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.

     

Primary classification and phylogeny of the Polemoniaceae, with comments on molecular cladistics

The system of classification of the Polemoniaceae currently in use was published by Grant in 1959. Much new evidence concerning relationships in the family has been obtained by numerous workers since 1959, and the old system is in need of revision. A revised system down to the genus level, based on conventional and unconventional characters, including molecular evidence, is presented here. Nineteen genera are grouped into eight tribes and two subfamilies. Three new tribes are described: Acanthogilieae, Loeselieae, and Leptodactyloneae. Several genera are transferred to new groups. The phylogeny of the family is discussed in the light of both the older and new evidence. The approach used in constructing both the 1959 and new systems is that of evolutionary systematics. Two recent (1996, 1997) family-wide surveys of cpDNA and rDNA use cladistic methods of analysis to arrive at sets of major groups. Some of this molecular evidence has been adopted for the present revised system. However, much incongruence still exists between the new sets of clades, on the one hand, and the present revised system or the still-viable parts of the 1959 system on the other hand. The incongruences call for an examination and comparison of the contrasting methods of evolutionary systematics and molecular cladistics. A fundamental flaw in the 1996 and 1997 treatments is the attempt to classify plants on the basis of single-gene gene trees.     

Nomenclature in the dock. Overclassification leads to instability: a case study in the horticulturally important genus Cyclamen (Myrsinaceae)

Nine different classifications have been produced in the last 70 years for the horticulturally valuable genus Cyclamen , a small genus with fewer than 30 species. These classifications, generated by intuitive methods and cladistic analyses, incorporated a total of four infrageneric ranks above that of species and were based on data from morphology, cytology and DNA sequencing. Our results, based on cladistic analyses of three independent data sources − nrDNA ITS, cpDNA trn L intron and morphological data − reveal good resolution only in nrDNA sequence data. However, when these three data sources are combined they provide stronger resolution and support for three major clades, only one of which, subgenus Psilanthum , has been consistently supported in previous classifications. The differing infrageneric classifications produced in Cyclamen result from varying taxon sampling, differing interpretation of morphological data, changes in the sources and analysis of data, and inconsistent application of names. Extensive subdivision of small genera in the absence of adequate data that could provide evidence for consistent patterns of relationship is premature and leads to a proliferation of names.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 146 , 339–349.     

Weintrauboa, a new genus of pimoid spiders from Japan and adjacent islands, with comments on the monophyly and diagnosis of the family Pimoidae and the genus Pimoa (Araneoidea, Araneae)

The spider genus Weintrauboa new genus (Araneae, Pimoidae) is described to place two species of pimoids from Japan and adjacent islands that were formerly classified in the linyphiid genus Labulla . Weintrauboa contortipes (Karsch) new comb., the type species, and W. chikunii (Oi) new comb. are redescribed. Parsimony analysis of morphological characters provides robust support for the monophyly of the genus Weintrauboa and corroborates the monophyly of Pimoa , Pimoidae, and the clade Linyphiidae plus Pimoidae. New diagnoses for Pimoa and Pimoidae are provided.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 139 , 261–281     

A Phylogenetic Analysis of Ilyocryptus Sars, 1862 (Cladocera: Ilyocryptidae)

Kotov and Štifter (2006) revised the taxonomy of the genus Ilyocryptus Sars, 1862 (Branchiopoda: Anomopoda: Ilyocryptidae) and concluded that 28 species can be recognized as valid for the world fauna. In order to test phylogenetic relationships between the species and to contribute to a better understanding of the genus, a cladistic (using branch‐and‐bound search) analysis was conducted for 25 Ilyocryptus species (two of them with two subspecies). In total, 32 morphological characters were used. An evolutionary‐morphological interpretation of the results was also made. Phylogenetic analysis revealed that Ilyocryptus elegans is an earlier derived member of the genus, while other species are separated into two main branches: agilis ‐ and sordidus ‐lines (without reference to type of moulting). Species with incomplete moulting and species with complete moulting do not form separate clusters, suggesting an independent origin of incomplete moulting within different species groups. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Anna Meyer and the distinction between grades and clades in early models of gastropod evolution

Abstract. Anna Meyer published her first (and apparently last) scientific paper in 1913, in which she reported, in part, on the organization of the renogenital systems in the "Diotocardia" and "Monotocardia," and the evolutionary signal present in this character suite. Meyer's phylogeny broke with conventional wisdom of her time and she reconstructed early gastropod evolution as a sequence of branching events rather than a continuous grade. Her phylogeny was ignored because it did not correspond to the well-ordered grades that came to dominate gastropod systematics for over 75 years, but her schematics of renogenital configurations have been featured in the literature for over 55 years, sometimes without citation and redrawn to show a different set of relationships. We hope that the translation of her paper from German into English ( http://www.ucmp.berkeley.edu/collections/archdat.html ) will make her contribution more accessible to workers.     

