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.     

Morphology and molecular phylogeny of Pauciconfibuloides amazonica gen. n. sp. n. (Platyhelminthes,Monogenoidea) parasitizing the Amazonian croaker Plagioscion squamosissimus

An integrative study was performed to understand the phylogenetic relationships of an undescribed, freshwater species of microcotylid parasitizing Plagioscion squamosissimus from the Amazon River Basin. Based on morphological and molecular analysis (18S rDNA and partial 28S rDNA genes), a new genus is proposed to accommodate this new species, Pauciconfibuloides amazonica gen. n. sp. n. The new genus is closely related to Protastomicrocotylinae and Pauciconfibula by sharing the vagina, male copulatory organ, and genital atrium all unarmed. However, Pauciconfibuloides gen. n. can be distinguished from those taxa by the prostatic system and position of the vaginal pore. Molecular phylogenetic inference suggests a sister relationship with species of Polylabris (Prostatomicrocotylinae), but to date, there are no available 18S or 28S rDNA sequences of Pauciconfibula to be compared. This is the first report of a microcotylid parasitizing a freshwater sciaenid from South America.     

Evolutionary relationships of endemic Draparnaldioides simplex C. Meyer et Skabitch. Green alga from Lake Baikal with non-Baikalian taxa of chaetophoraceae (Chlorophyta) family

The phylogenetic relationships between Baikalian endemic green alga Draparnaldioides simplex C. Meyer et Skabitch., 1976 and holarctic taxa of green algae have been studied using the 18S rDNA gene fragment and internal transcribed ITS1 and ITS2 spacers of nuclear DNA. The Baikalian genus Draparnaldioides was shown to be a separate taxon. The level of genetic difference between the studied species and non-Baikalian taxa of sister groups of green algae is insignificant, which indicates the young age of the genus Draparnaldioides and its recent radiation from the common ancestor with genera Draparnaldia and Chaetophora.     

Phylogenetic analyses of the rhipicephaline ticks indicate that the genus Rhipicephalus is paraphyletic

We inferred the phylogeny of 21 species and subspecies of ticks from the subfamilies Rhipicephalinae and Hyalomminae using cytochrome c oxidase subunit I (COI) and 12S rRNA mitochondrial gene sequences. Two members of the subfamily Haemaphysalinae were used for outgroup reference. The largest rhipicephaline genus, Rhipicephalus, was represented by ticks from six of the species groups, the second largest genus, Dermacentor, by species from two of three of its subgenera, and the genus Boophilus by 3 of its 5 species. We analyzed the 12S and COI sequences separately and together; statistically significant incongruence between the 12S rDNA and the COI sequences was not detected in the combined dataset using the incongruence length difference test. The combined dataset provided greater phylogenetic resolution than the individual datasets, and although the 12S rDNA data had only 25% of the parsimony-informative characters, it provided half of the total partitioned Bremer support for the combined dataset. We present the first hypothesis of phylogenetic relationships among some species groups of Rhipicephalus but our most controversial result was that the genus Rhipicephalus is apparently paraphyletic, unless species of Boophilus are included in it. The species of Rhipicephalus most closely related to Boophilus spp. were from the R. pravus and R. evertsi species groups, which may implicate an African origin for this important group of ticks.     

Phylogenetic relationships and biodiversity in Hylids (Anura: Hylidae) from French Guiana

We evaluated two biodiversity criteria, higher taxonomic diversity and phylogenetic diversity in French Guiana. For this, we used a recent assessment of the knowledge accumulated since 30 years of study on the amphibian species currently known in French Guiana. We focused on two well-represented genera, Hyla and Scinax, belonging to the subfamily Hylinae. We used partial sequences of two mitochondrial genes (16S rDNA and 12S rDNA, 813 bp) and two nuclear genes (tyrosinase and 18S rRNA, 1590 bp) covering a total of 2403 bp. According to the high bootstrap support in phylogenetic analysis of the complete dataset, the genus Scinax is a homophyletic clade formed by two species groups (rubra and rostrata) in French Guiana. The genus Hyla was confirmed to be a paraphyletic group formed by two species groups as well (30 chromosomes and the 'gladiator frogs'). We confirmed that these genera should be taxonomically reconsidered. Moreover, at the genus, subfamily and family levels, the use of only morphological characters or only molecular DNA markers would hamper estimations of biodiversity. Thus, we strongly advise the combined use of both morphology and molecular data (nuclear and mitochondrial markers).     

