Integration, phylogeny, and the hominid cranial base

Basicranial features were examined in catarrhine primates and early hominids in order to demonstrate how information about morphological integration can be incorporated into phylogenetic analysis. Hypotheses purporting to explain the functional and structural relationships of basicranial characters were tested using factor analysis. Characters found to be functionally or structurally related to each other were then further examined in order to determine whether there was evidence that they were phylogenetically independent. If phylogenetic independence could not be demonstrated, then the characters were presumed to be integrated and were grouped into a complex. That complex was then treated as if it were a single character for the purposes of cladistic analysis. Factor analysis revealed that five basicranial features may be structurally related to relative brain size in hominoids. Depending on how one defines phylogenetic independence, as few as two, or as many as all of those characters might be morphologically integrated. A cladistic analysis of early hominids based on basicranial features revealed that the use of integrated complexes had a substantial effect on the phylogenetic position of Australopithecus africanus, a species whose relationships are poorly resolved. Moreover, the use of complexes also had an effect on reanalyses of certain published cladistic data sets, implying that those studies might have been biased by patterns of basicranial integration. These results demonstrate that patterns of morphological integration need to be considered carefully in all morphology-based cladistic analyses, regardless of taxon or anatomical focus. However, an important caveat is that the functional and structural hypotheses tested here predicted much higher degrees of integration than were observed. This result warns strongly that hypotheses of integration must be tested before they can be adequately employed in phylogenetic analysis. The uncritical acceptance of an untested hypothesis of integration is likely to be as disruptive to a cladistic analysis as when integration is ignored.     

Inferring and testing hypotheses of cladistic character dependence by using character compatibility

The notion that two characters evolve independently is of interest for two reasons. First, theories of biological integration often predict that change in one character requires complementary change in another. Second, character independence is a basic assumption of most phylogenetic inference methods, and dependent characters might confound attempts at phylogenetic inference. Previously proposed tests of correlated character evolution require a model phylogeny and therefore assume that nonphylogenetic correlation has a negligible effect on initial tree construction. This paper develops "tree-free" methods for testing the independence of cladistic characters. These methods can test the character independence model as a hypothesis before phylogeny reconstruction, or can be used simply to test for correlated evolution. We first develop an approach for visualizing suites of correlated characters by using character compatibility. Two characters are compatible if they can be used to construct a tree without homoplasy. The approach is based on the examination of mutual compatibilities between characters. The number of times two characters i and j share compatibility with a third character is calculated, and a pairwise shared compatibility matrix is constructed. From this matrix, an association matrix analogous to a dissimilarity matrix is derived. Eigenvector analyses of this association matrix reveal suites of characters with similar compatibility patterns. A priori character subsets can be tested for significant correlation on these axes. Monte Carlo tests are performed to determine the expected distribution of mutual compatibilities, given various criteria from the original data set. These simulated distributions are then used to test whether the observed amounts of nonphylogenetic correlation in character suites can be attributed to chance alone. We have applied these methods to published morphological data for caecilian amphibians. The analyses corroborate instances of dependent evolution hypothesized by previous workers and also identify novel partitions. Phylogenetic analysis is performed after reducing correlated suites to single characters. The resulting cladogram has greater topological resolution and implies appreciably less change among the remaining characters than does a tree derived from the raw data matrix.     

中国慈姑属系统发育的研究

本文研究了中国慈姑属植物间的系统发育关系。选取了12个与该属系统发育有较重要关系的特征,将8个已知分类群与外类群刺果泽泻属进行了比较。应用数量分支分析的Farris-Wagner方法,建立了中国慈姑属系统发育分支图。讨论了各分类群间的系统发育关系、该属起源和数量分支分析方法等问题。     

Homologies in phylogenetic analyses—concept and tests

Analyzing morphological characters in a phylogenetic context comprises two steps, character analysis and cladistic analysis, which are equivalent to two independent tests for hypotheses on homology. The concept of homology concerns comparable parts of the same or different organisms if their correspondences are the consequence of the same genetic or epigenetic information, and consequently of the same origin. The concept of homology is more inclusive than the character concept. Characters are seen as parts of transformation series. In the first step of morphological character analyses correspondences and non-correspondences between two characters are analyzed. A range of different examination methods and accurate study contribute to the severity of test. The hypothesis that two characters are homologous is corroborated if the correspondences outweigh the non-correspondences because the non-correspondences contradict the homology hypothesis whereas the correspondences contradict the analogy hypothesis. Complex characters possess a higher empirical content than less complex characters because they are more severely testable. The cladistic analysis tests characters against other characters which have all passed the first test. Characters which are congruent with the most parsimonious topology are further corroborated; incongruent characters are not seen as ‘falsified’ but as not further corroborated and subject to re-analysis. To test both homologies and topologies repeatedly is consistent with Popperian testability, and it is in such cycles of research that hypotheses will be critically re-evaluated.     

