Morphological, palaeontological and molecular aspects of ichneumonoid phylogeny (Hymenoptera, Insecta)

Ichneumonoid phylogeny is revised on the basis of morphological, palaeontological and molecular evidence. The only previous formal cladistic study of the phylogeny of the families of the superfamily Ichneumonoidea made many assumptions about what families lower taxa belonged to and was based on a very limited set of characters, nearly all of which were uninformative at family level. We have subdivided both Ichneumonidae and Braconidae into major groups, investigated several new character systems, reinterpreted some characters, scored several character states for extinct taxa by examining impression fossils using environment chamber scanning electron microscopy, and included data for a significant new subfamily of Braconidae from Cretaceous amber of New Jersey. Sixteen different variants of the data set were each subjected to parsimony analysis without weighting and with successive approximations weighting employing both maximum and minimum values of both the retention and rescaled consistency indices. Each analysis resulted in one of seven different strict consensus trees. Consensus trees based on subsets of these trees, selected on the basis of the optimal character compatibility index (OCCI), resulted in an eighth distinct tree. All trees had the Braconidae monophyletic with the Trachypetinae as the basal clade, and also had a clade comprising various arrangements of Apozyginae, the Rhyssalinae group, Aphidiinae and 'other cyclostomes', but relationships among the remaining braconid groups varied between trees. Only one of the consensus trees had the Ichneumonidae (including Tanychorella ) monophyletic. The Eoichneumonidae + Tanychora are the sister group the Braconidae in two of the consensus trees. Paxylommatinae were basal in the clade comprising the Eoichneumonidae + Tanychora and the Braconidae. The preferred tree, based on the highest OCCI was used for interpreting character state transitions.     

Corroboration among Data Sets in Simultaneous Analysis: Hidden Support for Phylogenetic Relationships among Higher Level Artiodactyl Taxa

In the taxonomic congruence approach to systematics, data sets are analyzed separately, and corroboration among data sets is indicated by replicated components in topologies derived from the separate analyses. By contrast, in the total evidence and conditional combination approaches, characters from different data sets are mixed in combined phylogenetic analyses. In optimal topologies derived from such simultaneous analyses, support for a particular node may be attributed to one, some, or all of the individual data sets. Partitioned branch support (PBS) is one technique for describing the distribution of character support and conflict among data sets in simultaneous analysis. PBS is analogous to branch support (BS), but recognizes hidden support and conflicts that emerge with the combination of characters from different data sets. For both BS and PBS, support for a particular node is interpreted as the difference in cost between optimal and suboptimal topologies. A different measure, the clade stability index (CSI), assesses the robustness of a particular node through the successive removal of characters. Here, we introduce variations of the CSI, the data set removal index (DRI) and nodal data set influence (NDI), that indicate the stability of a particular node to the removal of entire data sets. Like PBS, the DRI and NDI summarize the influence of different data sets in simultaneous analysis. However, because these new methods and PBS use different perturbations to assess stability, DRI and NDI scores do not always predict PBS scores and vice versa. In this report, the DRI and NDI are compared to PBS and taxonomic congruence in a cladistic analysis of 17 data sets for Artiodactyla (Mammalia). Five indices of hidden support and conflict are defined and applied to the combined artiodactyl character set. These measures identify substantial hidden support for controversial relationships within Artiodactyla. Hidden character support is ignored in the taxonomic congruence approach to systematics, but the DRI, NDI, and PBS utilize this cryptic information in estimates of support among data sets for a given node.     

Phyletic patterns of early development in gastropod molluscs

Cell lineage data for 30 exemplar gastropod taxa representing all major subclades and the outgroup Polyplacophora were examined for phylogenetic signal using cladistic analysis. Most cell lineages show phyletic trends of acceleration or retardation relative to the outgroup and more basal ingroup taxa, and when coded this variation is phylo-genetically informative. PAUP analyses of a cell lineage data set under three sets of character ordering assumptions produced similar tree topologies. The topologies of the strict consensus trees for both ordered and Dollo (near irreversibility of character transformations) character assumptions were similar, whereas the unordered character assumption recovers the least phyletic information. The cell lineage cladograms are also in agreement with the fossil record of the timing and sequence of gastropod subclade origination. A long branch lies between the Patellogastropoda+Vetigastropoda grade and the Neritopsina+Apogastropoda clade. The geological timing of this long branch is correlated with the first large-scale terrestrially derived eutrophication of the near-shore marine habitat, and one possible explanation for this branch may be a developmental shift associated with the evolution of feeding larvae in response to the more productive conditions in the near-shore water column. Although character transformations are highly ordered in this data set, developmental rate characters (like all other morphological and molecular characters) are also subject to homoplasy. Finally, this study further supports the hypothesis that early development of gastropod molluscs has conserved a strong phyletic signal for about half a billion years.     

