Morphological phylogenetics of the sea spiders (Arthropoda: Pycnogonida)

Pycnogonids or sea spiders are a group of marine arthropods whose relations to the chelicerates have been an issue of controversy. Higher-level phylogenetic relationships among the lineages of sea spiders are investigated using 36 morphological characters from 37 species from all extant families and a Devonian pycnogonid fossil. This is one of the first attempts to analyze the higher-level relationships of the Pycnogonida using cladistic techniques. Character homoplasy (implied weights) is taken into account to construct a polytomous, most-parsimonious tree in which two major clades within Pycnogonida are obtained. Clade A includes Ammotheidae paraphyletic with Colossendeidae, Austrodecidae and Rhynchothoracidae, and clade B is formed by Nymphonidae, Callipallenidae (apparently paraphyletic), Pycnogonidae and Phoxichilidiidae. The analysis of equally weighted data is presented and helps to identify those characters less consistent. The reduction of the chelifores, palps and ovigers — shown independently within each of the clades as parallel evolution events — challenges the assumption of a gradual mode of reduction within the group, according to analysis of unordered vs ordered characters. Most of the phylogenetic affinities proposed here are compatible with traditional classifications. However, traditional taxonomic characters need to be complemented by sets of anatomical, molecular and developmental data, among others, to produce more robust phylogenetic hypotheses on the higher- and lower-level relationships of the sea spiders.     

Molecular phylogeny, character evolution, and biogeography of the grammitid fern genus Lellingeria (Polypodiaceae)

? Premise of the study: The recognition of monophyletic genera for groups that have high levels of homoplastic morphological characters and/or conflicting results obtained by different studies can be difficult. Such is the case in the grammitid ferns, a clade within the Polypodiaceae. In this study, we aim to resolve relationships among four clades of grammitid ferns, which have been previously recovered either as a polytomy or with conflicting topologies, with the goal of circumscribing monophyletic genera. ? Methods: The sampling included 89 specimens representing 61 species, and sequences were obtained for two genes (atpB and rbcL) and four intergenic spacers (atpB-rbcL, rps4-trnS, trnG-trnR, and trnL-trnF), resulting in a matrix of 5091 characters. The combined data set was analyzed using parsimony, likelihood, and Bayesian methods. Ninety-six morphological characters were optimized onto the generated trees, using the parsimony method. ? Key results: Lellingeria is composed of two main clades, the L. myosuroides and the Lellingeria s.s. clades, which together are sister to Melpomene. Sister to all three of these is a clade with two species of the polyphyletic genus Terpsichore. In the L. myosuroides clade, several dispersal events occurred between the neotropics, Africa, and the Pacific Islands, whereas Lellingeria s.s. is restricted to the neotropics, with about 60% of its diversity in the Andes. ? Conclusions: Overall, our results suggest that Lellingeria is monophyletic, with two clades that are easily characterized morphologically and biogeographically. Morphological characters describing the indument are the most important to define the clades within the ingroup. A small clade, previously considered in Terpsichore, should be recognized as a new genus.     

AFLPs resolve phylogeny and reveal mitochondrial introgression within a species flock of African electric fish (Mormyroidea: Teleostei)

Estimating species phylogeny from a single gene tree can be especially problematic for studies of species flocks in which diversification has been rapid. Here we compare a phylogenetic hypothesis derived from cytochrome b (cyt b) sequences with another based on amplified fragment length polymorphisms (AFLP) for 60 specimens of a monophyletic riverine species flock of mormyrid electric fishes collected in Gabon, west-central Africa. We analyze the aligned cyt b sequences by Wagner parsimony and AFLP data generated from 10 primer combinations using neighbor-joining from a Nei-Li distance matrix, Wagner parsimony, and Dollo parsimony. The different analysis methods yield AFLP tree topologies with few conflicting nodes. Recovered basal relationships in the group are similar between cyt b and AFLP analyses, but differ substantially at many of the more derived nodes. More of the clades recovered with the AFLP characters are consistent with the morphological characters used to designate operational taxonomic units in this group. These results support our hypothesis that the mitochondrial gene tree differs from the overall species phylogeny due at least in part to mitochondrial introgession among lineages. Mapping the two forms of electric organ found in this group onto the AFLP tree suggests that posteriorly innervated electrocytes with nonpenetrating stalks have independently evolved from anteriorly innervated, penetrating-stalk electrocytes at least three times.     

