Fifty years of character compatibility concepts at work

In the mid 19th century,systematic biologists realized that observable similarities and differences among a group of related species could be the basis for hypotheses about the evolutionary relationships among the species and their ancestors.Such hypotheses Can be expressed as characters.A character is comprised of two or more character states of species considered to be similar with respect to a basis for comparison.The states of a character may also be arranged into a character state tree to hypothesize speciation events associated with changes from one character state to another.In the mid 20th century.some systematists realized that sometimes paxrs of characters(or character state trees)could be incompatible as hypotheses,i.e.,they could not both be true.Through the 1950s,'60s and'70s,tests for,and ways to resolve,incompatibilities were used to estimate an ancestor relation based on mutually compatible characters.An estimate was often shown as a diagram connecting ancestors to their immediate descendants(not quite correctly)called a phylogenetic tree.More recently,other applications of compatibility concepts have been developed,including:identify characters that appear to be random in the context of their data set;combine estimates of ancestor relations for subsets of taxa in a larger collection into a single estimate(a so-called supertree)for the whole collection;and interpret geographic patterns in an evolutionary context.     

CHARACTER DISCRIMINATORY POWER,CHARACTER-SET CONGRUENCE,AND THE CLASSIFICATION OF INDIVIDUALS FROM HYBRID ZONES: AN EXAMPLE USING STONE CRABS (MENIPPE)

Many investigators categorize individuals from hybrid zones to facilitate comparisons among genotypic classes (e.g., parental, F₁, backcross) for comparative studies in which components of fitness or geographic variation are being analyzed. Frequently, multiple character sets representing genetically independent traits are used to classify these individuals and various methodologies are employed to combine the classifications obtained from the different character sets. We adapted the principles of total evidence and taxonomic congruence (two formalized approaches used by systematists in formulating phylogenetic hypotheses) to address the problem of discriminating hybridizing species and classifying individuals from hybrid zones. As our model, we used two morphological (coloration and morphometric) and two molecular (allozyme and mitochondrial DNA restriction-fragment-length polymorphism) character sets that differentiate two stone crab species (Menippe adina and M. mercenaria). Using principal-components analysis, we determined that combining character sets and eliminating characters or character sets that did not have large eigenvector coefficients for the principal component that best separated the two species yielded the highest level of discrimination between species and allowed us to classify a broad range of morpho-genotypes as hybrids. For the stone crabs, three diagnostic allozyme loci and five diagnostic coloration characters best separated the species. The two character sets were not completely congruent, but they agreed in their classification of 50% of the individuals from the hybrid zone and rarely strongly disagreed in their classifications. Classification discrepancies between the two character sets probably represent variation between traits in interspecific gene flow rather than intraspecific, ecologically mediated variation. Our results support the assertions of previous investigators who espoused the benefits associated with using multiple character sets to classify individuals from hybrid zones and demonstrate that, if character sets are reasonably congruent and numerically balanced, combining diagnostic characters from multiple character sets (a total-evidence approach) can enhance discriminatory power between species and facilitate the assignment of hybrid-zone individuals to genotypic classes. On the contrary, classifying hybrid-zone individuals using character sets separately (a taxonomic-congruence approach) provides the opportunity to compare levels of introgression between species and to assess reasons for discordance among the data sets.     

A phylogenetic analysis of the land plants

Phylogenetic systematics (cladistics) is a theory of phylogeny reconstruction and classification widely used in zoology. Taxa are grouped hierarchically by the sharing of derived (advanced) characters. The information is expressed in a cladogram, a best estimate of a phylogeny. Plant systematists generally use a phenetic system, grouping taxa on overall similarity which results in many groups being formed, at least in part, on the basis of shared primitive characters.
The methods of phylogenetic systematics are used to create a preliminary cladogram of land plants. The current classification of land plants is criticized for its inclusion of many groups which are not monophyletic.
Objections to the use of phylogenetic systematics in botany, apparent convergences within major groups and frequent hybridization, are shown to be invalid. It is concluded that cladistic analysis presents the best estimate of die natural hierarchy of organisms, and should be adopted by plant systematists in their assessment of plant interrelationships.     

