Character analysis in morphological phylogenetics: problems and solutions

Many aspects of morphological phylogenetics are controversial in the theoretical systematics literature and yet are often poorly explained and justified in empirical studies. In this paper, I argue that most morphological characters describe variation that is fundamentally quantitative, regardless of whether they are coded qualitatively or quantitatively by systematists. Given this view, three fundamental problems in morphological character analysis (definition, delimitation, and ordering of character states) may have a common solution: coding morphological characters as continuous quantitative traits. A new parsimony method (step-matrix gap-weighting, a modification of Thiele's approach) is proposed that allows quantitative traits to be analyzed as continuous variables. The problem of scaling or weighting quantitative characters relative to qualitative characters (and to each other) is reviewed, and three possible solutions are described. The new coding method is applied to data from hoplocercid lizards, and the results show the sensitivity of phylogenetic conclusions to different scaling methods. Although some authors reject the use of continuous, overlapping, quantitative characters in phylogenetic analysis, quantitative data from hoplocercid lizards that are coded using the new approach contain significant phylogenetic structure and exhibit levels of homoplasy similar to those seen in data that are coded qualitatively.     

A cladistic analysis of the nomadine bees (Hymenoptera: Apoidea)

Abstract. This study compares the results of Rozen's cladistic analysis of the larvae of fifteen genera of cleptoparasitic bees in the subfamily Nomadinae with an independent data set of adult characters for the same genera. Adult characters exhibited considerably higher levels of homoplasy and poorer resolution of cladistic relationships, with multiple equally parsimonious cladograms. However, comparison of a Nelson consensus tree based on adult characters with the cladogram based on larval characters reveals three components consistently supported in both analyses (the tribes Epeolini and Ammobatini, and Neopasites + Neolarra) , one component supported only by adult characters (Isepeolus + Protepeolus) , and one terminal component supported only by larval characters (Nomada + Ammobatini), as well as several more inclusive groupings based on larval characters that are difficult to compare with the adult consensus tree because it shows so much less resolution. When adult and larval characters are combined in a single data matrix, the resulting cladogram closely resembles the cladogram based on larval characters alone, although levels of homoplasy are considerably higher than in the larval analysis.
A preliminary analysis of adult characters for thirty-four genera in the Nomadinae also exhibited high levels of homoplasy and very large numbers of equally parsimonious cladograms. Nevertheless, certain consistent monophyletic groupings, most notably the Epeolini and Ammobatini, were also supported in this analysis. The one currently recognized tribe whose monophyly has received no support from any analysis is the Nomadini.
The relevance of these phylogenetic hypotheses to our understanding of host associations and variable features of egg morphology and oviposition behaviour in nomadine bees is briefly discussed.     

Phylogeny and biogeography of a large radiation of Andean lizards (Iguania, Stenocercus)

With 61 species occurring mostly in the Andes and adjacent lowland areas, Stenocercus lizards represent one of the most widespread and well-represented Andean vertebrate groups. Phylogenetic relationships among species of Stenocercus are inferred using different datasets based on mitochondrial DNA sequence data of 35 species and morphological data of 59 species. Among morphological data, polymorphic and meristic/morphometric characters are coded under the frequency parsimony and gap-weighting methods, respectively, and the accuracy of these methods is tested. When both types of characters are included, the resulting tree topology is more similar to the topologies obtained from analyses of DNA sequence data than those topologies obtained after exclusion of one or both types of characters. The phylogenetic hypotheses inferred including 59 species of Stenocercus (dataset 1) and excluding those species for which DNA data were not available (dataset 2) are generally congruent with each other, as well as with previously published hypotheses. The most parsimonious tree obtained from analysis of dataset 2 is used in a dispersal-vicariance analysis to infer ancestral areas and major biogeographical events. Species of Stenocercus are divided into two major clades. Clade A has diversified mostly in the central Andes, with a few species in the northern Andes and one species in the southern Andes. Clade B is more widespread, with species in the northern, central, and southern Andes, as well as in the Atlantic lowlands and Amazon basin. The most recent common ancestor of Stenocercus is inferred to have occurred in the eastern cordillera of the central Andes. Given morphological similarity and altitudinal distribution of some species nested in a northern-Andes clade, as well as the relatively recent uplift of this Andean region, it is possible that species in this clade have diverged as recently as the mid-Pliocene.     

