Phylogeny of the gastropod superfamily Cerithioidea using morphology and molecules

The Cerithioidea is an ecologically important superfamily of basal Caenogastropoda with speciose marine, brackish water, and freshwater lineages primarily in tropical, subtropical, and warm temperate regions of the world. They often represent significant components of the communities where they occur and have given rise to several spectacular endemic radiations in rivers and ancient lakes. Earlier attempts to resolve the phylogenetic history of the group have been based on smaller taxon and character subsets with incongruent results. Here the monophyly and phylogeny of the group is evaluated with expanded morphological and molecular (16S, 28S rRNA) data sets. For morphological analyses, 151 characters (shell, operculum, radula, alimentary tract, kidney, nervous system, reproductive anatomy, and sperm ultrastructure) were scored for 47 cerithioideans (representing 17 families) and nine outgroup taxa. To test monophyly of the Cerithioidea, extended molecular data sets of 16S and 28S sequences for 57 and 44 taxa, respectively, were compiled using new and previously published sources. For combined analyses, a pruned molecular data set was combined with the morphological partition. The morphological data were analysed alone using only parsimony; molecular and simultaneous analyses were performed using both parsimony and Bayesian inference. The effect of excluding unconserved regions of the alignments was also explored. All analyses, with the exception of the individual 16S and 28S data sets, support monophyly of the Cerithioidea as currently formulated. Of the 12 families represented by more than one terminal, only two (Planaxidae, Potamididae) are always supported as monophyletic; Batillariidae, Cerithiidae, Pachychilidae, Pleuroceridae, Semisulcospiridae, Thiaridae, and Turritellidae are monophyletic in most but not all topologies. The combination of diverse data sources (morphology, 16S and 28S sequences) and inclusion of unconserved regions of the alignments improved the recovery of monophyletic families. At deeper levels, a consensus is beginning to emerge in the recognition of three main assemblages, but whether these represent clades or grades is still unclear; the resolution of these assemblages and the branching order within them are sensitive to exclusion of unconserved regions and choice of optimality criterion. No clear conclusion is reached with respect to the number of freshwater invasions, with two invasions supported on some topologies and three supported on others. Progress toward a robust and stable resolution of cerithioidean relationships will require (1) strategically coordinated sampling for additional morphological and molecular data; (2) comprehensive anatomical treatments for several poorly documented limnic lineages (e.g. Melanopsidae, Thiaridae) and comparative data for poorly understood organ systems (e.g. renal system); (3) the addition of poorly known, minute, and/or rare marine taxa, to provide novel character combinations, insight into putative homologies, and to help anchor basal nodes and break up long branches. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 43–89.     

Molecular systematics of North American phoxinin genera (Actinopterygii: Cyprinidae) inferred from mitochondrial 12S and 16S ribosomal RNA sequences

The cyprinid fish fauna of North America is relatively large, with approximately 300 species, and all but one of these are considered phoxinins. The phylogenetic relationships of the North American phoxinins continue to pose difficulties for systematists. Results of morphological analyses are not consistent owing to differences interpreting and coding characters. Herein, we present phylogenetic analyses of mitochondrial 12S and 16S ribosomal RNA sequence data for representatives of nearly all genera of North American phoxinins. The data were analysed using parsimony, weighted parsimony, maximum likelihood and bayesian analyses. Results from weighted parsimony, likelihood and the bayesian analysis are largely consistent as they all account for differing substitution rates between transitions and transversions. Several major clades within the fauna can be recognized and are strongly supported by all analyses. These include the western clade, creek chub–plagopterin clade and the open posterior myodome clade. The shiner clade is nested in the open posterior myodome clade and is the most species-rich clade of North American phoxinins. Relationships within this clade were not well resolved by our analyses. This may reflect the inability of the mitochondrial RNA genes to resolve recent speciation events or taxon sampling within the shiner clade.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 139 , 63–80.     

