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.     

The phylogenetic relationships of the suborder Acanthuroidei (Teleostei: Perciformes) based on molecular and morphological evidence

Fragments of 12S and 16S mitochondrial DNA genes were sequenced for 14 acanthuroid taxa (representing all six families) and seven outgroup taxa. The combined data set contained 1399 bp after removal of all ambiguously aligned positions. Examination of site saturation indicated that loop regions of both genes are saturated for transitions, which led to a weighted parsimony analysis of the data set. The resulting tree topology generally agreed with previous morphological hypotheses, most notably placing the Luvaridae within the Acanthuroidei, but it also differed in several areas. The putative sister group of Acanthuroidei, Drepane, was recovered within the suborder, and the sister group of the family Acanthuridae, Zanclus, was likewise recovered within the family. Morphological characters were included to produce a combined data set of 1585 characters for 14 acanthuroid taxa and a single outgroup taxon. An analysis of the same 15 taxa was performed with only the DNA data for comparison. The total-evidence analysis supports the monophyly of the Acanthuridae. A parametric bootstrap suggests the possibility that the paraphyly of Acanthuridae indicated by the molecular analyses is the result of long-branch attraction. The disagreement between molecular and morphological data on the relationships of the basal acanthuroids and its putative sister taxon is unresolved.     

Phylogenetic relationships among superfamilies of Hymenoptera

The first comprehensive analysis of higher‐level phylogeny of the order Hymenoptera is presented. The analysis includes representatives of all extant superfamilies, scored for 392 morphological characters, and sequence data for four loci (18S, 28S, COI and EF‐1α). Including three outgroup taxa, 111 terminals were analyzed. Relationships within symphytans (sawflies) and Apocrita are mostly resolved. Well supported relationships include: Xyeloidea is monophyletic, Cephoidea is the sister group of Siricoidea + [Xiphydrioidea + (Orussoidea + Apocrita)]; Anaxyelidae is included in the Siricoidea, and together they are the sister group of Xiphydrioidea + (Orussoidea + Apocrita); Orussoidea is the sister group of Apocrita, Apocrita is monophyletic; Evanioidea is monophyletic; Aculeata is the sister group of Evanioidea; Proctotrupomorpha is monophyletic; Ichneumonoidea is the sister group of Proctotrupomorpha; Platygastroidea is sister group to Cynipoidea, and together they are sister group to the remaining Proctotrupomorpha; Proctotrupoidea s. str. is monophyletic; Mymarommatoidea is the sister group of Chalcidoidea; Mymarommatoidea + Chalcidoidea + Diaprioidea is monophyletic. Weakly supported relationships include: Stephanoidea is the sister group of the remaining Apocrita; Diaprioidea is monophyletic; Ceraphronoidea is the sister group of Megalyroidea, which together form the sister group of [Trigonaloidea (Aculeata + Evanioidea)]. Aside from paraphyly of Vespoidea within Aculeata, all currently recognized superfamilies are supported as monophyletic. The diapriid subfamily Ismarinae is raised to family status, Ismaridae stat. nov. © The Will Henning Society 2011.     

Intraspecific phylogenetic relationships in Ixeridium dentatum (Compositae) complex based on genetic and morphological evidence

Ixeridium dentatum (I. dentatum; family Compositae) forms a complex species through intraspecific differentiation. In this study, intraspecific taxa of I. dentatum were analyzed by counting chromosome numbers, sequencing internal transcribed spacer (ITS), and detecting amplified fragment length polymorphisms (AFLP) to explore phylogenetic relationships within I. dentatum. Analysis of ploidy levels showed that I. dentatum subsp. kitayamense and subsp. nipponicum were diploid (2n = 2x = 14), I. dentatum subsp. kimuranum was tetraploid (2n = 4x = 28), and other intraspecific taxa of I. dentatum were triploid (2n = 3x = 21). The ITS sequences contained only 13 variable sites (2.7 %) among intraspecific taxa, suggesting that the I. dentatum complex originated by autoploidy. Our AFLP-based analysis separated these taxa into five groups: (1) I. dentatum subsp. kimuranum and subsp. kitayamense; (2) subsp. nipponicum and var. albiflorum; (3) two types of subsp. dentatum and f. atropurpureum; (4) f. amplifolium; (5) subsp. ozense and new taxa, which were discovered in this study. The identified clusters significantly differed from morphological classifications. For example, morphologically similar variety and forms of I. dentatum subsp. nipponicum were separated into different groups. Taken together with the ploidy data, this study proposes a possible evolutionary history generating the current taxonomic combinations of the I. dentatum complex. The proposed model suggests that diverse taxa recently emerged during migration to lowlands.     