Minority rule supertrees? MRP,Compatibility, and Minimum Flip may display the least frequent groups

New examples are presented, showing that supertree methods such as matrix representation with parsimony, minimum flip trees, and compatibility analysis of the matrix representing the input trees, produce supertrees that cannot be interpreted as displaying the groups present in the majority of the input trees. These methods may produce a supertree displaying some groups present in the minority of the trees, and contradicted by the majority. Of the three methods, compatibility analysis is the least used, but it seems to be the one that differs the least from majority rule consensus. The three methods are similar in that they choose the supertree(s) that best fit the set of input trees (quantified as some measure of the fit to the matrix representation of the input trees); in the case of complete trees, it is argued that, for a supertree method to be equivalent to majority rule or frequency difference consensus, two necessary (but not sufficient) conditions must be met. First, the measure of fit between a supertree and an input tree must be symmetrical. Second, the fit for a character representing a group must be measured as absolute: either it fits or it does not fit. In the restricted case of complete and equally resolved input trees, compatibility analysis (unlike MRP and minimum flipping) fulfils these two conditions: it is symmetrical (i.e., as long as the trees have the same taxon sets and are equally resolved, the number of characters in the matrix representation of tree A that require homoplasy in tree B is always the same as the number of characters in the matrix representation of tree B that require homoplasy in tree A) and it measures fit as all‐or‐none. In the case of just two complete and equally resolved input trees, the two conditions (symmetry and absolute fit) are necessary and sufficient, which explains why the compatibility analysis of such trees behaves as majority consensus. With more than two such trees, these conditions are still necessary but no longer sufficient for the equivalence; in such cases, the compatibility supertree may differ significantly from the majority rule consensus, even when these conditions apply (as shown by example). MRP and minimum flipping are asymmetric and measure various degrees of fit for each character, which explains why they often behave very differently from majority rule procedures, and why they are very likely to have groups contradicted by each of the input trees, or groups supported by a minority of the input trees. © The Willi Hennig Society 2005.     

Assessing progress in systematics with continuous jackknife function analysis

Systematists expect their hypotheses to be asymptotically precise. As the number of phylogenetically informative characters for a set of taxa increases, the relationships implied should stabilize on some topology. If true, this increasing stability should clearly manifest itself if an index of congruence is plotted against the accumulating number of characters. Continuous jackknife function (CJF) analysis is a new graphical method that portrays the extent to which available data converge on a specified phylogenetic hypothesis, the reference tree. The method removes characters with increasing probability, analyzes the rarefied data matrices phylogenetically, and scores the clades shared between each of the resulting trees and the reference tree. As more characters are removed, the number of shared clades must decrease, but the rate of decrease will depend on how decisively the data support the reference tree. Curves for stable phylogenies are clearly asymptotic with nearly 100% congruence for a substantial part of the curve. Less stable phylogenies lose congruent nodes quickly as characters are excluded, resulting in a more linear or even a sigmoidal relationship. Curves can be interpreted as predictors of whether the addition of new data of the same type is likely to alter the hypothesis under test. Continuous jackknife function analysis makes statistical assumptions about the collection of character data. To the extent that CJF curves are sensitive to violations of unbiased character collection, they will be misleading as predictors. Convergence of data on a reference tree does not guarantee historical accuracy, but it does predict that the accumulation of further data under the sampling model will not lead to rapid changes in the hypothesis.     

