Scorpion higher phylogeny and classification, taxonomic anarchy, and standards for peer review in online publishing

Soleglad and Fet's (2003a) attempt to reconstruct the phylogeny of Recent (including extant) scorpions, the revised classification derived from it, and recent emendations, mostly published in their self‐edited online journal, Euscorpius, are deficient. Separate analyses of three independent matrices (morphology, 16S rDNA, 18S rDNA) were presented. In the morphological matrix, 52 binary and 10 tristate trichobothrial characters were replaced with one character comprising six ordered states representing trichobothrial “types”. The remaining matrix of 105 characters was further reduced to 33 “fundamental” characters (20% of the morphological dataset), the analysis of which appears to be the basis for the revised classification presented. The taxon sample for the morphological analysis included 14 supraspecific terminal taxa representing genera, the monophyly of only 7 (12.5%) of which has been confirmed. A composite terminal, assembled from the fragments of fossils that may not be confamilial let alone monophyletic, was created for the Palaeopisthacanthidae, employed as the primary outgroup for the analysis. Other important outgroup taxa, notably eurypterids, xiphosurans and other arachnids, were omitted entirely. The morphological characters presented contained numerous unjustifiable assumptions of character polarity and phylogenetic relationship. An approach to character coding, deliberately adopted to reduce “homoplasy”, biased the analysis towards a preconceived result. Structurally and topographically similar features in different taxa were explicitly assigned separate (often autapomorphic) states according to presumed phylogenetic relationships among the taxa in which they were observed. Putative “reversals” were coded as separate characters or states. Character transformation was forced by ordering, additive coding or Sankoff optimization through allegedly intermediate states for which there is no empirical evidence. Many characters were defined in a manner that demonstrates either a lack of understanding of, or disregard for, established methods and standards of morphological character coding. Some states display overlapping variation whereas others subsume variation that is not structurally or topographically similar. Polymorphic “states” were created for terminals with interspecific variation and unknown “states” for terminals that should have been scored unknown. Many characters were not evaluated for particular terminal taxa, but merely scored inapplicable although the structures and, consequently, the characters in question are present and therefore applicable to them. In view of the significant theoretical and empirical problems with the approach to cladistics taken by Soleglad and Fet, we find no justification for accepting either the results of their analyses or the revised classification derived from them. Pending the outcome of a rigorous phylogenetic analysis, published according to acceptable standards of scholarship in a peer‐reviewed journal, we revert to the suprageneric classification of Scorpiones reflected by the most recent peer‐reviewed, published treatments and reject all changes to the classification proposed by Soleglad, Fet and colleagues since 2001. We argue that an analysis and revised classification of the kind presented in various papers by these authors could not survive the peer‐review process of a mainstream scientific journal. The poor scholarship exemplified by these and other papers published in Euscorpius emphasize the importance of quality control associated with the emergent infrastructure of online publishing. A centralized register of taxa may be the only solution for ensuring quality control in the taxonomy of the future. © The Willi Hennig Society 2005.     

伞形科囊瓣芹属的表型分析

选取伞形科(Apiaceae)囊瓣芹属(Pternopetalum Franchet)32个分类群的60个形态学性状,利用DELTA系统的UPGMA算法进行了聚类分析。结果表明属下形成以五匹青(P.vulgare(Dunn)Hand.-Mazz.)和东亚囊瓣(P.tanakae(Franchet&Sav.)Hand.-Mazz.)为代表的两个主要表征群。两个主要表征群的分类结构和各自所包含的类群基本相应于前人研究中本属两个组的属下处理。根据全面相似性分析的结果和部分形态学特征的评估,确认了属下6个种的复合群:即五匹青、囊瓣芹(P.davidii Franchet)、散血芹(P.botrychioides(Dunn)Hand.-Mazz.)、洱源囊瓣芹(P.molle(Franchet)Hand.-Mazz.)、澜沧囊瓣芹(P.de-lavayi(Franchet)Hand.-Mazz.)和东亚囊瓣芹复合群。根据形态学特征在表型树上的分布分析表明:伞形花序的着生位置、花柱的形态、花柱基的形状和萼齿的大小等生殖特征可能是属下早期分化的关键性性状。属下主要变异类型(种的复合群和典型狭域特有种)对不同海拔区域和小生境的依赖,以及不显著的形态学分化表明:对横断山区较高的异质性生境的生态适应是囊瓣芹属类群多样化过程后期的一个重要特征。     

