A Family Level Analysis of Tardigrade Phylogeny

In the present study a character data set suitable for cladistic analysis at the family level was developed. A data matrix consisting of 50 morphological characters from 15 families of tardigrades was analyzed by maximum parsimony. Kinorhynchs, loriciferans, and gastrotrichs were used as outgroups. The results agree with the currently accepted hypothesis that Eutardigrada and Heterotardigrada are distinct monophyletic groups. Among the eutardigrades, Eohypsibiidae was found to be a sister group to Macrobiotidae+Hypsibiidae, while Milnesiidae was the basal eutardigrade family. The basal heterotardigrade family was found to be Oreellidae. Echiniscoideans grouped with some traditional Arthrotardigrada (Renaudarctidae, Coronarctidae+Batillipedidae) suggesting that the arthrotardigrades are not monophyletic. The 18S rRNA gene sequence of Batillipes mirus Richters, 1909 and Calohypsibius schusteri Nelson & McGlothlin, 1996 were obtained and their addition to a previously published dataset supports the monophyly of Heterotardigrada and of Parachela versus Apochela within the Eutardigrada.     

Phylogeny of oligochaetous Clitellata

Clitellata, with more than one third of all annelid species described, is briefly introduced, and an overview of the hypotheses of phylogenetic relationships among the groups traditionally referred to as oligochaetes is given. The presentation is placed in a historical context and describes the trend to move from intuitive, narrative approaches to more formal analyses of character patterns. Monophyly of the earthworms (the megadriles, or Metagynophora sensu Jamieson), or at least a major part of them (Crassiclitellata sensu Jamieson), and paraphyly of the ‘microdrile’ largely aquatic, groups are supported by both morphological and molecular data. Further, DNA sequences as well as spermatozoal ultrastructure corroborate that all leech-like taxa (Hirudinida, Acanthobdellida and Branchiobdellida) constitute a clade derived within ‘Oligochaeta’, closely related to the family Lumbriculidae. Molecular systematic studies also support relationships already identified on the basis of morphological data, e.g., the position of Naididae within Tubificidae, the position of Phreodrilidae close to, but outside, the same family, and the putative sistergroup relationship between the newly discovered Capilloventridae and the rest of Clitellata. A recent study using 18S rDNA suggests that Enchytraeidae is closely related to Metagynophora, and that these two taxa, which contain all terrestrial oligochaetous clitellates, form a clade derived from aquatic ‘microdriles’ This refutes a recent hypothesis proposing that the ancestor of Clitellata was terrestrial. To a great extent, however, the basal resolution of the oligochaetous clitellates remains unclear.     

Phylogeny of Palaearctic Syrphidae (Diptera): evidence from larval stages

We estimated the phylogeny of Palaearctic Syrphidae using 187 larval morphological characters obtained from about 65% of the fauna (85 supraspecific taxa represented by 118 species) and based the analysis at the generic, level. The root of the syrphid tree was established from an outgroup consisting of other Aschizan families: the Platypezidae, Phoridae and Pipunculidae, with the tree rooted on the Lonchopteridae. The Syrphidae was the most derived Aschizan family. The Pipunculidae was the sister group to the Syrphidae. Eumerus was basal within Syrphidae. A trend exists towards increasing complexity of integumental folds and grooves across the Aschiza. In movement, the integument collapses along the line of these grooves. Grooves are evidence of muscles forming functional groups. Elaboration of independent groups of muscles appears to underlie much of the evolution of larval form within Aschiza. The basal feeding modes of syrphid larvae are mycophagy and phytophagy. Above these feeding modes, all remaining syiphids fall into one of two lineages comprising entomophages and saprophages, each of which has a single origin within the apparently polyphyletic Volucella. Major morphological innovation is associated with shifts between feeding modes; within feeding modes, change is gradual and tends towards increasing complexity. Change is mostly in structures associated with the mouthparts, thorax, anal segment and locomotory organs. Generic diagnoses with biological and taxonomic notes and a key to genera using larval characters are provided.     