A priori assumptions about characters as a cause of incongruence between molecular and morphological hypotheses of primate interrelationships

When molecules and morphology produce incongruent hypotheses of primate interrelationships, the data are typically viewed as incompatible, and molecular hypotheses are often considered to be better indicators of phylogenetic history. However, it has been demonstrated that the choice of which taxa to include in cladistic analysis as well as assumptions about character weighting, character state transformation order, and outgroup choice all influence hypotheses of relationships and may positively influence tree topology, so that relationships between extant taxa are consistent with those found using molecular data. Thus, the source of incongruence between morphological and molecular trees may lie not in the morphological data themselves but in assumptions surrounding the ways characters evolve and their impact on cladistic analysis. In this study, we investigate the role that assumptions about character polarity and transformation order play in creating incongruence between primate phylogenies based on morphological data and those supported by multiple lines of molecular data. By releasing constraints imposed on published morphological analyses of primates from disparate clades and subjecting those data to parsimony analysis, we test the hypothesis that incongruence between morphology and molecules results from inherent flaws in morphological data. To quantify the difference between incongruent trees, we introduce a new method called branch slide distance (BSD). BSD mitigates many of the limitations attributed to other tree comparison methods, thus allowing for a more accurate measure of topological similarity. We find that releasing a priori constraints on character behavior often produces trees that are consistent with molecular trees. Case studies are presented that illustrate how congruence between molecules and unconstrained morphological data may provide insight into issues of polarity, transformation order, homology, and homoplasy.     

Cladistic Analysis of Human Evolution: Some Points on Character Selection

Cladistic analysis strongly depends on accurate character choice. Usually, characters include morphology or molecules, but other sources of evidence are also employed. These include stratigraphic ages of taxa and behavioural data. The inclusion of time is a controversial issue, which has no Darwinian basis. However, the cladistic treatment of stratigraphic age has the potential to resolve problematic phylogenies. Here, it is proposed that the use of stratigraphic data in phylogenetic inference should be seen as a temporary shortcut, to resolve complex phylogenies in the wait for new character and taxonomic samplings, because phylogenetic hypotheses should be based on biological evidence only. Archaeologists working on toolmaking can provide behavioural data in human prehistory. In fact, while a tool itself is not biological evidence, the movements of hands and arms needed to prepare it are biological evidence and can be compared and scored for cladistic analysis. Such an approach has been formalized in studies on functional morphology of some vertebrates. The taxonomic data set to be used in cladistic analysis should include as many taxa as possible, and also very incomplete specimens should be used. In many cases, incomplete specimens had the potential to resolve complex phylogenies by adding new character combinations that cannot be scored in molecule-based phylogenetic studies.     

How much can cladistics tell us about early hominid relationships?

Although cladistic analysis has been used to compare hypotheses of relationships among early hominids, the outcomes of different studies have depended entirely on the assumptions made by different investigators. Problems include the close genetic relationship of early hominid taxa, small fossil sample sizes, possible correlations among characters, and a lack of understanding about the evolutionary factors affecting characters. This study investigates the interaction of some of these problems affecting early hominid phylogenetics. Monte Carlo simulations of character state evolution in closely related taxa demonstrate that the sample sizes and close genetic relationships of early hominids do not permit cladistic analyses to obtain unequivocal results. Even with unrealistically good assumptions about the evolutionary dynamics affecting characters, the probability of the most parsimonious hypothesis being true is unacceptably small. In the face of these problems, even phylogenetic statements that are supported by a strong consensus of cladistic studies may nevertheless be in error, and such errors are likely to confound the placement of new specimens and taxa. Advancement in our knowledge of hominid phylogeny can depend only on a fuller understanding of the natural history and evolutionary dynamics of traits.     

