Phylogeny of the higher Libelluloidea (Anisoptera: Odonata): an exploration of the most speciose superfamily of dragonflies

Although libelluloid dragonflies are diverse, numerous, and commonly observed and studied, their phylogenetic history is uncertain. Over 150 years of taxonomic study of Libelluloidea Rambur, 1842, beginning with Hagen (1840), [Rambur, M.P., 1842. Neuropteres. Histoire naturelle des Insectes, Paris, pp. 534; Hagen, H., 1840. Synonymia Libellularum Europaearum. Dissertation inaugularis quam consensu et auctoritate gratiosi medicorum ordinis in academia albertina ad summos in medicina et chirurgia honores.] and Selys (1850), [de Selys Longchamps, E., 1850. Revue des Odonates ou Libellules d'Europe [avec la collaboration de H.A. Hagen]. Muquardt, Bruxelles; Leipzig, 1-408.], has failed to produce a consensus about family and subfamily relationships. The present study provides a well-substantiated phylogeny of the Libelluloidea generated from gene fragments of two independent genes, the 16S and 28S ribosomal RNA (rRNA), and using models that take into account non-independence of correlated rRNA sites. Ninety-three ingroup taxa and six outgroup taxa were amplified for the 28S fragment; 78 ingroup taxa and five outgroup taxa were amplified for the 16S fragment. Bayesian, likelihood and parsimony analyses of the combined data produce well-resolved phylogenetic hypotheses and several previously suggested monophyletic groups were supported by each analysis. Macromiinae, Corduliidae s. s., and Libellulidae are each monophyletic. The corduliid (s.l.) subfamilies Synthemistinae, Gomphomacromiinae, and Idionychinae form a monophyletic group, separate from the Corduliinae. Libellulidae comprises three previously accepted subfamilies (Urothemistinae, a very restricted Tetrathemistinae, and a modified Libellulinae) and five additional consistently recovered groups. None of the other previously proposed subfamilies are supported. Bayesian analyses run with an additional 71 sequences obtained from GenBank did not alter our conclusions. The evolution of adult and larval morphological characters is discussed here to suggest areas for future focus. This study shows the inherent problems in using poorly defined and sometimes inaccurately scored characters, basing groups on symplesiomorphies, and failure to recognize the widespread effects of character correlation and convergence, especially in aspects of wing venation.     

The troublesome parasites--molecular and morphological evidence that Apicomplexa belong to the dinoflagellate-ciliate clade.

Large insertions and deletions in the variable regions of eukaryotic 16S-like rRNA relative to the archaebacterial structure have been defined as a marker for rapidly evolving taxa. Deletions in the rRNA occur in the diplomonad Giardia and the microsporidian Vairimorpha, whereas insertions occur in Euglenozoa (Euglena and the kinetoplastids), Acanthamoeba, Naegleria, Physarum, Dictyostelium, the apicomplexan Plasmodium, the ciliate Euplotes, and some metazoa. Except Acanthamoeba and Euplotes, all of these protists were previously placed at the base of the eukaryote phylogeny. A re-analysis of the 16S-like rRNA and 5S rRNA data with the neighborliness method revealed a close relationship of Apicomplexa to the dinoflagellate-ciliate clade, most probably closer to the dinoflagellates. Morphological evidence that supports this grouping is the layer of sacs underneath the plasma membrane in all three taxa and the identical structure of trichocysts in the apicomplexan Spiromonas and dinoflagellates. The remaining rapidly evolving organisms might still be misplaced in the 16S-like rRNA trees.     

The phylogenetic relevance of thoracic musculature: a case study including a description of the thorax anatomy of Zygoptera (Insecta: Odonata) larvae

New morphological techniques allow for the evaluation of novel character systems that are potentially important for phylogenetic analysis. Only a few studies so far have used character systems from the insect thorax for phylogenetics; the reasons for this might include a lack of common terminology or established homology for pterygote insect thorax musculature. Still, recent studies have proposed common terminology and hypotheses of homology, now allowing for an evaluation of thoracic morphological character systems among the groups of winged insects. Using X ‐ray microtomography (μCT) we present a detailed study of the thorax musculature of O donata as an important phylogenetic character system, with a matrix of 298 characters with 697 character states, including novel data from the thoracic anatomy of eight damselfly larvae. We also included additional O donata, E phemeroptera and N eoptera taxa from the literature and demonstrate the phylogenetic relevance of this character system by reproducing phylogenetic topologies of established relationships. We also compared high‐resolution data from O donata larvae from our study and from recent literature with data from older literature in the adult O donata. All major clades were successfully recovered, (e.g. O donata, E piprocta, A nisoptera and Z ygoptera) with high node support, but obtained higher phylogenetic resolution with the larval data. The best phylogenetic resolution was achieved by combining the adult and larval characters. The taxon sampling and character matrix is the largest to date and underlines the potential relevance of the thorax musculature as an important phylogenetic character system.     