Sensitivity analysis of different methods of coding taxonomic polymorphism: an example from higher-level bat phylogeny

New information concerning strengths and weaknesses of different methods of coding taxonomic polymorphisms suggests that results of some previous studies may have been unintentionally biased by the methods employed. In this study, we demonstrate that a form of sensitivity analysis can be used to evaluate the effects of different methods of coding taxonomic polymorphisms on the outcome of phylogenetic analyses. Our earlier analysis of higher‐level relationships of bats (Mammalia: Chiroptera) employed superspecific taxa as terminals and scored taxonomic polymorphisms using ambiguity coding. Application of other methods of dealing with polymorphisms (excluding variable characters, inferring ancestral states, majority coding) to the same data yields phylogenetic results that differ somewhat from those originally reported based on ambiguity coding. Monophyly of some clades was supported in all analyses (e.g., Microchiroptera, Rhinopomatoidea, and Nataloidea), while other groups found to be monophyletic in the original study (e.g., neotropical Nataloidea) appeared unresolved or nonmonophyletic when other methods were used to code taxonomic polymorphisms. Several groupings that were apparently refuted in the initial study (e.g., Noctilionoidea including Mystacinidae) were supported in some analyses, reducing some of the apparent incongruence between the trees in our earlier analysis (which were based principally on morphology) and other trees based on molecular data. Perceived support for various groupings (branch support, bootstrap values) were in some cases significantly affected by the methods employed. These results indicate that sensitivity analysis provides a useful tool for evaluating effects of different methods of dealing with taxonomic polymorphism in superspecific terminal taxa. Variation in results obtained with different methods suggests that it is always preferable to sample at the species level when higher‐level taxa exhibit taxonomic polymorphism, thus avoiding methodological biases associated with different methods of dealing with taxonomic polymorphisms during data analysis.     

A phylogenetic analysis of Tubificinae and Limnodriloidinae (Annelida, Clitellata, Tubificidae) using sperm and somatic characters

Marotta, R., Ferraguti, M. & Erséus, C. (2003). A phylogenetic analysis of Tubificinae and Limnodriloidinae (Annelida, Clitellata, Tubificidae) using sperm and somatic characters. — Zoologica Scripta , 32 , 255–278.
The spermatozoa and the sperm aggregates of 13 species belonging to four genera ( Smithsonidrilus, Limnodriloides, Thalassodrilides, Doliodrilus ) in the tubificid subfamily Limnodriloidinae (Annelida, Oligochaeta) were studied and compared with the spermatozoal patterns already described in the subfamily Tubificinae. Two characters considered exclusive for the Tubificinae were found in the more spermatologically variable Limnodriloidinae: the production of two kinds of spermatozoa, eusperm and parasperm, and the presence, in the spermathecae, of sperm aggregates formed by a combination of the two sperm types. A parsimony analysis was performed on the spermatozoal data of the species examined and compared with that based on the somatic characters of the same species: a critical revision of the already codified eusperm characters was carried out and the ultrastructure of parasperm was used as a new subset of spermatozoal characters. In a total evidence approach, a further parsimony analysis was run using a matrix combining both sets of characters. This analysis suggested that the double sperm line and the sperm aggregates composed of both eusperm and parasperm may well be homologous in tubificines and limnodriloidines. It thus supported the previous notion that Tubificinae and Limnodriloidinae are closely related and indicated that these subfamilies may be sister taxa.     

