Relationships among the major lineages of Dictyoptera: the effect of outgroup selection on dictyopteran tree topology

Abstract Dictyoptera, comprising Blattaria, Isoptera, and Mantodea, are diverse in appearance and life history, and are strongly supported as monophyletic. We downloaded COII, 16S, 18S, and 28S sequences of 39 dictyopteran species from GenBank. Ribosomal RNA sequences were aligned manually with reference to secondary structure. We included morphological data (maximum of 175 characters) for 12 of these taxa and for an additional 15 dictyopteran taxa (for which we had only morphological data). We had two datasets, a 59‐taxon dataset with five outgroup taxa, from Phasmatodea (2 taxa), Mantophasmatodea (1 taxon), Embioptera (1 taxon), and Grylloblattodea (1 taxon), and a 62‐taxon dataset with three additional outgroup taxa from Plecoptera (1 taxon), Dermaptera (1 taxon) and Orthoptera (1 taxon). We analysed the combined molecular?morphological dataset using the doublet and MK models in Mr Bayes , and using a parsimony heuristic search in paup . Within the monophyletic Mantodea, Mantoida is recovered as sister to the rest of Mantodea, followed by Chaeteessa; the monophyly of most of the more derived families as defined currently is not supported. We recovered novel phylogenetic hypotheses about the taxa within Blattodea (following Hennig, containing Isoptera). Unique to our study, one Bayesian analysis places Polyphagoidea as sister to all other Dictyoptera; other analyses and/or the addition of certain orthopteran sequences, however, place Polyphagoidea more deeply within Dictyoptera. Isoptera falls within the cockroaches, sister to the genus Cryptocercus. Separate parsimony analyses of independent gene fragments suggest that gene selection is an important factor in tree reconstruction. When we varied the ingroup taxa and/or outgroup taxa, the internal dictyopteran relationships differed in the position of several taxa of interest, including Cryptocercus, Polyphaga, Periplaneta and Supella. This provides further evidence that the choice of both outgroup and ingroup taxa greatly affects tree topology.     

1 Taxon sampling and inferences about diatom phylogeny

Proper taxon sampling is one of the greatest challenges to understanding phylogenetic relationships, perhaps as important as choice of optimality criterion or data type. This has been demonstrated in diatoms where centric diatoms may either be strongly supported as monophyletic or paraphyletic when analyzing SSU rDNA sequences using the same optimality criterion. The effect of ingroup and outgroup taxon sampling on relationships of diatoms is explored for diatoms as a whole and for the order Thalassiosirales. In the latter case, SSU rDNA and rbcL sequence data result in phylogenetic relationships that appear to be strongly incongruent with morphology and broadly incongruent with the fossil record. For example, Cyclotella stelligera Cleve & Grunow behaves like a rogue taxon, jumping from place to place throughout the tree. Morphological data place C. stelligera near the base of the freshwater group as sister to the extinct genus Mesodictyon Theriot and Bradbury, suggesting that it is an old, long branch that might be expected to “misbehave” in poorly sampled trees. Cyclotella stelligera and C. bodanica Grunow delimit the diameter of morphological diversity in Cyclotella, so increased sampling of intermediate taxa will be critical to resolving this part of the tree. Morphology is sampled for a much greater number of taxa and many transitional states of putative synapomorphies seem to suggest a robust morphological hypothesis. The Thalassiosirales are unstable with regards to taxon sampling in the genetic data, suggesting that perhaps the morphological hypothesis is (for now) preferable.     

TNT version 1.5, including a full implementation of phylogenetic morphometrics

Version 1.5 of the computer program TNT completely integrates landmark data into phylogenetic analysis. Landmark data consist of coordinates (in two or three dimensions) for the terminal taxa; TNT reconstructs shapes for the internal nodes such that the difference between ancestor and descendant shapes for all tree branches sums up to a minimum; this sum is used as tree score. Landmark data can be analysed alone or in combination with standard characters; all the applicable commands and options in TNT can be used transparently after reading a landmark data set. The program continues implementing all the types of analyses in former versions, including discrete and continuous characters (which can now be read at any scale, and automatically rescaled by TNT). Using algorithms described in this paper, searches for landmark data can be made tens to hundreds of times faster than it was possible before (from T to 3T times faster, where T is the number of taxa), thus making phylogenetic analysis of landmarks feasible even on standard personal computers.     