Resolving phylogenetic signal from noise when divergence is rapid: a new look at the old problem of echinoderm class relationships

Resolving evolutionary relationships in groups that underwent fast radiation in deep time is a problem for molecular phylogeny, as the scant phylogenetic signal that characterises short internal branches is generally swamped by more recent substitutions. We implement an approach, that maps how the support for rival phylogenies changes when analysing subsets of sites with either faster and more heterogeneous rates or slower and more homogeneous rates, to address a long-standing problem in deuterostome phylogeny - the interrelationships of the eleutherozoan echinoderm classes. We show that miRNA genes are phylogenetically uninformative as to the relationships of asteroids, echinoids and ophiuroids, consistent with a rapid radiation of these groups as suggested by their fossil record. Using three nuclear rRNAs and seven nuclear housekeeping genes, we map the support for the three possible phylogenetic arrangements of asteroids, ophiuroids and echinoids when moving between subsets of the data with very similar or very different rates of evolution. Only one of the three possible topologies (asteroids (ophiuroids + echinoids)) strengthens when the most rate-homogeneous subset of data are analysed. The other two possible pairings become stronger in a less reliable data subset, which includes the fastest and thus homoplasy-rich data in our alignment. Thus, while superficial analysis of our concatenated alignment identifies asteroids and ophiuroids as sister taxa, more thorough analyses suggest that ophiuroids may be more closely related to echinoids. Divergence of these echinoderm groups, using a relaxed molecular clock, is estimated to have occurred within ∼5 million years. Our results illustrate that the analytic approach of phylogenetic signal dissection can be a powerful tool to investigate rapid radiations in deep geologic time.     

What makes an ophiuroid? A morphological study of the problematic Ordovician stelleroid Stenaster and the palaeobiology of the earliest asteroids and ophiuroids

Extant asteroids and ophiuroids [EchinodermataJ are distinguished by differences in arm support, water vascular system structures and in details of arm and jaw structure. However, some lower Palaeozoic taxa show combinations of both asteroid-like and ophiuroid-like characters and their morphology and functional biology is poorly understood. This paper redescribes one such taxon, the middle-upper Ordovician stellate echinoderm Stenaster and clarifies its phylogenetic status. Characters in common with extant and Ordovician ophiuroids, include arm support due primarily to ambulacral ossicles, presence of extensive longitudinal arm musculature, a mobile jaw and an internalised radial water vessel with internalised podial pores. In addition, Stenaster lacks several characters which are conventionally considered to be asteroid-like, for example an axillary, madreporitc, marginal ossicles and a true ambulacral groove. However, in overall shape Stenaster is remarkably asteroid-like, showing short, broad-based arms shared podial basins and a small disc. A cladistic analysis of early asteroids, ophiuroids and somasteroid taxa consistently places Stenaster within the ophiuroids and suggests secondary convergence to asteroids. In functional terms, Stenaster is interpreted as an ophiuroid which has secondarily adopted a semi-infaunal, deposit-feeding mode of life, analogous to that of some extant paxillosid asteroids.     

