Phylogeny and classification of the extant basal lineages of the Hymenoptera (Insecta)

The phylogeny of the basal hymenopteran lineages, including representatives of all ‘symphytan’ families, is anal; In total, 236 morphological characters were scored for 44 exemplars, including six outgroup, two xyelic tenthredinoid, five pamphilioid, three cephoid, five ‘siricoid’, one orussid, and six apocritan taxa. The datas analysed with parsimony under equal weights and under implied weights. The monophyly of the Hymenopte strongly supported but the sistergroup of the Hymenoptera cannot be identified with confidence. The relations of the ‘symphytan’ lineages are Xyeloidea +(Tenthredinoidea+ (Pamphilioidea + (Cephoidea + (Ariaxyelic (Siricidae + (Xiphydriidae +(Orussoidea+Apocrita))))))). Many of the relationships between the superfamilies, especially in the basal branching pattern, are only weakly corroborated. The monophyly of most superfamilies is supported, and all may be monophyletic except the ‘Siricoidea’, which is clearly paraphyletic. It is difficult to di whether the Siricidae or the Anaxyelidae are the closest relatives of Xiphydriidae + (Orussoidea + Apocrita). support for the sistergroup relationship between the Orussoidea and the Apocrita is substantial, putative apomorphies being provided by most character systems. There is also good evidence in favour of the monophj the Apocrita. The internal phylogeny of the Tenthredinoidea differs considerably from the results of earlier anal The Blasticotomidae are the sistergroup of the Tenthredinoidea s.s. Relationships at the base of the Tenthredini s.s. are weakly supported. It is uncertain whether the Tenthredinidae are monophyletic or comprise a 1 paraphyletic grade within the Tenthredinoidea s.s. The Diprionidae may be the sistergroup to Cimbicidae +(Argidae+ Pergidae). Most relationships within the Cimbicidae + (Argidae + Pergidae) clade are corroborated, with the exception of the monophyly of the Argidae. It is proposed to elevate the Anaxyelidae the Xiphydriida both to superfamily status. The family‐level classification of the Tenthredinoidea will probably have to be changed, but this must await further clarification of the phylogeny of this superfamily.     

Simultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis

The first simultaneous analysis of molecular and morphological data of basal hymenopterans that includes exemplars from all families is presented. DNA sequences (of approximately 2000–2700 bp for each taxon) from the nuclear genes 18S and 28S and the mitochondrial genes 16S and CO1 have been sequenced for 39 taxa (four outgroup taxa, 29 symphytans, and six apocritans). These DNA sequences and 236 morphological characters from Vihelmsen [Zool. J. Linnean Soc. 131 (2001) 393] were analyzed separately as well as simultaneously. All analyses were performed on unaligned sequences, using the optimization alignment (= direct optimization) method. Sensitivity analysis sensu Wheeler [Syst. Biol. 44 (1995) 321] was applied by analyzing the data under nine different combinations of analysis parameter values. The superfamily level relationships of basal hymenopterans as proposed by Vilhelmsen [Zool. J. Linnean Soc. 131 (2001) 393] and Ronquist et al. [Zool. Scr. 28 (1999) 13] are mostly confirmed, except that Pamphilioidea is the sister group to Tenthredinoidea s.l. and that Anaxyelidae (i.e., Syntexis libocedrii) and Siricidae are supported as a monophyletic group, partly reestablishing the traditional concept of Siricoidea. The resulting hypothesis that best represents the combined evidence from morphology and DNA sequences is (Xyeloidea (Tenthredinoidea s.l. Pamphilioidea) (Cephoidea (Siricoidea (Xiphydrioidea (Orussidae Apocrita))))), with Siricoidea = Anaxyelidae +Siricidae. The phylogenetic system within Tenthredinoidea s.l., derived from the combined evidence, is (Blasticotomidae (Tenthredinidae including Diprionidae (Cimbicidae (Argidae Pergidae)))).     

Phantoms of Gondwana?—phylogeny of the spider subfamily Mynogleninae (Araneae: Linyphiidae)

This is the first genus‐level phylogeny of the subfamily Mynogleninae. It is based on 190 morphological characters scored for 44 taxa: 37 mynoglenine taxa (ingroup) representing 15 of the 17 known genera and seven outgroup taxa representing the subfamilies Stemonyphantinae, Linyphiinae (Linyphiini and Micronetini), and Erigoninae, and a representative of the family Pimoidae, the sister‐group to Linyphiidae. No fewer than 147 of the morphological characters used in this study are new and defined for this study, and come mainly from male and female genitalia. Parsimony analysis with equal weights resulted in three most parsimonious trees of length 871. The monophyly of the subfamily Mynogleninae and the genera Novafroneta, Parafroneta, Laminafroneta, Afroneta, Promynoglenes, Metamynoglenes, and Haplinis are supported, whereas Pseudafroneta is paraphyletic. The remaining seven mynoglenine genera are either monotypic or represented by only one taxon. Diagnoses are given for all genera included in the analysis. The evolution of morphological traits is discussed and we summarize the diversity and distribution patterns of the 124 known species of mynoglenines. The preferred topology suggests a single origin of mynoglenines in New Zealand with two dispersal events to Africa, and does not support Gondwana origin.     