Phenetic studies in Nuphar Sm. (Nymphaeaceae):variation in sect. Nuphar

Previous taxonomic assessments of the hydrophytic genus Nuphar Sm. (Nymphaeaceae) have inadequately considered the range of morphological variation existing in the genus. A comprehensive statistical analysis of morphological features among the recognized taxa of Nuphar is presented here, first using 10 fruit characters to delimit the separation of two infrageneric groups of taxa, and secondly using 31 characters to quantify the morphological variation found within sect. Nuphar. Results from combined phenetic analyses provided empirical support for recognition of two infrageneric groups of species in the genus (largely by fruit, stigmatic disk margin, neck, and stigmatic disk size) and for separation of taxa within sect. Nuphar (by leaf size, and fruit disk and neck size). Statistical analyses demonstrate that extensive variation in ranges of character states exists among sect. Nuphar taxa. However, a suite of qualitative and quantitative characters can be used to recognize five species and three subspecies within this predominantly Old World assemblage.     

泡沙参复合体(桔梗科)的物种生物学研究——Ⅲ.性状的遗传变异及其分类价值

阐明性状变异的遗传基础是评估性状分类价值以及揭示类群关系和进化过程的前提。本文根据泡沙参复合体内6个天然居群的材料,利用居群样本分析、子代测定和杂交试验等手段,结合统计学方法对该复合体一些在以往类群划分中起鉴别作用的形态性状进行了遗传学分析。结果表明,叶形、叶缘锯齿数目和大小、茎叶被毛、花萼裂片齿数、花梗长短等性状都是遗传性比较强的性状,而且性状之间有很强的相关性。但是,这些性状在居群内呈现连续变异且变异幅度非常大,以致于变异的两个极端个体被分别作为不同的种处理。通过对野外居群样本的统计分析和对极端变异类型个体所进行的子代测定及其人工杂交,进一步证实上述性状是受多基因决定的数量性状,其变异幅度大,变异式样中并不存在任何程度的间断性,因而至少在本复合体内没有鉴别意义。因此,以往建立在上述性状变异基础上的3个类群(A.biformifolia Y.Z.Zhao;A.bockiana Diels和A.polydentata P.F.Tu et G.I.Xu)均不成立。最后,本文对形态性状变异的遗传基础及其与类群划分的关系进行了讨论。     

Biosystematic Studies on Adenophora potaninii Korsh. Complex (Campanulaceae) III. Genetic Variation and Taxonomic Value of Morphological Characters

Adenophora potaninii Korsh．complex is a morphologically variable group including six species．As shown in many species in the genus Adenophora,the variability of many morphological characters in the complex under investigation is amazingly great,which brings difficulties in the delimitation and indentification of taxa．In the present study,six populations representing five species in the complex were systematically sampled to investigate the pattern of morphological variation within population and to detect the genetic basis of the variation with progeny tests and controlled crosses．The results are as follows： Great morphological variation within population is found (Fig.1),including characters such as leaf shape,teeth number and size of leaf margins,teeth number of calyx lobes,and indumentum on the surface of stems and leaves,which were previously considered as diagnotic．Systematic sampling and statistical analysis show that the differences in the above characters exhibit continuous patterns of variation within population (Fig．1,2),though they are highly correlated (Table 2)．From progeny testing and crossing between two contrast types of individuals (oblong,dentate and pubescent leaves vs．narrow,entire and glabrous leaves)it is evident that those characters show continuous variability in segregating progenies (Fig.3,4)and appear to be influenced by large numbers of loci with individually slight effects．Since most wild populations were highly heterozygous for those characters,the individuals in one extreme of variation can produce their variable offsprings including individuals similar to those in the other extreme (Fig. 3). This is also true for the indumentum density on stems and teeth number of calyx lobes. In this complex, A. biformifolia Y. Z. Zhao, A. bockiana Diels and A. polydentata P.F. Tu et G. J. Xu were described exclusively based on leaf shapes, teeth number of leaf margins and calyx lobes, teeth size of leaf margins, and indumentum on the surface of stemsand leaves. It is demonstrated, however, that the variation of those characters is of a quantitative nature and show no discontinuities. As a result, genetic analysis of diagnostic characters along with their sympatric distribution and same habitats, strongly suggest that A.biformifolia as well as A. bockiana and A. polydentata are actually the extreme individuals within A. wawreana and A. potaninii respectively and should not be recognized as taxa at any taxonomic level.     

