The evolutionary history of Trichoptera (Insecta): A case of successful adaptation to life in freshwater

The insect order Trichoptera (caddisflies) forms the second most species‐rich monophyletic group of animals in freshwater. So far, several attempts have been made to elucidate its evolutionary history with both morphological and molecular data. However, none have attempted to analyse the time frame for its diversification. The order is divided into three suborders – Annulipalpia, Integripalpia and ‘Spicipalpia’. Historically, the most problematic taxon to place within the order is ‘Spicipalpia’, whose larvae do not build traditional cases or filtering nets like the majority of the caddisflies. They have previously been proposed to be the sister group of all other Trichoptera or more advanced within the order, with equivocal monophyly and with different interordinal placements among various studies. In order to resolve the evolutionary history of the caddisflies as well as timing their diversification, we utilized fragments of three nuclear (carbamoylphosphate synthethase, isocitrate dehydrogenase and RNA polymerase II) and one mitochondrial (cytochrome oxidase I) protein coding genes, with 16 fossil trichopteran taxa used for time calibration. The ‘spicipalpian’ families are recovered as ancestral to all other caddisflies, though paraphyletic. We recover stable relationships among most families and superfamilies, resolving many previously unrecognized phylogenetic affinities amongst extant families. The origin of Trichoptera is estimated to be around 234 Ma, i.e. Middle – Late Triassic.     

Phylogenetic position of rhyacophiloid caddisflies (Insecta, Trichoptera): a spermatological analysis of Rhyacophilidae and Glossosomatidae

Most caddisflies (Insecta, Trichoptera) are classified into two suborders, Annulipalpia and Integripalpia. However, the use of the derived characters that are regularly applied in systematic and phylogenetic analyses of Trichoptera is insufficient to determine with certainty the position of the families belonging to Rhyacophiloidea, which are considered by different authors to be either Annulipalpia, or Integripalpia, or even a separate suborder. Rhyacophiloidea comprise four overall similar families: free-living Rhyacophilidae and Hydrobiosidae, saddle-case making Glossosomatidae, and purse-case making Hydroptilidae. It was previously found that Annulipalpia spermatozoa have aberrant axonemes while Integripalpia spermatozoa display the plesiomorph 9 + 2 axoneme. The present spermatological analysis of the families Rhyacophilidae and Glossosomatidae shows that both have spermatozoa with aberrant axonemes lacking the two central microtubules found in the typical axoneme of insect spermatozoa. This is an apomorphic character shared with the superfamily Hydropsychoidea, indicating that from this point of view, Rhyacophiloidae are more closely related to Annulipalpia than to Integripalpia.     

Phylogenetic relationships among the lepidopteran and trichopteran suborders (Insecta) from the embryological standpoint1

Adopting the cladistic method in comparative embryology, 27 embryonic characters were analyzed to reconstruct the phylogenetic relationships among the lepidopteran and trichopteran suborders, viz., Annulipalpia, Integripalpia, Zeugloptera, Dacnonypha, Exoporia, Monotrysia, and Ditrysia. The resultant cladogram is basically coincident with that proposed by Kristensen . The order Trichoptera and Lepidoptera constitute a monophyletic group on the basis of one synapomorphy, the presence of well developed silk glands in embryos. The Trichoptera are separable from the Lepidoptera by the states of four characters. The Trichoptera, as a whole, are quite homogenous, and embryological data provide no rational ground for the separation of this order into the Annulipalpia and Integripalpia at a subordinal level. On the contrary, the embryonic development of the Lepidoptera becomes divergent from the most primitive condition to a specialized one according to suborders. The Zeugloptera are the sister group of all other Lepidoptera, because they share two apomorphies with the latter. The Dacnonypha are the most primitive next to the Zeugloptera, and have a sister-group relationship with the Exoporia + (Monotrysia + Ditrysia), being held together with the latter by five synapomorphies. Although the Exoporia retain almost as many plesiomorphic characters as the Dacnonypha, they have a sister-group relationship with the Monotrysia + Ditrysia, as inferred on the basis of two synapomorphies. The Monotrysia and Ditrysia have a sistergroup relationship, and are the most advanced groups in the Lepidoptera judging from their shared acquisition of many apomorphic characters.     