Phylogeny reconstruction in the neogene bryozoan metrarabdotos: A paleontologic evaluation of methodology

An adequate stratigraphic record can not only aid in both cladistic and stratophenetic reconstruction of phytogenies, but can also serve in estimating the temporal consistency of the resulting phylogenetic trees. For hypothetical data sets, cladistically constructed trees can be as consistent with the temporal distribution of sampled populations or species as those constructed stratophenetically. Empirical testing in taxonomic groups with sufficiently dense fossil records is needed to show whether, and under what conditions, this potential can be realized. A stratophenetic tree and cladistic trees based on several approaches to character weighting were constructed for Caribbean Neogene species of the bryozoan Metrarabdotos with multiple‐character data from closely spaced sequential populations. The modular morphology and highly punctuated evolutionary pattern of these species blur the distinction between continuous and discrete characters, so that all available characters are potentially of equal significance in establishing phytogenies, rather than just those with discrete states conventionally used in cladistic analysis. However, only the cladistic trees generated with all characters weighted to emphasize contribution to species discrimination have temporal consistencies that are clearly significant statistically and approach that of the stratophenetic tree in magnitude. These results provide a start toward establishing general guidelines for cladistic analysis of taxa with stratigraphie records too sparse for stratophenetic reconstruction.     

Phylogenetic relationships among families of the Scaphopoda (Mollusca)

Phylogenetic relationships among families in the molluscan class Scaphopoda were analysed using morphological characters and cladistic parsimony methods. A maximum parsimony analysis of 34 discrete characters, treated as unordered and equally weighted, from nine ingroup terminal taxa produced a single most parsimonious tree; supplementary analyses of tree length frequency distribution and Bremer support indices indicate a strong phylogenetic signal from the data and moderate to minimally supported clades. The traditional major division of the class, the orders Dentaliida and Gadilida, is supported as both taxa are confirmed as monophyletic clades. Within the Dentaliida, two clades are recognized, the first comprised of the families Dentaliidae and Fustiariidae, the second of the Rhabdidae and Calliodentaliidae; together, these groups comprise a third clade, which has the Gadilinidae as sister. Within the Gadilida, a nested series of relationships is found among [Entalinidae, [Pulsellidae, [Wemersoniellidae, Gadilidae]]]. These results lend cladistic support to earlier hypotheses of shared common ancestry for some families, but are at variance with other previous hypotheses of evolution in the Scaphopoda. Furthermore, analysis of constituent Gadilinidae representatives provide evidence for paraphyly of this family. The relationships supported here provide a working hypothesis that the development of new characters and greater breadth of taxonomic sampling can test, with a suggested primary goal of establishing monophyly at the family level.     

Angiosperm wood evolution and the potential contribution of paleontological data

Wood anatomy is often viewed as a source of independent data that may be used to assess evolutionary relationships among angiosperms. Comparative anatomical studies document suites of correlated characters that have been interpreted as general evolutionary trends, of which several have been asserted to be irreversible. Paleobotanical data summarized by Wheeler and Baas provide broad chronological corroboration of some wood anatomical trends, such as evolution from scalariform to simple perforation plates and long to short vessel elements. However, the focus on general evolutionary trends rather than on analyzing character distribution patterns in a cladistic phylogenetic context obscures a more detailed understanding of the evolution of wood anatomical features. Patterns of character evolution, including the assertions of irreversibility, need to be tested through cladistic analyses. In this paper selected wood anatomical features from families of Magnoliidae and “lower” Hamamelididae are summarized and mapped onto previously published cladograms as a preliminary means of testing previous hypotheses of wood evolution. The results show that many of the characters are homoplasious and have evolved both in accord with, and counter to, the hypothesized general trends in different groups of flowering plants. In general, changes that confirm generalized trends are more common than changes that are counter to those trends. Future studies should combine wood anatomical characters with other features as part of a cladistic analysis. Fossil woods have not yet contributed significantly to phylogenetic studies, but in the very few cases where they have been linked to fossil reproductive structures, the woods have provided a better understanding of wood anatomy in early members of some families. Data from fossil wood expand the diversity of anatomical structure known in some angiosperm taxa and thus provide additional evidence that might be used in phylogenetic analyses. Fossil woods have the greatest potential to affect phylogenetic analyses where they can be linked to other fossil organs. The best chance for establishing such a linkage is through the study of fossil charcoalified woods that co-occur with other dispersed mesofossils.     