The phylogenetic relationships of the physaloid genera (Solanaceae) based on morphological data

A group of genera, e.g., Chamaesaracha, Leucophysalis, Physaliastrum, Margaranthus, and Withania, in the subfamily Solanoideae (Solanaceae) is centered around the genus Physalis and has been named the physaloid group. It comprises a number of small and often poorly known genera, sometimes seen as united with Physalis and/or each other. A hypothesis of the phylogenetic relationships within this group, based on parsimony analyses of morphological data, is here presented for the first time. The result is discussed in relation to prevailing generic circumsciptions and taxonomic consequences. It is also compared with hypotheses of relationships based on cpDNA data.     

A phylogenetic analysis of Coelopidae (Diptera) based on morphological and DNA sequence data

The phylogenetic relationships of 22 species of Coelopidae are reconstructed based on a data matrix consisting of morphological and DNA sequence characters (16S rDNA, EF-1alpha). Optimal gap and transversion costs are determined via a sensitivity analysis and both equal weighting and a transversion cost of 2 are found to perform best based on taxonomic congruence, character incongruence, and tree support. The preferred phylogenetic hypothesis is fully resolved and well-supported by jackknife, bootstrap, and Bremer support values, but it is in conflict with the cladogram based on morphological characters alone. Most notably, the Coelopidae and the genus Coelopa are not monophyletic. However, partitioned Bremer Support and an analysis of node stability under different gap and transversion costs reveal that the critical clades rendering these taxa non-monophyletic are poorly supported. Furthermore, the monophyly of Coelopidae and Coelopa is not rejected in analyses using 16S rDNA that was manually aligned. The resolution of the tree based on this reduced data sets is, however, lower than for the tree based on the full data sets. Partitioned Bremer support values reveal that 16S rDNA characters provide the largest amount of tree support, but the support values are heavily dependent on analysis conditions. Problems with direct comparison of branch support values for trees derived using fixed alignments with those obtained under optimization alignment are discussed. Biogeographic history and available behavioral and genetic data are also discussed in light of this first cladogram for Coelopidae based on a quantitative phylogenetic analysis.     

Phylogenetic relationships of Microdontinae (Diptera: Syrphidae) based on molecular and morphological characters

The intrasubfamilial classification of Microdontinae Rondani (Diptera: Syrphidae) has been a challenge: until recently more than 300 out of more than 400 valid species names were classified in Microdon Meigen. We present phylogenetic analyses of molecular and morphological characters (both separate and combined) of Microdontinae. The morphological dataset contains 174 characters, scored for 189 taxa (9 outgroup), representing all 43 presently recognized genera and several subgenera and species groups. The molecular dataset, representing 90 ingroup species of 28 genera, comprises sequences of five partitions in total from the mitochondrial gene COI and the nuclear ribosomal genes 18S and 28S. We test the sister‐group relationship of Spheginobaccha with the other Microdontinae, attempt to elucidate phylogenetic relationships within the Microdontinae and discuss uncertainties in the classification of Microdontinae. Trees based on molecular characters alone are poorly resolved, but combined data are better resolved. Support for many deeper nodes is low, and placement of such nodes differs between parsimony and Bayesian analyses. However, Spheginobaccha is recovered as highly supported sister group in both. Both analyses agree on the early branching of Mixogaster, Schizoceratomyia, Afromicrodon and Paramicrodon. The taxonomical rank in relation to the other Syrphidae is discussed briefly. An additional analysis based on morphological characters only, including all 189 taxa, used implied weighting. A range of weighting strengths (k‐values) is applied, chosen such that values of character fit of the resulting trees are divided into regular intervals. Results of this analysis are used for discussing the phylogenetic relationships of genera unrepresented in the molecular dataset.     

Molecular evidence for phylogenetic relationships among buntings and American sparrows (Emberizidae)

To help clarify controversial phylogenetic relationships within the family Emberizidae, we sequenced 1238 bp of mitochondrial DNA from the cytochrome b gene and a flanking portion of ND5. Although the longspurs ( Calcarius ) and the snow buntings ( Plectrophenax ) have been grouped with the Old World buntings ( Emberiza ) in traditional classifications, our molecular phylogenies constructed with maximum likelihood and maximum parsimony place these genera basal to a clade in which the Old World buntings and North American sparrows are sister groups. Contrary to the hypothesis that the radiation within Emberiza is recent following a westward expansion of emberizid stock into Eurasia from North America, we found that the level of genetic divergence among Old World buntings approximates those among different genera in North American sparrows. Thus the radiation of the Emberizidae seems to have occurred at roughly the same time in the Palaearctic and Nearctic. Our results are consistent with earlier analyses of allozymes, but sequences from multiple genes and new morphological analyses are required to fully resolve phylogenetic relationships within the Emberizidae.     