Refining molluscan characters: morphology, character coding and a phylogeny of the Caenogastropoda

Midgut morphology of gastropod molluscs has been underutilized as a resource of characters for phylogenetic analysis. The exclusion of these features reflects the inference that they will be uninformative in determining phylogenetic relationships because they are functionally correlated. In general, it has been hypothesized that the style sac form of midgut is an adaptation to microphagy and becomes secondarily simplified in taxa that have adopted a macrophagous/carnivorous habit with a corresponding increase in extracellular digestion (i.e. radular trituration, gizzards and/or foregut glands). This assumption has resulted in the formulation of adaptive scenarios concerning gastropod alimentary systems, which are mapped onto phylogenetic hypotheses derived from other characters. However, any conclusions regarding phylogenetic utility, and therefore homology, must be realized within a cladistic context. For this analysis, a multi‐organ system anatomical data set was assembled for 16 caenogastropods and two outgroups. The data matrix comprises 64 characters and includes many systems poorly represented in previous broad‐based comparative surveys, such as the alimentary and reno‐pericardial systems. In addition, several taxa were included for which no comprehensive anatomical studies have been available (Cyclophoroidea, Ptenoglossa). Phylogenetic analysis with NONA 1.6 resulted in two most‐parsimonious trees with length 188, CI = 0.53 and RI = 0.63, differing only in the placement of Prunum apicinum and Conus jaspideus. The topology of the strict consensus (Macleaniella Theodoxus((Neocyclotus Marisa)((Lampanella((Petaloconchus Strombus)(Crepidula Bithyia)))(Littorina(Neverita(Cypraea(Nitidiscala(Panarona(Prunum Conus(Ilyanassa Urosalpinx)))))))))), is largely congruent with several independent estimates based on both morphological and molecular data, supporting caenogastropod monophyly and monphyly of the Architaenioglossa, Sorbeoconcha and Neogastropoda. To evaluate phylogenetic utility of the midgut, a broad sampling of taxa was included representing a diversity of feeding modes, food preferences and alimentary morphologies. Character optimization revealed that the evolution of midgut structure is highly mosaic, cutting broadly across patterns of feeding, diet and foregut complexity, to a degree previously unappreciated. In addition, features from the foregut (subradular organ, oesophageal folding) and midgut (position of gastric shield) are broadly distributed among large clades of caenogastropods, providing critical basal synapomorphies within the group. This demonstrates that the gut is an unexploited resource for important and informative characters in higher order systematics of caenogastropods. © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 137 , 447–554.     

Phylogenetic relationships within Serpulidae (Sabellida, Annelida) inferred from molecular and morphological data

We assessed phylogenetic relationships within Serpulidae (including Spirorbinae) using parsimony and Bayesian analyses of 18S rDNA, the D1 and D9−D10 regions of 28S rDNA, and 38 morphological characters. In total, 857 parsimony informative characters were used for 31 terminals, 29 serpulids and sabellid and sabellariid outgroups. Following ILD assessment the two sequence partitions and morphology were analysed separately and in combination. The morphological parsimony analysis was congruent with the results of the 2003 preliminary analysis by Kupriyanova in suggesting that a monophyletic Serpulinae and Spirorbinae form a clade, while the remaining serpulids form a basal grade comprising what are normally regarded as Filograninae. Bremer support values were, however, quite low throughout. In contrast, the combined analyses of molecular and morphological data sets provided highly resolved and well-supported trees, though with some conflict when compared to the morphology-only analysis. Spirorbinae was recovered as a sister group to a monophyletic group comprising both 'filogranin' taxa ( Salmacina , Filograna , Protis , and Protula ) and 'serpulin' taxa such as Chitinopoma , Metavermilia , and Vermiliopsis . Thus the traditionally formulated subfamilies Serpulinae and Filograninae are not monophyletic. This indicates that a major revision of serpulid taxonomy is needed at the more inclusive taxonomic levels. We refrain from doing so based on the present analyses since we feel that further taxon sampling and molecular sequencing are required. The evolution of features such as the operculum and larval development are discussed.     

Molecules,morphology, missing data and the phylogenetic position of a recently extinct madtom catfish (Actinopterygii: Ictaluridae)

Taxa missing large amounts of data pose challenges that may hinder the recovery of a well‐resolved, accurate phylogeny and leave questions surrounding their phylogenetic position. Systematists commonly have to contend with one or two species in a group for which there is little or no material available suitable for recovering molecular data. It is unclear whether these taxa can be better placed using analyses based on morphological data only, or should be included in broader analyses based on both morphological and molecular data. The extinct madtom catfish Noturus trautmani is known from few specimens for which molecular data are unavailable. We included this taxon in parsimony and Bayesian analyses of relationships of madtom catfishes based on a combination of morphological and molecular data. Results indicate that using a combination of morphological and molecular data does a better job at providing a phylogenetic placement for N. trautmani than morphology alone, even though it is missing all of its molecular characters. We provide a novel hypothesis of relationships among Noturus species and recommendations for classification within the group. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 60–75.     