Phylogeny of caddisflies (Insecta, Trichoptera)

Trichoptera are holometabolous insects with aquatic larvae that, together with the Lepidoptera, comprise the Amphiesmenoptera. Previous phylogenetic hypotheses and progress on our ongoing data collection are summarized. Fragments of the large and small subunit nuclear ribosomal RNAs (D1, D3, V4–5), the nuclear elongation factor 1 alpha gene and a fragment of mitochondrial cytochrome oxidase 1 (COI) were sequenced, and molecular data were combined with previously published morphological data. Equally and differentially weighted parsimony analyses were conducted in order to present a phylogeny of Trichoptera, including 43 of 45 families. Our phylogeny closely resembles that proposed by Herbert Ross with respect to the relationships among suborders, with a monophyletic Annulipalpia at the base of the tree, and a clade consisting of Spicipalpia plus a monophyletic Integripalpia. The monophyly of Spicipalpia is weakly supported in the combined equally weighted analysis, and Spicipalpia is paraphyletic in the differentially weighted analysis. Within Integripalpia, our phylogeny recovered monophyletic Plenitentoria, Brevitentoria and Sericostomatoidea. Leptoceroidea was unresolved in the equally weighted analysis and monophyletic in the differentially weighted analysis. Within Annulipalpia, we recovered a basal but paraphyletic Philopotamoidea and a monophyletic Hydropsychoidea.     

A comparative morphological study of lateral line systems in larvae and pupae of Trichoptera

The abdominal lateral line system in Trichoptera, consisting of filaments and lamellae with associated primary and secondary setae, was studied in larvae and pupae of 70 genera representing 26 families. Filaments are slender, generally bifid, tubular extensions of the cuticle that together form a fringe on the lateral abdominal surface of larvae and pupae of many but not all families of case-making Trichoptera (Integripalpia). Larvae and pupae of the Annulipalpia and Spicipalpia lack a lateral fringe of bifid filaments, but single filaments occur in larvae of a few unrelated genera. A lateral fringe may help in regulating the flow of water which is maintained through the case by abdominal undulation. Lamellae occur only in larvae of the Integripalpia, where they are variously distributed among families and genera, and probably have a sensory function. Three types of lamellae are recognized: forked, serrate and single. Filaments and lamellae have significant taxonomic value, and their patterns of occurrence raise questions about the phylogeny of Trichoptera.     

Phylogenetic analysis of the Malacostraca (Crustacea)

The Malacostraca comprises about 28 000 species with a broad disparity in morphology, anatomy, embryology, behaviour and ecology. The phylogenetic relationships of the major taxa are still under debate. Is the Leptostraca the sister group of the remaining Malacostraca, or is this taxon more closely related to other Crustacea? Does the Stomatopoda or the Bathynellacea represent the most basal taxon within the remaining taxa? Is the Peracarida monophyletic or are some peracarid taxa more closely related to other ‘caridoid’ taxa? Is the Thermosbaenacea part of the Peracarida or its sister group, and how much support is there for a taxon Amphipoda + Isopoda? To answer these questions a phylogenetic analysis of the Malacostraca combining different phylogenetic approaches was undertaken. In a first step, the monophyly of the Malacostraca including the Leptostraca is shown using the ‘Hennigian approach’. A computer cladistic analysis of the Malacostraca was carried out with NONA and PEE ‐WEE , based on 93 characters from morphology, anatomy and embryology. Nineteen higher malacostracan taxa are included in our analysis. Taxa whose representatives are exclusively fossils were not included. The Leptostraca was used as an operational out‐group. The present analysis supports the basal position of the Stomatopoda. Syncarida and Peracarida (including Thermosbaenacea) are supported as monophyletic, the Eucarida is not. Instead a sister‐group relationship is suggested between Euphausiacea and Peracarida (including Thermosbaenacea), with the Syncarida as the sister group to both taxa. Certain embryonic characters are interpreted as support for the monophyly of the Peracarida (without Thermosbaenacea) because convergences or reversals of these characters seem implausible. Within the Peracarida, the Mysidacea (Lophogastrida + Mysida) represents the sister group to the remaining taxa. A sister‐group relationship between Amphipoda and Isopoda is not supported.     