Phylogenetic implications of the morphology of the braincase of caecilian amphibians (Gymnophiona)

Caecilian morphology is strongly modified in association with their fossorial mode of life. Currently phylogenetic analyses of characters drawn from the morphology of caecilians lack resolution, as well as complementarity, with results of phylogenetic analyses that employ molecular data. Stemming from the hypothesis derived from the mammal literature that the braincase has the greatest potential (in comparison to other cranial units) to yield phylogenetic information, the braincase and intimately associated stapes of 27 species (23 genera) of extant caecilians were examined using images assembled via microcomputed tomography. Thirty‐four new morphological characters pertaining to the braincase and stapes were identified and tested for congruence with previously recognized morphological characters. The results reveal that when added to previous character matrices, characters of the braincase and stapes resolve generic‐level relationships in a way that is largely congruent with the results of molecular analyses. Analysis of a combined data set of molecular and morphological data provides a framework for conducting ancestral character state reconstructions, which resulted in the identification of 95 new synapomorphies for various clades and taxa, 27 of which appear to be unique for the taxa that possess them. Together these data demonstrate the utility of the application of characters of the braincase and stapes for resolving phylogenetic relationships for a group whose morphology is largely confounded by functional modifications. In addition this study provides evidence of the utility of the braincase in resolving problematic morphology‐based phylogeny outside of Amniota, in an amphibian group. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 160–201.     

Estimating diversification rates for higher taxa: BAMM can give problematic estimates of rates and rate shifts

Estimates of diversification rates are invaluable for many macroevolutionary studies. Recently, an approach called BAMM (Bayesian Analysis of Macro‐evolutionary Mixtures) has become widely used for estimating diversification rates and rate shifts. At the same time, several articles have concluded that estimates of net diversification rates from the method‐of‐moments (MS) estimators are inaccurate. Yet, no studies have compared the ability of these two methods to accurately estimate clade diversification rates. Here, we use simulations to compare their performance. We found that BAMM yielded relatively weak relationships between true and estimated diversification rates. This occurred because BAMM underestimated the number of rates shifts across each tree, and assigned high rates to small clades with low rates. Errors in both speciation and extinction rates contributed to these errors, showing that using BAMM to estimate only speciation rates is also problematic. In contrast, the MS estimators (particularly using stem group ages), yielded stronger relationships between true and estimated diversification rates, by roughly twofold. Furthermore, the MS approach remained relatively accurate when diversification rates were heterogeneous within clades, despite the widespread assumption that it requires constant rates within clades. Overall, we caution that BAMM may be problematic for estimating diversification rates and rate shifts.     

Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences

SUMMARY Insight into the origin and early evolution of the animal phyla requires an understanding of how animal groups are related to one another. Thus, we set out to explore animal phylogeny by analyzing with maximum parsimony 138 morphological characters from 40 metazoan groups, and 304 18S rDNA sequences, both separately and together. Both types of data agree that arthropods are not closely related to annelids: the former group with nematodes and other molting animals (Ecdysozoa), and the latter group with molluscs and other taxa with spiral cleavage. Furthermore, neither brachiopods nor chaetognaths group with deuterostomes; brachiopods are allied with the molluscs and annelids (Lophotrochozoa), whereas chaetognaths are allied with the ecdysozoans. The major discordance between the two types of data concerns the rooting of the bilaterians, and the bilaterian sister-taxon. Morphology suggests that the root is between deuterostomes and protostomes, with ctenophores the bilaterian sister-group, whereas 18S rDNA suggests that the root is within the Lophotrochozoa with acoel flatworms and gnathostomulids as basal bilaterians, and with cnidarians the bilaterian sister-group. We suggest that this basal position of acoels and gnathostomulids is artifactal because for 1000 replicate phylogenetic analyses with one random sequence as outgroup, the majority root with an acoel flatworm or gnathostomulid as the basal ingroup lineage. When these problematic taxa are eliminated from the matrix, the combined analysis suggests that the root lies between the deuterostomes and protostomes, and Ctenophora is the bilaterian sister-group. We suggest that because chaetognaths and lophophorates, taxa traditionally allied with deuterostomes, occupy basal positions within their respective protostomian clades, deuterostomy most likely represents a suite of characters plesiomorphic for bilaterians.     