The Ultrastructure of Chaenea teres and an Analysis of the Phylogeny of the Haptorid Ciliates

Chaenea teres has typical haptorid ultrastructure. The somatic monokinetid has two transverse microtubular ribbons, an overlapping postciliary microtubular ribbon, and a laterally directed kinetodesmal fiber. The evered cytopharynx forms a dome at the apical end of the cell. The base of the dome is surrounded by oral dikinetids. The left, anterior kinetosome of the oral pair is not ciliated and has a transverse microtubular ribbon, a nematodesmata and a single postciliary microtubule. The right, posterior kinetosome is ciliated and has only postciliary microtubules. The kinetosomes at the anterior ends of the somatic kinetics are close together and their transverse microtubules and nematodesmata contribute to the support of the cytopharynx. The transverse microtubules of these oralized somatic kinetosomes, together with those from the oral dikinetids, line the cytopharynx. Accessory or bulge microtubules arise perpendicular to the transverse microtubules. A dorsal brush of three kineties of clavate cilia is found on the cell surface just posterior to the oral region. Mucocysts and a single type of toxicyst are present. The toxicysts are confined to the oral region. There are multiple ovoid macronuclei that stain weakly. Micronuclei were not observed. Cladistic analysis indicates the Chaenea may be most closely related to Fuscheria and Acropisthium. The cladistic analysis also suggests that existing taxonomies of the subclass Haptoria need to be revised. We propose some modifications to Foissner & Foissner's classification that include transferring Helicoprorodon, Actinobolina, the buetschiliids, and the balantidiids to the order Haptorida and recognizing the close relationship between pleurostomes and spathidiids.     

Phylogeny of the Neotropical moth tribe Josiini (Notodontidae: Dioptinae): a hidden case of Miillerian mimicry

The Neotropical moth tribe Josiini (Notodontidae: Dioptinae) contains over 100 described species in 11 genera. All are diurnal, with brightly-coloured, presumably aposematic wing patterns. Larval hostplants are exclusively in the genus Passiflora (Passifloraceae) except for two new records, reported here, from Tumera (Turneraceae). A comparative morphological study of 26 representative josiine species yielded 86 characters from adults, larvae and pupae, all of which are figured and discussed. Phylogenetic analysis of these data produced a single most-parsimonious cladogram. According to the phylogenetic results: (1) monophyly of the Josiini is strongly supported; (2) the currently accepted generic classification is in disarray; (3) morphological character variation is extensive, and adult traits reflect phylogeny more effectively than do those of immature stages; (4) wing pattern types have undergone convergent evolution. A rare phenotype, longitudinal wing stripes, appears in two widely divergent clades, suggesting the evolution of Miillerian mimicry within the Josiini.     

Romance of the three domains: how cladistics transformed the classification of cellular organisms

Cladistics is a biological philosophy that uses genealogical relationship among species and an inferred sequence of divergence as the basis of classification. This review critically surveys the chronological development of biological classification from Aristotle through our postgenomic era with a central focus on cladistics. In 1957, Julian Huxley coined cladogenesis to denote splitting from subspeciation. In 1960, the English translation of Willi Hennig’s 1950 work, Systematic Phylogenetics, was published, which received strong opposition from pheneticists, such as numerical taxonomists Peter Sneath and Robert Sokal, and evolutionary taxonomist, Ernst Mayr, and sparked acrimonious debates in 1960–1980. In 1977–1990, Carl Woese pioneered in using small subunit rRNA gene sequences to delimitate the three domains of cellular life and established major prokaryotic phyla. Cladistics has since dominated taxonomy. Despite being compatible with modern microbiological observations, i.e. organisms with unusual phenotypes, restricted expression of characteristics and occasionally being uncultivable, increasing recognition of pervasiveness and abundance of horizontal gene transfer has challenged relevance and validity of cladistics. The mosaic nature of eukaryotic and prokaryotic genomes was also gradually discovered. In the mid-2000s, high-throughput and whole-genome sequencing became routine and complex geneologies of organisms have led to the proposal of a reticulated web of life. While genomics only indirectly leads to understanding of functional adaptations to ecological niches, computational modeling of entire organisms is underway and the gap between genomics and phenetics may soon be bridged. Controversies are not expected to settle as taxonomic classifications shall remain subjective to serve the human scientist, not the classified.     