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.     

Sperm structure of Trichoptera. IV. Rhyacophilidae and Glossosomatidae

The families Rhyacophilidae and Glossosomatidae (Trichoptera) are considered to be the most primitive ones within the order. We examined the spermatozoa of members of these families to see whether their ultrastructure is consistent with an ancestral position. Axonemal structures, after fixation with a tannic acid-containing fixative, have been shown to be particularly useful as taxonomical indicators. It was found that 4 members of Rhyacophilidae, representing 3 subgenera (Rhyacophila, Pararhyacophila, and Hyporhyacophila) all have motile spermatozoa, with a 9 + 9 + 2 axoneme in which inner (but no outer) dynein arms are present. The accessory tubules have a wall consisting of 17 protofilaments, decreasing to 16 near the distal end, whereas the examined member of Glossosomatidae, Catagapetus nigrans, has accessory tubules with 18 protofilaments and a 9 + 9 + 2 axoneme with inner dynein arms and with motility similar to the Rhyacophilidae. Sperm motility is consistent with the inclusion of these 2 families within the suborder Integripalpia, and the axonemal pattern 9 + 9 + 2 indicates that the families indeed occupy a primitive position within Trichoptera.     

Massive gene rearrangements of mitochondrial genomes and implications for the phylogeny of Trichoptera (Insecta)

Mitochondrial genomes have been widely used for phylogenetic reconstruction and evolutionary analysis in various groups of Insecta. Gene rearrangements in the mitogenome can be informative characters for phylogenetic reconstruction and adaptive evolution. Trichoptera is one of the most important groups of aquatic insects. Prior to this study, complete mitogenomes from Trichoptera were restricted to eight families, resulting in a biased view of their mitogenome structure and evolution. Here, we assemble new mitogenomes for 66 species by high-throughput sequencing. The mitogenomes of 19 families and 47 genera are documented for the first time. Combined with 16 previously published mitogenomes of Trichoptera, we find 14 kinds of gene rearrangement patterns novel for Trichoptera, including rearrangement of protein-coding genes, tRNAs and control regions. Simultaneously, we provide evidence for the occurrence of tandem duplication and non-random loss events in the mitogenomes of three families. Phylogenetic analyses show that Hydroptilidae was recovered as a sister group to Annulipalpia. The increased nucleotide substitution rate and adaptive evolution may have affected the mitochondrial gene rearrangements in Trichoptera. Our study offers new insights into the mechanisms and patterns of mitogenome rearrangements in Insecta at large and into the usefulness of mitogenomic gene order as a phylogenetic marker within Trichoptera.     

Phylogenesis of spermatogenesis in Annulipalpia caddisflies: An ultrastructural analysis on philopotamidae spermiogenesis

Characters currently used in phylogenetic analyses are insufficient for determining the status of several families of the order Trichoptera (caddisflies). Comparative spermatology can contribute to solving this problem. In the suborder Integripalpia, the sperm axoneme displays the pattern of 9 + 2 pairs of parallel microtubules found in many animal species. In the suborder Annulipalpia, however, axonemes bear remarkable aberrations. Consistently, in Chimarra florida (Philopotamidae, Annulipalpia) we found that the number of central microtubules varies from zero to four in axonemes of the spermatids and that spermatozoa lack axonemes. We propose that, similarly, the axoneme pattern became unstable in the Annulipalpia ancestor, from which branched two phylogenetic lines having different kinds of axoneme aberrations: (a) families in which the number of central microtubules of the axoneme exceeds two (e.g., Philopotamidae, Polycentropodidae) and (b) families in which the number of central microtubules of the axoneme does not exceed two (e.g., Hydropsychidae).     