A statistical approach to the evaluation of characters to estimate evolutionary relationships among the species of the aquatic subterranean genus, Iberobathynella (Crustacea, Syncarida)

The 13 known species of the genus Iberobathynella were studied. Twenty-six characters with usually two or three states were revealed to have low within-species variability but show clear differences among some species. These characters were hypothesized to have states convex on the branching pattern of the phylogenetic lines that gave rise to these 13 species (i.e. be uniquely derived). Each pair of these hypotheses was tested for logical compatibility; then, for each character, a new character was created by choosing equiprobably one of the possible permutations of the 13 species to rename the species in each state. Characters created in this random way would have convex states only by chance, not by evolution. This random character was tested with each of the remaining 25 for logical compatibility as hypotheses of convexity. For each character, one thousand such random characters were created and tested. Sixteen observed characters were compatible with more other observed characters than 90% of their randomly generated counterparts, and so were considered plausibly non-random. They were used to speculate on branching patterns of the phylogenetic lines among the 13 species.     

Morphometric variation in the hominoid orbital aperture: a case study with implications for the use of variable characters in Miocene catarrhine systematics

Variable characters are ubiquitous in hominoid systematics and present a number of unique problems for phylogenetic analyses that include extinct taxa. As yet, however, few studies have quantified ranges of variation in complex morphometric characters within extant taxa and then used those data to assess the consistency with which discrete character states can be applied to poorly represented fossil species. In this study, ranges of intrageneric morphometric variation in the shape of the hominoid orbital aperture are estimated using exact randomization of average pairwise taxonomic distances (ATDs) derived from size-adjusted centroid, height-width, and elliptic Fourier (EF) variables. Using both centroid and height-width variables, 19 of the 21 possible ATDs between individuals representing seven extinct catarrhine taxa (Aegyptopithecus, Afropithecus, Ankarapithecus, Ouranopithecus, Paranthropus, Sivapithecus and Turkanapithecus) can be observed within a single extant hominoid subspecies, although generally with low probabilities. A resampling study is employed as a means for gauging the effect that this intrataxonomic variation may have on the consistency with which discrete orbital shape character states can be delimited given the small sample sizes available for most Miocene catarrhine taxa preserving this feature (i.e., n=1). For each type of morphometric variable, 100 cluster (UPGMA) analyses of pairwise ATDs are performed in which a single individual is randomly selected from each hominoid genus and analyzed alongside known extinct taxa; consensus trees are computed in order to obtain the frequencies with which different shape clusters appeared in each of the three analyses. The two major clusters appearing most frequently in all three consensus trees are found in only 57% (centroid variables), 49% (height-width variables), and 36% (EF variables) of these trees. If ranges of variation within represented extinct taxa could also be estimated, these frequencies would certainly be far lower. Hominoids clearly exhibit considerable intrageneric, intraspecific, and even intrasubspecific variation in orbit shape, and substantial morphometric overlap exists between taxa; consequently, discrete character states delimiting these patterns of continuous variation are likely to be highly unreliable in phylogenetic analyses of living and extinct species, particularly as the number of terminal taxa increases. Morphological phylogenetic studies of extant catarrhines that assess the effect of different methods (e.g., use of objective a priori weighting or frequency coding of variable characters, inclusion vs. exclusion of variable characters, use of specific vs. supraspecific terminal taxa) on phylogenetic accuracy may help to improve the techniques that systematists employ to make phylogenetic inferences about extinct taxa.     