A phylogenetic analysis of relationships among genera of Conopidae (Diptera) based on molecular and morphological data

Members of the family Conopidae (Diptera) have been the focus of little targeted phylogenetic research. The most comprehensive test of phylogenetic support for the present subfamily classification of Conopidae is presented here using 66 specimens, including 59 species of Conopidae and seven outgroup taxa. Relationships among subfamily clades are also explored. A total of 6824 bp of DNA sequence data from five gene regions (12S ribosomal DNA, cytochrome c oxidase subunit I, cytochrome b, 28S ribosomal DNA and alanyl‐tRNA synthetase) are combined with 111 morphological characters in a combined analysis using both parsimony and Bayesian methods. Parsimony analysis recovers three shortest trees. Bayesian analysis recovers a nearly identical tree. Five monophyletic subfamilies of Conopidae are recovered. The rarely acknowledged Zodioninae is restored, including the genera Zodion and Parazodion. The genus Sicus is removed from Myopinae. Morphological synapomorphies are discussed for each subfamily and inter‐subfamily clade, including a comprehensive review of the character interpretaions of previous authors. Included are detailed comparative illustrations of male and female genitalia of representatives of all five subfamilies with new morphological interpretation.     

Molecular phylogeny of flat‐footed flies (Diptera: Platypezidae): main clades supported by new morphological evidence

The molecular phylogeny of flat‐footed flies is inferred from analysis of DNA sequence data from the five mitochondrial genes 12S, 16S, COI, COII and CytB, and the nuclear gene 28S and discussed with the recent systematics based on morphological features. The Bayesian inference, maximum likelihood and maximum parsimony analyses included 42 species of 18 genera, representing all four extant subfamilies (Microsaniinae, Melanderomyiinae, Callomyiinae and Platypezinae) and all known genera except one (Metaclythia). Representatives of the brachycerous taxa Lonchopteridae, Phoridae, Sciadocerinae (Phoridae) and Opetiidae are used as outgroups, and Lonchoptera was used to root the trees. Our results show Platypezidae consisting of two well‐supported clades, the first with the subfamilies Melanderomyiinae + Callomyiinae and the second formed by subfamily Platypezinae. Genus Microsania was resolved as a separate lineage distant from Platypezidae which clustered with Opetiidae as its sister group, both together forming a sister group to Platypezidae. At the generic level, the genus Agathomyia proved not to be monophyletic in any of the analyses. The species Chydaeopeza tibialis is sister to Agathomyia sexmaculata, and consequently, the genus Chydaeopeza Shatalkin, 1992 is a new junior synonym of Agathomyia Verrall, 1901. Bifurcated setae on legs of adult Platypezidae are documented as a new synapomorphy of the family, exclusive of Microsania. Outstretched wings and only a small overlap of their surfaces at resting position are considered a new synapomorphy for the subfamily Platypezinae. Other phylogenetically important characters defining main clades are documented, and their relevance/validity in phylogenetic studies is discussed. The current systematic concept of Platypezidae is discussed, and new phylogenetic hypotheses are proposed.     

Phylogenetic relationships in the Lejeuneaceae (Hepaticae) inferred using ITS sequences of nuclear ribosomal DNA

Sequences of the ITS1–5.8S–ITS2 region of nuclear ribosomal DNA were generated for 12 species from 9 genera of Lejeuneaceae and a single species of Jubulaceae (outgroup). The taxon sampling of Lejeuneaceae included representatives of the two widely recognized subfamilies, Lejeuneoideae and Ptychanthoideae. The molecular dataset was analysed independently and in combination with a morphological dataset. The nrITS dataset and the combined dataset resulted in identical topologies. The genus Bryopteris, sometimes treated as a separate family Bryopteridaceae, is nested within the Lejeuneaceae subfamily Ptychanthoideae. Lejeuneaceae subfamily Lejeuneoideae proved to be paraphyletic with the tribe Lejeuneeae sister to Ptychanthoideae, albeit without significant bootstrap support. The tribes Brachiolejeuneeae and Cheilolejeuneeae of Lejeuneoideae, established recently based on morphological evidence, are well supported in bootstrap analyses both of the ITS and the combined molecular–morphological datasets. The results support classifications of Lejeuneaceae based on morphological data and demonstrate the usefulness of the ITS region for phylogenetic studies within or among closely related genera of Lejeuneaceae.     

Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces: Cypriniformes) inferred from cytochrome <Emphasis Type="Italic">b</Emphasis> sequences

Complete mitochondrial cytochrome b sequences of 54 species, including 18 newly sequenced, were analyzed to infer the phylogenetic relationships within the family Cyprinidae in East Asia. Phylogenetic trees were generated using various tree-building methods, including Neighbor-joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods, with Myxocyprinus asiaticus (family Catostomidae) as the designated outgroup. The results from NJ and ML methods were mostly similar, supporting some existing subfamilies within Cyprinidae as monophyletic, such as Cultrinae, Xenocyprinae and Gobioninae (including Gobiobotinae). However, genera within the subfamily “Danioninae” did not form a monophyletic group. The subfamily Leuciscinae was divided into two unrelated groups: the “Leuciscinae” in East Asia forming as a monophyletic group together with Cultrinae and Xenocyprinae, while the Leuciscinae in Europe, Siberia, and North America as another monophyletic group. The monophyly of subfamily Cyprininae sensu Howes was supported by NJ and ML trees and is basal in the tree. The position of Acheilognathinae, a widely accepted monophyletic group represented by Rhodeus sericeus, was not resolved.     

PHYLOGENY OF THE RUBIACEAE AND THE LOGANIACEAE: CONGRUENCE OR CONFLICT BETWEEN MORPHOLOGICAL AND MOLECULAR DATA?

Phylogenetic analyses of 33 genera of Rubiaceae were performed using morphological and a few chemical characters. Parsimony analysis based on 29 characters resulted in eight equally parsimonious trees, with a consistency index of 0.40 and a retention index of 0.69. These results were compared to a phylogenetic analysis of the same genera based on chloroplast DNA restriction site data. There are discrepancies between the two analyses, but if we consider groupings reflected in the present classification there is much congruency. With the exception of four genera, all the genera are positioned in the same group of taxa in the two analyses. Clades of taxa representing three of the four subfamilies (~the Antirheoideae, ~the Rubioideae, and the ~Ixoroideae) are monophyletic, while the fourth subfamily Cinchonoideae is shown to be paraphyletic. Both analyses support a widened tribe Chiococceae, including the former subtribe Portlandiinae (Condamineeae). Furthermore, in both analyses the tribe Hamelieae is placed outside the subfamily Rubioideae where it is now housed. In search for the most plausible sister group to the Rubiaceae, the genus Cinchona (Rubiaceae) was analyzed together with 13 genera of the Loganiaceae, Nerium (Apocynaceae), and Exacum (Gentianaceae). Cornus (Comaceae), Olea (Oleaceae), and these two genera together were used as outgroups. The analysis, including 25 characters, 16 taxa, and with Cornus and Olea together as an outgroup, resulted in four equally parsimonious trees, with a consistency index of 0.53 and a retention index of 0.62. The non-Loganiaceae taxa Cinchona (Rubiaceae), Nerium (Apocynaceae), and Exacum (Gentianaceae) were all found to have their closest relatives within the Loganiaceae indicating that the Loganiaceae are paraphyletic and ought to be reclassified. As a result of the morphological data the most plausible sister group to the Rubiaceae is the tribe Gelsemieae of the Loganiaceae.     

Molecular phylogeny of Omaliinae (Coleoptera: Staphylinidae) and its implications for evolution of atypically long elytra in rove beetles

Staphylinidae, or rove beetles, are a megadiverse family known for their typically very short elytra exposing most of the abdomen, but the putatively early-derived subfamily Omaliinae and its relatives have been known to include multiple taxa with unusually long elytra. The ancestral elytral length of the family and of this subfamily have long been debated. We present a phylogenetic analysis of Omaliinae based on partial mitochondrial COI (1488 bp), COII (366 bp), 12S rDNA (353 bp), nuclear 18S rDNA (1814 bp), 28S rDNA (876 bp) and CAD (869 bp) data. In all, 51 species in 31 genera and four outgroup species were included. The concatenated sequences were analysed by both parsimony- and model-based (Bayesian and maximum likelihood) methods. The subfamily Omaliinae was not supported as a monophyletic group. The model-based analyses (Bayesian and maximum likelihood trees) showed Empelinae nested within Omaliinae (excluding Corneolabiini), whereas parsimony analysis found all three putative ingroup subfamilies, Empelinae, Glypholomatinae and Microsilphinae, grouped within Omaliinae. Within the Omaliinae, the tribes Coryphiini and Eusphalerini were each supported as monophyletic, whereas Anthophagini and Omaliini were each nonmonophyletic. We hypothesize that there have been at least four independent origins of long elytra from short elytra in the omaliine lineage.     