Systematics of the subfamily Haplorchiinae (Trematoda: Heterphyidae), based on nuclear ribosomal DNA genes and ITS2 region

Phylogenetic relationships of 6 species in the trematode subfamily Haplorchiinae were analyzed using small and large subunit of ribosomal DNA genes (18S rDNA and 28S rDNA) and internal transcribed spacer subunit II (ITS2) region as molecular markers. Maximum Likelihood and Bayesian inference analyses of combined rDNAs and ITS2 indicated a close relationship between the genera Haplorchis and Procerovum, while these two genera were distinct from Stellantchasmus falcatus. These phylogenetic relationships were consistent with the number of testes but not with the characters of the modification of the seminal vesicle or of the ventral sucker. Although three Haplorchis spp. were, together with Procerovum, in the same cluster, their mutual topology was incongruent between rDNA and ITS2 trees. Phylogenetic analyses using other molecular markers with more species are necessary to work out solid phylogenetic relationships among the species in this subfamily.     

DNA‐based phylogeny of the marine genus Heterodrilus (Annelida,Clitellata, Naididae)

Heterodrilus is a group of marine Naididae, common worldwide in subtropical and tropical areas, and unique among the oligochaetes by their tridentate chaetae. The phylogenetic relationships within the group are assessed from the nuclear 18S rDNA gene, and the mitochondrial cytochrome c oxidase subunit I (COI) and 16S rDNA genes. Sequence data were obtained from 16 Heterodrilus species and 13 out‐group taxa; 48 sequences are new for this study. The data were analysed by Bayesian inference. Monophyly of the genus is corroborated by the resulting tree, with Heterodrilus ersei (a taxon representing a small group of species with aberrant male genitalia) proposed to be outside all other sampled species. Although earlier regarded as a member of the subfamily Rhyacodrilinae, both molecular and morphological data seem to support that Heterodrilus is closely related to Phallodrilinae. However, the results are not conclusive as to whether the genus is the sister group of, or a group nested inside, or separate from this latter subfamily. The studied sample of species suggests at least two major clades in Heterodrilus with different geographical distributions, in one of the clades, most species are from the Indo‐West Pacific Ocean, while in the other, the majority are from the Western Atlantic Ocean. Morphological characters traditionally used in Heterodrilus taxonomy are optimized on the phylogenetic tree, revealing a high degree of homoplasy.     

Phylogeny of the Saprininae reveals interesting ecological shifts in the history of the subfamily (Coleoptera: Histeridae)

A morphological data set for the histerid beetle subfamily Saprininae comprising 95 adult morphological characters scored (multistate coding) from 72 terminal taxa and four outgroups was developed in order to analyse and determine the relationships amongst the genera and subgenera of the Saprininae subfamily. Cladograms were rooted with exemplars of Dendrophilinae (genus Dendrophilus), Bacaniini (genus Bacanius), Abraeinae (genus Chaetabraeus), and Anapleini (genus Anapleus). Parsimony‐based phylogenetic analyses were performed based on the type species of each genus and subgenus of the Saprininae occurring around the world, with the exception of three taxa: Paramyrmetes foveipennis (type species of the genus Paramyrmetes), Satrapister nitens (type species of the genus Satrapister) and Xerosaprinus (Auchmosaprinus) laciniatus (type species of the subgenus Auchmosaprinus) that were not available. In addition, in order to test the monophyly of several questionable genera, multiple exemplars were added in a few cases. The analysis also included an exemplar of an apparently undescribed genus. The results of the analysis confirm the monophyly of the subfamily supported by two unique synapomorphies: (1) presence of sensory structures of the antenna; and (2) presence of the antennal cavity, as well as several other weaker synapomorphies. However, the phylogeny inferred here shows mostly low support for the deeper branches and consequently no major changes in the Saprininae classification are proposed. The presented cladogram is discussed together with its implications for the evolution of the subfamily. The most informative characters and their respective states are outlined. Multiple shifts in lifestyles have evolved during the evolutionary history of the group. Taxa found near the root of the cladogram are mostly nidicolous or myrmecophilous, and inquiliny is presumed to be the plesiomorphic lifestyle of the subfamily. The nidicolous lifestyle has undergone several transformations to other lifestyles and myrmecophily has evolved three times independently during the evolution of the subfamily. Termitoxeny has evolved two times independently in the group whereas ecological adaptation for life in caves has likewise evolved two times independently. The analyses yielded a large clade of predominantly psammophilous taxa; psammophily is thought to have evolved once and has been subsequently lost several times. © 2014 The Linnean Society of London     

Evolution of fossil and living spider flies based on morphological and molecular data (Diptera,Acroceridae)