Morphometrics and character state recognition for cladistic analyses in theBletia reflexa complex (Orchidaceae)

Different criteria have been suggested for decisions on character state recognition for morphological characters showing continuous variation from taxon to taxon. A method proposed byMishler andDe Luna seeks to recognize as many character states as the groups of taxon means that are revealed by an analysis of variance (ANOVA) followed by multiple range tests. We apply this method as a guide in decisions of selecting taxonomic characters in species of theBletia reflexa complex. Seven species of the complex, represented by 156 individuals belonging to 54 populations, were the terminal taxa of the study. Character state codes were assigned to 20 characters. These characters together with 12 non-quantitative characters were incorporated into cladistic analyses. Results indicate that the complex is monophyletic only under one outgroup combination.     

Scale Biogenesis in Synurophycean Protists: Phylogenetic Implications

The Synurophyceae is a class of golden-brown, freshwater, photosynthetic flagellates with a world-wide distribution. A well-developed taxonomy exists where genera and species are distinguished by colony or cell morphology or by the siliceous scales that cover the cells. However, phylogenetic relationships within the class are poorly understood, and incongruous taxonomic concepts occur. This study reviews scale morphology from field-collected samples and controlled culturing experiments as well as from studies of scale biogenesis. The information is used to identify homologous silicification surfaces among taxa and to document the diversity of the resulting scale structures. Thirty-two character states are coded into 11 characters in a cladistic analysis of 13 pivotal taxa. Colonial species are emphasized. One most-parsimonious phylogenetic tree is found (HI = 0, CI = 1). Synura lapponica is shown to be most closely related to Tessellaria volvocina. S. sphagnicola emerges at the base of the tree. Mallomonas caudata and the S. petersenii clade emerge from within Sectio Synura. Chrysodidymus synuroideus appears as an ancestral taxon in the Synura spinosa-like clade (i.e., Series Spinosae). The poorly understood developmental bases for some characters, especially secondary scale structures, are identified and may help focus future research.     

The deep divergences of neornithine birds: a phylogenetic analysis of morphological characters

Consensus is elusive regarding the phylogenetic relationships among neornithine (crown clade) birds. The ongoing debate over their deep divergences is despite recent increases in available molecular sequence data and the publication of several larger morphological data sets. In the present study, the phylogenetic relationships among 43 neornithine higher taxa are addressed using a data set of 148 osteological and soft tissue characters, which is one of the largest to date. The Mesozoic non‐neornithine birds Apsaravis, Hesperornis, and Ichthyornis are used as outgroup taxa for this analysis. Thus, for the first time, a broad array of morphological characters (including both cranial and postcranial characters) are analyzed for an ingroup densely sampling Neornithes, with crown clade outgroups used to polarize these characters. The strict consensus cladogram of two most parsimonious trees resultant from 1000 replicate heuristic searches (random stepwise addition, tree‐bisection‐reconnection) recovered several previously identified clades; the at‐one‐time contentious clades Galloanseres (waterfowl, fowl, and allies) and Palaeognathae were supported. Most notably, our analysis recovered monophyly of Neoaves, i.e., all neognathous birds to the exclusion of the Galloanseres, although this clade was weakly supported. The recently proposed sister taxon relationship between Steatornithidae (oilbird) and Trogonidae (trogons) was recovered. The traditional taxon “Falconiformes” (Cathartidae, Sagittariidae, Accipitridae, and Falconidae) was not found to be monophyletic, as Strigiformes (owls) are placed as the sister taxon of (Falconidae + Accipitridae). Monophyly of the traditional “Gruiformes” (cranes and allies) and ”Ciconiiformes” (storks and allies) was also not recovered. The primary analysis resulted in support for a sister group relationship between Gaviidae (loons) and Podicipedidae (grebes)—foot‐propelled diving birds that share many features of the pelvis and hind limb. Exclusion of Gaviidae and reanalysis of the data set, however, recovered the sister group relationship between Phoenicopteridae (flamingos) and grebes recently proposed from molecular sequence data.     

Multiple Origins of Colonial Green Flagellates from Unicells: Evidence from Molecular and Organismal Characters

