Phylogenetic classification of the Drosophilidae Rondani (Diptera): the role of morphology in the postgenomic era

Molecular sequences now overwhelm morphology in phylogenetic inference. Nonetheless, most molecular studies are conducted on a limited number of taxa, as DNA rarely can be analysed from old museum types or fossils. During the last 20 years, more than 150 molecular studies have challenged the current phylogenetic classification of the family Drosophilidae Rondani based on morphological characters. Most studies concerned a single genus, Drosophila Fallén, and included only few representative species from 17 out of the 78 genera of the family. Therefore, these molecular studies were unable to provide an alternative classification scheme. A supermatrix analysis of seven nuclear and one mitochondrial genes (8248 bp) for 33 genera was conducted using outgroups from one calyptrate and four ephydroid families. The Bayesian phylogeny was consistent with previous molecular studies including whole genome sequences and divided the Drosophilidae into four monophyletic clades. Morphological characters, mostly male genitalia, then were compared thoroughly between the four clades and homologous character states were identified. These states were then checked for 70 genera and a revised phylogenetic, family‐group classification for the Drosophilidae is proposed. Two genera –Cladochaeta Coquillett and Diathoneura Duda – of the tribe Cladochaetini Grimaldi are transferred to the family Ephydridae. The Drosophilidae is divided into two subfamilies: Steganinae Hendel (30 genera) and Drosophilinae Rondani (43 genera). A further two genera, Apacrochaeta Duda and Sphyrnoceps de Meijere, are incertae sedis, and Palmophila Grimaldi, is synonymized with Drosophila syn.n. The Drosophilinae is subdivided into two tribes: the re‐elevated Colocasiomyini Okada (nine genera) and Drosophilini Okada. The paraphyly of the genus Drosophila was not resolved to avoid affecting the binomina of important laboratory model species; however, its subgeneric classification was revised in light of molecular and morphological data. Three subgenera, namely Chusqueophila Brncic, Phloridosa Sturtevant and Psilodorha Okada, were synonymized with the subgenus Drosophila (Drosophila) Fallén syns.n. Among the 45 species groups and 5 species complexes of Drosophila (Drosophila), 22 groups and 1 complex were transferred to the subgenus Drosophila (Siphlodora) Patterson & Mainland and 6 groups, 2 species subgroups and 3 complexes are considered incertae sedis within the genus Drosophila. Different morphological characters provide different signals at different phylogenetic scales: thoracic characters (wing venation and presternal shape) discriminate families; grasping and erection‐related characters discriminate subfamilies to tribes; whereas phallic paraphyses, i.e. auxiliary intromittent organs, discriminate genera and Drosophila subgenera. The study shows the necessity of analysing morphological characters within a molecular phylogenetic framework to translate molecular phylogenies into taxonomically‐comprehensive classifications.     

Phylogeny of the riodinid butterfly subtribe Theopeina (Lepidoptera: Riodinidae: Nymphidiini)

Abstract The almost exclusively Neotropical butterfly family Riodinidae is poorly represented in both ecological and systematic studies of Lepidoptera. A comparative morphological study of all seventy-five species in subtribe Theopeina (tribe Nymphidiini) yielded 104 characters, predominantly from wing pattern, male and female genitalia, and abdominal structures. All morphological characters and adults representing the range of wing pattern variation are illustrated. Phylogenetic analysis of the data produced a large number of most parsimonious cladograms, but the strict consensus of these, both when using equal weights and after successive weighting, is well resolved and the majority of terminal clades have high character and branch support. Theopeina is found to consist of five monophyletic genera, Protonymphidia , Archaeonympha , Calicosama , Behemothia and Theope (=  Parnes and Dinoplotis ), with the largest genus Theope containing thirteen monophyletic species groups, which are delineated to facilitate a discussion of broad evolutionary patterns in this morphologically diverse subtribe.     