EVOLUTIONARY CHARACTER ANALYSIS: TRACING CHARACTER CHANGE ON A CLADOGRAM

Abstract— There has been little formal discussion concerning character analysis in cladistics, even though characters and their character state trees are central to phylogenetic analyses. We refer to this field as Evolutionary Character Analysis. This paper defines the components of evolutionary character analysis: character state trees, transmodal characters, cladogram characters, attribute and character phylogenies; and the use of these components in phylogenetic inference and evolutionary studies. Character state trees and their effect on cladogram construction are discussed. A new method for numerically coding complex character state trees is described that further reduces the number of variables required to describe them. This method, ordinal coding, reduces the size of data matrices, and facilitates retrieval of state codes. This paper advocates the use of both biological evidence and evidence internal to the cladogram itself to construct character state trees (CSTs). We discuss general models of character evolution (morphocline analysis, Fitch minimum mutation model, etc.) and their role in forming CSTs. Character state trees formed with theories of character evolution are referred to as transmodal characters. These transmodal characters are contrasted with cladogram characters (Mickevich, 1982), and the place of each in a phylogenetic analysis is discussed. The method for determining cladogram characters is detailed with more complicated examples than found in previous publications. We advocate testing transmodal characters by comparing them with the resultant cladogram characters. This comparison involves transformation series analysis (TSA; Mickevich, 1982) which is viewed as an extension of reciprocal illumination. The TSA procedure and its place in hypothesis testing are reviewed. Tracing the evolution of characters interests both systematists and non-systematists alike. When character state trees (transmodal characters) are optimized on pre-existing phylogenies, character phylogenies and attribute phylogenies result. Attributes are defined as a feature that may or may not be homologous (i.e., ecological categories, plant hosts, etc.). We provide two illustrations of this approach, one involving the evolution of the anuran ear and another involving the coevolution of the butterfly Heliconius and its hostplants. Finally, the components of phylogenetic character analysis can be used to test more general evolutionary theories such as the biogenetic law and vicariance biogeography.     

New probability matrices for identification of Streptomyces

The character state data obtained for clusters defined in a previous phenetic classification were used to construct two probabilistic matrices for Streptomyces species. These superseded an original published identification matrix by exclusion of other genera and the inclusion of more Streptomyces species. Separate matrices were constructed for major and minor clusters. The minimum number of diagnostic characters for each matrix was selected by computer programs for determination of character separation indices (CHARSEP) and a selection of group diagnostic properties (DIACHAR). The resulting matrices consisted of 26 phena x 50 characters (major clusters) and 28 phena x 39 characters (minor clusters). Cluster overlap (OVERMAT program) was small in both matrices. Identification scores were used to evaluate both matrices. The theoretically best scores for the most typical example of each cluster (MOSTTYP program) were all satisfactory. Input of test data for randomly selected cluster representatives resulted in correct identification with high scores. The major cluster matrix was shown to be practically sound by its application to 35 unknown soil isolates, 77% of which were clearly identified. The minor cluster matrix provides tentative probabilistic identifications as the small number of strains in each cluster reduces its ability to withstand test variation. A diagnostic table for single-membered clusters, constructed using the CHARSEP and DIACHAR programs, was also produced.     

浙江天童国家森林公园微地形与植被结构的关系

植物群落的本质特征之一是群落中的植物和环境之间存在一定的相互关系。丘陵地区的地形由各种微地形单元构成,这些微地形单元在空间上的分化提供的异质化的生境导致了区域丰富的物种和群落多样性的形成。选择浙江东部低山丘陵地区具有典型代表意义的天童国家森林公园,在地形识别的基础上,结合详细的植被调查,分析了不同微地形单元物种组成及其林分结构的变化。结果表明,基于物种组成相似性,7个微地形单元可以归为2组,与通过侵蚀前线划分结果一致。依据物种在这2个小尺度地形单元的分布格局,可以划分出3个特征种组,即上部坡面分布型、下部坡面分布型和无统计偏差型。壳斗科、山茶科、冬青科和山矾科常绿物种是构成上部坡面植被的主要成分,而榆科、槭树科、胡桃科和漆树科等的落叶种及樟科常绿种则是构成下部坡面植被的主要成分。下部坡面各微地形单元的林分垂直构造比上部坡面复杂,由榆科、槭树科、胡桃科和漆树科生境先锋种形成的明显超高层以及超大个体的存在是其显著特征。但其密度低于上部坡面微地形单元。上部坡面的顶坡和谷头凹地明显缺乏乔木层的存在。侵蚀前线是丘陵地区不同生境最重要的划分界限,由其切分的上部坡面和下部坡面是评价物种组成和林分结构的两大基本功能区域。     