The phylogeny of spider flies is presented based on an analysis of DNA sequence data combined with morphological characters for both living and fossil species. We sampled 40 extant and extinct genera across all major lineages of Acroceridae, which were compared with outgroup taxa from various lower brachyceran families. In all, 81 morphological characters of 60 extant and 10 extinct ingroup species were combined with 7.1 kb of DNA sequences of two nuclear (CAD and 28S rDNA) and two mitochondrial genes (COI and 16S rDNA). Results strongly support the monophyly of Acroceridae, with major clades contained within classified here in five extant subfamilies (Acrocerinae, Cyrtinae stat. rev. , Ogcodinae stat. rev. , Panopinae and Philopotinae) and one extinct subfamily, Archocyrtinae. The evolution of important spider fly traits is discussed, including genitalia and wing venation. The status of the enigmatic Psilodera Gray and Pterodontia Gray as members of the Panopinae is confirmed based on both molecular and morphological data.     

The systematic position of Opistocystidae (Annelida,Clitellata) revealed by DNA data

Opistocystidae ?ernosvitov, 1936 is a largely Neotropical oligochaete taxon containing seven species. Its familial status has never been formally challenged, although possible close relationships with Naididae and Phreodrilidae have been noted. Mitochondrial 12S and 16S rDNA, and nuclear 18S rDNA, of a range of aquatic oligochaete taxa, including Trieminentia corderoi (Opistocystidae), were analysed by Bayesian inference. This showed that T. corderoi is a derived lineage within Naididae, closely related to Pristina and its monotypic subfamily Pristininae. Opistocystidae as a whole (with its three genera, Opistocysta, Trieminentia, and Crustipellis) is thus likely to be a group within Naididae.     

Phylogeny of the Braconinae (Hymenoptera: Braconidae): A new tribal order!

Generic relationships within the parasitoid wasp subfamily Braconinae are assessed based on a molecular phylogenetic analysis of four gene fragments: mitochondrial cytochrome c oxidase subunit I, 16S rDNA, nuclear 28S D2-D3 rDNA and elongation factor 1-alpha. Our results support the recognition of Aphrastobraconini, Braconini and Coeloidini plus three new tribes: Compsobraconini tribus nov ., Tropobraconini tribus nov . and Virgulibraconini tribus nov . The first of these new tribes is restricted to the New World; the second includes the Old World genera Tropobracon Cameron, Trispinaria Quicke and Grangerbracon Samartsev and Belokobylskij and possibly others, whereas the third comprises the Australian genus Virgulibracon Quicke, plus several other described and undescribed Australian genera. Consistent placement of Amyosoma Viereck with members of the Virgulibraconini tribus nov . is discussed, whereas Amyosoma is left currently unplaced. A preliminary key to tribes is presented, and the characters used to differentiate between Aphrastobraconini and Braconini are revised. Megacoeloides Quicke was never recovered with Coeloides, the type genus of Coeloidini, so it is treated as Braconinae incertae sedis. By combining molecular and morphological traits, nearly all valid genera are assigned to tribes, and the possible relationships of the remainder are discussed. Alienoclypeus Shenefelt, 1978 is synonymised with Atanycolus Förster, 1862 (Atanycolus insolitus (Shenefelt) comb. nov .). Several new genera have been revealed and will be described elsewhere.     

Global phylogeny and new classification of the Rapaninae (Gastropoda: Muricidae), dominant molluscan predators on tropical rocky seashores

The monophyly of the muricid subfamily Rapaninae has recently been confirmed with molecular techniques, but its composition and the relationships among its constituent genera remain unclear. We use four genes (28S rRNA, 12S rRNA, 16S rRNA and cytochrome c oxidase subunit I, COI) to construct a Bayesian phylogeny of 80 rapanine species (73% of the approximately 109 currently accepted), representing 27 of the 31 nominal genera. This is the most complete phylogeny of this taxonomically confusing subfamily yet produced. We propose a revised phylogenetic classification of the Rapaninae, assigning the recognized species to 28 genera. Most of the morphologically-defined rapanine genera are considered valid, including Purpura, Drupa, Thais and Nassa, but many of them are here restricted or redefined so that they are monophyletic. In particular the familiar genus Thais is narrowly restricted to a single species. Many groups previously accepted as subgenera, including Mancinella, Vasula, Thalessa and Thaisella, are here accorded full generic rank. We describe one new genus, Indothais. While we do not formally alter species-level taxonomy, we show molecular evidence for two cryptic species and several instances of probable species synonymy. We estimate the age of diversification of the Rapaninae as Late Cretaceous (75.9 Ma) and of many of its genera as Miocene.     