The phylogenetic relationships of the suborder Acanthuroidei (Teleostei: Perciformes) based on molecular and morphological evidence

Fragments of 12S and 16S mitochondrial DNA genes were sequenced for 14 acanthuroid taxa (representing all six families) and seven outgroup taxa. The combined data set contained 1399 bp after removal of all ambiguously aligned positions. Examination of site saturation indicated that loop regions of both genes are saturated for transitions, which led to a weighted parsimony analysis of the data set. The resulting tree topology generally agreed with previous morphological hypotheses, most notably placing the Luvaridae within the Acanthuroidei, but it also differed in several areas. The putative sister group of Acanthuroidei, Drepane, was recovered within the suborder, and the sister group of the family Acanthuridae, Zanclus, was likewise recovered within the family. Morphological characters were included to produce a combined data set of 1585 characters for 14 acanthuroid taxa and a single outgroup taxon. An analysis of the same 15 taxa was performed with only the DNA data for comparison. The total-evidence analysis supports the monophyly of the Acanthuridae. A parametric bootstrap suggests the possibility that the paraphyly of Acanthuridae indicated by the molecular analyses is the result of long-branch attraction. The disagreement between molecular and morphological data on the relationships of the basal acanthuroids and its putative sister taxon is unresolved.     

Phylogeny and evolution of developmental mode in temnopleurid echinoids

The phylogenetic relationships of 24 nominal species of temnopleurid echinoid were established using molecular and morphological data sets. The analysis combined sequence data from mitochondrial 16S rRNA and cytochrome c oxidase subunit I genes and the nuclear 18S-like small subunit rRNA gene with morphological data concerning coronal, lantern, spine, and pedicellarial traits. All four data sets contain similar phylogenetic information, although each provides support at a different taxonomic level. Two data congruence tests (Templeton's test and the incongruence length difference test) suggested no significant heterogeneity between the data sets, and all data were combined in a total evidence analysis. The resulting well-resolved phylogeny suggests that Microcyphus, Amblypneustes, and Holopneustes are not monophyletic genera, and that Temnopleurus (Temnopleurus) and Temnopleurus (Toreumatica) are not closely related and should not be regarded as subgenera. In contrast to previous morphological analyses, Mespilia is found to be more closely related to Temnotrema and Toreumatica than it is to Microcyphus. The phylogeny was used to test a series of hypotheses about the evolution of developmental patterns. All species of Amblypneustes, Holopneustes, and Microcyphus are lecithotrophic, and many of these taxa are restricted to southern Australia. Planktotrophy is the ancestral condition for the temnopleurids, and the 11 instances of lecithotrophic nonplanktotrophy in this clade can be accounted for by a single developmental transition that occurred an estimated 4.4-7.4 million years ago, apparently before the migration of Microcyphus to southern Australia. The switch to a nonplanktotrophic mode of development is unidirectional with no evidence of reversals.     

Molecular phylogenetics of the Pectinidae (Mollusca: Bivalvia) and effect of increased taxon sampling and outgroup selection on tree topology

Evolutionary relationships of the Pectinidae were examined using two mitochondrial genes (12S rRNA, 16S rRNA) and one nuclear gene (Histone H3) for 46 species. Outgroup taxa from Propeamussidae, Spondylidae and Limidae were also sequenced to examine the impact of outgroup choice on pectinid topologies. Our phylogenetic analyses resolved the Pectinidae as monophyletic, but many of the subfamilies and tribes within the family do not form monophyletic clades. The paraphyletic Aequipectinini group is the most basal member of the Pectinidae, with the Chlamydinae and Palliolinae representing the most recently derived pectinid groups. These results are in contrast with the current morphological hypothesis of Pectinidae evolution, which suggests the Chlamydinae and Pallioline are basal groups within the Pectinidae. Ingroup topology was found to be sensitive to outgroup choice and increasing taxon sampling within the Pectinidae resulted in more robust phylogenies.     

Phylogeny and systematics of the subfamily Bryocorinae based on morphology with emphasis on the tribe Dicyphini sensu Schuh,

The classification of the hyperdiverse true bug family Miridae is far from settled, and is particularly contentious for the cosmopolitan subfamily Bryocorinae. The morphological diversity within the subfamily is pronounced, and a lack of explicit character formulation hampers stability in the classification. Molecular partitions are few and only a handful of taxa have been sequenced. In this study the phylogeny of the subfamily Bryocorinae has been analysed based on morphological data alone, with an emphasis on evaluating the tribe Dicyphina sensu Schuh, 1976, within which distinct groups of taxa exist. A broad sample of taxa was examined from each of the bryocorine tribes. A broad range of outgroup taxa from most of the other mirid subfamilies was also examined to test for bryocorine monophyly, ingroup relationships and to determine character polarity. In total a matrix comprising 44 ingroup, 15 outgroup taxa and 111 morphological characters was constructed. The phylogenetic analysis resulted in a monophyletic subfamily Bryocorinae sensu Schuh (1976, 1995), except for the genus Palaucoris, which is nested within Cylapinae. The tribe Dicyphini sensu Schuh (1976, 1995) has been rejected. The subtribe Odoniellina is synonymized with the subtribe Monaloniina and the subtribes Dicyphina, Monaloniina and Eccritotarsina are now elevated to tribal level, with the Dicyphini now restricted in composition and definition. The genus Felisacus is highly autapomorphic and a new tribe – the Felisacini – is erected for the included taxa. This phylogeny of the tribes of the Bryocorinae comprises the following sister‐group relationships: Dicyphini ((Bryocorini + Eccritotarsini)(Felisicini + Monaloniini)).     