Convergence in the distribution patterns of Europe’s plants and mammals is due to environmental forcing

Aim Our aims were to test: (1) the extent to which vascular plant associations are related in space to mammalian associations, and (2) whether the plant associations are more closely related than the mammalian associations to climate and to a published environmental stratification of Europe. Location Europe, as defined by the following boundaries: 11° W, 32° E, 71° N and 35° N. Methods The analysis is based on presence/absence records of mammal species and plant species with a resolution of 50 km × 50 km. The similarity of the overall spatial structure was tested using a partial Mantel test while controlling for the effect of geographical proximity. To further identify the main spatial components in the datasets, we used k‐means clustering and principal components analysis. The resulting geographical patterns were compared with one another, with climate variables and with the environmental stratification of Europe. Results The clustering of the plant data forms coherent areas that can be interpreted as reflections of floristic regions that are controlled to a large extent by climate and topography. In terms of the correlation between distance matrices, the relationship between plants and mammals is relatively strong. The relationships between mammals and climate, and between plants and climate, are more complex but always statistically significant. There is no evidence that the plant clusters are more closely related than the mammalian clusters to climate, although plant clusters are closer to environmental data than to climate. Main conclusions The clustering patterns of mammals and plants form groups that agree with one another in their spatial extent. The forcing of floristic patterns into coherent entities appears mainly to be caused by climatic variables (temperature, temperature range and rainfall), mediated by elevation differences. The formation of individual plant clusters is also related to species numbers and to local and regional floristic differences. The close correlation between the floristic and faunal patterns suggests that the mammal and plant distributions are controlled by the same environmental variables, although the extent to which the mammals are controlled directly by climate or through the influence of vegetation requires more detailed study.     

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.     

Energy and structural analysis of double nucleic acid triplets

In order to investigate the energy and structural character of RNA-RNA triplets and RNA-DNA duplex base triplets, 64 sets of three-dimensional models of RNA-DNA duplex base triplets and mRNA-tRNA triplex base triplets were constructed and optimized by homologous modeling method using the software InsightII. The comparative statistical method and cluster analysis were adopted to study these features. The result showed: (i) all energy parameters of monomer RNA-DNA hybrid triplets and ternary complexes appeared significantly different; and some parameters related with overall molecules such as overall energy, bond energy and coulomb energy have statistically significant correlations between the structures in vacuum and aquatic solutions while other parameters, including theta energy, phi energy, hydrogen bond energy and non-bond energy, changed significantly, but not continuously. (ii) However, the case of mRNA-tRNA triplets was much more complicated in that only the bond energy's correlation coefficient is -0.8. Typically, the main contribution of GC pairs and G/A/U bases were interesting. The models of RNA-DNA hybrid triplets and mRNA-tRNA triplet should be helpful for the study of base pairing in codons and the biological effectiveness of antisense nucleic acids.     

What Can Molecular and Morphological Markers Tell Us About Plant Hybridization?

The study of hybrids and their evolutionary significance is often based on a number of tacit assumptions regarding character expression in hybrids. This article examines morphological, chemical, and molecular character expression in hybrids to determine whether traditionally recognized properties of hybrid plants, such as hybrid intermediacy and character coherence, are actually supported by empirical evidence, and also examines the impact of hybrids on phylogenetic analyses. We show that hybrids are a mosaic of both parental and intermediate morphological characters rather than just intermediate ones, and that a large proportion of first (64%) and later generation hybrids (89%) exhibit extreme or novel characters. Chemical character expression in hybrids is more predictable, with predominantly additive or complementary expression for both first generation hybrids (68%) and hybrid taxa (54%). Likewise, the genetic basis, and thus the expression of molecular characters, is well-worked out and predictable, although non-Mendelian inheritance has been reported in a few instances for molecular markers as well.