Conodonts Meet Cladistics: Recovering Relationships and Assessing the Completeness of the Conodont Fossil Record

A numerical cladistic analysis of the conodont family Palmatolepidae has been undertaken to determine the applicability of the technique to group-wide systematic revision. Results suggest a new hypothesis of relationships that is considerably more parsimonious than trees compatible with existing hypotheses of relationships, or trees that are even loosely constrained stratigraphically. This may occur either because the fossil record is incomplete, because taxon sampling for the cladistic analysis is low, or because the most parsimonious trees approximate the true tree less well than do stratigraphically-constrained trees (or because of a combination of these factors). Although more taxa and more characters would be preferable in choosing between these possibilities, the tree derived solely from morphological data is adopted. Thus, stratigraphic data can be used to test hypotheses of relationships and construct phylogenies; hypotheses of relationships can be used to test the completeness of the conodont fossil record. Existing schemes of classification within the Palmatolepidae are rejected because most groups within them are either polyphyletic or paraphyletic. A new scheme is presented. Character changes suggest correlated, progressive and mosaic evolution within the Palmatolepidae. Parsimony analysis of partitioned datasets indicates that more phylogenetic information can be recovered from S rather than P or M element positions, although data from all three positional groups are preferable to data from just one. Thus, multielement taxonomy is essential to the resolution of conodont interrelationships.     

Phylogenetic evidence for the herbaceous origin of angiosperms

The ancestral angiosperm is commonly interpreted as an arborescent to shrubby magnolialean with large, multiparted, complex flowers. We examined this hypothesis using a phylogenetic analysis of new and reevaluated characters polarizabled with outgroup comparison. Our cladistic analysis of basal angiosperms placed the nonmagnolialeanChloranthaceae andPiperaceae at the bottom of the tree. We further inferred the probable ancestral states of characters not polarizable with outgroup comparison by examining their distribution among taxa at the base of our cladogram. The sum of ancestral character states suggests that the protoangiosperm was a diminutive, rhizomatous to scrambling perennial herb, with small, simple flowers.     

Cranial shape and correlated characters in crocodilian evolution

Crocodilians show a high degree of cranial variation and convergence throughout their 80 million-year fossil record that complicates their phylogenetic reconstruction. Conflicting phylogenetic results from different data partitions and character homoplasies typify crocodilian phylogeny, and differences between molecular and morphological phylogenetic hypotheses are believed to be associated with the slender-snout skull shape of Gavialis gangeticus and Tomistoma schlegelii. Slender-snout skulls are one of five identified eusuchian cranial ecomorph shape categories (ESCs) thought to reflect functional or ecological specialization. This paper tested the effect of transitions among general, blunt and slender ESCs on cranial character-state distributions in phylogeny using the concentrated changes test. In addition, 'tree-free' character compatibility analysis of character independence was conducted on the morphological character matrix to determine if character correlations are observed independent of specific tree topologies. Results suggest cranial ESCs do affect cranial character-state gains in phylogeny. Concentrated changes identify a broad suite of character-state changes that significantly correlate with transitions to slender, general and blunt ESCs on morphological, molecular and combined-data tree topologies, but numbers of correlated characters for each category differ according to topology. Character compatibility analysis results do not mirror the concentrated changes test results and reflect hierarchically distributed support throughout the data. As cranial ESCs affect character-state transitions, it is possible that nonphylogenetic variables could affect inferences of crocodilian phylogeny by affecting cranial morphology.     

Meta-analysis of character utility and phylogenetic information content in cladistic studies of ammonoids

While previous workers have argued persuasively that ammonoid workers should use cladistic approaches to reconstruct phylogeny, relatively few cladistic studies have been published to date. An essential yet challenging part of cladistic analysis is the selection of characters. Are certain types of characters more likely to show homoplasy? Are certain aspects of shell anatomy more likely to contain phylogenetically informative characters? Are datasets with more characters inherently better? To answer these questions, a meta-analysis of character data from published ammonoid phylogenies was performed. I compiled 14 datasets, published between 1989 and 2007, representing parsimony-based phylogenetic analyses of ammonoids. These studies defined a combined total of 323 characters, which were grouped into categories reflecting different aspects of anatomy: shell size and shape, ornament, suture, early ontogeny, body chamber and apertural modifications. Tree searches were re-run to determine overall tree statistics, parsimony permutation tail probability (PTP) tests were calculated to assess the phylogenetic information content of the matrices, and retention and rescaled consistency indices for each character were calculated. My analyses revealed that studies with higher character/taxon ratios did not necessarily produce trees with more information content and less homoplasy, as measured by retention or rescaled consistency indices, because additional characters were often parsimony-uninformative. Rather, studies with relatively few characters could produce high-quality trees if the characters were well-chosen and character states carefully defined. Characters related to the body chamber and adult aperture typically had retention indices of either 0 or 1, rarely in between, indicating that they either worked perfectly or not at all. Suture characters tended to have higher indices than shell shape or ornament characters, suggesting more phylogenetic information and less homoplasy in the suture line than in shell traits. These results should aid in the selection of characters for future cladistic studies of ammonoids.     