A phylogeny of Vetigastropoda and other “archaeogastropods”: re-organizing old gastropod clades

Abstract. The phylogenetic relationships among the “archaeogastropod” clades Patellogastropoda, Vetigastropoda, Neritimorpha, and Neomphalina are uncertain; the phylogenetic placement of these clades varies across different analyses, and particularly among those using morphological characteristics and those relying on molecular data. This study explores the relationships among these groups using a combined analysis with seven molecular loci (18S rRNA, 28S rRNA, histone H3, 16S rRNA, cytochrome c oxidase subunit I [COI], myosin heavy-chain type II, and elongation factor-1α [EF-1α]) sequenced for 31 ingroup taxa and eight outgroup taxa. The deep evolutionary splits among these groups have made resolution of stable relationships difficult, and so EF-1α and myosin are used in an attempt to re-examine these ancient radiation events. Three phylogenetic analyses were performed utilizing all seven genes: a single-step direct optimization analysis using parsimony, and two-step approaches using parsimony and maximum likelihood. A single-step direct optimization parsimony analysis was also performed using only five molecular loci (18S rRNA, 28S rRNA, histone H3, 16S rRNA, and COI) in order to determine the utility of EF-1α and myosin in resolving deep relationships. In the likelihood and POY optimal phylogenetic analyses, Gastropoda, Caenogastropoda, Neritimorpha, Neomphalina, and Patellogastropoda were monophyletic. Additionally, Neomphalina and Pleurotomariidae fell outside the remaining vetigastropods, indicating the need for further investigation into the relationship of these groups with other gastropods.     

RNA SEQUENCE DATA IN PHYLOGENETIC RECONSTRUCTION: TESTING THE LIMITS OF ITS RESOLUTION

Abstract— 18S ribosomal RNA sequences from 11 echinoderms are analysed using parsimony to investigate phylogenetic relationships. Their estimated divergence limes range from less than 20 Ma to more than 550 Ma before present. Phylogenies based on 18S rRNA sequence data are compared with well-established morphological phylogenies to discover at what evolutionary distance the two approaches start to produce incongruent results. Three regions of the 18S rRNA molecule are analysed separately and together, and paired and unpaired sites are also treated separately and combined.
Results show that a parsimony analysis of sequence data produces reliable results only when taxa have diverged more recently than about 100 Ma. At greater evolutionary distances (up to 250 Ma), paired nucleotides produce more reliable results than unpaired, while paired and unpaired data combined produce intermediate results. All trees within about 1% of the most parsimonious solution ought to be accepted. Transversions give results almost as reliable as paired regions though there were relatively few informative sites. The relationships of echinoderm classes, which diverged 450–550 Ma ago, are unresolved by 18S rRNA data.     

Sea urchins, sea stars and brittle stars from Terra Nova Bay (Ross Sea, Antarctica)

Although echinoderms constitute some of the most conspicuous taxa of the Antarctic benthic communities, the echinoderm fauna of Terra Nova has not been described yet. The present study provides the first species list of echinoids, ophiuroids and asteroids from Terra Nova Bay (30–500 m depth) and describes the depth distribution of these species. Preliminary observations of the summer reproductive condition of some of the species are also included.     

