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.     

Responses of a generalist and a specialist parasitoid (Hymenoptera: Eucoilidae) to Drosophilid larval kairomones

Foraging parasitoids are thought to need more specific information than generalists on the presence, identity, availability, and suitability of their insect host species. In the present paper, we compare responses to host kairomones by two phylogenetically related parasitoid species that attack Drosophilidae and that differ in the width of their host range. As predicted, the behavioral response of the parasitoids to host kairomones reflected their difference in host range. The response of the specialist parasitoid Leptopilina boulardiwas restricted to contact kairomones from its natural hosts and one closely related species. In contrast, the generalist parasitoid Leptopilina heterotomaresponded to contact kairomones of a variety of Drosophilidae species.     

EVOLUTION OF MULTIPLE KINDS OF FEMALE SPERM-STORAGE ORGANS IN DROSOPHILA

Females of all species belonging to the family Drosophilidae have two kinds of sperm-storage organs: paired spherical spermathecae and a single elongate tubular seminal receptacle. We examined 113 species belonging to the genus Drosophila and closely allied genera and describe variation in female sperm-storage organ use and morphology. The macroevolutionary pattern of organ dysfunction and morphological divergence suggests that ancestrally both kinds of organs stored sperm. Loss of use of the spermathecae has evolved at least 13 times; evolutionary regain of spermathecal function has rarely if ever occurred. Loss of use of the seminal receptacle has likely occurred only once; in this case, all descendant species possess unusually elaborate spermathecae. Data further indicate that the seminal receptacle is the primary sperm-storage organ in Drosophila. This organ exhibits a pattern of strong correlated evolution with the length of sperm. The evolution of multiple kinds of female sperm-storage organs and the rapidly divergent and correlated evolution of sperm and female reproductive tract morphology are discussed.     

Diversity and host associations of dipteran insects exploiting fungal fruiting bodies in Hokuriku,central Japan

To clarify the diversity and host associations of dipteran insects exploiting fungal fruiting bodies, we collected fruiting bodies at 18 localities in Hokuriku region, central Japan, from 2012 to 2015 and examined them for the emergence of insects. In total, 14,107 dipteran individuals belonging to 20 families emerged from fungi of 8 orders, 25 families, 49 genera and 129 species. Approximately 79% of dipteran individuals belonged to three families, Phoridae, Muscidae and Drosophilidae. The faunal similarity at the family level was relatively high between central (warm‐temperate) and northern (cool‐temperate) areas of Japan. However, the species composition of Drosophilidae was much different between central and northern Japan. The difference in the species composition was discussed in relation to the climatic conditions and fungal flora. None of the species from Drosophilidae, Phoridae, Muscidae, Mycetophilidae, Lonchaeidae and Chloropidae were specialists (they exploited more than one species of fungi), but they showed differences their fungi preference. Adults of some families, especially Drosophilidae, were frequently collected from fruiting bodies, but those of other families were seldom collected, probably reflecting differences in adult feeding ecology.     

The phylogenetic relationships of flies in the family Drosophilidae deduced from mtDNA sequences.

The phylogenetic relationships of several taxa from representative genera, subgenera, groups, and subgroups in the Drosophilidae were examined using sequences from a 905-bp mtDNA fragment. Conventional cloning and sequencing techniques were used to obtain nucleotide sequences. In addition, polymerase chain reaction primers were designed for the rapid amplification and sequencing of this region for the species examined in the Drosophilidae. Phylogenetic analysis was done by cladistic techniques. Because of the coding nature of the 905-bp mtDNA fragment, several separate analyses of these sequences were performed. The genera Scaptomyza and Hirtodrosophila occupy ancestral branching positions in the molecular phylogeny. The genera Chymomyza and Zaprionus have intermediate branching positions, while the subgenera Drosophila and Sophophora are in the most derived position in the molecular phylogeny. Within the subgenus Sophophora, there is little resolution using these sequences, while within the subgenus Drosophila, D. melanica, D. funebris, and D. pinicola form a clade in a derived part of the phylogeny, with D. robusta and D. immigrans branching in an intermediate position in the phylogeny. D. mercatorum, a member of the repleta species group, occupies an ancestral position in the molecular phylogeny.     

Distribution and conservation of sequences homologous to the 1731 retrotransposon in Drosophila

The distribution of 1731 retrotransposon-hybridizing sequences in the family Drosophilidae has been studied using a 1731 probe from Drosophila melanogaster. Squash blot and Southern blot analyses of 42 species reveal that the 1731 sequences are widespread within both the Sophophora and Drosophila subgenera and are also present in the genera Scaptomyza and Zaprionus. Hence the 1731 retrotransposon family appears to have a long evolutionary history in the Drosophilidae genome. Differences of hybridization signal intensity suggested that the 1731 sequence is well conserved only in the three species most closely related to D. melanogaster (D. simulans, D. mauritiana, and D. sechellia). A survey of insertion sites in numerous different populations of the previous four species by in situ hybridization to polytene chromosomes has shown in all cases both chromocentric hybridizations and a low number of sites (0-5) on the chromosomal arms. This number of sites is among the lowest observed in D. melanogaster and D. simulans when 1731 is compared with other retrotransposon families. In addition, we have observed species-specific patterns of the chromocentric hybridization signal, suggesting rapid modifications of the beta-heterochromatin components since the radiation of the melanogaster subgroup.      

