency indices (CIs, which measure homoplasy) within data sets for the two types of characters. In a second analysis we compared overall CIs for 8 data sets comprised entirely of behavioral characters with overall CIs for 32 morphological data sets and found no significant difference between the two types of data sets. For both analyses, 95% confidence limits on the difference between the two types of characters indicate that, even if given the benefit of the doubt, morphological characters could not have substantially higher mean CIs than behavioral characters. These results do not support the idea that behavioral characters are less useful than morphological characters for the estimation of phylogeny.     

Additive Variation Maintained under Stabilizing Selection: A Two-Locus Model of Pleiotropy for Two Quantitative Characters

A model with two diallelic loci controlling two additive quantitative characters is suggested. One of the loci has a similar effect on both characters, whereas the second locus has an antagonistic effect on two characters. Both characters experience direct stabilizing selection. The model yields a stable polymorphic state, with both characters maintaining genetic variation. The genetic correlation between the characters at the equilibrium is zero, in spite of the pleiotropic effects of the loci controlling them.     

检索表的矛盾分析及其实践意义(综述)

通过对生物检索表结构的分析,认为检索表的根本矛盾是标本具有的个性性状与检索表使用的共性性状的矛盾。单道检索表的主要矛盾是检索表对性状的有条件使用与单个标本性状有限性之间的矛盾,因而单道检索表未能很好地解决其基本矛盾,使得其应用范围和使用效果受到诸多影响。多道检索表的主要矛盾是性状数据库内性状的有限性与物种具有的个性性状的无限性之间的矛盾,不存在个性与共性的矛盾,即解决了根本矛盾问题,便于检索应用。     

Evolutionary rates of secondary sexual and non-sexual characters among birds

The rate of evolutionary morphological change in secondary sexual characters among species has traditionally been assumed to exceed that for non-sexual characters, giving rise to a larger degree of divergence. We used a large data set of independent evolutionary events of exaggerated secondary sexual feather characters across all birds to test whether that was the case. Comparative analyses revealed that secondary sexual tail feather characters diverged more than wing feathers in females, and we also found that secondary sexual head feather characters diverged more than tarsi in males, when only including intra-order comparisons in the analyses. These results are in the predicted direction, with secondary sexual characters diverging more than ordinary morphological traits, partially supporting the general impression that secondary sexual characters are more variable among species than ordinary morphological characters. However, the degree of divergence among secondary sexual characters was generally not much larger than that among ordinary characters. Some non-significant differences in divergence between secondary sexual characters and ordinary characters could be explained by the cost-reducing function of ordinary morphological traits. There was no evidence of significant differences in divergence between sexes for secondary sexual characters, maybe because of genetic correlations in morphology between the sexes. However, male tarsi diverged more than female tarsi, and sexual selection might play a role in this difference in divergence. This revised version was published online in July 2006 with corrections to the Cover Date.     

苦瓜主要品质性状的遗传变异、相关和通径分析

对23份苦瓜材料的10个品质性状进行了研究。结果表明,苦瓜维生素C、还原糖、有机酸、果瘤、果色、果刺和苦味遗传变异系数大,遗传力高;水分含量遗传变异系数很小;风味遗传变异系数较小,遗传力低。苦瓜4个内在营养品质之间相关性小,而4个外观品质性状之间关系密切。两个味觉品质与4个内在营养品质之间相关性小,但与4个外观品质之间关系密切。内在营养品质与外观品质之间有一定关系。通径分析提出通过降低果实的苦味和有机酸含量来提高风味品质;通过水分含量和果瘤两性状的直接选择来实现对维生素C的间接选择。     

The races of maize: III. choices of appropriate characters for racial classification

Analyses of variance for 111 characters from 55 races and subraces of maize from eastern South America grown at Piracicaba, S. P., Brazil, between 1960 and 1965, indicated that those characters which were least affected by environmental factors and interactions were reproductive characters. In particular, the component of variance due to differences among races for certain ear and kernel characters was greater than the sum of the corresponding components due to differences among years and race by year interactions. The converse was true for all vegetative characters. Tassel characters tended to be intermediate between ear and plant characters. While some indices had larger components of variance attributable to racial differences than to the effects of environment and/or environmental interaction, some commonly used ones, such as cob/rachis and rachilla/kernel indices, proved to be quite susceptible to environmental influences. Again, indices based upon solely vegetative characters were consistently influenced more strongly by environmental factors and interaction than were those based on reproductive characters.     