Generic revision and phylogeny of Microweiseinae (Coleoptera: Coccinellidae)

The monophyly and phylogenetic relationships of the subfamily Microweiseinae were investigated. Twenty‐three in‐group taxa, representing all known genera of Microweiseinae (except for Microcapillata Gordon) were included in a cladistic analysis, based on 45 adult morphological characters. The parsimony analysis of the resulting data matrix supported the monophyly of Microweiseinae, Carinodulini, Serangiini and Microweiseini (inclusive of Sukunahikonini). The recognition of Sukunahikonini renders Microweiseini paraphyletic, and consequently both tribes were synonymized, retaining Microweiseini as a senior family‐group name ( syn.n. ). Genera and tribes of Microweiseinae are diagnosed thoroughly, illustrated and keys to their identification are provided. The following nomenclatural changes were made: Hikonasukuna Sasaji and Orculus Sicard are synonymized with Scymnomorphus Weise ( syn.n. ); Gnathoweisea Gordon is synonymized with Microweisea Cockerell ( syn.n. ); Hikonasukuna monticola Sasaji and Orculus castaneus Sicard are transferred to Scymnomorphus ( comb.n. ); Smilia planiceps Casey, Gnathoweisea hageni Gordon, Gnathoweisea ferox Gordon, Gnathoweisea micula Gordon and Gnathoweisea texana Gordon are transferred to Microweisea ( comb.n ). Three new genera are described: Allenius gen.n. for Allenius californianus sp.n. (type species) from Mexico and Allenius iviei sp.n. from U.S.A.; Gordoneus gen.n. (type species Gnathoweisea schwarzi Gordon from U.S.A.); and Cathedrana gen.n. (type species Cathedrana natalensis sp.n. from South Africa). The first African member of Carinodulini, Carinodulina ruwenzorii sp.n. is described. The genera Microweisea, Coccidophilus, Serangium and Delphastus are well‐known predators of sternorrynchous Hemiptera, such as scale insects (Diaspididae) and whiteflies (Aleyrodidae), and play a significant role in agricultural ecosystems as biocontrol agents. Host data and biological records are summarized for each genus.     

Phylogeny of the tribe Abrotrichini (Cricetidae,Sigmodontinae): integrating morphological and molecular evidence into a new classification

The tribe Abrotrichini (five genera and 14 living species) is a small clade within the speciose subfamily Sigmodontinae (Rodentia, Cricetidae), representing one of the extant successful radiations of mammals at southern high latitudes of the Neotropics. Its distribution is mostly Andean, reaching its greatest diversity in southern Argentina and Chile. We evaluate the phylogenetic relationships within this tribe through parsimony and Bayesian approaches based on 99 morphological characters (including 19 integumental characters, 38 skull characters, 31 dental characters, three postcranial skeletal characters, seven from the male accessory glands and phallus and one from the digestive system) and six molecular markers (one mitochondrial and five nuclear). We include representatives of all, except one, of the currently recognized species of living Abrotrichini plus one fossil form. Based on total evidence, we recovered a primary division between the genus Abrothrix and a group including the long‐clawed Abrotrichini, Chelemys, Geoxus, Notiomys and Pearsonomys. Both clades are recognized and named here as subtribes. The large degree of morphological variation observed within Abrothrix suggests that species in the genus fall into four groups, which we recognize as subgenera. In addition, the two known species of Chelemys do not form a monophyletic group, and Geoxus was recovered as paraphyletic with respect to Pearsonomys. To reconcile classification and phylogenetics, we describe a new genus for Chelemys macronyx and include Pearsonomys as a junior synonym of Geoxus. Our results highlight the importance of both morphology and molecules in resolving the phylogenetic relationships within this tribe. Based on biogeographical analyses, we hypothesize that Abrotrichini originated in south‐western South America by vicariance and then diversified mostly by successive dispersal events.     

The saline nuisance chironomid Carteronica longilobus (Diptera: Chironomidae): a systematic reappraisal

Abstract. Carteronica Kieffer and Nilodorum Kieffer sensu auctt. are synonymized with Kiefferulus Goetghebuer on the basis of cladistic analysis. An expanded diagnosis for all stages of Kiefferulus and a checklist of included species is given. K.longilobus comb.n. from Carteronica , a saline tolerant nuisance pest, is redescribed in all its life history stages. The following additional new combinations are proposed: K.brevibucca (Kieffer), K.brevipalpis (Kieffer), K.rugosum (Freeman), K.tainanus (Kieffer), K.umbraticola (Yamamoto). Many new characters from larval ventromental plates are illustrated and their use in phylo-genetic analysis is discussed.     