Phylogeny, Evolution and Historical Zoogeography of Ticks: A Review of Recent Progress

There has been much progress in our understanding of the phylogeny and evolution of ticks, particularly hard ticks, in the past 5 years. Indeed, a consensus about the phylogeny of the hard ticks has emerged. Our current working hypothesis for the phylogeny of ticks is quite different to the working hypothesis of 5 years ago. So that the classification reflects our knowledge of ticks, several changes to the nomenclature of ticks are imminent. One subfamily, the Hyalomminae, will probably be sunk, yet another, the Bothriocrotoninae n. subfamily, will be created. Bothriocrotoninae n. subfamily, and Bothriocroton n. genus, are being created to house an early-diverging (‘basal’) lineage of endemic Australian ticks that used to be in the genus Aponomma (ticks of reptiles). There has been progress in our understanding of the subfamily Rhipicephalinae. The genus Rhipicephalus is almost certainly paraphyletic with respect to the genus Boophilus. Thus, the genus Boophilus will probably become a subgenus of Rhipicephalus. This change to the nomenclature, unlike other options, will keep the name Boophilus in common usage. Rhipicephalus (Boophilus) microplus may still called B. microplus, and Rhipicephalus (Boophilus) annulatus may still be called B. annulatus, but the nomenclature will have been changed to reflect our knowledge of the phylogeny and evolution of these ticks. New insights into the historical zoogeography of ticks will also be presented. This revised version was published online in July 2006 with corrections to the Cover Date.     

Phylogeny of the nominotypical subgenus of Culex (Diptera: Culicidae): insights from analyses of anatomical data into interspecific relationships and species groups in an unresolved tree

The aim of this study was to produce the first objective and comprehensive phylogenetic analysis of the speciose subgenus Culex based on morphological data. We used implied and equally weighted parsimony methods to analyse a dataset comprised of 286 characters of the larval, pupal, and adult stages of 150 species of the subgenus and an outgroup of 17 species. We determined the optimal support by summing the GC supports for each MPC, selecting the cladograms with the highest supports to generate a strict consensus tree. We then collapsed the branches with GC support < 1 to obtain the ‘best’ topography of relationships. The analyses largely failed to resolve relationships among the species and the informal groups in which they are currently placed based on morphological similarities and differences. All analyses, however, support the monophyly of genus Culex. With the exception of the Atriceps Group, the analyses failed to find positive support for any of the informal species groups (monophyly of the Duttoni Group could not be established because only one of the two species of the group was included in the analyses). Since the analyses would seem to include sufficient data for phylogenetic reconstruction, lack of resolution appears to be the result of inadequate or conflicting character data, and perhaps incorrect homology assessments. Molecular and other biological data are needed to gain insights into the evolution of subgenus Culex. Nevertheless, we discuss the placement of several taxa in the current morphology-based classification of the subgenus based on insights realized during the study.

     

Flagellate Phylogeny: A Study in Conflicts*

SYNOPSIS. Information relating to the ultrastructure of 4 organellar systems of flagellates—nuclei (including mitosis), flagella, mitochondria and chloroplasts—is examined for bearing on the probable phylogeny of the principal flagellate groups, first considered singly and then in combination. The mitotic mechanism has not proved to be as conservative a character as might be hoped, but still remains characteristic for the average condition in many of the groups. Flagellar features are useful if allowance is made for the reduction or multiplication of the basic pair, and the loss of lateral and terminal hairs seems to have occurred independently several times. The presence of paraxial rods within flagella may be a useful indication of affinity. Rootlet systems are not dealt with in detail here, although the possible similarity between axial microtubular sheets in axostylar flagellates and some members of the green algae containing “manchettes” is noted. The basic patterns of chloroplast internal structure are summarized and their general agreement with other characters is affirmed, noting however that cryptomonads may be closer to the green flagellates (including euglenoids) than is generally accepted. Attention is drawn to the potential value of internal mitochondrial morphology as an indicator of large assemblages. Finally, a “tree” based on multiple cell organizational features is presented and discussed.     