Fossils and ferns in the resolution of land plant phylogeny

Fifty-two taxa of living and extinct vascular plants were evaluated in an unconstrained numerical cladistic analysis using 101 morphological characters to simultaneously resolve the phylogenetic relationships of ferns sensu lato. Included in the analysis were ferns assignable to the Cladoxylales, Stauropteridales, Rhacophytales, Zygopteridales, Ophioglossales, Marattiales, Filicales, and Hydropteridales, as well as a rhyniophyte, a trimerophyte, equisetophytes, lignophytes, and the psilotophytesPsilotum andTmesipteris. The results placed ferns and fernlike plants in three distinct clades, indicating that ferns s.l. are a polyphyletic grade group. Fern clades consist of extinct stauropterids; extinct cladoxylaleans, rhacophytaleans, and zygopteridaleans; and eusporangiates and leptosporangiates with living and extinct species. Psilotophytes occur near the base of the tree rather than nesting with the Filicales, as hypothesized by some. These results place Ophioglossales as the sister group to Marattiales plus the leptosporangiates, supporting the hypothesis that Ophioglossales represent ferns rather than progymnosperms. These analyses are a first attempt, which includes extinct plants, to develop cladistic hypotheses for the overall topology of fern phylogeny and to lay the groundwork for more detailed analyses of relationships among the homosporous leptosporangiates.     

HYBRIDS AND PHYLOGENETIC SYSTEMATICS I. PATTERNS OF CHARACTER EXPRESSION IN HYBRIDS AND THEIR IMPLICATIONS FOR CLADISTIC ANALYSIS

Interspecific hybridization is considered common among plants, but the methods of cladistic systematics produce only divergently branching phylogenetic hypotheses and thus cannot give the correct phylogeny if an analysis includes hybrids. Empirical studies of the impact of known hybrids on phylogenetic analysis are lacking, and are necessary to begin to understand the problems that we face if hybrids are often included in cladistic analysis. Examination of the implications of hybrids for cladistics must begin with patterns of character expression in hybrids. This study includes 17 hybrids and their nine parental taxa that are Central American species of Aphelandra (Acanthaceae), analyzed using a set of 50 morphological characters. The hybrids are overwhelmingly intermediate as quantitatively scored for phylogenetic analysis. They express maternal and paternal, and primitive and derived characters in equal frequencies, showing no evidence of predominant inheritance of derived character states as has been assumed by most cladists who have considered hybrids theoretically. Because of their known genetic constitution, hybrids were useful in homology assessment and ordering character states. The parental character set was generally robust, but some changes were made to reflect the special evidence offered by the hybrids. These hybrids suggest that the inclusion of hybrids in phylogenetic analysis will not lead to unresolved cladograms with rampant homoplasy, as has been predicted by other authors. Instead, the patterns of character inheritance in these hybrids lead to the prediction that a hybrid will be placed by phylogenetic analysis as a basal lineage to the clade that includes its most derived parent, with relatively little effect on homoplasy. These predictions will be evaluated by incorporation of the hybrids in phylogenetic analyses, to be reported in a subsequent paper.     

Evolution of the Vertebrate Central Nervous System: Patterns and Processes

AS brains do not fossilize, most proposed phylogenetic sequencesfor central nervous system characters must be based on the patternsof variation of those characters in living organisms. Similarly,hypotheses regarding how brains change through time, and theevolutionary processes that produce these changes, are ultimatelybased on the character patterns recognized. It is critical inthese analyses to distinguish between homologous and homoplasouscharacters if errors in the reconstruction and interpretationof phylogenies are to be minimized. Definitions of homologyand homoplasy are reviewed, as are the concepts that bear ontheir application. Cladistic definitions are adopted, and criteriafor distinguishing homologous from homoplasous characters arediscussed. Analysis of a number of CNS characters that are usuallyassumed to be homologous reveals that homoplasous charactersappear among them. As in other organ systems, homoplasous charactersare actually common. A number of previous hypotheses regardingCNS evolution are reviewed in the context of new data on neuralconnections and their cladistic analysis. Some of these hypothesesmay be falsified by a cladistic treatment of CNS characters,whereas sufficient data do not exist to evaluate others.     