Phylogenetic Relationships Among Quolls Revisited: The mtDNA Control Region as a Useful Tool

There has been a great deal of interest in determining phylogenetic relationships within the family Dasyuridae due to the widespread distribution, ecological diversity, and relative plesiomorphy of this taxon within the Australasian marsupial radiation. In the past, it has been extremely problematic to determine the phylogenetic relationships among species within Dasyurus, with numerous studies using both morphological and molecular characters providing different topologies. Here, the mitochondrial DNA (mtDNA) control region is used as a novel set of characters in an attempt to identify relationships among the six closely related extant species. Sequences were obtained from multiple individuals representing all extant species of quolls including, when possible, individuals from different geographical regions. Sequences were analyzed using both parsimony criteria and neighbor-joining methods. Results presented here concur with those of Krajewski et al. (1997) in (1) placing D. geoffroii in a highly supported clade with D. spartacus, (2) resolving a monophyletic group of D. albopunctatus + D. geoffroii + D. spartacus, and (3) placing D. hallucatus as the sister taxon to all other species of quolls. Results also show two highly supported and geographically distinct clades of D. maculatus (Tasmanian and mainland) that do not correspond to the currently used subspecific nomenclature. Preliminary results also indicate that there are different clades among geographic groups of D. hallucatus that warrant further investigation. The mtDNA control region is a highly variable locus and may be used in forensic tests for species identification in this genus.     

Major clades of parmelioid lichens (Parmeliaceae, Ascomycota) and the evolution of their morphological and chemical diversity

Parmelioid lichens comprise about 1500 species and have a worldwide distribution. Numerous species are widely distributed and well known, including important bioindicators for atmospheric pollution. The phylogeny and classification of parmelioid lichens has been a matter of debate for several decades. Previous studies using molecular data have helped to establish hypotheses of the phylogeny of certain clades within this group. In this study, we infer the phylogeny of major clades of parmelioid lichens using DNA sequence data from two nuclear loci and one mitochondrial locus from 145 specimens (117 species) that represent the morphological and chemical diversity in these taxa. Parmelioid lichens are not monophyletic; however, a core group is strongly supported as monophyletic, excluding Arctoparmelia and Melanelia s. str., and including Parmeliopsis and Parmelaria. Within this group, seven well-supported clades are found, but the relationships among them remain unresolved. Stochastic mapping on a MC/MCMC tree sampling was employed to infer the evolution of two morphological and two chemical traits believed to be important for the evolutionary success of these lichens, and have also been used as major characters for classification. The results suggest that these characters have been gained and lost multiple times during the diversification of parmelioid lichens.     

Exploring rate variation among and within sites in a densely sampled tree: species level phylogenetics of north american tiger beetles (genus cicindela)

Species-level phylogenetic studies require fast-evolving nucleotide positions to resolve relationships among close relatives, but these sites may be highly homoplastic and perhaps uninformative or even misleading deeper in the tree. Here we describe a species-level analysis of tiger beetles in the genus Cicindela (Coleoptera: Cicindelidae) for 132 terminal taxa and 1897 nucleotide positions from three regions of mtDNA, comprising 75% coverage of species occurring in North America. Evenly weighted parsimony analysis recovered four major clades representing radiations confined to North and Central America. Relationships near the tips were well supported but signal was contradictory at deeper nodes. Two major categories (3rd positions and all others) can be distinguished in likelihood analysis of character variation, of which only the fast-changing 3rd position characters were affected by saturation. However, their downweighting under a variety of criteria did not improve the tree topology at basal nodes. There was weak conflict between 3rd and non-3rd position characters deep in the tree, but support levels declined towards the root for all categories, even on trees that were reconstructed from 3rd and non-3rd positions separately. Statistical analysis of parsimony-based character transitions along branches showed a largely homogeneous distribution of change along the root-to-tip axis. The comparison of character transitions among the four major portions of the tree revealed deviations from stochastic distribution for the non-3rd positions, but not for 3rd positions. Hence, variability of functionally constrained non-3rd positions differs between clades and may be dependent on the character states at other sites, consistent with the covarion model of molecular evolution. The results suggest that some properties of 3rd positions are less problematic for phylogenetic reconstruction than other categories despite their high total homoplasy. In densely sampled data sets of closely related species, the disadvantages of weighting schemes according to homoplasy levels outweigh the benefits, showing the difficulty of devising meaningful weighting schemes that are applicable universally throughout the tree.     