The tropical African legume Scorodophloeus clade includes two undescribed Hymenostegia segregate genera and Micklethwaitia,a rare,monospecific genus from Mozambique

Legume subfamily Caesalpinioideae accommodates approximately 2250 species in 171 genera which traditionally are placed in four tribes: Caesalpinieae, Cassieae, Cercideae and Detarieae. The monophyletic tribe Detarieae includes the Amherstieae subclade which contains about 55 genera. Our knowledge of the relationships among those genera is good in some cases but for many other genera phylogenetic relationships have been unclear. The non-monophyletic nature of at least two amherstioid genera, Cynometra and Hymenostegia has also complicated the picture. During the course of a multi-disciplinary study of Hymenostegia sensu lato, which includes phylogenetic analyses based on matK and trnL data, we have recovered the “Scorodophloeus clade”, an exclusively tropical African clade of four genera which includes the eponymous genus Scorodophloeus, two undescribed generic segregates of Hymenostegia sensu lato, and the previously unsampled rare monospecific genus Micklethwaitia from Mozambique. Zenkerella is suggested as a possible sister genus to the Scorodophloeus clade. A distribution map is presented of the seven species that belong to the Scorodophloeus clade.     

Molecular phylogeny of Allograpta (Diptera, Syrphidae) reveals diversity of lineages and non-monophyly of phytophagous taxa

Phylogenetic relationships of genera Allograpta, Sphaerophoria and Exallandra (Diptera, Syrphidae) were analyzed based on sequence data from the mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) and the nuclear 28S and 18S ribosomal RNA genes. The three genera are members of the subfamily Syrphinae, where nearly all members feed as larvae on soft-bodied Hemiptera and other arthropods. Phytophagous species have recently been discovered in two subgenera of Allograpta, sg Fazia and a new subgenus from Costa Rica. Phylogenetic analyses of the combined datasets were performed using parsimony, under static alignment and direct optimization, maximum likelihood and Bayesian inference. Congruent topologies obtained from all the analyses indicate paraphyly of the genus Allograpta with respect to Sphaerophoria and Exallandra. Exallandra appears embedded in the genus Sphaerophoria, and both genera are placed within Allograpta. The distribution of phytophagous taxa in Allograpta indicates that plant feeding evolved at least twice in this group.     

On the systematics of the fungus gnat subfamily Mycetophilinae (Diptera): a combined morphological and molecular approach

The phylogenetic relationships within the fungus gnat subfamily Mycetophilinae (Diptera) are addressed using a combined morphological and molecular approach. Twenty-four species, representing nine genera of the tribe Mycetophilini and 15 genera of the tribe Exechiini, were included in the study. Analyses include nucleotide sequences of mitochondrial (cytochrome oxidase I and 16S), and nuclear (18S and 28S rDNA) genes, in addition to 65 morphological characters. A combined parsimony analysis, including all characters, supports the monophyly of the subfamily Mycetophilinae and two of its tribes, Exechiini and Mycetophilini. There is also statistical support for a Mycetophila- group and a Phronia- group within the tribe Mycetophilini. The Phronia- group includes the genera Phronia , Macrobrachius and Trichonta . The Mycetophila- group includes the genera Mycetophila , Epicypta , Platurocypta , Sceptonia and Zygomyia . A Bayesian analysis based on the nucleotide sequences alone also support these clades within Mycetophilini except for the position of Dynatosoma which is recovered as the sister taxon to the Phronia- group. A somewhat different pattern, however, is observed for the tribe Exechiini – neither molecular data nor the combined data set support unambiguously any intergeneric relationships within Exechiini.     

Phylogenetic Classification at Generic Level in the Absence of Distinct Phylogenetic Patterns of Phenotypical Variation: A Case Study in Graphidaceae (Ascomycota)

Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed.     

Position of the genera <Emphasis Type="Italic">Lycenchelys</Emphasis> Gill and <Emphasis Type="Italic">Lycodapus</Emphasis> Gilbert in the family zoarcidae (Perciformes: Zoarcoidei) inferred from molecular genetic analysis

Sequence variation of the mitochondrial COI, cytochrome b, and 16S RNA genes, as well as nuclear RNF213 gene was examined in the genera Lycenchelys and Lycodapus with the purpose of determination of their positions in the system of the family Zoarcidae. It was demonstrated that the genus Lycodapus was considerably closer to the generic group of Lycogramminae (Lycogrammoides, Bothrocara, Allolepis, Bothrocarhichthys) than the genus Lycenchelys. However, on the phylogenetic trees both of these genera were located in the clade of the subfamily Lycodinae. Genetic heterogeneity of the genus Lycenchelys, represented by two species groups differing in distribution patterns (northeastern Pacific and Antarctic) and showing more profound differences than the genera of subfamily Lycodinae, was demonstrated.