Turtle origins: insights from phylogenetic retrofitting and molecular scaffolds

Adding new taxa to morphological phylogenetic analyses without substantially revising the set of included characters is a common practice, with drawbacks (undersampling of relevant characters) and potential benefits (character selection is not biased by preconceptions over the affinities of the ‘retrofitted’ taxon). Retrofitting turtles (Testudines) and other taxa to recent reptile phylogenies consistently places turtles with anapsid‐grade parareptiles (especially Eunotosaurus and/or pareiasauromorphs), under both Bayesian and parsimony analyses. This morphological evidence for turtle–parareptile affinities appears to contradict the robust genomic evidence that extant (living) turtles are nested within diapsids as sister to extant archosaurs (birds and crocodilians). However, the morphological data are almost equally consistent with a turtle–archosaur clade: enforcing this molecular scaffold onto the morphological data does not greatly increase tree length (parsimony) or reduce likelihood (Bayesian inference). Moreover, under certain analytic conditions, Eunotosaurus groups with turtles and thus also falls within the turtle–archosaur clade. This result raises the possibility that turtles could simultaneously be most closely related to a taxon traditionally considered a parareptile (Eunotosaurus) and still have archosaurs as their closest extant sister group.     

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.     

Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules

The largest Recent family of Bivalvia, the marine Veneridae with approximately 800 species, comprises one of the least understood and most poorly defined molluscan taxa, despite including some of the most economically important and abundant bivalves, for example quahog, Pismo clams, and Manila clams. A review of previous phylogenetic analyses including the superfamily Veneroidea (Veneridae, Petricolidae, Glauconomidae, Turtoniidae, Neoleptonidae) and within the Veneridae shows minimal taxon sampling leading to weak conclusions and few supported synapomorphies. New phylogenetic analyses on 114 taxa tested the monophyly of Veneroidea, Veneridae, and 17 nominal venerid subfamilies, using morphological (conchological, anatomical) data and molecular sequences from mitochondrial (16S, cytochrome oxidase I) and nuclear (28S, histone 3) genes. Morphological analyses using 45 exemplar taxa and 23 traditional characters were highly homoplastic and failed to reconstruct traditional veneroid classification. Full morphological analyses (31 characters) supported the monophyly of Veneroidea and Veneridae but only when certain taxa were excluded, revealing analytical difficulties caused by a suite of characters associated with neotenous or miniaturized morphology. Molecular analyses resulted in substantially higher clade consistency. The combined molecular data set resulted in significant support for a particular topology. The monophyly of Veneridae was supported only when Petricolidae and Turtoniidae were subsumed, and recognized as members with derived or neotenous morphologies, respectively. Morphological character mapping on molecular trees retained a high level of homoplasy, but revealed synapomorphies for major branch points and supported six subfamily groups (Dosiniinae, Gemminae, Samarangiinae, Sunettinae, Tapetinae, combined Chioninae + Venerinae). Glauconomidae and Neoleptonidae are provisionally maintained in Veneroidea pending further study; Petricolinae and Turtoniinae are placed in Veneridae. © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society, 2006, 148 , 439–521.     

A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular data set

The first scolopocryptopid centipede known from the fossil record is a specimen of the subfamily Scolopocryptopinae in Miocene amber from Chiapas, southern Mexico. It is described here as Scolopocryptops simojovelensis sp. nov. , displaying a distinct combination of morphological characters compared to extant congeners. Anatomical details of the fossil specimen were acquired by non‐invasive 3D synchrotron microtomography using X‐ray phase contrast. The phylogenetic position of the new species is inferred based on a combination of morphological data with sequences for six genes (nuclear 18S and 28S rRNA, nuclear protein‐coding histone H3, and mitochondrial 12S rRNA, 16S rRNA, and protein‐coding cytochrome c oxidase subunit I) for extant Scolopendromorpha. The data set includes eight extant species of Scolopocryptops and Dinocryptops from North America, east Asia, and the Pacific, rooted with novel sequence data for other blind scolopendromorphs. The molecular and combined data sets, analysed in a parsimony/direct optimization framework, identified a stable pattern of two main clades within Scolopocryptopinae. North American and Asian species of Scolopocryptops are united as a clade supported by both morphological and molecular characters. Its sister group is a Neotropical clade in which the type species of Dinocryptops is nested within a paraphyletic assemblage of Scolopocryptops species; Dinocryptops is placed in synonymy with Scolopocryptops. The strength of support for the relationships of extant taxa from the molecular data allow the Chiapas fossil to be assigned with precision, despite ambiguity in the morphological data; the fossil is resolved as sister species to the extant Laurasian clade. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 768–786.     