Two undescribed species of Phylloporia from Mexico based on morphological and phylogenetic evidence

Phylloporia rzedowskii and Phylloporia ulloai, both collected in tropical forests of the Sierra of the Huasteca Potosina, San Luis Potosi, Mexico, are described as new species. The main critical morphological features that characterize them are the pileus shape, the pore diameter, the basidiospores shape and size, and, possibly, their ecology, such as the host relationships (specificity/preference). Both species also form distinct clades in phylogenetic analysis based on partial DNA sequences data from the nuclear ribosomal LSU. An identification key for 10 species reported from the Americas is proposed.     

Molecular dating and phylogenetic relationships among Teiidae (Squamata) inferred by molecular and morphological data

We present a phylogenetic analysis of teiid lizards based on partitioned and combined analyses of 12S and 16S mitochondrial DNA sequences, and morphological and ultrastructural characters. There were some divergences between 12S and 16S cladograms, but phylogenetic analyses of the combined molecular data corroborated the monophyly of Tupinambinae, Teiinae, and "cnemidophorines", with high support values. The total combined analysis (molecules+morphology) produced similar results, with well-supported Teiinae and "cnemidophorines". We present an evolutionary scenario for the evolution of Teiidae, based on molecular dating of evolutionary events using Bayesian methods, ancestral areas analysis, the fossil record, the geographic distribution of genera, and environmental and geologic changes during the Tertiary. According to this scenario, (1) all current teiid genera, except Aspidoscelis, originated in isolation in South America; (2) most teiid genera originated during the Eocene, a period characterized by savanna expansion in South America; and (3) Cnemidophorus originated in South America, after which some populations dispersed to Central America during the Late Miocene.     

Determination of phylogenetic position ofPipizini (Diptera: Syrphidae): based on molecular biological and morphological data

Based on the sequence analysis of 5.8S subunit and internal transcribed spacers (ITS) of ribosomal RNA gene (rDNA), the molecular phylogenetic tree of representative species of Pipizini and three groups of Syrphidae with different feeding habits (seven species belong to six genera) was constructed. Meanwhile, the phylogenetic tree of tribes (including Pipizini and other 17 tribes of Syrphidae) was constructed using morphological characteristics of adults and larvae and the number of chromosomes. Both the results show that the relationship between Pipizini and predatory groups is closer than that between Pipizini and saprophagous groups. So it is suggested that Pipizini be transferred from Milesiinae to Syrphinae.     

A morphological analysis of marsupial mammal higher-level phylogenetic relationships

Phylogenetic relationships among marsupial taxa have proven to be more complex than the simple grouping of species by continent. Recent marsupials are distributed across the New World, Australia, New Guinea, and certain neighboring islands. Morphological characteristics of various groups bridge different geographical areas. We investigated the origin of these characteristics by assembling a morphological data matrix consisting of a new suite of 149 postcranial characters and incorporated a series of previously published data on the craniodental (76 characters) and soft tissue (5 characters) anatomy. Twenty‐one marsupial terminal taxa representing all the major radiations of marsupials and 10 outgroups, most of which are exceptionally well‐preserved fossils such as Vincelestes, Ukhaatherium, and a few basal metatherian taxa, were investigated. A maximum parsimony analysis was conducted, resulting in one most parsimonious tree. Relationships among outgroups are congruent with current understanding of mammalian phylogeny. All currently accepted marsupial orders were recovered by the analysis. We confirmed previous results showing the South American “monito del monte”Dromiciops nested within the Australasian radiation. Within this australidelphian clade, Dromiciops was closely allied with the Diprotodontia. The South American paucituberculates appeared more closely related to the Australidelphia than to the American Didelphimorphia. The marsupial mole Notoryctes and the Peramelia were closely allied to each other and in turn were the sister group of the Dromiciops plus Diprotodontia clade. This pattern of relationships left Dasyuromorphia as the most basal offshoot of the Australidelphia. Whereas this tree topology recovers some signal that had been detected by previous studies, morphological and/or molecular, some novel hypotheses are also supported.     