Phylogeny of the orb-web building spiders (Araneae, Orbiculariae: Deinopoidea, Araneoidea)

This phylogenetic analysis of 31 exemplar taxa treats the 12 families of Araneoidea (Anapidae, Araneidae, Cyatholipidae, Linyphiidae, Mysmenidae, Nesticidae, Pimoidae, Symphytognathidae, Synotaxidae, Tetragnathidae, Theridiidae, and Theridiosomatidae). The data set comprises 93 characters: 23 from male genitalia, 3 from female genitalia, 18 from cephalothorax morphology, 6 from abdomen morphology, 14 from limb morphology, 15 from the spinnerets, and 14 from web architecture and other behaviour. Criteria for tree choice were minimum length parsimony and parsimony under implied weights. The outgroup for Araneoidea is Deinopoidea (Deinopidae and Uloboridae). The preferred shortest tree specifies the relationships ((Uloboridae, Deinopidae) (Araneidae (Tetragnathidae ((Theridiosomatidae (Mysmenidae (Symphytognathidae, Anapidae))) ((Linyphiidae, Pimoidae) ((Theridiidae, Nesticidae) (Cyatholipidae, Synotaxidae))))))). The monophyly of Tetragnathidae (including metines and nephilines), the symphytognathoids, theridiid-nesticid lineage, and Synotaxidae are confirmed. Cyatholipidae are sister to Synotaxidae, not closely related to either the Araneidae or Linyphiidae, as previously suggested. Four new clades are proposed: the cyatholipoids (Cyatholipidae plus Synotaxidae), the 'spineless femur clade' (theridioid lineage plus cyatholipoids), the 'araneoid sheet web builders' (linyphioids plus the spineless femur clade), and the 'reduced piriform clade' (symphytognathoids plus araneoid sheet web builders). The results imply a coherent scenario for web evolution in which the monophyletic orb gives rise to the monophyletic araneoid sheet, which in turn gives rise to the gumfoot web of the theridiid-nesticid lineage. While the spinning complement of single pairs of glands does not change much over the evolution of the group, multiple sets of glands are dramatically reduced in number, implying that derived araneoids are incapable of spinning many silk fibers at the same time.     

Phylogeny of flatfishes (Pleuronectiformes): comparisons and contradictions of molecular and morpho-anatomical data

Several species of flatfishes (Pleuronectiformes) have been studied by isoenzyme electrophoresis and DNA/DNA hybridization to establish the evolutionary relationships of this group of fishes. This molecular data-based phylogeny has been compared to previously described phylogenies based on morpho-anatomical criteria. A number of discrepancies are observed and discussed. The high degree of genetic divergence observed within the families of Pleuronectiformes indicates that their origin seems to be much older than suggested by their striking morphological similarity.     

CLADISTICS OF THE BRYOPSIDALES: A PRELIMINARY ANALYSIS

The Bryopsidales contains some of the most species rich and ecologically dominant algae in tropical ecosystems. However, the evolutionary relationships among the 29 genera and several hundred species of this order remain poorly resolved. Because of a lack of known reproductive characters for many taxa, evolutionary hypotheses grouped genera by similarities in morphological characters. To apply standard cladistical analyses to further our understanding of this group, this study presents the first comprehensive compilation of reported morphological, reproductive, and subcellular characteristics for genera in the Bryopsidales. Computer-assisted cladistical analyses ultimately identified phylogenetically informative and uninformative characters. Although the topology of the trees generated in this study is expected to change as additional data are added to this matrix, many traditional groupings and recent groupings based on molecular data were supported.     

Systematics of the genus Mayazomus (Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics

The schizomid genus Mayazomus Reddell & Cockendolpher, 1995, endemic to south‐eastern Mexico, currently comprises seven species. It was originally proposed to accommodate two species, from Chiapas and Tabasco. Recently, five additional species from Chiapas were described. The monophyly of the genus has never been tested using cladistic analysis. We undertook a phylogenetic analysis using the seven described species of Mayazomus as the ingroup, ten exemplar species representing the most similar New World hubbardiids as the outgroup, and one protoschizomid species to root the tree. The analysis was based on 130 morphological characters (continuous and discrete characters). The resulting topologies recovered Mayazomus as paraphyletic, with Heteronochrus estor Armas & Viquez, 2010, from Guatemala nested within the genus; therefore, we formally propose its synonymy herein. Mayazomus appears to be most closely related to Rowlandius Reddell & Cokendolpher, 1995, a South American genus. This contribution also provides new characters derived from the pedipalp setae with important phylogenetic information; as well as the implementation of morphometric ratios, as continuous characters, to partially codify the shape of the male flagellum. The relationships recovered amongst the outgroups used in this contribution are a reliable baseline for future analyses of the phylogeny of the New World schizomids.     