Generalized frequency coding: a method of preparing polymorphic multistate characters for phylogenetic analysis

A new method of coding polymorphic multiistate characters for phylogenetic analysis is presented. By dividing such characters into subcharacters, their frequency distributions can be represented with discrete states. Differential weighting is used to counter the effect of representing one character with multiple characters. The new method, generalized frequency coding (GFC), is potentially superior to previously used methods in that it incorporates more information and is applicable to both qualitative and quantitative characters. When applied to a previously published data set that includes both types of polymorphic multistate characters, the method performed well, as assessed with g1 and nonparametric bootstrap statistics and giving results congruent with those of other studies. The data set was also used to compare GFC with both gap-weighting and Manhattan distance step matrix coding. On these grounds and for philosophical reasons, we consider GFC to be a better estimator of phylogeny.     

Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes): effects of character exclusion, data partitioning and missing data

The phylogenetic relationships, biogeography and classification of, and morpho‐behavioral (M/B) evolution in, gamebirds (Aves: Galliformes) are investigated. In‐group taxa (rooted on representatives of the Anseriformes) include 158 species representing all suprageneric galliform taxa and 65 genera. The characters include 102 M/B attributes and 4452 nucleic acid base pairs from mitochondrial cytochrome b (CYT B), NADH dehydrogenase subunit 2 (ND2), 12S ribosomal DNA (12S) and control region (CR), and nuclear ovomucoid intron G (OVO‐G). Analysis of the combined character data set yielded a single, completely resolved cladogram that had the highest levels of jackknife support, which suggests a need for a revised classification for the phasianine galliforms. Adding 102 M/B characters to the combined CYT B and ND2 partitions (2184 characters) decisively overturns the topology suggested by analysis of the two mtDNA partitions alone, refuting the view that M/B characters should be excluded from phylogenetic analyses because of their relatively small number and putative character state ambiguity. Exclusion of the OVO‐G partition (with > 70% missing data) from the combined data set had no effect on cladistic structure, but slightly lowered jackknife support at several nodes. Exclusion of third positions of codons in an analysis of a CYT B + ND2 partition resulted in a massive loss of resolution and support, and even failed to recover the monophyly of the Galliformes with jackknife support. A combined analysis of putatively less informative, “non‐coding” characters (CYT B/ND2 third position sites + CR +12S + OVO‐G sequences) yielded a highly resolved consensus cladogram congruent with the combined‐evidence cladogram. Traditionally recognized suprageneric galliform taxa emerging in the combined cladogram are: the families Megapodiidae (megapodes), Cracidae (cracids), Numididae (guineafowls), Odontophoridae (New World quails) and Phasianidae (pheasants, pavonines, partridges, quails, francolins, spurfowls and grouse) and the subfamilies Cracinae (curassows, chachalacas and the horned guan), Penelopinae (remaining guans), Pavoninae sensu lato (peafowls, peacock pheasants and argus pheasants), Tetraoninae (grouse) and Phasianinae (pheasants minus Gallus). The monophyly of some traditional groupings (e.g., the perdicinae: partridges/quails/francolins) is rejected decisively, contrasted by the emergence of other unexpected groupings. The most remarkable phylogenetic results are the placement of endemic African galliforms as sisters to geographically far‐distant taxa in Asia and the Americas. Biogeographically, the combined‐data cladogram supports the hypothesis that basal lineages of galliforms diverged prior to the Cretaceous/Tertiary (K‐T) Event and that the subsequent cladogenesis was influenced by the break‐up of Gondwana. The evolution of gamebirds in Africa, Asia and the Americas has a far more complicated historical biogeography than suggested to date. With regard to character evolution: spurs appear to have evolved at least twice within the Galliformes; a relatively large number of tail feathers (≥ 14) at least three times; polygyny at least twice; and sexual dimorphism many times. © The Willi Hennig Society 2006.     