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.     

PHYLOGENETIC INTERRELATIONSHIPS AND REDUCTIVE EVOLUTION IN NEOTROPICAL CHARACIDIIN FISHES (CHARACIFORMES, OSTARIOPHYSI)

Abstract— Miniaturization, which results in the presence of numerous apparently paedomorphic characters associated with reduced size, is a common phenomenon among neotropical fishes, with over 85 miniature species distributed among the five major ordinal groups. Eleven species are recognized as miniatures within the Characidiinae, a monophyletic subunit of Characiformes. A reconstruction of characidiin phylogeny is used to analyze the history of miniaturization events. Former hypotheses of origin of miniaturization among characidiins are rejected, underscoring the need for phylogenetic frameworks in the study of ontogenetic changes associated with the phenomenon of miniaturization. The 11 instances of miniature species can be most parsimoniously attributed to three independent miniaturization events within the Characidiinae.
Reductive characters comprise a large proportion of phylogenetically informative characters within the Characidiinae. In the largest group of miniatures, reductive characters represent more than half of the character state transformations affecting supraspecific relationships among Elachocharax, Klausewitzia, Odontocharacidium and Microcharacidium . An analysis of patterns of character state distributions fails to reject the null hypothesis of character independence. A distinction is made between the concepts of character independence, defined as the origination of character states from different (non-simultaneous) evolutionary events, and character correlation, defined as the association of character states in terminal taxa. Character correlation is not a sufficient criterion to reject Hennig's auxiliary principle, according to which the "presence of apomorphous characters in different species is always reason for suspecting kinship, and their origin by convergence should not be assumed a priori". High values of character correlation are the expected result of congruent patterns of character distribution.     

Inferring hominoid and early hominid phylogeny using craniodental characters: the role of fossil taxa

Recent discoveries of new fossil hominid species have been accompanied by several phylogenetic hypotheses. All of these hypotheses are based on a consideration of hominid craniodental morphology. However, Collard and Wood (2000) suggested that cladograms derived from craniodental data are inconsistent with the prevailing hypothesis of ape phylogeny based on molecular data. The implication of their study is that craniodental characters are unreliable indicators of phylogeny in hominoids and fossil hominids but, notably, their analysis did not include extinct species. We report here on a cladistic analysis designed to test whether the inclusion of fossil taxa affects the ability of morphological characters to recover the molecular ape phylogeny. In the process of doing so, the study tests both Collard and Wood's (2000) hypothesis of character reliability, and the several recently proposed hypotheses of early hominid phylogeny. One hundred and ninety-eight craniodental characters were examined, including 109 traits that traditionally have been of interest in prior studies of hominoid and early hominid phylogeny, and 89 craniometric traits that represent size-corrected linear dimensions measured between standard cranial landmarks. The characters were partitioned into two data sets. One set contained all of the characters, and the other omitted the craniometric characters. Six parsimony analyses were performed; each data set was analyzed three times, once using an ingroup that consisted only of extant hominoids, a second time using an ingroup of extant hominoids and extinct early hominids, and a third time excluding Kenyanthropus platyops. Results suggest that the inclusion of fossil taxa can play a significant role in phylogenetic analysis. Analyses that examined only extant taxa produced most parsimonious cladograms that were inconsistent with the ape molecular tree. In contrast, analyses that included fossil hominids were consistent with that tree. This consistency refutes the basis for the hypothesis that craniodental characters are unreliable for reconstructing phylogenetic relationships. Regarding early hominids, the relationships of Sahelanthropus tchadensis and Ardipithecus ramidus were relatively unstable. However, there is tentative support for the hypotheses that S. tchadensis is the sister taxon of all other hominids. There is support for the hypothesis that A. anamensis is the sister taxon of all hominids except S. tchadensis and Ar. ramidus. There is no compelling support for the hypothesis that Kenyanthropus platyops shares especially close affinities with Homo rudolfensis. Rather, K. platyops is nested within the Homo + Paranthropus + Australopithecus africanus clade. If K. platyops is a valid species, these relationships suggest that Homo and Paranthropus are likely to have diverged from other hominids much earlier than previously supposed. There is no support for the hypothesis that A. garhi is either the sister taxon or direct ancestor of the genus Homo. Phylogenetic relationships indicate that Australopithecus is paraphyletic. Thus, A. anamensis and A. garhi should be allocated to new genera.