Phylogenetic analysis of pelecaniformes (aves) based on osteological data: implications for waterbird phylogeny and fossil calibration studies

Background

Debate regarding the monophyly and relationships of the avian order Pelecaniformes represents a classic example of discord between morphological and molecular estimates of phylogeny. This lack of consensus hampers interpretation of the group''s fossil record, which has major implications for understanding patterns of character evolution (e.g., the evolution of wing-propelled diving) and temporal diversification (e.g., the origins of modern families). Relationships of the Pelecaniformes were inferred through parsimony analyses of an osteological dataset encompassing 59 taxa and 464 characters. The relationships of the Plotopteridae, an extinct family of wing-propelled divers, and several other fossil pelecaniforms (Limnofregata, Prophaethon, Lithoptila, ?Borvocarbo stoeffelensis) were also assessed. The antiquity of these taxa and their purported status as stem members of extant families makes them valuable for studies of higher-level avian diversification.

Methodology/Principal Findings

Pelecaniform monophyly is not recovered, with Phaethontidae recovered as distantly related to all other pelecaniforms, which are supported as a monophyletic Steganopodes. Some anatomical partitions of the dataset possess different phylogenetic signals, and partitioned analyses reveal that these discrepancies are localized outside of Steganopodes, and primarily due to a few labile taxa. The Plotopteridae are recovered as the sister taxon to Phalacrocoracoidea, and the relationships of other fossil pelecaniforms representing key calibration points are well supported, including Limnofregata (sister taxon to Fregatidae), Prophaethon and Lithoptila (successive sister taxa to Phaethontidae), and ?Borvocarbo stoeffelensis (sister taxon to Phalacrocoracidae). These relationships are invariant when ‘backbone’ constraints based on recent avian phylogenies are imposed.

Conclusions/Significance

Relationships of extant pelecaniforms inferred from morphology are more congruent with molecular phylogenies than previously assumed, though notable conflicts remain. The phylogenetic position of the Plotopteridae implies that wing-propelled diving evolved independently in plotopterids and penguins, representing a remarkable case of convergent evolution. Despite robust support for the placement of fossil taxa representing key calibration points, the successive outgroup relationships of several “stem fossil + crown family” clades are variable and poorly supported across recent studies of avian phylogeny. Thus, the impact these fossils have on inferred patterns of temporal diversification depends heavily on the resolution of deep nodes in avian phylogeny.     

Comparative and functional morphology of wing coupling structures in Trichoptera: Annulipalpia

Several orders of morphologically four‐winged insects have evolved mechanisms that enforce a union between the mesothoracic and metathoracic wings (forewings and hindwings) during the wing beat cycle. Such mechanisms result in a morphologically tetrapterous insect flying as if it were functionally dipterous, and these mechanisms have been described for several insect orders. The caddisfly suborders Annulipalpia and Integripalpia (Trichoptera) each have evolved a wing coupling apparatus, with at least three systems having evolved within the suborder Annulipalpia. The comparative and inferred functional morphology of the putative wing coupling mechanisms is described for the annulipalpian families Hydropsychidae (subfamilies Macronematinae and Hydropsychinae), Polycentropodidae and Ecnomidae, and a novel form‐functional complex putatively involved with at‐rest forewing‐forewing coupling is described for Hydropsychidae: Smicrideinae. It is proposed that the morphology of the wing coupling apparatuses of Hydropsychinae and Macronematinae are apomorphies for those clades. J. Morphol. 2009. © 2009 Wiley‐Liss, Inc.     

Phylogeny,divergence times and biogeography of window flies (Scenopinidae) and the therevoid clade (Diptera: Asiloidea)