Taxonomic revision of the genus Stauropoctonus Brauns, 1889 (Hymenoptera: Ichneumonidae: Ophioninae) in Japan

The Japanese species of the ichneumonid genus Stauropoctonus Brauns, 1889 are revised. As a result, three species are recognized. Stauropoctonus infuscus (Uchida, 1928 ) stat. rev. , previously synonymized with S. bombycivorus (Gravenhorst, 1829 ), is recognized as a valid species and re‐described. Stauropoctonus bombycivorus, which has already been recorded in Japan, is also recognized and re‐described based on Japanese specimens. Stauropoctonus aurantiacus sp. nov. is described based on a single male specimen from Yakushima Island, Kagoshima Prefecture, Japan. Stauropoctonus nigrithorax Lee & Kim, 2002 syn. nov. is newly synonymized with S. bombycivorus. Additionally, a key to the Stauropoctonus species and discussions on their phenology and collection methods are provided.     

Pythiopina,an enigmatic subtribe of darkling beetles (Coleoptera: Tenebrionidae: Pedinini): taxonomic revision,microtomography, ecological niche models and phylogenetic position

Morphological, anatomical, and distributional data concerning the S outh A frican endemic beetle subtribe P ythiopina (T enebrionidae: P edinini) are revised. Five species, representing two genera, are recognized. Included in this total is one new species (Meglyphus mariae K amiński sp.n. ). The following species are placed in synonymy: Meglyphus ciliatipes [=Meglyphus calitzensis syn.n. ]; Meglyphus laenoides [=Meglyphus andreaei syn.n. ; =Meglyphus namaqua syn.n. ]. Microtomographic models for all valid P ythiopina species, including the holotype of the newly described species, are presented and analysed. Endoskeleton morphology (specifically characters of the tentorium and metendosternite) proved to be informative at the specific and generic levels. An identification key is provided to all known species of the subtribe. Environmental niche models are presented for the majority of species. A molecular phylogeny of P edinini based on six genetic loci (28S : D 1–D 3 region; 28S : D 4–D 5 region, COII , A rgK , CAD 2, wg) was also produced to explore the phylogenetic position of P ythiopina. This analysis is the first to include representatives of all seven subtribes of P edinini, and supports a sister relationship between P ythiopina and the P alaearctic subtribe D endarina. Results also suggest the existence of a second pair of sister taxa within P edinini (in addition to M elambiina) with an amphitropical A frican distribution. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:285AD87A‐46B1‐4FE9‐BC57‐949EA1F70D49 .     

Long‐proboscid brachyceran flies in Cretaceous amber (Diptera: Stratiomyomorpha: Zhangsolvidae)

The monophyletic family Zhangsolvidae comprises stout‐bodied brachyceran flies with a long proboscis and occurring only in the Cretaceous, originally known in shale from the Early Cretaceous Laiyang Formation (Fm.) in China (Zhangsolva Nagatomi & Yang), subsequently from limestones of the Early Cretaceous Crato Fm. of Brazil. Cratomyoides Wilkommen is synonymized with Cratomyia Mazzarolo & Amorim, both from the Crato Fm.; Cratomyiidae is synonymized with Zhangsolvidae. Two genera and three species of Zhangsolvidae are described: Buccinatormyia magnifica Arillo, Peñalver & Pérez‐de la Fuente, gen. et sp.n. and B. soplaensis Arillo, Peñalver & Pérez‐de la Fuente, sp.n. , in Albian amber from Las Peñosas Fm. in Spain; and Linguatormyia teletacta Grimaldi, gen. et sp.n. , in Upper Albian–Lower Cenomanian amber from Hukawng Valley in Myanmar. Buccinatormyia soplaensis and Linguatormyia teletacta are unique among all Brachycera, extant or extinct, by their remarkably long, flagellate antennae, about 1.6× the body length in the latter species. A phylogenetic analysis of 52 morphological characters for 35 taxa is presented, 11 taxa being Cretaceous species, which supports placement of the family within Stratiomyomorpha, although not to any particular family within the infraorder. This published work has been registered in Zoobank, http://zoobank.org/urn:lsid:zoobank.org:pub:F32CF887‐7C37‐45D5‐BD6B‐135FE9B729A7 .     