There is even less empirical support for the concept of character coherence than hybrid intermediacy. Although morphological character coherence has been reported in both artificial and natural hybrid populations, it appears to be the exception rather than the rule. This idiosyncratic relationship among morphological characters is shown to be the norm for the relationship of morphological to molecular characters, as well as for the relationship among molecular characters.

Hybrids are shown to have little impact on the topology of nonhybrid taxa in phylogenetic trees. However, the expression of primitive vs. derived character states, the placement of hybrids in cladograms, the number of equally parsimonious trees produced, and the effects of hybrids on phylogenetic topology do not appear to be predictable. Thus, cladistic identification of hybrid taxa is difficult and may not be possible based on phenotypic data, regardless of the analytical tools used.     

Geometric and traditional morphometrics for the assessment of character state identity: multivariate statistical analyses of character variation in the genus Arrenurus (Acari,Hydrachnidia, Arrenuridae)

Geometric and traditional morphometric approaches are tested to describe and reveal taxonomic characters and character states in variation of shape and size of idiosoma morphology in the Arrenuridae. Patterns of variation of idiosoma and glandularia features of males from 11 Mexican species of Arrenurus (Megaluracarus) and two species of subgenus Dadayella were explored with five landmark configurations and three sets of interlandmark distances. Separate principal component analyses (PCA) and canonical variate analyses (CVA) were performed for each data set. The eight multivariate analyses of variance among 13 a priori groups (species) detected significantly different morphometric variants, which were interpreted as different taxonomic character states. Patterns of character state similarity among species were examined with unweighted‐pair grouping method using averages (UPGMA) cluster analyses on Mahalanobis distances. Analyses of five landmark configurations revealed important taxonomical variation in the anterior idiosoma outline (10 character states), the outline of the posterior region or cauda (13 states), the distribution of postocularia, and the second and third pairs of dorsoglandularia (nine states), the fourth pair of dorsoglandularia (three states), and ventroglandularia on the posterior side of idiosoma (nine character states). Multivariate analyses of three sets of distance measurements also resulted in the detection of potential taxonomic characters related to idiosoma size (12 character states), postocularia and dorsoglandularia (13 states), and ventroglandularia (nine character states). Morphometric analyses of distances and shapes provide a formal basis for the interpretation of taxonomic characters, and for the discovery of character states. These characters should be investigated further in a wider sample of species for the phylogenetic systematics of these water mites. In the meantime, idiosoma regions and structures were tested for congruence in a phylogenetic analysis, and were proposed as homologous among the species sampled.     

Nystroemiaceae,a new family of Permian gymnosperms from China with an unusual combination of features

Nystroemiaceae is proposed as a new family of gymnosperms from the Permian of Cathaysia that adds to the diversity of gymnosperms known from this critical time in seed plant evolution. This family is characterized by bifurcating and highly branched pinnate ovuliferous organs bearing bicornute ovules (seeds) and entire leaves with anastomozing veins that are born on complex and modern-looking branching systems with clear axillary branching. The reconstruction is based on numerous large specimens from two localities in North China, in which the different plant parts are attached to each other. The ovulate structures show some apparently plesiomorphic (primitive) character states more typical of early seed plants, whereas the leaves and branches show the clearly apomorphic (derived) character states of broad-leaved gymnosperms.     

Somatic hybridization between male sterile Nicotiana tabacum and N. glutinosa through protoplast fusion

Summary Protoplasts derived from suspension cultured cells of cytoplasmic male sterile Nicotiana tabacum (N. debneyi cytoplasm) and of fertile N. glutinosa were fused with the aid of polyethylene glycol (PEG). Out of 1,089 colonies developed from PEG-treated protoplasts, 29 restored whole plants.A somatic hybrid plant was selected on the basis of isoelectrofocusing analysis of Fraction I protein in leaves of regenerated plants. A newly created hybrid contained small subunits of both parents but only a N. glutinosa type large subunit.Male sterile character was conserved in a hybrid plant while leaf morphology was intermediate between the parents. By tobacco mosaic virus infection tests, the hybrid's leaves showed resistant symptoms, hypersensitive local lesions, which were due to N. glutinosa nuclear genome expression.Abbreviations PEG Polyethylene glycol - TMV Tobacco mosaic virus     