Phylogenetic relationships and evolution of Orbiniidae (Annelida, Polychaeta) based on molecular data

The phylogenetic relationships of orbiniid taxa were reconstructed based on sequence data of the mitochondrial 16S rRNA and nuclear 18S rRNA genes. Both genes were analysed separately and in combination using maximum likelihood, Bayesian inference and maximum parsimony. Regardless of the method used, a clade consisting of the investigated Orbiniidae, Methanoaricia dendrobranchiata and Questa was strongly supported by the 18S dataset. The analysis of the combined dataset suggests inclusion of M. dendrobranchiata within the Orbiniidae with close relationships to species of Orbinia and Phylo, rather than as a sister taxon to all other orbiniids. Evidence is given for the paraphyletic status of Leitoscoloplos , Naineris , Orbinia , Phylo and Scoloplos , which represent the most species-rich genera of the Orbiniidae. It is thus reasoned that the morphological characters presently used for genus diagnosis are not informative for cladistic analysis. No support is found for the hypothesis that taxa of the Protoariciinae represent juveniles of Orbiniinae. Instead, in the case of Protoaricia oerstedi , strong support for a progenetic origin is found.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 59−73.     

Somatic musculature of Tardigrada: phylogenetic signal and metameric patterns

Although studies describing molecular‐based phylogenies within tardigrades are now frequently being published, this is not the case for studies combining molecular and morphological characters. Tardigrade phylogeny is still based, from a morphological point of view, almost exclusively on chitinous structures and little attention has been given to detecting and using novel morphological data. Consequently, we analysed the musculature of seven tardigrade species belonging to the main phyletic lines by confocal laser scanning microscopy and compared these morphological results with new molecular analyses (18S+28S rRNA genes). Finally, we analysed all the data with a total evidence approach. A consilience in the phylogenetic relationships among orders and superfamilies of tardigrades was obtained among the evolutionary trees obtained from morphological, molecular and total evidence approaches. Comparative analysis on the musculature allowed the identification of serial homologies and repeated metameric patterns along the longitudinal animal body axis. A phenomenon of mosaic evolution was detected in musculature anatomy, as dorsal musculature was found to be highly modified with respect to the other body muscle groups, probably related to the evolution of dorsal cuticular plates. An understanding of tardigrade musculature anatomy will give fundamental information to understand the evolution of segmental pattern within Panarthropoda. © 2013 The Linnean Society of London     

The origin of modern amphibians: a re‐evaluation

There are currently three competing hypotheses seeking to explain the evolutionary origins of modern amphibians. The lepospondyl hypothesis holds that the lysorophian lepospondyls constitute the sister taxon to all lissamphibians. The temnospondyl hypothesis suggests that modern amphibians are most closely related to the dissorophoid temnospondyls. Finally, the polyphyletic hypothesis posits that the modern amphibian orders have separate evolutionary origins from among different groups of Palaeozoic tetrapods. Here, we review the character matrices used in previous studies. These data sets differ significantly in choice of characters. Therefore, we built a matrix based on data from all three hypotheses and analysed key taxa phylogenetically using both Bayesian inference and parsimony. Uncorrected, the supermatrix yielded inconclusive results, demonstrating the presence of at least two phylogenetic optima. When the data were corrected according to new observations on Doleserpeton, Eocaecilia, and other fossil forms, the phylogeny supported the temnospondyl hypothesis of lissamphibian origins. This conclusion is also supported by a careful study of character changes in the individual lineages. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 457–469.     