Do different disparity proxies converge on a common signal? Insights from the cranial morphometrics and evolutionary history of Pterosauria (Diapsida: Archosauria)

Disparity, or morphological diversity, is often quantified by evolutionary biologists investigating the macroevolutionary history of clades over geological timescales. Disparity is typically quantified using proxies for morphology, such as measurements, discrete anatomical characters, or geometric morphometrics. If different proxies produce differing results, then the accurate quantification of disparity in deep time may be problematic. However, despite this, few studies have attempted to examine disparity of a single clade using multiple morphological proxies. Here, as a case study for this question, we examine the disparity of the volant Mesozoic fossil reptile clade Pterosauria, an intensively studied group that achieved substantial morphological, ecological and taxonomic diversity during their 145+ million-year evolutionary history. We characterize broadscale patterns of cranial morphological disparity for pterosaurs for the first time using landmark-based geometric morphometrics and make comparisons to calculations of pterosaur disparity based on alternative metrics. Landmark-based disparity calculations suggest that monofenestratan pterosaurs were more diverse cranially than basal non-monofenestratan pterosaurs (at least when the aberrant anurognathids are excluded), and that peak cranial disparity may have occurred in the Early Cretaceous, relatively late in pterosaur evolution. Significantly, our cranial disparity results are broadly congruent with those based on whole skeleton discrete character and limb proportion data sets, indicating that these divergent approaches document a consistent pattern of pterosaur morphological evolution. Therefore, pterosaurs provide an exemplar case demonstrating that different proxies for morphological form can converge on the same disparity signal, which is encouraging because often only one such proxy is available for extinct clades represented by fossils. Furthermore, mapping phylogeny into cranial morphospace demonstrates that pterosaur cranial morphology is significantly correlated with, and potentially constrained by, phylogenetic relationships.     

Phylogeny of prickly poppies,Argemone (Papaveraceae), and the evolution of morphological and alkaloid characters based on ITS nrDNA sequence variation

Evolutionary relationships withinArgemone (Papaveraceae) were inferred from nucleotide variation in nuclear ribosomal DNA. A complete representation of the genus was achieved by using herbarium material to a large extent (74%). Four distinct clades can be recognized based on the molecular results. The support for the different clades varies greatly due to a very uneven distribution of characters. Although some clades are largely unresolved, some unexpected relationships, for example the sister group relationship of the relict speciesA. subintegrifolia to the rest ofArgemone, were found. The evolution of morphological and alkaloid characters against the background of the obtained phylogeny is discussed. Whereas the morphological characters provide some support for the phylogeny found, the alkaloid characters turned out not to contain much phylogenetic information. Past difficulties in recognizing phylogenetic relationships withinArgemone result from largely continuous morphological variation and from parallelisms correlated with and probably caused by polyploidization.     

Multi-gene phylogenies indicate ascomal wall morphology is a better predictor of phylogenetic relationships than ascospore morphology in the Sordariales (Ascomycota, Fungi)

Ascospore characters have commonly been used for distinguishing ascomycete taxa, while ascomal wall characters have received little attention. Although taxa in the Sordariales possess a wide range of variation in their ascomal walls and ascospores, genera have traditionally been delimited based on differences in their ascospore morphology. Phylogenetic relationships of multiple representatives from each of several genera representing the range in ascomal wall and ascospore morphologies in the Sordariales were estimated using partial nuclear DNA sequences from the 28S ribosomal large subunit (LSU), beta-tubulin, and ribosomal polymerase II subunit 2 (RPB2) genes. These genes also were compared for their utility in predicting phylogenetic relationships in this group of fungi. Maximum parsimony and Bayesian analyses conducted on separate and combined data sets indicate that ascospore morphology is extremely homoplastic and not useful for delimiting genera. Genera represented by more than one species were paraphyletic or polyphyletic in nearly all analyses; 17 species of Cercophora segregated into at least nine different clades, while six species of Podospora occurred in five clades in the LSU tree. However, taxa with similar ascomal wall morphologies clustered in five well-supported clades suggesting that ascomal wall morphology is a better indicator of generic relationships in certain clades in the Sordariales. The RPB2 gene possessed over twice the number of parsimony-informative characters than either the LSU or beta-tubulin gene and consequently, provided the most support for the greatest number of clades.     