Ultrastructure of the spermatozoa of the flatworms Phaenocelis peleca and Boninia divae (Platyhelminthes, Polycladida)

The ultrastructure of spermatozoa of the acotylean Phaenocelis peleca and the cotylean Boninia divae is described. All spermatozoa are filiform and biflagellate with a 9+"1" microtubular pattern in the axoneme. Sperm characters in P. peleca follow the morphologies described for other acotyleans, with axonemes exiting the sperm shaft at the distal end and remaining in close contact with the sperm membrane. The nucleus occupies the proximal region of the shaft, and two types of dense bodies and mitochondria are located at the distal end. Unlike other members of the Cotylea, the axonemes of B. divae spermatozoa are incorporated into the sperm shaft, leaving the shaft at some distance from the distal end and then remaining free. This type of morphology is characteristic for acotyleans. Additionally, the spermatozoa of B. divae contain only one type of dense bodies plus a unique structure, which we call a central core. The nucleus in this species is unique as well; it shows periodic constrictions and rings of electron-dense granules, characters that further contribute to the distinct status of Boniniidae.     

Spermatozoa and sperm aggregates in the vestimentiferan Lamellibrachia luymesi compared with those of Riftia pachyptila (Polychaeta: Siboglinidae: Vestimentifera)

The spermatozoa and the sperm bundles of the vestimentiferans Riftia pachyptila and Lamellibrachia luymesi (Annelida: Siboglinidae) were studied using several microscopical techniques (transmission and scanning electron microscopy, and confocal microscopy) and compared with some other annelid sperm. The spermatozoa and sperm bundles of both species show a similar structure, but they differ in the dimensions of the components of individual cells and in the number of spermatozoa forming each sperm bundle. The spermatozoa of R. pachyptila and L. luymesi are filiform cells composed, in sequence, by an acrosome in the form of a thread-like helical vesicle, an elongated coiled nucleus surrounded by two helical mitochondria, and a long flagellum. In the spermatozoa of both species, the apical portion of the nucleus is completely devoid of chromatin and is delimited by a thickened nuclear envelope with a fibrillar appearance. Both species have sperm bundles that resemble buds, having a calyx-like portion formed by the helical heads, and a stalk-like portion formed by the tightly packed flagella. A parsimony analysis based on spermatozoal characters showed monophyly of the Siboglinidae and the Vestimentifera. We propose a new set of autapomorphies characterizing vestimentiferan spermatozoa. Our analysis suggests that spermatozoal characters are useful to the understanding of the phylogeny of the group.     

Comparative analysis of apoptotic pathways in rat, mouse, and hamster spermatozoa

Apoptosis is a type of cell death characterized by the activation of a family of cysteine-proteases called caspases. We made a comparative study to determine the presence of several caspases and other regulators of apoptosis in rat, mouse, and hamster spermatozoa. Our results showed that the three species have both active and inactive caspases-8 and -3, the proapoptotic protein BID, p53, and the endogenous caspase inhibitor cIAP-1. However, we did not find evidence for the presence of active caspase-9. The acrosome reaction (i.e., the exocytic process of sperm acrosome) and sperm viability were not affected by the presence of a general caspase inhibitor. On the other hand, valinomycin, which promotes caspase-dependent cell death in somatic cells, induced caspase-independent cell death in spermatozoa. TRAIL, a ligand whose receptor induces apoptosis in malignant cells, did not have any effect in the viability of mouse spermatozoa, despise the presence of its receptor in rat and mouse, but not in hamster spermatozoa. Therefore, our results strongly suggest that rodent spermatozoa have some components of the apoptotic pathway. However, the role of caspases in mammalian spermatozoa appears to be unrelated to sperm survival or to the acrosome reaction under physiological conditions.     