Taking phylogenetics beyond pattern analysis: can models of genome dynamics guide predictions about homoplasy in morphological and behavioral data sets?

Despite the considerable amount of interest in phylogeny reconstruction, patterns of homoplasy in morphological and behavioral data have received only limited attention to date, whereas the patterns of homoplasy in molecular data are relatively well understood. First, because the number of alternative molecular character states is strictly limited (particularly for nucleotide sequence data), higher rates of substitution generate higher levels of homoplasy. Second, depending on the relative proportions of constrained and unconstrained sites, each molecular data set has a time frame of applicability outside of which resolution becomes ambiguous. There is good evidence to suggest that numbers of alternative character states for morphological and even behavioral data may be similarly limited and that higher rates of evolution are often linked to higher rates of homoplasy. Like molecular data sets, morphological and behavioral data sets contain rapidly evolving characters as well as more conservative elements. Morphologies and behaviors related to sexual recognition and reproduction show low levels of intraspecific variation, but high levels of lability between species, making them crucial for species identification but often poor as markers of relationship at greater time depths. The organization theory of speciation derived by Carson is a model based on genome dynamics, and it predicts exactly this window of applicability for characters related to sexual reproduction. Nonsexual characters related to environmental adaptation should be applicable at greater phylogenetic depths. A better understanding of patterns of homoplasy enables a more sophisticated approach to the assessment of the relative reliabilities of alternative tree topologies.     

HOMOPLASY AS PATTERN: MULTIVARIATE ANALYSIS OF MORPHOLOGICAL CONVERGENCE IN ANSERIFORMES

Abstract— A multivariatc model for taxa and characters is presented that represents taxa as points in an ordination space such that shared derived character states define groups of taxa or regions in this space. This model is compared, in terms of concepts of information content and explanatory power, to the eladistie model that relates characters and taxa to a hierarchical pattern. While a cladogram may be identified with a phylogenetic hypothesis, the ordination pattern may be equated with hypotheses about similarities among the taxa in habitat, feeding mode, or other ecological factors.
This basic data-pattern model is appropriate for the explanation of the character convergences implied by a particular phylogenetic hypothesis. Under the assumptions of the model, the underlying ordination pattern may be inferred from the observed character data using robust ordination procedures recently developed in community ecology.
As an illustration of the method, the morphological convergences derived from a recent phylogenetic hypothesis for genera of Anseriformes are analysed. In the resulting two-dimensional ordination, the genera are arranged such that the convergenlly derived states form regions in the space. While this pattern implies that some of the taxa that are close together in the space are phylogcnetically dissimilar , taxa that are close together in the space are found to be similar in their mode of feeding. Thus, the ordination demonstrates that taxa sharing these morphological convergences tend to utilize habitat in the same way in terms of mode of feeding.
The explanatory power of the pattern and the degree of recovery of habitat information are tested against null hypotheses using Monte Carlo simulations.
Extensions of the method are discussed, including applications to studies of parasite—host relationships and to biogeography.     

Morphometric analysis of Alaskan members of the genus Potentilla sect. Niveae (Rosaceae)

A morphometric study of Potentilla nivea, P unijlora, and P hookeriana, as well as the close relative of the latter, P furcata, has been carried out, and the quantitative data subjected to Canonical Discriminant Analysis. The four taxa belong to the arctic-alpine section Niveae of Potentilla, and material for the analysis was collected in Alaska, U. S. A. The a priori defined groups are based on petiole hair type, the qualitative, and only, character traditionally used to distinguish taxa within Potentilla sect. Niveae. The hair types recognized previously by taxonomists have been vaguely defined, and the intraspecific variation of other morphological characters has never been discussed. Ordination by canonical discriminant analysis was performed to characterize mean differences among species, to obtain insight into group differences, and to estimate character weights from correlations between canonical variates and original variables. The four taxa differ significantly in the canonical analysis of six quantitative characters. Leaflet length, incision depth (length of leaflet teeth), and ovule number are shown to be the most important discriminators. A key to the four taxa, taking into account the intra- vesus interspecific variation, as well as character weights, is provided.     