Hylid frog phylogeny and sampling strategies for speciose clades

How should characters and taxa be sampled to resolve efficiently the phylogeny of ancient and highly speciose groups? We addressed this question empirically in the treefrog family Hylidae, which contains > 800 species and may be nonmonophyletic with respect to other anuran families. We sampled 81 species (54 hylids and 27 outgroups) for two mitochondrial genes (12S, ND1), two nuclear genes (POMC, c-myc), and morphology (144 characters) in an attempt to resolve higher-level relationships. We then added 117 taxa to the combined data set, many of which were sampled for only one gene (12S). Despite the relative incompleteness of the majority of taxa, the resulting trees placed all taxa in the expected higher-level clades with strong support, despite some taxa being > 90% incomplete. Furthermore, we found no relationship between the completeness of a taxon and the support (parsimony bootstrap or Bayesian posterior probabilities) for its localized placement on the tree. Separate analysis of the data set with the most taxa (12S) gives a somewhat problematic estimate of higher-level relationships, suggesting that data sets scored only for some taxa (ND1, nuclear genes, morphology) are important in determining the outcome of the combined analysis. The results show that hemiphractine hylids are not closely related to other hylids and should be recognized as a distinct family. They also show that the speciose genus Hyla is polyphyletic, but that its species can be arranged into three monophyletic genera. A new classification of hylid frogs is proposed. Several potentially misleading signals in the morphological data are discussed.     

Giant taxon‐character matrices: quality of character constructions remains critical regardless of size

Giant morphological data matrices are increasingly common in cladistic analyses of vertebrate phylogeny, reporting numbers of characters never seen or expected before. However, the concern for size is usually not followed by an equivalent, if any, concern for character construction/selection criteria. Therefore, the question of whether quantity parallels quality for such influential works remains open. Here, we provide the largest compilation known to us of character construction methods and criteria, as derived from previous studies, and from our own de novo conceptualizations. Problematic character constructions inhibit the capacity of phylogenetic analyses to recover meaningful homology hypotheses and thus accurate clade structures. Upon a revision of two of the currently largest morphological datasets used to test squamate phylogeny, more than one‐third of the almost 1000 characters analysed were classified within at least one of our categories of “types” of characters that should be avoided in cladistic investigations. These characters were removed or recoded, and the data matrices re‐analysed, resulting in substantial changes in the sister group relationships for squamates, as compared to the original studies. Our results urge caution against certain types of character choices and constructions, also providing a methodological basis upon which problematic characters might be avoided.     

Phylogeny of the water strider genus Rheumatobates (Heteroptera: Gerridae)

The genus Rheumatobates comprises thirty‐seven species and subspecies of New World water striders belonging to subfamily Rhagadotarsinae. Among species, males vary dramatically in the degree and nature of modifications of the antennae, three pairs of legs and abdominal and genital segments. Characters describing this modification have traditionally been used to differentiate and group species. The general assumption has been that modified species belong to one group and unmodified species to another. These two ‘species groups’ are subdivided into ‘subgroups’, but little effort has been made to resolve relationships among them. We conduct the first numerical cladistic analysis of Rheumatobates using a data set comprised of 102 characters, primarily describing modification of male external morphology. To address concerns about the inclusion of characters to be optimized on the phylogeny, characters describing modification of antennae and hind legs were included and then excluded in separate analyses. A preferred phylogeny was chosen from the four equally parsimonious cladograms found after successive reweighting of characters. There was good resolution at all levels of the phylogeny. Most of the major clades and terminal relationships were moderately to strongly supported, whereas the basal relationships were less well supported. The general assumption that unmodified and modified species form two monophyletic groups was not supported. However, traditionally recognized ‘subgroups’ within the modified species group were largely upheld. The analysis also suggested several major clades and relationships among these clades that were not previously recognized. The exclusion of characters describing modification of antennae and hind legs did not change the resolved major clades of the reconstructed phylogeny.     