ON CONSENSUS, COLLAPSIBILITY, AND CLADE CONCORDANCE

Abstract — Consensus in cladistics is reviewed. Consensus trees, which summarize the agreement in grouping among a set of cladograms, are distinguished from compromise trees, which may contain groups that do not appear in all the cladograms being compared. Only a strict or Nelson tree is an actual consensus. This distinction has implications for the concept of support for cladograms: only those branches supported under all possible optimizations are unambiguously supported. We refer to such cladograms as strictly supported, in contrast to the semistrictly (ambiguously) supported cladograms output by various current microcomputer programs for cladistic analysis. Such semistrictly supported cladograms may be collapsed, however, by a variety of options in various programs. Consideration of collapsibility and optimization on multifurcations leads to some conclusions on the use of consensus. Consensus tree length provides information about character conflict that occurs between, not within, cladograms. We propose the clade concordance index, which employs the consensus tree length to measure inter-cladogram character conflict for all characters among a set of cladograms.     

Origin of Ginkgo biloba L. Phylogenetic approach

A cladistic analysis on fossil and modern Gymnosperms (20 taxa) is presented and discussed with particular mention of Ginkgo biloba L. origin. The consensus tree obtained from 68 characters (59 informative characters) shows a monophyletic clade containing all plants bearing micropylate ovules ('Micropylophytes'). Medullosales appear at the base of this clade. Ginkgo forms the sister group of the Dicranophyllales + Coniferales. The obtained phylogeny implies that the Ginkgoales ancestor is to be found during the Upper Carboniferous.     

A preliminary cladistic study of the families of the superorder Lamiiflorae

LU AN-MING, 1990. A preliminary cladistic study of the families of the superorder Lamiiflorae. A preliminary cladistic analysis was undertaken to evaluate the relationships between families of the superorder Lamiiflorae sensu Dahlgren. Several character complexes were surveyed, and ultimately 29 informative characters were used for the study. Three families, Clethraceae, Oleaceae and Solanaceae were selected for outgroup comparison and polarization of the characters. A data matrix was constructed for the 23 ingroup families. The data matrix was analysed with the cladistic parsimony program Hennig86. Three equally parsimonious cladograms were found. Many family interrelationships could not be resolved, although several groups were common to all three cladograms, as shown by a strict consensus tree. The Retziaceae emerged as the sister group to the remaining families. About half of those appeared in a large polytomy in the consensus tree. There was also one possibly monophyletic complex of families involving the Lamiales with the families Verbenaceae, Lamiaceae, Phrymaceae and Callitrichaceae as well as the three isolated families Trapellaceae, Hippuridaceae, and Hydrostachyaceae. Within this complex, Verbenaceae and Lamiaceae came out as sister groups, as did Callitrichaceae and Hydrostachyaceae, with Hippuridaceae as sister group to them. However, the results must be regarded as tentative.     

Evolutionary relationships of the cup-fungus genus Peziza and Pezizaceae inferred from multiple nuclear genes: RPB2, beta-tubulin, and LSU rDNA

To provide a robust phylogeny of Pezizaceae, partial sequences from two nuclear protein-coding genes, RPB2 (encoding the second largest subunit of RNA polymerase II) and beta-tubulin, were obtained from 69 and 72 specimens, respectively, to analyze with nuclear ribosomal large subunit RNA gene sequences (LSU). The three-gene data set includes 32 species of Peziza, and 27 species from nine additional epigeous and six hypogeous (truffle) pezizaceous genera. Analyses of the combined LSU, RPB2, and beta-tubulin data set using parsimony, maximum likelihood, and Bayesian approaches identify 14 fine-scale lineages within Pezizaceae. Species of Peziza occur in eight of the lineages, spread among other genera of the family, confirming the non-monophyly of the genus. Although parsimony analyses of the three-gene data set produced a nearly completely resolved strict consensus tree, with increased confidence, relationships between the lineages are still resolved with mostly weak bootstrap support. Bayesian analyses of the three-gene data, however, show support for several more inclusive clades, mostly congruent with Bayesian analyses of RPB2. No strongly supported incongruence was found among phylogenies derived from the separate LSU, RPB2, and beta-tubulin data sets. The RPB2 region appeared to be the most informative single gene region based on resolution and clade support, and accounts for the greatest number of potentially parsimony informative characters within the combined data set, followed by the LSU and the beta-tubulin region. The results indicate that third codon positions in beta-tubulin are saturated, especially for sites that provide information about the deeper relationships. Nevertheless, almost all phylogenetic signal in beta-tubulin is due to third positions changes, with almost no signal in first and second codons, and contribute phylogenetic information at the "fine-scale" level within the Pezizaceae. The Pezizaceae is supported as monophyletic in analyses of the three-gene data set, but its sister-group relationships is not resolved with support. The results advocate the use of RPB2 as a marker for ascomycete phylogenetics at the inter-generic level, whereas the beta-tubulin gene appears less useful.     