中国凤仙花科植物叶表皮特征及其分类学意义

利用光学显微镜观察凤仙花科106份样本材料、36种代表植物的叶表皮微形态特征。结果表明:该科植物叶表皮微形态特征种内稳定,对于种间及属间关系的界定具有重要的分类学价值。上表皮细胞的形状及垂周壁的式样种间差异明显,各分类群间有明显的界限,是种间界定的重要依据,因此上表皮微形态特征具有重要的的分类学价值,基于上表皮的微形态特征将研究的36种代表植物划分为5个类型。下表皮的微形态特征虽更为多样,种间差异显著,可用于种间界定,但对于属下划分难以提供有价值的性状。该科植物叶表皮微形态特征与宏观形态特征的相关性较弱,与地理分布格局的相关性较强,关系更为密切。同一地理分布区域内的种类宏观形态特征虽然差别明显,但叶表皮微形态特征却表现出较强的一致性,这似乎也反映了叶表皮微形态这一性状受环境饰变的影响比较明显。综上所述,叶表皮微形态特征可为凤仙花科的系统发育,尤其是凤仙花属种间界定提供有价值的分类学佐证     

MACROEVOLUTIONARY PATTERNS OF MORPHOLOGICAL DIVERSIFICATION AMONG PARASITIC FLATWORMS (PLATYHELMINTHES: CERCOMERIA)

Patterns of parasite morphological diversification were investigated using a morphological data base for the parasitic platyhelminths comprising 1,459 characters analyzed using phylogenetic systematic methods. Only 10.8% of the 1,882 character transformations are losses, casting doubt on views that parasites are secondarily simplified and exhibit degenerate evolution. Chi-squared analysis indicates that character loss in the Digenea and Monogenea occurs in proportion to total change and is disproportionately lower within the Eucestoda. In the Digenea fewer female characters and more male characters have been lost than expected by the total number of characters in that group, and more male and more nonreproductive characters have been lost in proportion to their distribution across groups. In the Monogenea fewer nonreproductive and more larval characters have been lost than expected within the group, and female character loss is high relative to other groups. In the Eucestoda fewer female and more larval characters have been lost than expected within the group, whereas loss of male and nonreproductive character is low, and loss of larval characters is high, compared to the other groups. Patterns of character loss result partially from characters that show repeated (homoplasious) loss in different groups. High consistency index and low homoplasy slope ratio values indicate that the parasitic platyhelminths show unusually low levels of homoplasy, casting doubt on views that parasite morphology is unusually adaptively plastic. Homoplasy within the monogeneans occurs in proportion to overall character change, is slightly higher than expected in the digeneans, and is much lower than expected within the eucestodes. Homoplasy occurs less often than expected in larval characters, and more often than expected in nonreproductive characters in the Digenea. Monogeneans show more homoplasy than expected for larval characters both within and among groups. Eucestodes show fewer homoplasious male and nonreproductive, and more homoplasious larval, characters than expected within the group, and higher homoplasy in larval characters and lower homoplasy in female and nonreproductive characters among groups.     

Testing phylogenetic implications of eggshell characters in side-necked turtles (Testudines: Pleurodira)

Amniote egg and eggshell morphology is a rich source of characters to link aspects of reproductive biology with systematics. Extensive work concerning both anatomy and phylogenetic assignability has been done on fossil bird and dinosaur eggs, but little is known for extant sauropsids. The utility of eggshell characters for phylogenetic analyses is tested and discussed for extant side-necked turtles (Pleurodira), and the diversity of egg ultrastructure is examined in several species. Egg gross morphology and eggshell ultrastructure of 12 species of extant side-necked turtles was documented using scanning electron microscopy. Thirteen eggshell characters were scored and mapped on a composite phylogeny and ancestral character states were reconstructed. Many of the characters do not show a phylogenetic signal according to a test comparing the number of steps on the chosen phylogeny with that on randomly generated trees. The presence of conservative, clade-supporting features could be demonstrated, and the following clades are supported by several characters: the Elseya-Emydura entity, short-necked Australasian chelids, is backed by two characters, and two additional characters could potentially support this group. Three characters support the monophyly of South American chelids, whereas two characters argue for the exclusion of Hydromedusa, a long-necked form resembling Australian chelids rather than South American forms, from this clade.     

Quantitative handling of characters useful in snake systematics with particular reference to intraspecific variation in the Ringed Snake Natrix natrix (L.)