Phylogenetic relationships of subfamilies and circumscription of tribes in the family Hesperiidae (Lepidoptera: Hesperioidea)

A comprehensive tribal‐level classification for the world’s subfamilies of Hesperiidae, the skipper butterflies, is proposed for the first time. Phylogenetic relationships between tribes and subfamilies are inferred using DNA sequence data from three gene regions (cytochrome oxidase subunit I‐subunit II, elongation factor‐1α and wingless). Monophyly of the family is strongly supported, as are some of the traditionally recognized subfamilies, with the following relationships: (Coeliadinae + (“Pyrginae” + (Heteropterinae + (Trapezitinae + Hesperiinae)))). The subfamily Pyrginae of contemporary authors was recovered as a paraphyletic grade of taxa. The formerly recognized subfamily Pyrrhopyginae, although monophyletic, is downgraded to a tribe of the “Pyrginae”. The former subfamily Megathyminae is an infra‐tribal group of the Hesperiinae. The Australian endemic Euschemon rafflesia is a hesperiid, possibly related to “Pyrginae” (Eudamini). Most of the traditionally recognized groups and subgroups of genera currently employed to partition the subfamilies of the Hesperiidae are not monophyletic. We recognize eight pyrgine and six hesperiine tribes, including the new tribe Moncini. © The Willi Hennig Society 2008.     

Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae)

The slipper lobsters belong to the family Scyllaridae which contains a total of 20 genera and 89 species distributed across four subfamilies (Arctidinae, Ibacinae, Scyllarinae, and Theninae). We have collected nucleotide sequence data from regions of five different genes (16S, 18S, COI, 28S, H3) to estimate phylogenetic relationships among 54 species from the Scyllaridae with a focus on the species rich subfamily Scyllarinae. We have included in our analyses at least one representative from all 20 genera in the Scyllaridae and 35 of the 52 species within the Scyllarinae. Our resulting phylogenetic estimate shows the subfamilies are monophyletic, except for Ibacinae, which has paraphyletic relationships among genera. Many of the genera within the Scyllarinae form non-monophyletic groups, while the genera from all other subfamilies form well supported clades. We discuss the implications of this history on the evolution of morphological characters and ecological transitions (nearshore vs. offshore) within the slipper lobsters. Finally, we identify, through ancestral state character reconstructions, key morphological features diagnostic of the major clades of diversity within the Scyllaridae and relate this character evolution to current taxonomy and classification.     

Phylogeny of the North American vaejovid scorpion subfamily Syntropinae Kraepelin, 1905, based on morphology,mitochondrial and nuclear DNA

The first rigorous analysis of the phylogeny of the North American vaejovid scorpion subfamily Syntropinae is presented. The analysis is based on 250 morphological characters and 4221 aligned DNA nucleotides from three mitochondrial and two nuclear gene markers, for 145 terminal taxa, representing 47 species in 11 ingroup genera, and 15 species in eight outgroup genera. The monophyly and composition of Syntropinae and its component genera, as proposed by Soleglad and Fet, are tested. The following taxa are demonstrated to be para‐ or polyphyletic: Smeringurinae; Syntropinae; Vaejovinae; Stahnkeini; Syntropini; Syntropina; Thorelliina; Hoffmannius; Kochius; and Thorellius. The spinose (hooked or toothed) margin of the distal barb of the sclerotized hemi‐mating plug is demonstrated to be a unique, unambiguous synapomorphy for Syntropinae, uniting taxa previously assigned to different subfamilies. Results of the analysis demonstrate a novel phylogenetic relationship for the subfamily, comprising six major clades and 11 genera, justify the establishment of six new genera, and they offer new insights about the systematics and historical biogeography of the subfamily, and the information content of morphological character systems.     