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.     

Morphometrics and character state recognition for cladistic analyses in theBletia reflexa complex (Orchidaceae)

Different criteria have been suggested for decisions on character state recognition for morphological characters showing continuous variation from taxon to taxon. A method proposed byMishler andDe Luna seeks to recognize as many character states as the groups of taxon means that are revealed by an analysis of variance (ANOVA) followed by multiple range tests. We apply this method as a guide in decisions of selecting taxonomic characters in species of theBletia reflexa complex. Seven species of the complex, represented by 156 individuals belonging to 54 populations, were the terminal taxa of the study. Character state codes were assigned to 20 characters. These characters together with 12 non-quantitative characters were incorporated into cladistic analyses. Results indicate that the complex is monophyletic only under one outgroup combination.     

Morphological and molecular variation in tiger beetles of the Cicindela hybrida complex: is an ‘integrative taxonomy’ possible?

Current taxon assignments at the species level are frequently discordant with DNA-based analyses. Recent studies on tiger beetles in the Cicindela hybrida complex identified discordance between mtDNA patterns and the entities currently defined by the taxonomic literature. To test the accuracy of morphologically delimited groups, five named taxa (species) from 24 representative sampling sites across Europe were scored for 41 external morphological characters. Three of the named taxa were 'diagnosable', that is, defined by between one and three characters unique to each group. Newly sequenced ITS1 and existing mitochondrial cox1 markers established 20 and 22 different haplotypes, respectively, but only cox1 produced (four) diagnosable units. Phylogenetic analysis and statistical parsimony networks showed poor congruence of character variation with the taxonomic entities (and each other). Variation in morphological characters was therefore tested directly for association with DNA-based nesting groups at various hierarchical levels using permutational contingency analysis. Significant statistical associations of 11 (of 13 variable) morphological characters were observed with nesting groups from ITS1 and mitochondrial DNA markers, predominantly at the 4-step level. The analysis demonstrates the need for formal tests of congruence with morphological variation at the level of individual characters, a step that is omitted from recent studies of 'integrative taxonomy'. In addition, statistical correlation of particular morphological characters with DNA-based nesting groups can identify the lowest hierarchical level at which various character sets show congruence, as a means to define evolutionarily separated entities supported by diverse data sources.     

Of teeth and trees: A fossil tip‐dating approach to infer divergence times of extinct and extant squaliform sharks

Fossil tip‐dating allows for the inclusion of morphological data in divergence time estimates based on both extant and extinct taxa. Neoselachii have a cartilaginous skeleton, which is less prone to fossilization compared to skeletons of Osteichthyans. Therefore, the majority of the neoselachian fossil record is comprised of single teeth, which fossilize more easily. Neoselachian teeth can be found in large numbers as they are continuously replaced. Tooth morphologies are of major importance on multiple taxonomic levels for identification of shark and ray taxa. Here, we review dental morphological characters of squalomorph sharks and test these for their phylogenetic signal. Subsequently, we combine DNA sequence data (concatenated exon sequences) with dental morphological characters from 85 fossil and extant taxa to simultaneously infer the phylogeny and re‐estimate divergence times using information of 61 fossil tip‐dates as well as eight node age calibrations of squalomorph sharks. Our findings show that the phylogenetic placement of fossil taxa is mostly in accordance with their previous taxonomic allocation. An exception is the phylogenetic placement of the extinct genus ?Protospinax , which remains unclear. We conclude that the high number of fossil taxa as well as the comprehensive DNA sequence data for extant taxa may compensate for the limited number of morphological characters identifiable on teeth, serving as a backbone for reliably estimating the phylogeny of both extinct and extant taxa. In general, tip‐dating mostly estimates older node ages compared to previous studies based on calibrated molecular clocks.     