Phylogeny of Syrphidae (Diptera) inferred from combined analysis of molecular and morphological characters

Abstract.  Syrphidae (Diptera) commonly called hoverflies, includes more than 5000 species world-wide. The aim of this study was to address the systematic position of the disputed elements in the intrafamilial classification of Syrphidae, namely the monophyly of Eristalinae and the placement of Microdontini and Pipizini, as well as the position of particular genera ( Nausigaster , Alipumilio , Spheginobaccha ). Sequence data from nuclear 28S rRNA and mitochondrial COI genes in conjunction with larval and adult morphological characters of fifty-one syrphid taxa were analysed using optimization alignment to explore phylogenetic relationships among included taxa. A species of Platypezidae, Agathomyia unicolor , was used as outgroup, and also including one representative ( Jassidophaga villosa ) of the sister-group of Syrphidae, Pipunculidae. Sensitivity of the data was assessed under six different parameter values. A stability tree summarized the results. Microdontini, including Spheginobaccha , was placed basally, and Pipizini appeared as the sister-group to subfamily Syrphinae. The monophyly of subfamily Eristalinae was supported. The results support at least two independent origins of entomophagy in syrphids, and frequent shifts between larval feeding habitats within the saprophagous eristalines.     

Phylogeny of pholcid spiders (Araneae: Pholcidae): combined analysis using morphology and molecules

The spider family Pholcidae comprises a large number of mainly tropical, web-weaving spiders, and is among the most diverse and dominant spider groups in the world. The phylogeny of this family has so far been investigated exclusively using morphological data. Here, we present the first molecular data for the family analyzed in a phylogenetic context. Four different gene regions (12S rRNA, 16S rRNA, cytochrome c oxidase subunit I, 28S rRNA) and 45 morphological characters were scored for 31 pholcid and three outgroup taxa. The data were analyzed both for individual genes, combined molecular data, and molecular plus morphological data, using parsimony, maximum likelihood, and Bayesian methods. Some of the phylogenetic hypotheses obtained previously using morphology alone were also supported by our results, like the monophyly of pholcines and of the New World clade. On the other hand, some of the previous hypotheses could be discarded with some confidence (monophyly of holocnemines, the position of Priscula), and still others need further investigation (the position of holocnemines, ninetines, and Metagonia). The data obtained provide an excellent basis for future investigations of phylogenetic patterns both within the family and among spider families.     

Vestigial ophiopluteal structures in the lecithotrophic larvae of Ophionereis schayeri (Ophiuroidea)

Evolution of echinoderm development from a feeding to a non-feeding mode can be examined by studying non-feeding larvae with structures that appear to be vestiges derived from a feeding ancestral state. The lecithotrophic larvae of the Australian brittle star Ophionereis schayeri possess such features, and the early development of this species was documented by light and scanning electron microscopy. The embryos undergo irregular cleavage, resulting in the formation of different sized blastomeres, with subsequent development through a wrinkled blastula stage. The lecithotrophic larva of O. schayeri possesses several vestigial ophiopluteal structures, including a continuous ciliated band, a larval gut, and a larval skeleton. The ciliated band is a reduced expression of the continuous ciliated band typical of ophioplutei. The larval gut is a transiently complete system, but an esophageal plug and rapid closure of the blastopore renders it nonfunctional. The larval skeleton, though reduced, consists of four rods corresponding to the body, posterolateral, anterolateral, and postoral rods characteristic of an ophiopluteus. Due to a heterochrony in larval skeletogenesis, the postoral rods develop early and simultaneously with the other rods. Compared with the larvae of other lecithotrophic ophiuroids, the larva of O. schayeri is one of the most reduced ophiopluteal forms reported to date.     

Development of the nervous system in the brittle star Amphipholis kochii

There are several studies of neural development in various echinoderms, but few on ophiuroids, which develop indirectly via the production of pluteus larvae, as do echinoids. To determine the extent of similarity of neuroanatomy and neural development in the ophiuroids with other echinoderm larvae, we investigated the development of the nervous system in the brittle star Amphipholis kochii (Echinodermata: Ophiuroidea) by immunohistochemistry. Immunoreactive cells first appeared bilaterally in the animal pole at the late gastrula stage, and there was little migration of the neural precursors during A. kochii ontogeny, as is also the case in echinoids and holothuroids. On the other hand, neural specification in the presumptive ciliary band near the base of the arms does occur in ophiuroid larvae and is a feature they share with echinoids and ophiuroids. The ophiopluteus larval nervous system is similar to that of auricularia larvae on the whole, including the lack of a fine network of neurites in the epidermis and the presence of neural connections across the oral epidermis. Ophioplutei possess a pair of bilateral apical organs that differ from those of echinoid echinoplutei in terms of relative position. They also possess coiled cilia, which may possess a sensory function, but in the same location as the serotonergic apical ganglia. These coiled cilia are thought to be a derived structure in pluteus-like larvae. Our results suggest that the neural specification in the animal plate in ophiuroids, holothuroids, and echinoids is a plesiomorphic feature of the Ambulacraria, whereas neural specification at the base of the larval arms may be a more derived state restricted to pluteus-like larvae.     