Phylogenetic hypotheses generated from cladistic analysis of organismal and molecular data are shown to be generally congruent and/or complementary for comparisons of unicellular and colonial green algae in the Chlorophyceae. Cladistic analysis of organismal character data corroborates the alliance of colonial Stephanosphaera with unicellular Haematococcus (Haematococcaceae sensu Smith), inferred from previous studies of nuclear-encoded rRNA sequence data. The organismal data also support monophyly of the colonial Volvocaceae (sensu Smith). Alliances of other unicellular taxa, including those ascribed to the "Euchlamydomonas" Hauptgruppe (sensu Ettl), are not resolved by organismal characters principally because the structure of the data is skewed to shared ancestral characters (symplesiomorphies) and unique characters (autapomorphies) which define individual taxa only. Reanalysis of rRNA sequence data, with additional sequence data for critical taxa, does not support monophyly of the colonial Volvocaceae (sensu Smith). However, these data are weak in the support of the alternate hypothesis of nomnonophyly. In contrast, relationships among most unicellular flagellates are unambiguously resolved by the molecular data. Although the failure of the sequence data to resolve relationships among colonial flagellates appears to be due to a sampling of conservative sequences, an ancient, rapid radiation event or taxon sampling bias may also be contributing to the ambiguity problem. Results from analysis of a combined data set (organismal and molecular) are generally consistent with the inferences of the organismal character data regarding the colonial flagellates and are also consistent with the inferences of the sequence data regarding the unicellular taxa.     

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.     

Assigning fossil specimens to a given recent classification when the distribution of character variation is not normal

To help assign fossil material to Recent taxa we present a methodology that offers systematic quantitative tools to explore several continuous characters. It also enables the quantitative determination of which characters amongst several alternatives give results more consistent with a given classification.

The Gini Mean Difference ('Gini') is the expected absolute difference between two randomly drawn observations. In a fossil assemblage comprising several taxa, the Gini of the overall assemblage may be decomposed into three components: the weighted sum of intra‐taxon Gini, the index of overlap, and the inter‐taxon Gini. The parameter that is additional to alternative methods is the overlap index, which serves as a quantitative measure for evaluating the quality of identification. The Gini is advantageous in that it does not require the assumption of a normal distribution in character variation.

The Gini methodology is described in both mathematical and non‐mathematical terms. We demonstrate it by application to a hypothetical gastropod genus consisting of five species, in which we show in orderly, quantitative terms that one character is better for identification of the various species than another character.     

Scorpion higher phylogeny and classification, taxonomic anarchy, and standards for peer review in online publishing

Soleglad and Fet's (2003a) attempt to reconstruct the phylogeny of Recent (including extant) scorpions, the revised classification derived from it, and recent emendations, mostly published in their self‐edited online journal, Euscorpius, are deficient. Separate analyses of three independent matrices (morphology, 16S rDNA, 18S rDNA) were presented. In the morphological matrix, 52 binary and 10 tristate trichobothrial characters were replaced with one character comprising six ordered states representing trichobothrial “types”. The remaining matrix of 105 characters was further reduced to 33 “fundamental” characters (20% of the morphological dataset), the analysis of which appears to be the basis for the revised classification presented. The taxon sample for the morphological analysis included 14 supraspecific terminal taxa representing genera, the monophyly of only 7 (12.5%) of which has been confirmed. A composite terminal, assembled from the fragments of fossils that may not be confamilial let alone monophyletic, was created for the Palaeopisthacanthidae, employed as the primary outgroup for the analysis. Other important outgroup taxa, notably eurypterids, xiphosurans and other arachnids, were omitted entirely. The morphological characters presented contained numerous unjustifiable assumptions of character polarity and phylogenetic relationship. An approach to character coding, deliberately adopted to reduce “homoplasy”, biased the analysis towards a preconceived result. Structurally and topographically similar features in different taxa were explicitly assigned separate (often autapomorphic) states according to presumed phylogenetic relationships among the taxa in which they were observed. Putative “reversals” were coded as separate characters or states. Character transformation was forced by ordering, additive coding or Sankoff optimization through allegedly intermediate states for which there is no empirical evidence. Many characters were defined in a manner that demonstrates either a lack of understanding of, or disregard for, established methods and standards of morphological character coding. Some states display overlapping variation whereas others subsume variation that is not structurally or topographically similar. Polymorphic “states” were created for terminals with interspecific variation and unknown “states” for terminals that should have been scored unknown. Many characters were not evaluated for particular terminal taxa, but merely scored inapplicable although the structures and, consequently, the characters in question are present and therefore applicable to them. In view of the significant theoretical and empirical problems with the approach to cladistics taken by Soleglad and Fet, we find no justification for accepting either the results of their analyses or the revised classification derived from them. Pending the outcome of a rigorous phylogenetic analysis, published according to acceptable standards of scholarship in a peer‐reviewed journal, we revert to the suprageneric classification of Scorpiones reflected by the most recent peer‐reviewed, published treatments and reject all changes to the classification proposed by Soleglad, Fet and colleagues since 2001. We argue that an analysis and revised classification of the kind presented in various papers by these authors could not survive the peer‐review process of a mainstream scientific journal. The poor scholarship exemplified by these and other papers published in Euscorpius emphasize the importance of quality control associated with the emergent infrastructure of online publishing. A centralized register of taxa may be the only solution for ensuring quality control in the taxonomy of the future. © The Willi Hennig Society 2005.     