ANOTHER MONOPHYLY INDEX: REVISITING THE JACKKNIFE

Abstract — Randomization routines have quickly gained wide usage in phylogenetic systematies. Introduced a decade ago, the jackknife has rarely been applied in cladistic methodology. This data resampling technique was re-investigated here as a means to discover the effect that taxon removal may have on the stability of the results obtained from parsimony analyses. This study shows that the removal of even a single taxon in an analysis can cause a solution of relatively few multiple equally parsimonious trees in an inclusive matrix to result in hundreds of equally parsimonious trees with the single removal of a taxon. On the other hand, removal of other taxa can stabilize the results to fewer trees. An index of clade stability, the Jackknife Monophyly Index (JMI) is developed which, like the bootstrap, applies a value to each clade according to its frequency of occurrence in jackknife pseudoreplicates. Unlike the bootstrap and earlier application of the jackknife, alternative suboptimal hypotheses are not forwarded by this method. Only those clades in the most parsimonious tree(s) are given JMI values. The behaviour of this index is investigated both in relation to a hypothetical and a real data set, as well as how it performs in comparison to the bootstrap. The JMI is found to not be influenced by uninformative characters or relative synapomorphy number, unlike the bootstrap.     

Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species

MOTIVATION: Through the most extensive phylogenomic analysis carried out to date, complete genomes of 11 eukaryotic species have been examined in order to find the homologous of more than 25,000 amino acid sequences. These sequences correspond to the exons of more than 3000 genes and were used as presence/absence characters to test one of the most controversial hypotheses concerning animal evolution, namely the Ecdysozoa hypothesis. Distance, maximum parsimony and Bayesian methods of phylogenetic reconstruction were used to test the hypothesis. RESULTS: The reliability of the ecdysozoa, grouping arthropods and nematodes in a single clade was unequivocally rejected in all the consensus trees. The Coelomata clade, grouping arthropods and chordates, was supported by the highest statistical confidence in all the reconstructions. The study of the dependence of the genomes' tree accuracy on the number of exons used, demonstrated that an unexpectedly larger number of characters are necessary to obtain robust phylogenies. Previous studies supporting ecdysozoa, could not guarantee an accurate phylogeny because the number of characters used was clearly below the minimum required.     

Soft anatomy, diffuse homoplasy, and the relationships of lizards and snakes

Most previous phylogenetic analyses of squamates (‘lizards’ and snakes) employing large character sets have focused on osteology. Soft anatomical traits bearing on this problem have usually been considered in small subsets. Here, a comprehensive phylogenetic analysis of squamate soft anatomy is attempted. 126 informative characters are assessed for 23 squamate lineages, representing snakes, amphisbaenians, dibamids, and all the traditionally recognized ‘families’ of lizards. The traditionally recognized groupings Iguania, Scleroglossa, Gekkota, Scincomorpha, Anguimorpha and Varanoidea are corroborated in this analysis. More controversial taxa are resolved as follows. Xantusiids, amphisbaenians and dibamids cluster with gekkotans, and snakes are strongly allied with anguimorphs in general, and varanids in particular. Nearly all these clades are congruent with those found in a recent comprehensive osteological analysis; the strong support for snake‐varanid relationships found in both studies is particularly notable. This congruence is surprising given that previous studies of soft anatomy tended to give differing and often heterodox results. These previous results can be attributed to overrepresentation of misleading characters in small isolated data sets. Such misleading signals are minimized when data sets are combined. For instance, the snake‐varanid clade is contradicted by many characters, and analyses of particular organ systems therefore give differing results. However, characters that are incongruent with the snake‐varanid clade also disagree with each other (diffuse homoplasy), rather than forming coherent support for some particular alternative clade (concerted homoplasy). In a combined analysis these incongruent but diffuse characters cancel each other out to leave a very strong (and orthodox) phylogenetic signal. These results underscore the view that the raw amount of homoplasy — as revealed by consistency and retention indices — is not the only determinant of phylogenetic signal; the distribution of that homoplasy is also important. Thus, questioning a phylogenetic hypothesis (e.g. the snake‐varanid clade) by identifying numerous conflicting characters is insufficient — the structure of the conflicting characters should be assessed in a rigorous phylogenetic analysis.     