Gelechioidea (Insecta: Lepidoptera) systematics: a reexamination using combined morphology and mitochondrial DNA data

Phylogenies of Gelechioidea (Insecta: Lepidoptera) historically have been in disagreement and definitions vary at the family and subfamily levels. Addition of new taxa or new characters drastically changes relationships indicating that current phylogenetic schemes require more investigation. This study is the first phylogenetic analysis of Gelechioidea to include molecular data. Here we present a combined analysis using Maximum Parsimony to investigate sister-group relationships within Gelechioidea. The addition of Cytochrome oxidase I and II to revised published morphological matrices gives 453 parsimony informative characters for the 42 taxa for which we have sequence data. The combined analysis resulted in two trees with mostly novel sister-group relationships. These results challenge current concepts of Gelechioidea, suggesting that traditional morphological characters that have united taxa may not be homologous structures and are in need of further investigation. A combination of morphological data with new molecular data will be the most robust method of study for Gelechioidea phylogenetics.     

What can the mitochondrial genome reveal about higher‐level phylogeny of the molluscan class Cephalopoda?

We present the first analysis of cephalopod mitochondrial gene order and construct phylogenies based on gene order using Bayesian, distance, and parsimony analysis methods. Analyses included all species of cephalopod for which the whole mitochondrial genome has been sequenced. Where resolution was obtained, these analyses supported division of Neocoleoidea, in which all recent coleoid Cephalopoda can be placed, into Octopodiformes and Decapodiformes. For the same taxa, we also constructed a phylogeny in a maximum likelihood framework based on amino‐acid coded sequence data of all mitochondrial protein coding genes. As well as supporting Octopodiformes and Decapodiformes, amino‐acid analyses established support for Teuthoidea (Oegospida and Myopsida) to the exclusion of Sepiidae, and supported a monophyletic Oegopsida. Partial mitochondrial sequences of additional higher‐level taxa for which whole genome data were not available were subsequently included in the amino‐acid analysis to provide additional information on phylogeny. Spirulida was found to be basal amongst Decapodiformes. Mapping of morphological characters onto our phylogeny and consideration of palaeontological evidence suggests that our phylogeny reflects true evolutionary relationships. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 573–586.     

Evolution of habitat preference in Clitellata (Annelida)

Clitellata (earthworms, leeches, and allies) is a clade of segmented annelid worms that comprise more than 5000 species found worldwide in many aquatic and terrestrial habitats. According to current views, the first clitellates were either aquatic (marine or freshwater) or terrestrial. To address this question further, we assessed the phylogenetic relationships among clitellates using parsimony, maximum likelihood and Bayesian analyses of 175 annelid 18S ribosomal DNA sequences. We then defined two ecological characters (Habitat and Aquatic‐environment preferences) and mapped those characters on the trees from the three analyses, using parsimony character‐state reconstruction (i.e. Fitch optimization). We accommodated phylogenetic uncertainty in the character mapping by reconstructing character evolution on all the trees resulting from parsimony and maximum likelihood bootstrap analyses and, in the Bayesian inference, on the trees sampled using the Markov chain Monte Carlo algorithm. Our analyses revealed that an ‘aquatic’ ancestral state for clitellates is a robust result. By using alterations of coding characters and constrained analyses, we also demonstrated that the hypothesis for a terrestrial origin of clitellates is not supported. Our analyses also suggest that the most recent ancestor of clitellates originated from a freshwater environment. However, we stress the importance of adding sequences of some rare marine taxa to more rigorously assess the freshwater origin of Clitellata. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 447–464.     

Phylogenetic interrelationships,taxonomy, and reductive evolution in the Neotropical electric fish genus Hypopygus (Teleostei,Ostariophysi, Gymnotiformes)

A phylogenetic reconstruction of the Neotropical electric fish genus Hypopygus based on 47 parsimony‐informative morphological characters is presented. A series of synapomorphies support the hypothesis of monophyly of Hypopygus, and partially resolve species‐level relationships within the genus. Hypopygus species are recognized here as miniaturized fishes based on two criteria; first, a derived condition of diminutive body size, and; second, the presence of a suite of reductive morphological characters, including partial or total losses, simplifications, and reductions of the anal‐fin rays, scales, cranial bones, and laterosensory canal system. Reductive characters associated with miniaturization comprise 45% of the total number of characters in the phylogenetic reconstruction of the genus. Miniaturization and reductive morphological evolution in Hypopygus are discussed here in the phylogenetic context. A taxonomic revision of Hypopygus is presented, in which five new species are described, two species previously assigned to the genus are redescribed, and a single known species of Stegostenopos is redescribed and included in Hypopygus as a junior synonym. Distribution maps and a key for all eight valid species of Hypopygus are provided, based on the examination of 5014 catalogued museum specimens. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 1096–1156.     