Phylogenetic relationships in the tribe Oxyptilini (Lepidoptera,Pterophoridae, Pterophorinae) based on morphological data of adults

The monophyly of the tribe Oxyptilini and phylogenetic relationships of the genera embraced in this tribe were examined using 171 (75 binary and 96 multistate) characters of adult morphology. The study material included 98 species of 30 genera, representing all previously recognized genera of Oxyptilini, together with the genera Sphenarches, Antarches, Diacrotricha, and Cosmoclostis, four species of Oidaematophorini, three species of Platyptiliini, as well as three and two other species belonging to Pterophorini and Exelastini respectively. Two Agdistis species were used as outgroups. The cladistic analysis resulted in six equally parsimonious trees. A majority of the recovered synapomorphic characters have previously been used in the taxonomy of the subfamily. However, 25 novel characters were found. The monophyly of Oxyptilini was supported, although only with homoplastic characters and low amounts of tree confidence; the genera Capperia, Procapperia, Paracapperia, Oxyptilus, Megalorhipida, and Trichoptilus were found to be nonmonophyletic; Sphenarches and Antarches were recovered as members of Oxyptilini; the two genera Cosmoclostis and Diacrotricha were placed out of Oxyptilini, inside the tribe Pterophorini; and close affinity of the genus Dejongia to Stangeia, Stenodacma, Megalorhipida, Trichoptilus, and Buckleria species was revealed. Four new combinations, Cosmoclostis lanceata (Arenberger) comb. nov. , Nippoptilia regulus (Meyrick) comb. nov. , Capperia tadzhica (Zagulajev) comb. nov. , and Buckleria negotiosus (Meyrick) comb. nov. are proposed; Capperia insomnis Townsend was considered as a senior synonym of Procapperia hackeri Arenberger syn. nov. , Buckleria negotiosus (Meyrick) as a senior synonym of Buckleria vanderwolfi Gielis syn. nov. , and Oxyptilus variegatus Meyrick syn. nov. as a junior synonym of Oxyptilus secutor Meyrick. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 484–547.     

Monophyly and phylogenetic placement of the spider genus Labulla Simon, 1884 (Araneae, Linyphiidae) and description of the new genus Pecado

The genus Labulla Simon is circumscribed in phylogenetic terms to include the species Labulla thoracica (Wider), L. flahaulti Simon and L. machadoi sp. nov. The genital anatomy of the genus is described in detail and the taxonomy of the genus is reviewed. The monophyly of Labulla is supported by numerous morphological apomorphies of the male palp and female epigynum. Based on a cladistic analysis, a new genus, Pecado gen. nov. , is erected to place Labulla impudica Denis, from Northern Africa. Lepthyphantes insularis Saito and ' Labulla ' nepula Tikader, both formerly included in Labulla , are not congeneric with the type species of Labulla .  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 359–404.     

The interrelationships of all major groups of Platyhelminthes: phylogenetic evidence from morphology and molecules

We used a data matrix of 65 morphological characters from 25 ingroup and 6 outgroup taxa, and an alignment comprising complete 18S rDNA sequences from 82 species of parasitic and free-living Platyhelminthes and from 19 species of lower invertebrates to analyse phylogenetic relationships of various platyhelminth taxa. Of the 1358 unambiguously alignablc molecular positions, 995 were variable and 757 were phylogenctically informative (parsimony criterion); complete 18S rDNA sequences ranged in length from 1755 to 2873 bp. Main conclusions are: Ncodermata are monophylctic, and the Trematoda, Monogenca and Cestoda within them are monophylctic as well. The sister group of the Ncodermata is all the other Ncoophora; the Kalyptorhynchia, Typhloplanida, Dalyelliida and Tcmnocephalida form one clade, and the last three another. Monophyly of the Seriata is rejected, but Polycladida/ Macrostomida/Haplopharyngida are monophylctic, as arc the last two taxa. As a consequence, validity of the taxon Trepaxonemata is rejected. Further studies must show the correct position of the Acocla and Nemertodermatida. It is stressed that morphological and molecular data in some respects lead to contradictory results, for instance concerning the position of the Fecampiidac/ Urastoma/Ichthyophaga and the relative position of the Lccithoepitheliata. Denser sampling of taxa for molecular data, complementary sequences from independent genes, and inclusion of additional morphological data are necessary to resolve these contradictions.     

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.     