Revision of New Zealand Orthotylinae (Insecta: Hemiptera: Miridae)

Abstract

Six genera and 11 species of Orthotylinae are now known from New Zealand. Zanchius Distant is newly recorded. One new genus, Tridiplous, and seven new species of endemic New Zealand Orthotylini are described and illustrated. Four new species are described in Tridiplous: T. burrus, T. parvapiatus, T. penmani, and T. virens, and three new species are described in Zanchius: Z. ater, Z. rubicrux, and Z. totus. Keys are provided to identify New Zealand taxa of the tribes of Orthotylinae, genera and species of Halticini, genera of Orthotylini, and species of Tridiplous and Zanchius. The bugs are illustrated with colour habitus photos, and drawings including male and female genitalia. Economic importance is discussed.     

Improved tribal delimitation of the subfamily Dictyopharinae and description of new genera and new species (Homoptera,Fulgoroidea, Dictyopharidae)

Ten new genera, five new subgenera, and five new species are described in the family Dictyopharidae. Three generic names are synonymized. A new name is proposed for the generic homonym. Dictyophara kazeruna Dlabola is transferred to the genus Callodictya Melichar. The genus Sinodictya Matsumura, with the type species Sinodictya tukana Matsumura, is redescribed. A new key to the tribes of the subfamily Dictyopharinae is given. The composition and characters of the tribes Taosini and Lappidini are revised. All the genera of the subfamily Dictyopharinae are listed according to their tribal position. New records are given for some interesting species.     

Rhagodiinae: A new subtribe in the Chenopodiaceae

A new subtribe, Rhagodiinae, is described in the tribe Chenopodieae of the Chenopodiaceae. Three genera are included in this new subtribe: Rhagodia with 8 species, Einadia with 3 species, and Holmbergia with a single species. All the species are fully described and keys to the genera and species are given. Four new combinations are proposed: Rhagodia deltophylla, Einadia nutans, Einadia hastata and Einadia triandra.     

Shaping of Drosophila Alcohol Dehydrogenase Through Evolution: Relationship with Enzyme Functionality

Drosophilidae is a large, widely distributed family of Diptera including 61 genera, of which Drosophila is the most representative. Drosophila feeding is part of the saprophytic trophic chain, because of its dependence upon decomposing organic matter. Many species have adapted to fermenting fruit feeding or to artificial (man-made) fermentation habitats, such as cellars and breweries. Actually, the efficient exploitation of niches with alcohols is considered one of the reasons for the worldwide success of this genus. Drosophila alcohol dehydrogenase (ADH), a member of the short-chain dehydrogenase/reductase family (SDR), is responsible for the oxidation of alcohols, but its direct involvement in fitness, including alcohol tolerance and utilization, gives rise to much controversy. Thus, it remains unclear whether ADH differentiation through evolution is somehow associated with natural adaptation to new feeding niches, and thus maybe to Drosophila speciation, or if it is a simple reflection of neutral divergence correlated with time separation between species. To build a hypothesis which could shed light on this dilemma, we analyzed the amino acid variability found in the 57 protein ADH sequences reported up to now, identified the taxon-specific residues, and localized them in a three-dimensional ADH model. Our results define three regions whose shaping has been crucial for ADH differentiation and would be compatible with a contribution of ADH to Drosophila speciation. Received: 11 August 1997 / Accepted: 30 December 1997     

A phylogeny of Drosophilidae using the Amyrel gene: questioning the Drosophila melanogaster species group boundaries

In this study, the phylogenetic relationships of 164 species of the family Drosophilidae are discussed, using the Amyrel gene, a member of the α -amylase multigene family. This study focuses on numerous species groups in the subgenera Sophophora and Drosophila of the genus Drosophila but also includes other closely related genera. Nucleotide data were analysed by several methods: maximum parsimony, neighbour joining, maximum likelihood and Bayesian inference. Heterogeneity of base composition (mainly low GC contents in the species groups willistoni and saltans ) has been addressed. In all analyses, the genus Drosophila appeared paraphyletic. The subgenus Sophophora clearly appeared to be a monophyletic group, showing well-resolved clades, with the Neotropical groups arising in a basal position. Here, it is proposed to raise the species subgroups ananassae and montium to the rank of species group, and to restrict the melanogaster species group to the melanogaster subgroup plus the 'Oriental' subgroups, among which the suzukii subgroup is polyphyletic. Some related genera such as Zaprionus , Liodrosophila , Scaptomyza and Hirtodrosophila are clustered with, or inside the subgenus Drosophila , which is therefore paraphyletic and should be reviewed.     