The phylogeny of charadriiform birds (shorebirds and allies) – reassessing the conflict between morphology and molecules

Multiple molecular analyses provide a congruent and well‐supported phylogeny of the charadriiform family‐level taxa, which conflicts with previous hypotheses based on osteological data. In order to revise the latter and to identify new characters of phylogenetic significance, skeletons of most charadriiform family‐level taxa were examined and 49 characters analysed. Tree topology was sensitive to outgroup choice, but the result of the analysis rooted with Columbidae (doves and pigeons) recovered a monophyletic Scolopaci, Charadrii, and nonturnicid Lari. With regard to the inclusion of Alcidae and Glareolidae in the Lari, the results of the present study are also in better concordance with the new molecular phylogenies than previous analyses of morphological data. Furthermore, for the first time an apomorphy of a clade including Thinocoridae, Pedionomidae, Rostratulidae, and Jacanidae was identified. Inclusion of Turnicidae in the Lari could not be supported, but there is no strong morphological evidence for an alternative placement. Pluvianus shares derived osteological features with the Burhinidae, and its position in the molecular analyses likewise cannot be corroborated with morphological data. Based on the topology of the molecular consensus tree, the ancestral state of selected characters is reconstructed. It is finally noted that recent calibrations of molecular analyses, which indicate an origin of extant charadriiform lineages in the Cretaceous, are based on incorrectly identified fossils. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 916–934.     

Anatomy of a cladistic analysis

The sequential stages culminating in the publication of a morphological cladistic analysis of weevils in the Exophthalmus genus complex (Coleoptera: Curculionidae: Entiminae) are reviewed, with an emphasis on how early‐stage homology assessments were gradually evaluated and refined in light of intermittent phylogenetic insights. In all, 60 incremental versions of the evolving character matrix were congealed and analysed, starting with an assembly of 52 taxa and ten traditionally deployed diagnostic characters, and ending with 90 taxa and 143 characters that reflect significantly more narrow assessments of phylogenetic similarity and scope. Standard matrix properties and analytical tree statistics were traced throughout the analytical process, and series of incongruence length indifference tests were used to identify critical points of topology change among succeeding matrix versions. This kind of parsimony‐contingent rescoping is generally representative of the inferential process of character individuation within individual and across multiple cladistic analyses. The expected long‐term outcome is a maturing observational terminology in which precise inferences of homology are parsimony‐contingent, and the notions of homology and parsimony are inextricably linked. This contingent view of cladistic character individuation is contrasted with current approaches to developing phenotype ontologies based on homology‐neutral structural equivalence expressions. Recommendations are made to transparently embrace the parsimony‐contingent nature of cladistic homology.     

A combined evidence phylogenetic analysis of Anguimorpha (Reptilia: Squamata)

Anguimorpha is a clade of limbed and limbless squamates with ca. 196 extant species and a known fossil record spanning the past 130 million years. Morphology‐based and molecule‐based phylogenetic analyses disagree on several key points. The analyses differ consistently in the placements of monstersaurs (e.g. Gila Monsters), shinisaurs (Crocodile Lizards), the anguid Anniella (American Legless Lizards), carusioids (Knobby Lizards), and the major clades within Varanus (Monitor Lizards). Given different data sources with such different phylogenetic hypotheses, Anguimorpha is an excellent candidate for a combined phylogenetic analysis. We constructed a data matrix consisting of 175 fossil and extant anguimorphs, and 2281 parsimony‐informative characters (315 morphological characters and 1969 molecular characters). We analysed these data using the computer program TNT using the “new technology search” with the ratchet. Our result is novel and shows similarities with both morphological and molecular trees, but is identical to neither. We find that a global combined evidence analysis (GCA) does not recover a holophyletic Varanoidea, but omission of fossil taxa reveals cryptic molecular support for that group. We describe these results and others from global morphological analysis, extant‐only morphological analysis, molecular data‐only analyses, combined evidence analysis of extant taxa, and GCA. © The Willi Hennig Society 2010.