Towards a new classification of the giant paraphyletic genus Cyperus (Cyperaceae): phylogenetic relationships and generic delimitation in C4 Cyperus

Maximum likelihood and Bayesian inference analyses of nuclear ribosomal DNA (ETS1f) and plastid DNA (rpl32‐trnL, trnH‐psbA) sequence data are presented for ‘C₄ Cyperus’ (Cyperaceae). The term ‘C₄ Cyperus’ encompasses all species of Cyperus s.l. that use C₄ photosynthesis linked with chlorocyperoid vegetative anatomy. Sampling comprises 107 specimens of 104 different taxa, including many of the subdivisions of C₄ Cyperus s.s. and all C₄ segregate genera (Alinula, Ascolepis, Kyllinga, Lipocarpha, Pycreus, Queenslandiella, Remirea, Sphaerocyperus and Volkiella). According to our results, C₄ Cyperus is a well‐supported monophyletic clade nested in C₃ Cyperus. Despite the lack of resolution along the backbone of the C₄ Cyperus clade and for some internal branches, several well‐supported clades can be distinguished. The first clade in C₄ Cyperus is formed by Cyperus cuspidatus and C. waterloti. Other recognizable and well‐supported clades correspond to segregate genera, i.e. Ascolepis, Lipocarpha including Volkiella, and Kyllinga. Species of C₄ Cyperus s.s. form a core grade in which the C₄ segregate genera are embedded. Pycreus, the largest segregate genus composed of c. 120 species, is not monophyletic as it includes several C₄ species of Cyperus s.s. This study establishes a phylogenetic framework for revising the classification and character evolution in Cyperus s.l. © 2013 The Linnean Society of London     

The interrelationships of the echinoderm classes: morphological and molecular evidence

The relationship between the five echinoderm classes has perplexed phylogeneticists for some time. Although each of the crinoids (C), asteroids (A), ophiuroids (O), echinoids (E) and holothuroids (H) are morphologically distinct, evidence from larval and adult morphology, molecular biology, and stratigraphy have failed to provide a single consensus solution. We have reviewed all available morphological and molecular data, added new data and reanalysed independent data sets individually and in combination, in order to resolve echinoderm class relationships. In total, we present 21 larval and 50 adult morphological characters, partial 28S-like large subunit rRNA gene data for 39 taxa and complete 18S-like small subunit rRNA gene data for 37 taxa. For a 5 taxon problem there are 105 possible rooted tree topologies, and yet we were consistently presented with three competing hypotheses when data sets were analysed both individually and in combination. The total evidence solution favoured (outgroup(C(A(O(E, H))))) although the alternative tree topology, (outgroup(C(O(A(E, H))))) was only one step longer and (outgroup(C((A, O),(E, H)))) was two steps longer. Only these three trees are serious contenders and the distribution of morphological characters suggests we should discount the solution placing ophiuroids as sister group to an asteroid+echinoid + holothurian clade. Thus we are left with (outgroup(C(A(O(E, H))))) and (outgroup(C((A, O),(E, H)))) as the two most plausible phylogenetic hypotheses. Our data showed high levels of phylogenetic signal and these trees best fit the available data.     

Parallelism,parsimony, and the phytogeny of the lemuridae

In spite of the increasing popularity of cladistic methods in studies of primate systematics, few authors have investigated the effects of parallel evolution when such methods are applied to empirical data. To counter the effects of parallelism, cladistic techniques rely on the principle of evolutionary parsimony. When parsimony procedures are used to reconstruct the phylogeny of the Lemuridae, nine highly parsimonious phylogenies can be deduced. Further choice among these competing hypotheses of relationship is determined by the extent to which one embraces the parsimony principle. The phylogeny obtained by the most rigorous adherence to the parsimony principle is one which is wholly consistent with traditional evolutionary classifications of the Lemuridae. Moderate levels of parallelism can lead to the generation of several plausible, alternative phylogenetic hypotheses; less than 25% of the characters analyzed here need have evolved in parallel, yet they are largely responsible for the ambiguity of the nine different lemurid phylogenies. This suggests that phylogeny reconstructions based entirely on cladistic methods do not provide a suitable basis for the construction of classifications for groups such as the order Primates, where the degree of parallelism is likely to be quite high.     

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, classification, and biogeography of the cycloteline Therevinae (Insecta: Diptera: Thereavidae)