Evolutionary relationships of euthyneuran gastropods (Mollusca): a cladistic re-evaluation of morphological characters

Morphological characters of the Euthyneura available from the literature were re-evaluated in terms of terminology and primary homology. A total of 77 characters and 75 taxa were retained in a data matrix. Several assumptions on character weights and types were tested. In the cladistic analyses, it appeared that the data matrix was highly homoplastic, and only robust nodes (those which were little modified by variations in weight and coding of characters) were retained in a concensus tree. The evolutionary histories of all characters and monophylies of higher euthyneuran taxa were discussed. The following interrelationships of the taxa were obtained in a consensus tree: the clade Heterobranchia includes paraphyletic allogastropod taxa which emerge basally, and the clade Euthyneura. The latter includes the clade Pulmonata and at least 10 opisthobranch clades of unresolved relationship (Thecosomata, Gymnosomata, Acochlidioidea, Pyramidelloidea, Runcinoidea, Cephalaspidea, Sacoglossa, Umbraculoidea, Pleurobranchoidea, Nudibranchia). The Pulmonata include basommatophoran paraphyletic taxa and the clade Geophila (Onchidiidae, Soleolifera, Stylommatophora). The position of the Sacoglossa and the monophyly of the Notaspidea are also discussed.  © 2002 The Linnean Society of London, Zoological Journal of the Linnean Society , 2002, 135 , 403–470.     

Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.     

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

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

Strange bayes indeed: uniform topological priors imply non-uniform clade priors

While Bayesian analysis has become common in phylogenetics, the effects of topological prior probabilities on tree inference have not been investigated. In Bayesian analyses, the prior probability of topologies is almost always considered equal for all possible trees, and clade support is calculated from the majority rule consensus of the approximated posterior distribution of topologies. These uniform priors on tree topologies imply non-uniform prior probabilities of clades, which are dependent on the number of taxa in a clade as well as the number of taxa in the analysis. As such, uniform topological priors do not model ignorance with respect to clades. Here, we demonstrate that Bayesian clade support, bootstrap support, and jackknife support from 17 empirical studies are significantly and positively correlated with non-uniform clade priors resulting from uniform topological priors. Further, we demonstrate that this effect disappears for bootstrap and jackknife when data sets are free from character conflict, but remains pronounced for Bayesian clade supports, regardless of tree shape. Finally, we propose the use of a Bayes factor to account for the fact that uniform topological priors do not model ignorance with respect to clade probability.     

Phylogeny of Henicopidae (Chilopoda: Lithobiomorpha): a combined analysis of morphology and five molecular loci

Abstract. Relationships in Henicopidae, the dominant southern temperate clade of Lithobiomorpha, are appraised based on parsimony analysis of forty-nine morphological characters and sequence data from five loci (nuclear ribosomal RNAs 18S and 28S, mitochondrial ribosomal RNAs 12S and 16S, protein-coding mitochondrial cytochrome c oxidase I). A combined analysis of these data used direct character optimization, and tested stability of hypotheses through parameter-sensitivity analysis. The morphology dataset highlighted the mandibles as a source of new characters. Morphology, as well as the most congruent parameters for the sequence data and combined analysis, resolved Zygethobiini within Henicopini. Groups retrieved by combined analysis of the sequences and combination with morphology for all parameters include Anopsobiinae/Henicopinae, Lamyctes + Lamyctinus + Henicops , Paralamyctes ( Paralamyctes ), and a clade that groups the southeastern Australian/New Zealand Paralamyctes ( Haasiella ) and P . ( Thingathinga ). Paralamyctes (including Haasiella ) is a Gondwanan clade in the most congruent cladograms based on all molecular data and combination with morphological data. Biogeographic analysis of subtrees for Paralamyctes resolved the interrelationships of Gondwana as (Patagonia ((New South Wales + southeastern Queensland) ((Tasmania) (southern Africa + India) (New Zealand + north Queensland)))).     