What is a Suiforme (Artiodactyla)?: Contribution of Cranioskeletal and Mitochondrial DNA Data

Suiformes (Artiodactyla) traditionally includes three families: Suidae, Tayassuidae, and Hippopotamidae but the monophyly of this suborder has recently been questioned from molecular data. A maximum parsimony analysis of molecular, morphological, and combined data was performed on the same set of taxa including representatives of the three Artiodactyla suborders (Suiformes, Ruminantia, and Tylopoda) and Perissodactyla as outgroup. Mitochondrial (cytochromeband 12S rRNA) sequence comparisons support the monophyly of Suina (Suidae and Tayassuidae) and Ancodonta (Hippopotamidae) but not the monophyly of Suiformes. Inversely, our preliminary morphological analysis supports the monophyly of Suiformes whereas relationships among the three families are not resolved. The combined data set does not resolve the relationships between Suina, Ancodonta, and Ruminantia. These results are discussed in relation to morphological characters and paleontological data. Some improvements are suggested to clarify the morphological definition of Suiformes and relationships among them.     

Developmental plasticity in Macrophiothrix brittlestars: are morphologically convergent larvae also convergently plastic?

The pluteus larval forms of sea urchins (echinoids) and brittlestars (ophiuroids) use an internal skeleton to project arms that bear a long ciliated band used in swimming and feeding. The length of this ciliated band influences rates of maximum food clearance for larvae of both echinoderm classes and affects rates of growth and development in the plankton. Phylogenetic and morphological evidence, however, tend to support the view that the pluteus morphologies of the two classes are independently derived. Studies with echinoplutei have shown that investment in skeletal growth and ciliated band length changes in response to food conditions, with poorly fed larvae investing more in growth of the larval skeleton and arms either absolutely or in relation to other larval or developing postlarval structures. We present evidence for similar plasticity of skeletal growth in ophioplutei. We examined four species in the brittlestar genus Macrophiothrix that spanned a 3.8-fold range in egg size. Sibling larvae in 14 male-female crosses were reared with high (H) or low (L) food rations, and measurements were recorded for five skeletal arm rods and three non-arm body dimensions. The expression of adaptive plasticity (significantly longer arms in L versus H cultures on a given day) was apparent for most crosses in M. koehleri, the species with the smallest egg size. In the single cross for M. longipeda, larvae from L cultures had longer arms for their body length or stomach width than did larvae from H cultures. In these cases, plasticity was similar in timing, persistence, and magnitude to previously published results from echinoplutei. If internal skeletons are independently derived in the two classes, then plasticity in the expression of this homoplastic trait may itself be homoplastic.     

Phylogeny of Palaearctic wheatears (genus Oenanthe)--congruence between morphometric and molecular data

Wheatears of the genus Oenanthe are birds specialized to desert ecosystems in the Palaearctic region from Morocco to China. Although they have been the subject of many morphological and ecological studies, no molecular data have been used to elucidate their phylogenetic relationships, and, their relationships are still debated. Here we use DNA sequences of 1180 bp of two mitochondrial genes, 16S rRNA and cytochrome oxidase subunit I, from 32 individuals from Middle East and North Africa, and Bayesian methods to derive a phylogeny for 11 species of Oenanthe. The resulting tree supported three major clades: (A) O. alboniger, O. chrysopygia, O. lugens, O. finschii, O. leucopyga, O. picata, O. moesta, (B) O. deserti and O. pleschanka; and (C) O. isabellina and O. oenanthe. These results largely differ from previous hypotheses based on analysis of morphological and chromatic characters. However, the two clades (B) and (C) were also supported by a phenetic analysis of new morphometric data presented here, indicating that characters related to colouration and ecology in Oenanthe are more strongly influenced by homoplasy than those of body shape.