PATTERNS OF VARIATION IN LEVELS OF HOMOPLASY

Patterns of variation in levels of homoplasy were explored through statistical analyses of standardized consistency indexes. Data were obtained from 60 recent cladistic analyses of a wide variety of organisms based on several different kinds of characters. Consistency index is highly correlated with the number of taxa included in an analysis, with homoplasy increasing as the number of taxa increases. This observation is compatible with a simple model of character evolution in which 1) the probability of character-state change increases with the total number of branches in a tree and 2) the number of possible states of a character is limited. Consistency index does not show a significant relationship to the number of characters utilized in an analysis or to the taxonomic rank of the terminal taxa. When the relationship between consistency index and number of taxa is taken into account, there is no significant difference between plant and animal data sets in the amount of homoplasy. Likewise, the level of homoplasy in morphological and molecular data sets does not appear to differ significantly, although there are still too few molecular studies to be confident of this result. Future comparisons of consistency indexes, including studies along the lines established here, must take into account the influence of the number of taxa on homoplasy.     

Vagaries in the delimitation of character states in quantitative variation--an experimental study

An experimental study on the delimitation of character states in continuous variation indicates that (1) the way data are presented influences the assignment of character states and (2) states in the same data set are delimited in various ways by different individuals. Forty-nine individuals were given a set of graphs denoting variation of 10 characters in the genus Kalmia (Ericaceae) and outgroups, all identification having been removed from the graphs. The variation was represented in one of three ways: as 95% confidence intervals on a linear scale, as 95% confidence intervals on a log10 scale, or with bars showing SD x 2 on a linear scale. No two individuals scored a set of graphs in the same way, and only one character in one representation was scored identically by all individuals; the scoring for this character was completely different when the ordinate was changed from linear to logarithmic. Together, the 49 individuals delimited states within each character between 9 and 16 different ways. In general, variation represented by 2 x SD bars elicited the largest numbers of different scorings, yet with a relatively low number of states; the complexity of the patterns in the graphs in this representation was greatest. Expert knowledge appears to be of dubious value in delimiting states in such variation, and if such characters are to be used in phylogenetic analyses, states could be delimited by people who know nothing of the details of the study being scored; in any case, presentation of data and an explicit protocol to follow when delimiting states are essential. In converting data of this type into character states, psychological factors are particularly likely to come into play. Other implications of our experiments include the severe underdetermination of some phylogenetic hypotheses by observation and the heterogeneous nature of morphological data.     

Origins and relationships of primitive members of the Opisthobranchia (Mollusca: Gastropoda)

An examination of possible prosobranch precursors of opisthobranchs and pulmonates suggests that archaeogastropods are poor candidates, as they lack the complex female glands which characterize all higher gastropods. Similarities between members of the Rissoacea and Cerithiacea with the Opisthobranchia and Pulmonata are here considered to be a result of parallel evolution. Much of the basis for suggesting phylogenetic aRinities between members of these taxa hinges on the supposition that pyramidellids are opisthobranchs. This contention is questioned, as the euthyneurous nervous system and hermaphroditic reproductive system share weak structural and positional homologies with opisthobranchs. The range of morphological variation within the Pyramidellidae should be more thoroughly investigated, as this taxon is poorly known. The reproductive system of members of the Littorinacea is largely homologous with that found in the least derived opisthobranchs and pulmonates. This, when considered in conjunction with other morphological and palaeontological evidence, suggests that the least derived mesogastropods, the Littorinacea, provide a more precise model of the opisthobranch-pulmonate ancestor among living prosobranchs. The specialization of the digestive system in littorinaceans suggests that morphological divergence has taken place following the cladogenesis of these taxa, and that a direct ancestor/descendent relationship cannot be implied from extant littorinaceans. The status of Acteon and other acteonids as archetypal opisthobranchs is questioned. Moditication 01 all morphological systems, with the exception of the shell and mantle complex, diminish the position of the Acteonidae as ancestral opisthobranchs. Members of the Ringiculidae more closely approach the ancestral form, but have undergone modification, as well. No extant opisthobranch retains all plesiomorphic character states. For this reason, in addition to the fact that contusion exists as to the plesiomorphic conditions of some characters within the Opisthobranchia, a hypothetical ancestral opisthobranch is characterized. It appears that parallel evolution, which confounds the relationships of certain prosobranchs and opisthobranchs, is also evident within the Opisthobranchia. Much of the confusion that has surrounded the determination of phylogenetic relationships within the Opisthobranchia relates directly to the high incidence of parallelism throughout the subclass.     