Cladistic analysis of molecular and morphological data

Considerable progress has been made recently in phylogenetic reconstruction in a number of groups of organisms. This progress coincides with two major advances in systematics: new sources have been found for potentially informative characters (i. e., molecular data) and (more importantly) new approaches have been developed for extracting historical information from old or new characters (i. e., Hennigian phylogenetic systematics or cladistics). The basic assumptions of cladistics (the existence and splitting of lineages marked by discrete, heritable, and independent characters, transformation of which occurs at a rate slower than divergence of lineages) are discussed and defended. Molecular characters are potentially greater in quantity than (and usually independent of) more traditional morphological characters, yet their great simplicity (i. e., fewer potential character states; problems with determining homology), and difficulty of sufficient sampling (particularly from fossils) can lead to special difficulties. Expectations of the phylogenetic behavior of different types of data are investigated from a theoretical standpoint, based primarily on variation in the central parameter λ (branch length in terms of expected number of character changes per segment of a tree), which also leads to possibilities for character and character state weighting. Also considered are prospects for representing diverse yet clearly monophyletic clades in larger-scale cladistic analyses, e. g., the exemplar method vs. “compartmentalization” (a new approach involving substituting an inferred “archetype” for a large clade accepted as monophyletic based on previous analyses). It is concluded that parsimony is to be preferred for synthetic, “total evidence” analyses because it appears to be a robust method, is applicable to all types of data, and has an explicit and interpretable evolutionary basis. © 1994 Wiley-Liss, Inc.     

Morphological phylogeny of army ants and other dorylomorphs (Hymenoptera: Formicidae)

Abstract. The dorylomorph group of ants comprises the three subfamilies of army ants (Aenictinae, Dorylinae, Ecitoninae) together with the subfamilies Aenictogitoninae, Cerapachyinae, and Leptanilloidinae. We describe new morphological characters and synthesize data from the literature in order to present the first hypothesis of phylogenetic relationships among all dorylomorph genera. These data include the first available character information from the newly discovered male caste of Leptanilloidinae. We used ant taxa from Leptanillinae, Myrmeciinae, and the poneromorph (Ponerinae sensu lato) subfamilies Amblyoponinae, Ectatomminae, and Paraponerinae as outgroups. We scored a total of 126 characters from twenty-two terminal taxa and used these data to conduct maximum parsimony and bootstrap analyses. The single most-parsimonious tree and bootstrap results support a single origin of army ants. The Old World army ant genus Dorylus forms a monophyletic group with the enigmatic genus Aenictogiton, which is currently known only from males; the second Old World army ant genus Aenictus is sister to this clade. This result generates the prediction that females of Aenictogiton, when discovered, will be observed to possess the army ant syndrome of behavioural and reproductive traits. The monophyly of the New World army ants (Ecitoninae) is supported very strongly, and within this group the genera Eciton, Nomamyrmex, and Labidus form a robust clade. The monophyly of Leptanilloidinae is also upheld. The subfamily Cerapachyinae appears paraphyletic, although this conclusion is not supported by strong bootstrap results. Relationships among genera of Cerapachyinae similarly are not resolved robustly, although parsimony results suggest clades consisting of (Acanthostichus + Cylindromyrmex) and (Cerapachys + Sphinctomyrmex). We tested for the effect of incompletely known taxa by conducting a secondary analysis in which the two genera containing ∼50% missing character data (Aenictogiton and Asphinctanilloides) were removed. The strict consensus of the seventeen most-parsimonious trees from this secondary analysis is poorly resolved outside the army ants and contains no clades conflicting with the primary analysis. The position of Leptanilla shifts from forming the sister group to Leptanilloidinae (without high bootstrap support) in the primary analysis, to falling within a polytomy at the base of the root of the dorylomorphs when incompletely known taxa are removed. This instability suggests that the placement of Leptanilla within the dorylomorphs in our primary analysis may be spurious.