This paper is based on the numerous characters used in a biometric study of the intraspecific variation of Natrix natrix (L.). These characters are drawn from the internal morphology, scalation, colour pattern, body proportions, dentition and dermal sense organs. The criteria involved in selecting these characters for taxonomic work are considered.
The alternative methods for quantifying the above features are discussed and so are the theoretical problems involved in coding the continuous characters.
The value of the characters in studying the geographic variation, ontogenetic variation and sexual dimorphism in N. natrix is indicated.
The use of a wider range of characters than just the scalation and colour pattern is urged when diagnosing the lower taxonomic levels of ophidians. The neglected internal morphology may well be able to supply characters to this end.     

青藏高原和内蒙古高原典型草地植物叶片肾型和哑铃型气孔器气孔特征及其与环境的关系

该研究利用植物制片技术,以中国青藏高原和内蒙古高原典型草地常见种或优势种植物的叶片为研究对象,通过比较分析叶片哑铃型气孔器和肾型气孔器的特征及其与环境因子的关系,揭示植物叶片两类气孔器对环境因子的响应策略。结果表明:(1)叶片哑铃型气孔器气孔指标的变异系数小于肾型气孔器。(2)叶片哑铃型气孔器气孔指标与环境气候指标的关系弱于肾型气孔器。(3)叶片哑铃型气孔器气孔特征与环境关系在叶片上下表面之间存在显著差异,而肾型气孔器气孔特征与环境因子的关系在叶片上下表面之间无显著差异。(4)叶片哑铃型气孔器的气孔特征与降水关系密切,而肾型气孔器气孔特征与温度关系密切。(5)同一种气孔器的气孔特征在两个地区(青藏高原和内蒙古高原)间存在显著差异。研究认为,肾型气孔器和哑铃型气孔器的气孔特征及其与环境之间的关系存在差异,在分析气孔特征时有必要将肾形与哑铃形保卫细胞形成的气孔器加以区分,该研究结果有助于进一步理解中国草地植物叶气孔特征对气候变化的响应与适应策略。     

Evaluating the efficacy of continuous quantitative characters for reconstructing the phylogeny of a morphologically homogeneous spider taxon (Araneae, Mygalomorphae, Antrodiaetidae, Antrodiaetus)

The use of continuous quantitative characters for phylogenetic analyses has long been contentious in the systematics literature. Recent studies argue for and against their use, but there have been relatively few attempts to evaluate whether these characters provide an accurate estimate of phylogeny, despite the fact that a number of methods have been developed to analyze these types of data for phylogenetic inference. A tree topology will be produced for a given methodology and set of characters, but little can be concluded with regards to the accuracy of phylogenetic signal without an independent evaluation of those characters. We assess the performance of continuous quantitative characters for the mygalomorph spider genus Antrodiaetus, a group that is morphologically homogeneous and one for which few discrete (morphological) characters have been observed. Phylogenetic signal contained in continuous quantitative characters is compared to an independently derived phylogeny inferred on the basis of multiple nuclear and mitochondrial gene loci. Tree topology randomizations, regression techniques, and topological tests all demonstrate that continuous quantitative characters in Antrodiaetus conflict with the phylogenetic signal contained in the gene trees. Our results show that the use of continuous quantitative characters for phylogenetic reconstruction may be inappropriate for reconstructing Antrodiaetus phylogeny and indicate that due caution should be exercised before employing this character type in the absence of other independently derived sources of characters.     

Continuous characters analyzed as such

Quantitative and continuous characters have rarely been included in cladistic analyses of morphological data; when included, they have always been discretized, using a variety of ad hoc methods. As continuous characters are typically additive, they can be optimized with well known algorithms, so that with a proper implementation they could be easily analyzed without discretization. The program TNT has recently incorporated algorithms for analysis of continuous characters. One of the problems that has been pointed out with existing methods for discretization is that they can attribute different states to terminals that do not differ significantly—or vice versa. With the implementation in TNT, this problem is diminished (or avoided entirely) by simply assigning to each terminal a range that goes from the mean minus one (or two) SE to the mean plus one (or two) SE; given normal distributions, terminals that do not overlap thus differ significantly (more significantly if using more than 1 SE). Three real data sets (for scorpions, spiders and lizards) comprising both discrete and quantitative characters are analyzed to study the performance of continuous characters. One of the matrices has a reduced number of continuous characters, and thus continuous characters analyzed by themselves produce only poorly resolved trees; the support for many of the groups supported by the discrete characters alone, however, is increased when the continuous characters are added to the analysis. The other two matrices have larger numbers of continuous characters, so that the results of separate analyses for the discrete and the continuous characters can be more meaningfully compared. In both cases, the continuous characters (analyzed alone) result in trees that are relatively similar to the trees produced by the discrete characters alone. These results suggest that continuous characters carry indeed phylogenetic information, and that (if they have been observed) there is no real reason to exclude them from the analysis. © The Willi Hennig Society 2006.     