Arion transsylvanus (Mollusca,Pulmonata, Arionidae): rediscovery of a cryptic species

Jordaens, K., Pinceel, J., Van Houtte, N., Breugelmans, K. & Backeljau, T. (2010). Arion transsylvanus (Mollusca, Pulmonata, Arionidae): rediscovery of a cryptic species. —Zoologica Scripta, 39, 343–362. Cryptic species are abundant among invertebrates and are often hard to recognise. Molecular markers are an extremely useful tool to delineate cryptic taxa, although they should be applied with caution because different genes and techniques may yield different outcomes. We illustrate how cross‐validation by molecular and morphological data can be applied to optimise taxonomic interpretations when cryptic species are involved. This is performed for the terrestrial slug Arion subfuscus species complex which represents a historical ‘taxonomic garbage can’. Gonad morphology, allozymes and mtDNA data consistently showed that slugs from Romania and a location in E Poland represent a strongly differentiated taxon within this complex. These slugs are therefore formally redescribed and assigned to A. transsylvanus Simroth 1885 ; a forgotten nominal taxon from Transylvania. Diagnostic characters, including DNA sequences for the mitochondrial 16S rDNA are presented. Animals with the morphology of A. brunneus Lehmann 1862 , a nominal taxon which has also been reported from Romania, have the gonad type, allozyme alleles and 16S rDNA haplotypes of either A. fuscus, A. subfuscus or A. transsylvanus. Therefore, A. brunneus is regarded as a colour morph shared by several species and hence, A. transsylvanus is probably the only A. subfuscus‐like species in the Romanian Carpathians.     

Osteology of the Late Jurassic Portuguese sauropod dinosaur Lusotitan atalaiensis (Macronaria) and the evolutionary history of basal titanosauriforms

Titanosauriforms represent a diverse and globally distributed clade of neosauropod dinosaurs, but their inter‐relationships remain poorly understood. Here we redescribe Lusotitan atalaiensis from the Late Jurassic Lourinhã Formation of Portugal, a taxon previously referred to Brachiosaurus. The lectotype includes cervical, dorsal, and caudal vertebrae, and elements from the forelimb, hindlimb, and pelvic girdle. Lusotitan is a valid taxon and can be diagnosed by six autapomorphies, including the presence of elongate postzygapophyses that project well beyond the posterior margin of the neural arch in anterior‐to‐middle caudal vertebrae. A new phylogenetic analysis, focused on elucidating the evolutionary relationships of basal titanosauriforms, is presented, comprising 63 taxa scored for 279 characters. Many of these characters are heavily revised or novel to our study, and a number of ingroup taxa have never previously been incorporated into a phylogenetic analysis. We treated quantitative characters as discrete and continuous data in two parallel analyses, and explored the effect of implied weighting. Although we recovered monophyletic brachiosaurid and somphospondylan sister clades within Titanosauriformes, their compositions were affected by alternative treatments of quantitative data and, especially, by the weighting of such data. This suggests that the treatment of quantitative data is important and the wrong decisions might lead to incorrect tree topologies. In particular, the diversity of Titanosauria was greatly increased by the use of implied weights. Our results support the generic separation of the contemporaneous taxa Brachiosaurus, Giraffatitan, and Lusotitan, with the latter recovered as either a brachiosaurid or the sister taxon to Titanosauriformes. Although Janenschia was recovered as a basal macronarian, outside Titanosauria, the sympatric Australodocus provides body fossil evidence for the pre‐Cretaceous origin of titanosaurs. We recovered evidence for a sauropod with close affinities to the Chinese taxon Mamenchisaurus in the Late Jurassic Tendaguru beds of Africa, and present new information demonstrating the wider distribution of caudal pneumaticity within Titanosauria. The earliest known titanosauriform body fossils are from the late Oxfordian (Late Jurassic), although trackway evidence indicates a Middle Jurassic origin. Diversity increased throughout the Late Jurassic, and titanosauriforms did not undergo a severe extinction across the Jurassic/Cretaceous boundary, in contrast to diplodocids and non‐neosauropods. Titanosauriform diversity increased in the Barremian and Aptian–Albian as a result of radiations of derived somphospondylans and lithostrotians, respectively, but there was a severe drop (up to 40%) in species numbers at, or near, the Albian/Cenomanian boundary, representing a faunal turnover whereby basal titanosauriforms were replaced by derived titanosaurs, although this transition occurred in a spatiotemporally staggered fashion. © 2013 The Linnean Society of London