Phylogeny of ensign scale insects (Hemiptera: Coccoidea: Ortheziidae) based on the morphology of Recent and fossil females

The Ortheziidae (ensign scale insects) is a morphologically well‐defined family. The morphology and occurrence in the fossil record suggests a probable early origin of the family in scale insect evolution. The present phylogenetic analysis – based on 69 morphological characters of female ortheziids, using 39 exemplar Recent species – provides the first analytical assessment of relationships among living genera of the family, as well as the relationships of eight fossil species, based on complete, well‐preserved specimens in amber. Monophyly of the subfamilies Newsteadiinae, Ortheziinae and Ortheziolinae is supported, but Nipponortheziinae is found to be paraphyletic by inclusion of the Ortheziolinae. Thus, the subfamily Ortheziolinae is reduced in rank to tribe Ortheziolini stat.n. , which now includes Matileortheziola Kozár & Foldi, Ortheziolacoccus Kozár, Ortheziolamameti Kozár and Ortheziola?ulc. Consequently, the tribes Matileortheziolini, Ortheziolacoccini and Ortheziolamametini are synonymized ( syn.n. ) here under Ortheziolini. Five new species and one new genus of fossil ensign scales are described from three amber deposits: Burmorthezia gen.n. with type species Burmorthezia kotejai sp.n. and also B. insolita sp.n ., both in mid‐Cretaceous Burmese amber (98 Ma) and Arctorthezia baltica sp.n. in Eocene Baltic amber (c. 43 Ma) based on second‐instar nymphs; Mixorthezia kozari sp.n . and M. dominicana sp.n . in Miocene Dominican amber (c. 17 Ma) based on adult females. Fossil placements are unambiguous, with Burmorthezia forming a stem to crown‐group (Recent and Tertiary) Ortheziidae. A summary of described fossil ortheziids is provided.     

Hepaticae Borneenses (Oxford University Expedition to Sarawak, 1932)

Abstract

The taxonomic status of Barbula montenegrina Breidl. &; Szyszyl., a putative synonym of Tortula lingulata Lindb., was re-evaluated, considering its morphological characters and the habitat conditions of the known localities. The taxon is typified here and synonymized with Tortula muralis subsp. obtusifolia (Schwägr.) Culm.     

Phylogeny and biogeography of Carminator (Hymenoptera: Megalyridae)

Carminator Shaw is a small genus of parasitic wasps that is mainly distributed in Southeast Asia. Eight species are recognized here, including Carminator coronatus sp.n. and Carminator gracilis sp.n. A data set comprising 54 morphological characters and including all the known species of Carminator, as well as four out‐group taxa (two Cryptalyra spp., one Ettchellsia sp. and one Megalyra sp.), was assembled and analysed. Carminator is retrieved as monophyletic. All weighted analyses place Carminator affinis as the sister group to the rest of the genus. A northern clade comprising species occurring on the Japanese Isles, Taiwan and Vietnam (Carminator japonicus (Carminator gracilis sp.n. (Carminator cavus + Carminator helios))) is strongly supported and nested inside the more southerly distributed species. C. helios is found on Nakanoshima Island, which emerged post‐Pliocene, and so C. helios is considered to have dispersed there via a land‐bridge connection from the Ryukyu Islands. A key to all known species of Carminator is provided.     