The impact of natural odors on affective states in humans

Laboratory studies have shown a significant influence of certain fragrances on affective as well as cognitive states in humans. The aim of the current study was to measure the relationship between complex, natural odors and affective states, that is, calmness, alertness, and mood, in the field. In 4 experiments, the emotional impact, intensity, and hedonics of complex, natural plant odors were assessed in 32 healthy human subjects and compared with control conditions involving a similar outdoor environment without the tested fragrant plants. In all experiments, the selected fragrances were evaluated as more intense than the odors in the control conditions but pleasantness ratings differed only in 2 of the 4 experiments. The fragrances improved subjective ratings of calmness, alertness, and mood depending on the sequence of the conditions but independent of visual features of the environment. In contrast, a fifth experiment which tested the influence of natural and artificial pleasant odors and an artificial unpleasant odor on calmness, alertness, and mood in 22 subjects showed that the unpleasant odor impaired these affective states in humans independent of the order of presentation. On the other hand, no effects of the pleasant odors on mood and calmness were observed in this experiment.     

Amino acid sequence versus morphological data and the interordinal relationships of mammals

To a large extent, the mutual affinities of the mammalian orders continue to puzzle systematists, even though comparative anatomy and amino acid sequencing offer a massive data base from which these relationships could potentially be adduced. In the present paper the consistency index--the number of character states less the number of characters in a data set, divided by the total number of changes in the character states on a cladogram--was used to examine the relative resolving powers of recently published morphological and molecular- sequence data. Consistency indices were calculated for previously published alpha crystallin A chain and myoglobin amino acid-sequence cladograms and for four original amino acid-sequence cladograms (alpha crystallin A, myoglobin, and alpha and beta hemoglobin); these were found to be comparable to the consistency indices of morphologically based cladograms. Qualitative comparisons between the morphologically based and molecularly based trees were also made; only moderate congruence between the two was observed. Moreover, there was a general lack of congruence between the cladograms specified by each of the four proteins. Amino acid-sequence and morphological data agreed on the placement of edentates as an early eutherian offshoot and on the grouping of hyracoids, proboscideans, and sirenians. Otherwise there was only limited congruence: morphology strongly supported the grouping of lagomorphs and rodents and the alliance of pholidotes and edentates, but sequence analyses did not. The placement of tubulidentates differed widely among proteins. Morphology indicated the close association of sirenians with proboscideans; proteins suggested a pairing of sirenians with hyracoids. Sequence data did not identify many (morphologically well-diagnosed) orders as monophyletic (e.g., Lagomorpha).(ABSTRACT TRUNCATED AT 250 WORDS)      

How can third codon positions outperform first and second codon positions in phylogenetic inference? An empirical example from the seed plants

Greater phylogenetic signal is often found in parsimony-based analyses of third codon positions of protein-coding genes relative to their corresponding first and second codon positions, even for early-derived ("basal") clades. We used the Soltis et al. (2000; Bot. J. Linn. Soc. 133:381-461) data matrix of atpB and rbcL from 567 seed plants to quantify how each of six factors (observed character-state space, frequencies of observed character states, substitution probabilities among nucleotides, rate heterogeneity among sites, overall rate of evolution, and number of parsimony-informative characters) contributed to this phenomenon. Each of these six factors was estimated from the original data matrix for parsimony-informative third codon positions considered separately from first and second codon positions combined. One of the most parsimonious trees found was used as the constraint topology; branch lengths were estimated using likelihood-based distances, and characters were simulated on this tree. Differential frequencies of observed character states were found to be the most limiting of the factors simulated for all three codon positions. Differential frequencies of observed character states and differential substitution probabilities among states were relatively advantageous for first and second codon positions. In contrast, differential numbers of observed character states, differential rate heterogeneity among sites, the greater number of parsimony-informative characters, and the higher overall rate of evolution were relatively advantageous for third codon positions. The amount of possible synapomorphy was predictive of the overall success of resolution.