MITOCHONDRIAL DNA PHYLOGENIES FOR THE DROSOPHILA OBSCURA GROUP

Species belonging to the obscura group of the genus Drosophila have long held a central position in evolutionary studies, especially in experimental population genetics. Despite the considerable amount of accumulated knowledge, many of the phylogenetic relationships of the species in the group remain unclear. Here we present DNA sequence data for the mitochondrial gene cytochrome oxidase I (COI) for 13 species native to both the Old and New Worlds. We combine these data with seven other mitochondrial gene sequences from previous studies, for a total of over 3 kb per species. Strongly supported conclusions include: (1) the two North American subgroups, pseudoobscura and affinis, are each monophyletic; and (2) among Eurasian species two unambiguous clades are identified, one containing D. tristis, D. ambigua, and D. obscura and the other containing D. guanche, D. subobscura, and D. madeirensis. Constructing firm hypotheses connecting these four major clades is problematic with all datasets. Major ambiguities are the number of invasions giving rise to the North American obscura species and the relationships among the Eurasian species. The inadequacy of the mtDNA data to resolve these ambiguities does not reside in lack of changes; the transversions-only parsimony tree has 283 informative characters. Rather, the problems are likely intrinsic to the history of the group: while radiating in temperate Eurasia, North America was colonized once or twice, followed by one or two radiations in the New World.     

Phylogenetic Classification at Generic Level in the Absence of Distinct Phylogenetic Patterns of Phenotypical Variation: A Case Study in Graphidaceae (Ascomycota)

Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed.     

A preliminary phylogeny of the 'didymocarpoid Gesneriaceae' based on three molecular data sets: Incongruence with available tribal classifications

The 'didymocarpoid Gesneriaceae' (traditional subfam. Cyrtandroideae excluding Epithemateae) are the largest group of Old World Gesneriaceae, comprising 85 genera and 1800 species. We attempt to resolve their hitherto poorly understood generic relationships using three molecular markers on 145 species, of which 128 belong to didymocarpoid Gesneriaceae. Our analyses demonstrate that consistent topological relationships can be retrieved from data sets with missing data using subsamples and different combinations of gene sequences. We show that all available classifications in Old World Gesneriaceae are artificial and do not reflect natural relationships. At the base of the didymocarpoids are grades of clades comprising isolated genera and small groups from Asia and Europe. These are followed by a clade comprising the African and Madagascan genera. The remaining clades represent the advanced Asiatic and Malesian genera. They include a major group with mostly twisted capsules. The much larger group of remaining genera comprises exclusively genera with straight capsules and the huge genus Cyrtandra with indehiscent fruits. Several genera such as Briggsia, Henckelia, and Chirita are not monophyletic; Chirita is even distributed throughout five clades. This degree of incongruence between molecular phylogenies, traditional classifications, and generic delimitations indicates the problems with classifications based on, sometimes a single, morphological characters.     

A phylogenetic analysis of the arachnid orders based on morphological characters

Morphological evidence for resolving relationships among arachnid orders was surveyed and assembled in a matrix comprising 59 euchelicerate genera (41 extant, 18 fossil) and 202 binary and unordered multistate characters. Parsimony analysis of extant genera recovered a monophyletic Arachnida with the topology (Palpigradi (Acaromorpha (Tetrapulmonata (Haplocnemata, Stomothecata nom. nov. )))), with Acaromorpha containing Ricinulei and Acari, Tetrapulmonata containing Araneae and Pedipalpi (Amblypygi, Uropygi), Haplocnemata (Pseudoscorpiones, Solifugae) and Stomothecata (Scorpiones, Opiliones). However, nodal support and results from exploratory implied weights analysis indicated that relationships among the five clades were effectively unresolved. Analysis of extant and fossil genera recovered a clade, Pantetrapulmonata nom nov. , with the topology (Trigonotarbida (Araneae (Haptopoda (Pedipalpi)))). Arachnida was recovered as monophyletic with the internal relationships (Stomothecata (Palpigradi, Acaromorpha (Haplocnemata, Pantetrapulmonata))). Nodal support and exploratory implied weights indicated that relationships among these five clades were effectively unresolved. Thus, some interordinal relationships were strongly and/or consistently supported by morphology, but arachnid phylogeny is unresolved at its deepest levels. Alternative hypotheses proposed in the recent literature were evaluated by constraining analyses to recover hypothesized clades, an exercise that often resulted in the collapse of otherwise well-supported clades. These results suggest that attempts to resolve specific nodes based on individual characters, lists of similarities, evolutionary scenarios, etc., are problematic, as they ignore broader impacts on homoplasy and analytical effects on non-target nodes.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 221–265.