Large numbers of mice established by in vitro fertilization with cryopreserved spermatozoa: implications and applications for genetic resource banks, mutagenesis screens, and mouse backcrosses

Recent advances in the methodologies for cryopreservation of mouse spermatozoa have opened up a number of opportunities for mouse geneticists. We have investigated various applications for this relatively new technology and have explored the potential of sperm freezing coupled with IVF for archiving, stock building, and the rapid establishment of backcrosses. Firstly, we investigated the use of sperm freezing for the archiving of (C3H/HeH × BALB/c)F₁ progeny from a large-scale mutagenesis program. We have demonstrated that it is possible to establish efficient, comprehensive, and deep archives and that potentially thousands of offspring can be derived from the frozen spermatozoa of a single mutant male mouse. Secondly, we examined the efficacy of sperm freezing for a number of other genotypes. For at least some genotypes, frozen spermatozoa can be utilized to rapidly build stock far more quickly than by conventional methods. Finally, we demonstrated that it is feasible to use frozen spermatozoa from the mouse mutant archive for the rapid generation of mutant backcross progeny. Received: 8 February 1999 / Accepted: 5 May 1999     

Lipophilic compounds in femoral secretions of male collared lizards,Crotaphytus bicinctores (Iguania,Crotaphytidae)

In many lizards, chemical compounds from the femoral gland secretions are used in intraspecific communication, but most studies describing these chemicals are for lizard species included in the Scleroglossa clade, whereas lizards within the Iguanian clade have been much less studied, probably because these lizards were considered to rely more on visual cues. However, many iguanian lizards have abundant femoral secretions and are able of chemosensory conspecific recognition, which might be based on compounds secreted by femoral glands. By using GC–MS analyses, we found 58 lipophilic compounds in femoral gland secretions of male Great Basin collared lizard, Crotaphytus bicinctores (Iguania, Crotaphytidae). Main compounds were steroids (mainly two triunsaturated steroids and cholesterol), carboxylic acids (mainly hexadecanoic acid), waxy esters of long chain fatty acids, alcohols (mainly hexadecanol), aldehydes and other minor compounds. We compared these compounds with those found in other lizard species and discussed the potential signaling function of some compounds and how the xeric habitat of this lizard could have conditioned the composition of secretions.     

Phylogenetic relationships of corytophanid lizards (Iguania, Squamata, Reptilia) based on partitioned and total evidence analyses of sperm morphology, gross morphology, and DNA data

We conducted partitioned and combined Bayesian and parsimony phylogenetic analyses of corytophanid lizards (Iguania) using mtDNA, gross morphology, and sperm ultrastructure data sets. Bayesian and parsimony hypotheses showed little disagreement. The combined analysis, but not any of the partitioned ones, showed strong support for the monophyly of Corytophanidae and its three genera, Basiliscus , Corytophanes , and Laemanctus . Basiliscus is the sister taxon of a well-supported clade formed by Corytophanes and Laemanctus . The relationships of species within Basiliscus and Corytophanes received weak support, regardless of the method used. We defend those relationships as feasible and open to further testing. Data derived from the ultrastructure of spermatozoa are potentially a good source of characters for systematic inferences of Iguania and its major lineages. A Brooks Parsimony Analysis based on the geographic distributions of corytophanids and the phylogenetic tree obtained from the combined analysis suggested a Central American origin of the group, a recent colonization of northern South America, and the role of epeirogenic uplifts and the formation of lowlands during the late Tertiary in the differentiation of corytophanids.     

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.     

Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation

Iguanian lizards form a diverse clade whose members have been the focus of many comparative studies of ecology, behavior, and evolution. Despite the importance of phylogeny to such studies, interrelationships among many iguanian clades remain uncertain. Within the Old World clade Acrodonta, Agamidae is sometimes found to be paraphyletic with respect to Chamaeleonidae, and recent molecular studies have produced conflicting results for many major clades. Within the largely New World clade Pleurodonta, relationships among the 12 currently recognized major subclades (mostly ranked as families) have been largely unresolved or poorly supported in previous studies. To clarify iguanian evolutionary history, we first infer phylogenies using concatenated maximum-likelihood (ML) and Bayesian analyses of DNA sequence data from 29 nuclear protein-coding genes for 47 iguanian and 29 outgroup taxa. We then estimate a relaxed-clock Bayesian chronogram for iguanians using BEAST. All three methods produce identical topologies. Within Acrodonta, we find strong support for monophyly of Agamidae with respect to Chamaeleonidae, and for almost all relationships within agamids. Within Pleurodonta, we find strong Bayesian support for almost all relationships, and strong ML support for some interfamilial relationships and for monophyly of almost all families (excepting Polychrotidae). Our phylogenetic results suggest a non-traditional biogeographic scenario in which pleurodonts originated in the Northern Hemisphere and subsequently spread southward into South America. The pleurodont portion of the tree is characterized by several very short, deep branches, raising the possibility of deep coalescences that may confound concatenated analyses. We therefore also use 27 of these genes to implement a coalescent-based species-tree approach for pleurodonts. Although this analysis strongly supports monophyly of the pleurodont families, interfamilial relationships are generally different from those in the concatenated tree, and support is uniformly poor. However, a species-tree analysis using only the seven most variable loci yields higher support and more congruence with the concatenated tree. This suggests that low support in the 27-gene species-tree analysis may be an artifact of the many loci that are uninformative for very short branches. This may be a general problem for the application of species-tree methods to rapid radiations, even with phylogenomic data sets. Finally, we correct the non-monophyly of Polychrotidae by recognizing the pleurodont genus Anolis (sensu lato) as a separate family (Dactyloidae), and we correct the non-monophyly of the agamid genus Physignathus by resurrection of the genus Istiurus for the former Physignathus lesueurii.     

The effects of carnitine,glycerylphosphorylcholine, caffeine,and egg yolk on the motility of rat epididymal spermatozoa

Experiments were performed to further the understanding of epididymal processes involved in the acquisition of sperm motility. Samples of luminal contents were collected by micropuncture from four regions of the rat epididymis. These samples were incubated in various diluents to observe the effects of the diluents on sperm motility. Consonant with previous reports, 40 mM glycerylphosphorylcholine (GPC) and 60 mM DL-carnitine reduced overall motility scores of cauda epididymidal spermatozoa but did not prevent normal initiation of motility. Additionally, control sperm cells and cells treated with carnitine could reinitiate full motility after becoming immotile. Spermatozoa treated with GPC could not reinitiate motility. The sperm cells in our system thus react to GPC and carnitine in fundamentally different ways, the exact nature of which remains to be determined. Spermatozoa from the distal caput epididymidis evidenced high motility scores when diluted in a 5% egg yolk + 10 mM caffeine diluent. It was demonstrated, however, that the subjective appearance of full motility in these immature cells was not supported by actual progressive motility as measured in an assay of linear distance traveled. It was concluded that neither 10 mM caffeine, 5% egg yolk, nor their combination was sufficient to induce progressive motility in immature rat spermatozoa.     

The zymogen form of acrosin in testicular,epididymal, and ejaculated spermatozoa from ram

The sperm-specific proteinase acrosin (EC 3.4.21.10) is found in spermatozoa as a zymogen. We have looked for different forms of this zymogen in testicular, epididymal, and ejaculated spermatozoa from ram and have compared total sperm extracts made immediately after cell disruption with extracts made later from isolated sperm heads. We have concluded that the autoactivatable zymogen form, known generally as proacrosin, is the only form of acrosin within intact mature ram spermatozoa; no other zymogen form was detected, although lower levels of proacrosin were found in some samples of testicular spermatozoa. From studies of the activation process, it appears that ram proacrosin is truly autoactivatable; no evidence could be found for the involvement of any auxiliary enzyme. Estimations of the molecular weight of proacrosin using gel chromatography (60,000) and SDS-polyacrylamide gel electrophoresis (51,300) indicated that the zymogen is monomeric. Comparison with the molecular weight of ram acrosin (44,000 or 40,000, using the two respective methods) indicated that a single acrosin molecule is derived from each zymogen molecule. The sperm acrosin inhibitor (molecular weight 11,000 or 8,000) was present in testicular spermatozoa as well as in ejaculated spermatozoa; there was no evidence that it was produced as a result of zymogen activation.     

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.