The evolution of the ‘therevoid’ clade, with an emphasis on window flies (Scenopinidae), is presented by combining DNA sequence data with morphological characters for living and fossil species. The therevoid clade represents a group of four families (Apsilocephalidae, Evocoidae, Scenopinidae and Therevidae) of lower brachyceran Diptera in the superfamily Asiloidea. A comprehensive phylogenetic analysis using parsimony and likelihood methods was undertaken using extensive taxon sampling from all families and subfamilies, and compared with outgroup taxa sampled from the related families Asilidae, Mydidae, Apioceridae and Empididae. Fifty‐nine morphological characters (adult, larval and pupal) were combined with 6.4 kb of DNA sequences for two ribosomal genes (16S and 18S ribosomal DNA) and three protein‐encoding genes [cytochrome oxidase I (COI), triose phosphate isomerase (TPI) and the CPSase region of carbamoyl‐phosphate synthase‐aspartate transcarbamoylase‐dihydroorotase (CAD)]. Results from combined analyses of morphological and molecular data for 78 taxa representing all families of the therevoid clade are presented. Specific hypotheses of the relationship between respective families and subfamilies were tested statistically using four‐cluster likelihood mapping. The therevoid clade is a well‐supported monophyletic group within Asiloidea, with Evocoidae sister to Apsilocephalidae and Therevidae sister to Scenopinidae. Temporal and zoogeographical aspects of therevoid clade evolution were investigated using Bayesian divergence time estimates and Lagrange ancestral range scenarios. The effect of inclusion of fossils as terminal taxa on phylogenetic and divergence time estimation was investigated, with morphological scoring for fossil representatives included in the analyses rather than used simply as minimum age constraints. In each analysis there was either improvement in estimation, or only marginal and localized loss in tree resolution, and with younger estimates of divergence time across the tree. The historical biogeography of the therevoid clade was examined with multiple trans‐Antarctic vicariance events between Australasia and South America evident during the Late Cretaceous to early Palaeogene. Scenopininae is newly subdivided into two tribes, Metatrichini trib.n. and Scenopinini Fallén stat.r. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:4974EBF8‐3117‐4189‐B6DE‐7D5BF9B23E53 .     

PHYLOGENETIC RELATIONSHIPS IN SEED PLANTS

Abstract— The phylogenetic relationships of nineteen extant and fossil seed plants are considered. Analysis of 31 characters produced ten topologically similar and equally parsimonious cladograms. A strict consensus tree derived from these cladograms places Lyginopteris as the sister taxon to the other seed plants included. Within this clade all the taxa considered, except medullosans and cycads, form a single monophyletic group defined by the presence of flattened seeds and saccate pollen ("platy-sperms"). Relationships between medullosans, cycads, and "platysperms" were not resolved, but within the "platysperm" clade conifers and cordaites ( Cordaixylon, Mesoxylon ) + Ginkgo form a monophyletic group ("coniferophytes"). The "higher platysperms" (glossopterids, Caytonia , corystosperms, Bennettitales, Pentoxylon , Gnetales, and angiosperms) are also monophyletic, but their relationship to "coniferophytes," peltasperms, and Callistophyton is unresolved. Pentoxylon is placed as sister taxon to the Bennettitales, and together they form the sister group to a clade in which Gnetales and angiosperm are sister taxa. The Bennettitales + Pentoxylon + Gnetales + angiosperms ("anthophytes") form a monophyletic sister group to the corystosperms. This analysis is compared with current classifications of seed plants. It does not support a close relationship between Bennettitales and cycads, it provides no evidence for seed plant polyphyly, and it strongly suggests that the current concept of seed ferns has little value in a phylogenetic context.     

Comments on hexanchiform phylogeny (Pisces, Neoselachii)

The Hexanchiformes (Cow Sharks) are regarded as a monophyletic taxon. Cladistic analysis shows that among the various neoselachian taxa proposed so far as the sister group of the Hexanchiformes a sister group relationship between the Hexanchiformes and a (still unnamed) taxon comprising the Squaliformes and Pristiophoriformes appears as the most probable hypothesis. In addition, MAISEY and WOLFRAM'S (1984) concept of hexanchiform interrelationships is critically reviewed. An alternative cladogram of hexanchiform interrelationships is developed which includes Recent as well as fossil hexanchiform taxa. In this cladogram the living genera Hexancbus and Notorynchus are sister groups and both taxa together form the sister group of the Recent Heptranchias. The fossil taxa +Notidanoides, +“Hexanchus” gracilis, +Notidanodon and +Weltonia are arranged in the stem lineage of recent Hexanchiformes.     