Phylogeny of Veneridae (Bivalvia) based on mitochondrial genomes

Veneridae is one of the most diverse families of bivalve molluscs. However, their phylogenetic relationships among subfamilies have been debated for years. To explore phylogenetic relationships of Veneridae, we sequenced 13 complete mitochondrial genome sequences from eight subfamilies and compared with available complete mitochondrial genome of other Veneridae taxa (18 previously reported sequences). Phylogenetic analyses using probabilistic methods recovered two highly supported clades. In addition, the protein‐coding gene order revealed a highly conserved pattern among the same subclade lineages. According to our molecular analyses, Tapetinae should be recognized as a valid subfamily, but the genera formed para‐polyphyletic clades. Chioninae was recovered not monophyletic that differs from a previously molecular phylogeny. Furthermore, the reconstructed chronogram calibrated with fossils recovered the Veneridae have originated during the early Permian (about 290 million years ago). Noticeably, programmed frameshift was found in the nad4 gene of Leukoma jedoensis, Anomalodiscus squamosus and Antigona lamellaris and cob gene of L. jedoensis. This is the first time that the presence of the programmed frameshift has been found in the protein‐coding genes of Heterodonta species. Our results improved the phylogenetic resolution within Veneridae, and a more taxonomic sampling analysis of the subfamily Chioninae is supposed to construct.     

THE KRANZ SYNDROME IN THE GRAMINEAE AS INDICATED BY CARBON ISOTOPIC RATIOS

The Kranz syndrome, as indicated by relatively high ¹³C/¹²C ratios is characteristic of 16 ½ tribes and about ½ of the species of the Gramineae. Data are given for 198 species from 129 genera and 47 tribes, and from at least 6 subfamilies of grasses. This information is correlated with data from the literature on anatomical and physiological characters of both Kranz and non-Kranz grasses. All subfamilies, tribes, and genera seem to be uniformly all Kranz or non-Kranz except the subfamily Panicoideae and the genus Panicum which have both Kranz and non-Kranz species represented.     

Morphology-based phylogeny of the treehopper family Membracidae (Hemiptera: Cicadomorpha: Membracoidea)

A parsimony‐based phylogenetic analysis of eighty‐three morphological characters of adults and immatures of seventy representatives of the tribes and subfamilies of Membracidae and two outgroup taxa was conducted to evaluate the status and relationships of these taxa. Centrotinae apparently gave rise to Nessorhinini and Oxyrhachini (both formerly treated as subfamilies, now syn.n. and syn.reinst., respectively, of Centrotinae). In contrast to previous analyses, a clade comprising Nicomiinae, Centronodinae, Centrodontinae, and the unplaced genera Holdgatiella Evans, Euwalkeria Goding and Antillotolania Ramos was recovered, but relationships within this clade were not well resolved. Nodonica bispinigera, gen.n. and sp.n., is described and placed in Centrodontini based on its sister‐group relationship to a clade comprising previously described genera of this tribe. Membracinae and Heteronotinae were consistently monophyletic. Neither Darninae nor Smiliinae, as previously defined, was monophyletic on the maximally parsimonious cladograms, but constraining both as monophyletic groups required only one additional step. The monophyly of Stegaspidinae, including Deiroderes Ramos (unplaced in Membracidae), was supported on some but not all equally parsimonious cladograms. More detailed analyses of individual subfamilies, as well as morphological data on the undescribed immatures of several membracid tribes and genera, will be needed to elucidate relationships among tribes and genera. A key to the subfamilies and tribes is provided.     

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)).     

Molecular phylogeny of black fungus gnats (Diptera: Sciaroidea: Sciaridae) and the evolution of larval habitats

The phylogeny of the family Sciaridae is reconstructed, based on maximum likelihood, maximum parsimony, and Bayesian analyses of 4809 bp from two mitochondrial (COI and 16S) and two nuclear (18S and 28S) genes for 100 taxa including the outgroup taxa. According to the present phylogenetic analyses, Sciaridae comprise three subfamilies and two genus groups: Sciarinae, Chaetosciara group, Cratyninae, and Pseudolycoriella group + Megalosphyinae. Our molecular results are largely congruent with one of the former hypotheses based on morphological data with respect to the monophyly of genera and subfamilies (Sciarinae, Megalosphyinae, and part of postulated “new subfamily”); however, the subfamily Cratyninae is shown to be polyphyletic, and the genera Bradysia, Corynoptera, Leptosciarella, Lycoriella, and Phytosciara are also recognized as non-monophyletic groups. While the ancestral larval habitat state of the family Sciaridae, based on Bayesian inference, is dead plant material (plant litter + rotten wood), the common ancestors of Phytosciara and Bradysia are inferred to living plants habitat. Therefore, shifts in larval habitats from dead plant material to living plants may have occurred within the Sciaridae at least once. Based on the results, we discuss phylogenetic relationships within the family, and present an evolutionary scenario of development of larval habitats.