Phylogeny, biogeography and reproductive trends in the Onychophora

A cladistic analysis places the Onychophora between Polychaeta and Arthropoda. The 'Uniramia'concept is not supported. No justification was found for either onychophoran family to be considered ancestral. A cladogram of fossil genera indicates the common ancestor to have long oncopods, armoured plates and an annulated body. Later forms show adaptations to life in reduced spaces. Physiological data suggest that the Onychophora became adapted to land via the littoral zone, before the Late Ordovician. Adhesive glands evolved for defence on land. Peripatopsidae and Peripatidae were distinct by the late Triassic. The occurrence of onychophorans probably dates from post-Pliocene in New Guinea and southern Australia, and post-Early Cretaceous in Chile, the southern half of Southeast Asia, Mesoamerica and the Caribbean. After the Early Cretaceous, the peripatids of tropical Africa lost terrestrial contact with those of South America. A new biogeographic technique, formalized here under the name retrovicariance, indicates that the Peripatidae of Equatorial Africa and the Neotropics are sister-groups. Typical inbreeding adaptations found in some onychophorans include: female-biased sex ratios; gregarious development; relatively constant time of development and number of offspring in each clutch; male polygamy and shorter life span; frequent sibmating in the microhabitat of development, and sperm storage by females, so that a single insemination fertilizes all ova.     

Toward a Better Understanding of the Phylogeny of the Asplanchnidae (Rotifera)

We investigated the phylogenetic relationships of Family Asplanchnidae using both morphological and molecular data. The morphological database, comprising 23 characters from 19 taxa (15 Asplanchnidae and 4 outgroups), was compiled from a survey of the literature and our own observations; the molecular data (ITS and V4 region nuclear regions and mitochondrial cox1) was sequenced from specimens that we collected. Our analysis of the morphological data set (maximum parsimony) yielded 12 most-parsimonious trees with a tree length of 27 steps. From this analysis we conclude (1) Asplanchnidae is a monophyletic group as are the three genera comprising it, (2) there is no compelling support for the argument that Asplanchna should be separated into two discrete genera, and (3) there is some support for the proposal that Asplanchnidae and Synchaetidae are sister groups. Our analysis of the molecular data set supports the first two of these conclusions while the sister group of the family varied depending on the gene region analyzed and families and genera included. Current understanding of the phylogeny of Asplanchnidae is hampered by the need for additional informative morphological characters and a lack of molecular data for the genus Harringia and several other members of the Asplanchnidae.     

Phylogeny and molecular dating of the cerato-platanin-encoding genes

The cerato-platanin family consists of proteins that can induce immune responses, cause necrosis, change chemotaxis and locomotion and may be related to the growth and development of various fungi. In this work, we analyzed the phylogenetic relationships among genes encoding members of the cerato-platanin family and computed the divergence times of the genes and corresponding fungi. The results showed that cerato-platanin-encoding genes could be classified into 10 groups but did not cluster according to fungal classes or their functions. The genes transferred horizontally and showed duplication. Molecular dating and adaptive evolution analyses indicated that the cerato-platanin gene originated with the appearance of saprophytes and that the gene was under positive selection. This finding suggests that cerato-platanin-encoding genes evolved with the development of fungal parasitic characteristics.     

Systematics of the Miocene–Recent bryozoan genus Pentapora (Cheilostomata)

The four existing species of the ascophoran bryozoan Pentapora Fisher, 1807 are revised, and two new fossil species are introduced: Pentapora lacryma sp. nov. from the Pliocene Coralline Crag Formation of Suffolk, and Pentapora clipeus sp. nov. from the Pliocene of Emilia, Italy. The Arctic species Pentapora boreale Kuklinski & Hayward possesses a lyrula, does not belong in Pentapora, and is a junior synonym of Raymondcia rigida (Lorenz). The morphology of the autozooids is relatively uniform within the genus, and the main distinguishing characters are those of the ovicells and, particularly, the giant avicularia that are developed sporadically in all species apart from Pentapora foliacea, popularly known as ‘Ross coral’. A phylogenetic analysis based on skeletal characters returned a single shortest tree in which the three species of Pentapora from the North Atlantic (P. foliacea, Pentapora pertusa, and P. lacryma sp. nov. ) form a clade crownward of the three basal species from the Mediterranean (Pentapora ottomulleriana, Pentapora fascialis, and P. clipeus sp. nov. ). © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 17–39.