Phylogeny of Trichoptera (caddisflies): characterization of signal and noise within multiple datasets

Trichoptera are holometabolous insects with aquatic larvae that, together with the Lepidoptera, make up the Amphiesmenoptera. Despite extensive previous morphological work, little phylogenetic agreement has been reached about the relationship among the three suborders--Annulipalpia, Spicipalpia, and Integripalpia--or about the monophyly of Spicipalpia. In an effort to resolve this conflict, we sequenced fragments of the large and small subunit nuclear ribosomal RNAs (1078 nt; D1, D3, V4-5), the nuclear elongation factor 1 alpha gene (EF-1 alpha; 1098 nt), and a fragment of mitochondrial cytochrome oxidase I (COI; 411 nt). Seventy adult and larval morphological characters were reanalyzed and added to molecular data in a combined analysis. We evaluated signal and homoplasy in each of the molecular datasets and attempted to rank the particular datasets according to how appropriate they were for inferring relationships among suborders. This evaluation included testing for conflict among datasets, comparing tree lengths among alternative hypotheses, measuring the left-skew of tree-length distributions from maximally divergent sets of taxa, evaluating the recovery of expected clades, visualizing whether or not substitutions were accumulating with time, and estimating nucleotide compositional bias. Although all these measures cast doubt on the reliability of the deep-level signal coming from the nucleotides of the COI and EF-1 alpha genes, these data could still be included in combined analyses without overturning the results from the most conservative marker, the rRNA. The different datasets were found to be evolving under extremely different rates. A site-specific likelihood method for dealing with combined data with nonoverlapping parameters was proposed, and a similar weighting scheme under parsimony was evaluated. Among our phylogenetic conclusions, we found Annulipalpia to be the most basal of the three suborders, with Spicipalpia and Integripalpia forming a clade. Monophyly of Annulipalpia and Integripalpia was confirmed, but the relationships among spicipalpians remain equivocal.     

A phylogeny of fossil and living neocoleoid cephalopods

Coleoid cephalopod phylogeny is well studied via both molecular and morphological data, yet although some agreement has been reached (e.g. that extant Decapodiformes and Octopoda are monophyletic) many details remain poorly resolved. Fossil coleoids, for which much data exists, have hitherto not been incorporated into analyses. Their inclusion is highly desirable for the support of neontological phylogenies, to better reconstruct character‐state histories, and to investigate the placement of the fossil groups themselves. In this study we present and analyse a morphological data matrix including both extinct and extant taxa. Homology assumptions in our data are discussed. Our results are presented both with and without the constraint of a monophyletic Decapodiformes imposed. When analysed with this constraint our results are strikingly congruent with those from molecular phylogeny, for instance placing Idiosepius in a basal position within Decapodiformes, and recovering Oegopsida and Bathyteuthoidea (although as grades). Our results support an Octopodiformes clade (“vampire squid” Vampyroteuthis as sister to Octopoda) and an octopodiform interpretation for most fossil coleoids. They suggest the fossil sister taxon to the octopods to be Plesioteuthididae. Most fossil higher taxa are supported, although many genera, especially within suborder Teudopseina, appear para‐ or polyphyletic.     

Global interrelationships of Plesiosauria (Reptilia,Sauropterygia) and the pivotal role of taxon sampling in determining the outcome of phylogenetic analyses

Previous attempts to resolve plesiosaurian phylogeny are reviewed and a new phylogenetic data set of 66 taxa (67% of ingroup taxa examined directly) and 178 characters (eight new) is presented. We recover two key novel results: a monophyletic Plesiosauridae comprising Plesiosaurus dolichodeirus, Hydrorion brachypterygius, Microcleidus homalospondylus, Occitanosaurus tournemirensis and Seeleyosaurus guilelmiimperatoris; and five plesiosaurian taxa recovered outside the split between Plesiosauroidea and Pliosauroidea. These taxa are Attenborosaurus conybeari, ‘Plesiosaurus’macrocephalus and a clade comprising Archaeonectrus rostratus, Macroplata tenuiceps and BMNH 49202. Based on this result, a new name, Neoplesiosauria, is erected for the clade comprising Plesiosauroidea and Pliosauroidea. Taxon subsamples of the new dataset are used to simulate previous investigations of global plesiosaurian relationships. Based on these simulations, most major differences between previous global phylogenetic hypotheses can be attributed to differences in taxon sampling. These include the position of Leptocleididae and Polycotylidae and the monophyly or paraphyly of Rhomaleosauridae. On this basis we favour the results recovered by our, larger analysis. Leptocleididae and Polycotylidae are sister taxa, forming a monophyletic clade within Plesiosauroidea, indicating that the large‐headed, short‐necked ‘pliosauromorph’ body plan evolved twice within Plesiosauria. Rhomaleosauridae forms the monophyletic sister taxon of Pliosauridae within Pliosauroidea. Problems are identified with previous phylogenetic definitions of plesiosaurian clades and new, stem‐based definitions are presented that should maintain their integrity over a range of phylogenetic hypotheses. New, rank‐free clade names Cryptoclidia and Leptocleidia are erected to replace the superfamilies Cryptoclidoidea and Leptocleidoidea. These were problematic as they were nested within the superfamily Plesiosauroidea. The incongruence length difference test indicates no significant difference in levels of homoplasy between cranial and postcranial characters.     

Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly

The dipteran clade Calyptratae is comprised of approximately 18 000 described species (12% of the known dipteran diversity) and includes well‐known taxa such as houseflies, tsetse flies, blowflies and botflies, which have a close association with humans. However, the phylogenetic relationships within this insect radiation are very poorly understood and controversial. Here we propose a higher‐level phylogenetic hypothesis for the Calyptratae based on an extensive DNA sequence dataset for 11 noncalyptrate outgroups and 247 calyptrate species representing all commonly accepted families in the Oestroidea and Hippoboscoidea, as well as those of the muscoid grade. DNA sequences for genes in the mitochondrial (12S, 16S, cytochrome c oxidase subunit I and cytochrome b) and nuclear genome [18S, 28S, the carbamoyl phosphate synthetase region of CAD (rudimentary), Elongation factor one alpha] were used to reconstruct the relationships. We discuss problems relating to the alignment and analysis of large datasets and emphasize the advantages of utilizing a guide tree‐based approach for the alignment of the DNA sequences and using the leaf stability index to identify ‘wildcard’ taxa whose excessive instability obscures the phylogenetic signal. Our analyses support the monophyly of the Calyptratae and demonstrate that the superfamily Oestroidea is nested within the muscoid grade. We confirm that the monotypic family Mystacinobiidae is an oestroid and further revise the composition of the Oestroidea by demonstrating that the previously unplaced and still undescribed ‘McAlpine’s fly’ is nested within this superfamily as a probable sister group to Mystacinobiidae. Within the Oestroidea we confirm with molecular data that the Calliphoridae are a paraphyletic grade of lineages. The families Sarcophagidae and Rhiniidae are monophyletic, but support for the monophyly of Tachinidae and Rhinophoridae depends on analytical technique (e.g. parsimony or maximum likelihood). The superfamilies Hippoboscoidea and Oestroidea are consistently found to be monophyletic, and the paraphyly of the muscoid grade is confirmed. In the overall relationships for the calyptrates, the Hippoboscoidea are sister group to the remaining Calyptratae, and the Fanniidae are sister group to the nonhippoboscoid calyptrates, whose relationships can be summarized as (Muscidae (Oestroidea (Scathophagidae, Anthomyiidae))).     

Polychaete phylogeny based on morphological data – a comparison of current attempts

Annelid phylogeny is one of the largest unresolved problems within the Metazoa. This is due to the enormous age of this taxon and also strongly influenced by the current discussion on the position of the Arthropoda, which traditionally is hypothesized to be the annelid sister taxon. Within the framework of recent discussions on the position of the Annelida, the ground pattern of this taxon is either a clitellate-like, parapodia-less dwelling organism or an organisms that resembles errant polychaetes in having parapodia and gills and probably being a predator. To solve this problem different attempts have been made in the past, cladistic analysis, scenario based plausibility considerations and a successive search for sister taxa base on isolated characters. These attempts are presented and critically discussed. There is at least strong support for the Annelida as wells as for several of its taxa above the level of traditional families; the monophyly of the Polychaeta, however, remains questionable. The term taxon is used here in the sense of group of things that share certain characteristics. Biological taxa are not necessarily monophyletic, although many of them turned out to be. In terms of phylogenetic systematics taxa should be monophyletic.