Variation in monoculture and in mixture for grain yield and other characters in spring barley

Fourteen north-west European spring barley cultivars were grown alone or in binary mixtures sampled according to a partial diallel scheme. On the basis of the association between cultivars in mixture and monoculture, three groups of characters were distinguished. Group A characters, plant height, ear weight/tiller, grain yield/tiller, number of grains/tiller and 1000-grain weight, showed strong positive associations between performance in monoculture and mixture. Group B characters, number of tillers/plant and harvest index showed incomplete positive associations, while for group C characters, dry matter/plant, ear weight/plant, grain yield/plant and number of grains/plant, associations were weak or non-existent. Compound characters in group C showed less genetic variation in monoculture and lower general competitive effects in mixture than component characters in groups A or B. These results clearly indicate that while selection for grain yield and other characters on a per plant basis (group C characters) is confounded by intergenotypic competition, characters such as the yield components number of grains/tiller and 1000-grain weight (group A characters) are hardly affected in this range of cultivars. Selection for opposing group A characters may start in the F₂ generation, while any selection for group B and C characters should be delayed until later generations. The merits of indirect selection for yield using visual assessment of yield components are discussed. Separate analyses obtained by the inclusion of spring wheat cv. Timmo in monoculture and in the set of mixtures indicated that the use of spring wheat plants to minimise intergenotypic competition ranges from superfluous (group A characters) to useless (group C characters). A large degree of mixture advantage and the lack of complementary dominance and suppression between competitor and associate was attributed to the relatively low density of plants in the experiment which, though suitable for single plant selection, is not typical of normal seed rates for cropping.     

A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference

AFLPs (and to a lesser extent ISSRs and RAPDs) are increasingly being used for phylogenetic inference among closely related species. Presence/absence characters for each AFLP allele treat all absences as homologous to one another. With three or more alleles, terminals are grouped by their shared absence of alleles in character-based phylogenetic-inference methods in a manner that is not redundant with their shared presence of an alternative allele. We conducted simulations to quantify how severe the negative effect of using presence/absence characters of individual bands is for phylogenetic inference relative to standard multistate characters. We examined alternative tree topologies, relative branch lengths, numbers of characters, rates of evolution, and numbers of alternative alleles, using both parsimony and Nei-and-Li distance analyses. Multistate parsimony generally outperformed presence/absence parsimony, which in turn outperformed Nei-and-Li distance. Increasing the character-state space (i.e., the number of alternative character states available) was found to be advantageous for all three methods of analysis examined, but was most advantageous for multistate parsimony. However, the advantage of multistate parsimony relative to Nei-and-Li distance decreased when applied to more divergent characters. More parsimony-informative variation generally alleviated the problem associated with scoring multistate characters as presence/absence characters. The ensemble consistency index was lower for presence/absence characters relative to multistate characters.     

野牡丹族数量分类的初步研究

用ＵＰＧＭＡ聚合法对野牡丹族的４２个性状进行Ｒ分析和对该族华南及台湾地区１５个分类群进行Ｑ分析．Ｒ分析的结果反映了性状之间相关进化及性状与分类群之间相关进化的规律性．Ｑ分析对这些分类群的分类系统做了初步的定量研究．其结论与经典分类基本吻合．Ｑ分析的结果还支持将台湾产的耳药花并入野牡丹属。     

生物性状的系统分析理论──多元分析在生物性状分析中的应用研究

本文首次提出了生物性状的系统分析理论,指出了多元分析在生物性状应用研究中,应使统计分析模型适应于生物性状之间的相互作用规律,而不应是使生物性状适应于统计分析模型。生物性状多元分析时,统计上或任何人为增加或减少某些性状将影响生物性状之间的相互作用的大小,并得出不符合生物规律的错误结论,只有根据生物性状的系统理论分析生物性状之间的相互作用关系,才能准确评价各性状之间的相互作用大小。