A multivariate analysis of morphological variation in the Hemizygia bracteosa complex (Lamiaceae, Ocimeae)

The variation and recognition of taxa within the Hemizygia bracteosa complex was examined using multivariate techniques. Morphological characters were sampled on 197 herbarium specimens. Phenetically H. bracteosa and H. welwitschii overlap in many floral characters. However differences in leaf characters and habit maintain their morphological distinctness from each other and they are therefore upheld as species. Hemizygia ornata, synonymized under H. welwitschii in recent treatments of the genus Hemizygia, differentiates from H. welwitschii on the basis of differences in leaf and floral characters and its reinstatement at specific level is here proposed. The concept of H. linearis is revised on account of the type specimen separating from all other elements of the taxon used in the analyses. The latter form a coherent group with H. petrensis and H. canescens thus negating any attempt to give any of them specific recognition. It is proposed that they should be synonymized under the earliest name H. canescens. The specific boundary of H. petiolata is revised but its specific status maintained.     

Molecules,morphology and Mimeoma scarabs: evolutionary and taxonomic implications for a palm‐associated scarab group

Cyclocephaline scarabs, the second largest tribe of rhinoceros beetles, are important pollinators of early‐diverging angiosperm families in the tropics. The evolutionary history of cyclocephaline genera is poorly resolved and several genera are thought to be nonmonophyletic. We assess the monophyly of Mimeoma Casey, a group of Neotropical palm‐feeding scarabs, and its relationship to Cyclocephala with a phylogenetic analysis of 2899 bp of DNA sequence data and 18 morphological characters. All five species of Mimeoma were included in analyses along with species of Cyclocephala Dejean, Dyscinetus Harold and Tomarus Erichson as outgroup taxa. Nearly complete 28S, 12S and CO1 data were collected from 26 of 29 specimens, of which 16 samples were pinned, museum specimens. 28S data strongly support a nonmonophyletic Mimeoma; mitochondrial data (CO1 and 12S) suggest that Mimeoma species are nested within an apical clade of other Cyclocephala species; combined molecular and morphological data identify two strongly supported clades of Mimeoma species but do not support their sister relationship. Combined data show that Mimeoma species are nested within Cyclocephala, thus rendering Cyclocephala paraphyletic. Mimeoma is synonymized within Cyclocephala resulting in the following new combinations: Cyclocephala acuta Arrow n.comb ., Cyclocephala englemani (Ratcliffe) n.comb ., Cyclocephala maculata Burmeister n.comb ., Cyclocephala nigra (Endrödi) n.comb . and Cyclocephala signatoides Höhne n.comb . Our results demonstrate that pinned, museum specimens can be used to obtain DNA sequence data (particularly high‐copy gene regions) for evolutionary studies, and provide the first empirical support that host‐plant associations within cyclocephaline scarab clades are conserved at the plant family‐level.     

Phylogeny of Gracilariaceae (Rhodophyta): evidence from plastid and mitochondrial nucleotide sequences

Gracilariaceae are mostly pantropical red algae and include ~230 species in seven genera. Infrafamilial classification of the group has long been based on reproductive characters, but previous phylogenies have shown that traditionally circumscribed groups are not monophyletic. We performed phylogenetic analyses using two plastid (universal plastid amplicon and rbcL) and one mitochondrial (cox1) loci from a greatly expanded number of taxa to better assess generic relationships and understand patterns of character distributions. Our analyses produce the most well‐supported phylogeny of the family to date, and indicate that key characteristics of spermatangia and cystocarp type do not delineate genera as commonly suggested. Our results further indicate that Hydropuntia is not monophyletic. Given their morphological overlap with closely related members of Gracilaria, we propose that Hydropuntia be synonymized with the former. Our results additionally expand the known ranges of several Gracilariaceae species to include Brazil. Lastly, we demonstrate that the recently described Gracilaria yoneshigueana should be synonymized as G. domingensis based on morphological and molecular characters. These results demonstrate the utility of DNA barcoding for understanding poorly known and fragmentary materials of cryptic red algae.     

Evolution,pollination, and systematics of the tribeNeottieae (Orchidaceae)

The various classifications of the orchid tribeNeottieae are reviewed and a new classification is proposed that divides the tribe into three subtribes,Neottiinae, Limodorinae, andCephalantherinae, based primarily on characters of the column (gynostemium). A cladistic analysis illustrates that these three subtribes are more closely related to one another than either is to any other group in subfam.Neottioideae, although there are very few apomorphic characters for the tribe. Pollination biology is also discussed showing links between breeding systems and distribution. There is also a possible role between column and labellum morphology and the emergence of a deceptive pollination syndrome from one of reward.     