Generic delimitation of the genera Brevilongium and Otoglossum (Orchidaceae) with description of new species from Colombia and Panama

A discussion on the generic delimitation of the orchid genera Brevilongium and Otoglossum is presented. Additional notes on Ecuadorella are provided. A comparison of the morphological characters of the genera is presented together with a key to their identification. Moreover, two new species of Brevilongium and four species of Otoglossum are described and illustrated. The taxonomic affinities of the new taxa are briefly discussed. Keys to the identification of Brevilongium and the Colombian species of Otoglossum are provided.     

New species of Metadesmolaimus and Stephanolaimus (Nematoda: Chromadoria) from Northern Ireland with reviews of the genera

Two new species of freeliving marine nematodes belonging to the genera Metadesmolaimus and Stephanolaimus are fully described and illustrated. Figures and tables are given to aid identification of all of the valid species of each of the genera. The new species, Metadesmolaimus gaelicus and Stephanolaimus jayasreei, are described from a sandy beach in Co. Down, Northern Ireland but they have also been recorded from Scottish localities.     

Three new genera of Leptophlebiidae (Ephemeroptera) from New Zealand

Abstract

Three new genera—Austroclima, Mauiulus, and Cryophlebia—are established for species of Leptophlebiidae from New Zealand. The following new combinations are included: Austroclima sepia (Phillips) and Cryophlebia aucklandensis (Peters). Atalophlebioides sepia is redescribed as Austroclima sepia and a neotype is designated. Two new species, Austroclima jollyae and Mauiulus luma, are described. All life stages are described, and the relationships of each genus are discussed. Keys are given to male and female imagos, subimagos, and nymphs of each species, and to all New Zealand genera with species previously placed in Atalophlebioides.     

Chromosome numbers of miscellaneous Malagasy Acanthaceae

Meiotic chromosome numbers are reported for 12 species in eight genera of Acanthaceae from Madagascar. Chromosome numbers of 11 species are reported for the first time. Counts inMendoncia (n=19) andNeuracanthus (n=20) are the first for these genera. A new chromosome number (n=30) is reported inJusticia. Systematic implications of the chromosome counts are addressed and basic chromosome numbers for these eight genera of Malagasy Acanthaceae are discussed.     

Phylogeny and taxonomic revision of all genera of Conopidae (Diptera) based on morphological data

All global genera of the fly family Conopidae are revised here. A cladistic analysis of 117 morphological characters recorded from 154 species, including representatives of 59 genera and subgenera, recovers a phylogenetic hypothesis for the family. This hypothesis is used as the basis of a new classification for the family. Both Sicini and Zodionini are removed from Myopinae and elevated to subfamilial status. A new tribe, Thecophorini, is proposed within Myopinae to accommodate Thecophora, Scatoccemyia, and Pseudoconops. Two genera, Pseudomyopa and Parazodion, are removed from Dalmanniinae and placed in Myopinae and Zodioninae, respectively. Conopinae is divided into 11 tribes, seven of which are newly described (Asiconopini, Caenoconopini, Gyroconopini, Microconopini, Neoconopini, and Siniconopini). Some examined species are transferred to different or new genera and subgenera. A new genus, Schedophysoconops gen. nov. , and subgenus Asiconops (Aegloconops) subgen. nov. within Conopinae are described. A review of character evolution and phylogeography is included in light of the new classification. A catalogue of all genus‐group names is included with new emendations noted.     

Phylogenetic analysis of the family Ariidae (Ostariophysi: Siluriformes), with a hypothesis on the monophyly and relationships of the genera

Ariid monophyly and intrafamilial relationships are investigated based on cladistic analysis of 230 morphological characters. Terminal taxa examined include whenever possible type‐species, or the most morphologically similar species to the type‐species of the nominal genera, and the largest possible number of species, including cleared and stained specimens, available in zoological collections. Previous hypotheses about monophyly of the Ariidae are strongly corroborated by new synapomorphies discovered in the present study. The subfamily Galeichthyinae and the remaining ariids are strongly supported by new morphological characters. The monotypic subfamily Bagreinae is recognized as the sister group to all nongaleichthyin ariids, supported by a large series of exclusive synapomorphies. A new concept of Ariinae is presented: the subfamily is found to be unequivocally monophyletic and includes all ariid genera, except Galeichthys and Bagre. New data supporting the monophyly of the genera included in the Ariinae are introduced and previous hypotheses of monophyly, species composition, morphological definition, and relationships are reviewed and discussed.