The evolution of pharyngeal bones and teeth in Gobioninae fishes (Teleostei: Cyprinidae) analyzed with phylogenetic comparative methods

The subfamily Gobioninae is a subgroup in the specious fish family Cyprinidae, which bears high diversity in morphological and ecological dimensions and has its most components distributed in East Asia. In this study, the pharyngeal bones and teeth of 39 species belonging to 19 genera of the Gobioninae were examined, with the phylogenetic comparative method (PCM) and correlation methods employed to analyze the character evolution. Three characters on pharyngeal bones (shape of the pharyngeal bones, extension for attachment of the pharyngo-cleithralis internus posterior (PCIP) muscle, and teeth-bearing area) and six characters of pharyngeal teeth (shape of the five teeth in the main row, number of rows of the teeth) were identified and compared. When the character states were mapped on a molecular phylogenetic tree, it was found that, to adapt to different masticatory operations, different Gobioninae species have various morphological types of pharyngeal bones and teeth: some have intermediate pharyngeal bones bearing multiple rows of diverse teeth (conical, coarsely compressed, and compressed), others have broad pharyngeal bones bearing a single row of molar teeth, and still others have narrow pharyngeal bones bearing a single row of extremely compressed teeth. Tests on the phylogenetic signal and evolutionary associations revealed that evolution of the examined characters was all phylogenetically constrained and correlated. Owing to the homoplasy in evolution, it was suggested that the conventional method of using pharyngeal bones and teeth for phylogenetic reconstruction of cyprinid fishes should not be encouraged.     

When molecules and morphology clash: reconciling conflicting phylogenies of the Metazoa by considering secondary character loss

Molecular and morphological data sets have yielded conflicting phylogenies for the Metazoa. So far, no general explanation for the existence of this conflict has been suggested. However, I believe that a neglected aspect of metazoan cladistics has introduced a systematic and substantial bias into morphological phylogenetic analyses. Most characters used for metazoan cladistics are coded as binary absence/presence characters. For most of these characters, the absence states are assumed to be uninformative default plesiomorphies, if they are defined at all. This character coding strategy could seriously underestimate the number of informative apomorphic absences or secondary character losses. Because nodes in morphological metazoan phylogenies are typically supported by relatively small numbers of characters each with a potentially strong impact on tree topology, failure to distinguish between primary absence and secondary loss of characters before a cladistic analysis may mislead morphological cladistics. This may falsely suggest conflict with molecular phylogenies, which are not sensitive to this bias. To test the existence of this bias, I compare the phylogenetic placement of a variety of metazoan taxa in molecular and morphological trees. In all instances investigated here, phylogenetic conflict can be resolved by allowing for secondary loss of morphological characters, which were assumed to be primitively absent in cladistic analyses. These findings suggest that we should be cautious in interpreting the results of morphological metazoan cladistic analyses and additionally illustrate the value of a more functional approach to comparative morphology in certain circumstances.     

The accuracy of methods for coding and sampling higher-level taxa for phylogenetic analysis: a simulation study

Many phylogenetic analyses, particularly morphological studies, use higher taxa (e.g., genera, families) rather than species as terminal taxa. This general approach requires dealing with interspecific variation among the species that make up the higher taxon. In this paper, I review different parsimony methods for coding and sampling higher taxa and compare their relative accuracies using computer simulations. Despite their widespread use, methods that involve coding higher taxa as terminals perform poorly in simulations, relative to splitting up the higher taxa and using species as terminals. Among the methods that use higher taxa as terminals, coding a taxon based on the most common condition among the included species (majority or modal coding) is generally more accurate than other coding methods, such as coding taxa as missing or polymorphic. The success of the majority method, and results of further simulations, suggest that in many cases "common equals primitive" within variable taxa, at least for low and intermediate rates of character change. The fixed-only method (excluding variable characters) performs very poorly, a result that is indirectly supported by analyses of published data for squamate reptiles. Sampling only a single species per higher taxon also yields low accuracy under many conditions. Along with recent studies of intraspecific polymorphism, the results of this study show the general importance of (1) including characters despite variation within taxa and (2) using methods that incorporate detailed information on the distribution of states within variable taxa.