Phylogenetic interrelationships,taxonomy, and reductive evolution in the Neotropical electric fish genus Hypopygus (Teleostei,Ostariophysi, Gymnotiformes)

A phylogenetic reconstruction of the Neotropical electric fish genus Hypopygus based on 47 parsimony‐informative morphological characters is presented. A series of synapomorphies support the hypothesis of monophyly of Hypopygus, and partially resolve species‐level relationships within the genus. Hypopygus species are recognized here as miniaturized fishes based on two criteria; first, a derived condition of diminutive body size, and; second, the presence of a suite of reductive morphological characters, including partial or total losses, simplifications, and reductions of the anal‐fin rays, scales, cranial bones, and laterosensory canal system. Reductive characters associated with miniaturization comprise 45% of the total number of characters in the phylogenetic reconstruction of the genus. Miniaturization and reductive morphological evolution in Hypopygus are discussed here in the phylogenetic context. A taxonomic revision of Hypopygus is presented, in which five new species are described, two species previously assigned to the genus are redescribed, and a single known species of Stegostenopos is redescribed and included in Hypopygus as a junior synonym. Distribution maps and a key for all eight valid species of Hypopygus are provided, based on the examination of 5014 catalogued museum specimens. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 1096–1156.     

Towards a phylogeny of the flesh flies (Diptera: Sarcophagidae): morphology and phylogenetic implications of the acrophallus in the subfamily Sarcophaginae

The morphology of the acrophallus, the distal portion of the male phallus carrying the phallotreme, was studied in 72 exemplar species representing 56 genera and subgenera of the flesh fly subfamily Sarcophaginae. For 42 of those species, scanning electron microscopy was used to clarify the phallic morphology. Terms used to describe the male genitalia were updated based on new interpretations of homology. Male genitalic characters, combined with other morphological characters of adult males and females and of larvae, were used to construct a phylogeny. The monophyly of the subfamily was supported, and some generic‐level sister‐group relationships proposed in the literature, but without previous cladistic analyses, were also supported. The genus Blaesoxipha Loew, as currently recognized, was not monophyletic in our analysis. The genus Helicobia Coquillett is synonymized with Sarcophaga Meigen syn. nov. and treated as a subgenus of the latter. The Sarcophaga subgenera Neobellieria Blanchard and Mehria Enderlein were not monophyletic. Many of the clades in the analysis were supported primarily or exclusively by male genitalic character states, highlighting the importance of the male genitalia as a source of morphological characters for sarcophagine phylogeny. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 740–778.     

Morphometric analyses and new taxonomic circumscription of South American species of Flourensia (Asteraceae,Heliantheae, Enceliinae)

Flourensia (Asteraceae, Heliantheae, Enceliinae) is an amphitropical genus of resinous subshrubs, shrubs and small trees with 13 North American and 20 South American species among which disagreement on the species limits of some members still exists. To resolve the taxonomy of the South American taxa, we carried out a combination of clustering (Ward's method with Gower distance coefficient) and ordination analyses (Principal Coordinate Analyses) based on 34 vegetative and reproductive characters scored from herbarium material, including types. Based on the results, we recognize 12 South American species: F. angustifolia, F. cajabambensis, F. fiebrigii, F. heterolepis, F. hirtissima, F. macrophylla, F. niederleinii; F. peruviana, F. polycephala, F. thurifera, F. tortuosa and F. suffrutescens. A number of species are placed in synonymy: Flourensia blakeana and F. hirta are synonymized under the name F. fiebrigii; Flourensia campestris, F. leptopoda, F. oolepis and F. riparia are synonymized under F. thurifera; Flourensia macroligulata is synonymized under F. tortuosa, and Flourensia polyclada is synonymized under F. suffrutescens. A taxonomic treatment of four redefined species as well as a key and distribution maps to all South American Flourensia species are provided.