Twenty-one members of the Laurasian group of Therevinae (Diptera: Therevidae) are compared using 65 adult morphological characters. Cladistic analysis using parsimony on the 17 ingroup and 4 outgroup taxa provides a well-supported hypothesis of relationships among taxa within the Gyclotelini, tribe nov. The Cyclotelini is a monophyletic assemblage of mostly New World genera, including Anolinga , gen. nov. , Breviperna Irwin, Coleiana , gen. nov. , Crebraseta , gen. nov. , Cyclotelus Walker, Mesonana , gen.nov. , and Ozodiceromyia Bigot. In addition, three Old World genera, Ammothereva Lyneborg, Bugulaverpa , gen. nov. , and Procyclotelus Nagatomi & Lyneborg, are included in the tribe. These ten genera are divided into two monophyletic genus-groups, the Brevipema-group and the Cyclotelus-group. Keys are provided for the genera of Cyclotelini. The tribe, the two informal genus-groups, and all genera are diagnosed; five new genera and six new species are proposed. The biogeographical histories of the genera are discussed in terms of their cladistic relationships using methods of cladistic biogeography. Two major vicariant events account for the current distribution of the tribe. The first relates to the Beringian land bridge connecting western North America and eastern Asia. Second, New World cyclotelines were profoundly affected by the Early Eocene breakup of the archipelagic bridge between North and South America, and the distributions support the hypotheses favouring the continental origin of the Greater Antilles.     

Sturmius epiphytus n. gen. n. spec, from Colombia, a taxon of the Symphypleona (Insecta, Collembola) with an unexpected character combination

From epiphytic mosses and ferns of remnants of mountain forest in the páramo region of Colombia, Sturmius epiphytus n. gen. n. spec, a taxon that resembles the Katianniformia, is described, the appendices anales of which are, however, directed towards the posterior. Analysis of characters allows a statement of the systematic position: in phylogenetic systematics, Sturmius epiphytus and the Katianniformia form a monophylum Anteriora as the sister group of the Sminthuriformia; in Linnean categories, for Sturmius n. gen., a new family Sturmiidae must be established with a new superfamily Sturmioidea as the sister group of a new superfamily Katiannoidea.     

Overlap Indices: Tools to quantify the amount of anatomical overlap among groups of incomplete terminal taxa in phylogenetic analyses

Phylogenetic analyses of morphological data are often characterized by missing data due to incomplete operational taxonomic units, as in fossils. This incomplete knowledge derives from various reasons, including—in the case of fossils—the numerous filters an organism has to pass through during taphonomy, fossilization, weathering and collecting. Whereas several methods have been proposed to address issues raised by the inclusion of incomplete terminal taxa, until recently no tool existed to easily quantify the amount of anatomical overlap within a particular clade. The Overlap Indices provide such values and might prove useful for comparative cladistics. We herein describe these new indices and their applications in detail and provide an example file for their calculation. A case study of diplodocid sauropod dinosaurs shows how the Overlap Indices will help to explore and quantify, which one of a number of conflicting tree topologies is supported by more anatomical traits, which skeletal regions are underrepresented in a particular phylogenetic matrix, and which taxon would improve character state score completeness.     

A phylogenetic analysis of the Conchostraca and Cladocera (Crustacea, Branchiopoda, Diplostraca)

A computer-assisted cladistic analysis on morphological characters of the Diplostraca (Conchostraca and Cladocera) has been undertaken for the first time. The morphological information has been obtained from literature and transformed into 56 suitable characters. The analysis included 47 ingroup taxa, comprising five conchostracan taxa (four families of the Spinicaudata and the Laevicaudata) and 42 genera of the Cladocera. A detailed character discussion is presented which will be a useful working base for future phylogenetic studies on the group. A number of systematic groups were, with differing degrees of certainty, supported in all 218 equally short trees. These are the Diplostraca, Cladocera, Gymnomera (Onychopoda and Haplopoda), Onychopoda, Podonidae, Cercopagididae, Anomopoda, Daphniidae, Moininae, Scapholeberinae, Chydoridae, Chydorinae and Sididae. The Spinicaudata were only supported on some of the 218 equally short trees while no support was found for the Conchostraca. Two taxa—the Macrothricidae and Aloninae—were relatively strongly indicated to be paraphyletic. A suggested classificatory hierarchy, without indication of absolute rank, is presented.     

The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record

The pattern, timing and extent of the evolutionary radiation of anatomically modern birds (Neornithes) remains contentious: dramatically different timescales for this major event in vertebrate evolution have been recovered by the 'clock-like' modelling of molecular sequence data and from evidence extracted from the known fossil record. Because current synthesis would lead us to believe that fossil and nonfossil evidence conflict with regard to the neornithine timescale, especially at its base, it is high time that available data are reconciled to determine more exactly the evolutionary radiation of modern birds. In this review we highlight current understanding of the early fossil history of Neornithes in conjunction with available phylogenetic resolution for the major extant clades, as well as recent advancements in genetic methods that have constrained time estimates for major evolutionary divergences. Although the use of molecular approaches for timing the radiation of Neornithes is emphasized, the tenet of this review remains the fossil record of the major neornithine subdivisions and better-preserved taxa. Fossils allowing clear phylogenetic constraint of taxa are central to future work in the production of accurate molecular calibrations of the neornithine evolutionary timescale.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 141 , 153–177.