Utility of the white gene in estimating phylogenetic relationships among mosquitoes (Diptera: Culicidae)

The utility of a nuclear protein-coding gene for reconstructing phylogenetic relationships within the family Culicidae was explored. Relationships among 13 species representing three subfamilies and nine genera of Culicidae were analyzed using a 762-bp fragment of coding sequence from the eye color gene, white. Outgroups for the study were two species from the sister group Chaoboridae. Sequences were determined from clone PCR products amplified from genomic DNA, and aligned following conceptual intron splicing and amino acid translation. Third codon positions were characterized by high levels of divergence and biased nucleotide composition, the intensity and direction of which varied among taxa. Equal weighting of all characters resulted in parsimony and neighboring-joining trees at odds with the generally accepted phylogenetic hypothesis based on morphology and rDNA sequences. The application of differential weighting schemes recovered the traditional hypothesis, in which the subfamily Anophelinae formed the basal clade. The subfamily Toxorhynchitinae occupied an intermediate position, and was a sister group to the subfamily Culicinae. Within Culicinae, the genera Sabethes and Tripteroides formed an ancestral clade, while the Culex-Deinocerites and Aedes- Haemagogus clades occupied increasingly derived positions in the molecular phylogeny. An intron present in the Culicinae- Toxorhynchitinae lineage and one outgroup taxon was absent in the basal Anophelinae lineage and the second outgroup taxon, suggesting that intron insertions or deletions may not always be reliable systematic characters.      

Exoribonuclease superfamilies: structural analysis and phylogenetic distribution

Exoribonucleases play an important role in all aspects of RNA metabolism. Biochemical and genetic analyses in recent years have identified many new RNases and it is now clear that a single cell can contain multiple enzymes of this class. Here, we analyze the structure and phylogenetic distribution of the known exoribonucleases. Based on extensive sequence analysis and on their catalytic properties, all of the exoribonucleases and their homologs have been grouped into six superfamilies and various subfamilies. We identify common motifs that can be used to characterize newly-discovered exoribonucleases, and based on these motifs we correct some previously misassigned proteins. This analysis may serve as a useful first step for developing a nomenclature for this group of enzymes.     

A phylogenetic hypothesis for Asilidae based on a total evidence analysis of morphological and DNA sequence data (Insecta: Diptera: Brachycera: Asiloidea)

An hypothesis of phylogenetic relationships of Asilidae and its constituent taxa is presented, combining morphological and DNA sequence data in a total evidence framework. It is based on 77 robber fly species, 11 Asiloidea outgroup species, 211 morphological characters of the adult fly, and approximately 7300 bp of nuclear DNA from five genes (18S and 28S rDNA, AATS, CAD, and EF-1α protein-encoding DNA). The equally weighted, simultaneous parsimony analysis under dynamic homology in POY resulted in a single most parsimonious cladogram with a cost of 27,582 (iterative pass optimization; 27,703 under regular direct optimization). Six of the 12 included subfamily taxa are recovered as monophyletic. Trigonomiminae, previously always considered as monophyletic based on morphology, is shown to be non-monophyletic. Two of the three Trigonomiminae genera, Holcocephala Jaennicke, 1867 and Rhipidocephala Hermann, 1926, group unexpectedly as the sister taxon to all other Asilidae. Laphriinae, previously seen in the latter position, is the sister group of the remaining Asilidae. Five other subfamily taxa, i.e. Brachyrhopalinae, Dasypogoninae, Stenopogoninae, Tillobromatinae, and Willistonininae, are also shown to be non-monophyletic. The phylogenetic relationships among the higher-level taxa are partly at odds with findings of a recently published morphological study based on more extensive taxon sampling. The total evidence hypothesis is considered as the most informative one, but the respective topologies from the total-evidence, morphology-only, and molecular-only analyses are compared and contrasted in order to discuss the signals from morphological versus molecular data, and to analyze whether the molecular data outcompete the fewer morphological characters. A clade Apioceridae+Mydidae is corroborated as the sister taxon to Asilidae.     

Determination of phylogenetic position of Pipizini (Diptera: Syrphidae): based on molecular biological and morphological data

Based on the sequence analysis of 5.8S subunit and internal transcribed spacers (ITS ) of ribosomal RNA gene (rDNA), the molecular phylogenetic tree of representative species of Pipizini and three groups of Syrphidae with different feeding habits (seven species belong to six genera) was constructed. Meanwhile, the phylogenetic tree of tribes (including Pipizini and other 17 tribes of Syrphidae) was constructed using morphological characteristics of adults and larvae and the number of chromosomes. Both the results show that the relationship between Pipizini and predatory groups is closer than that between Pipizini and saprophagous groups. So it is suggested that Pipizini be transferred from Milesiinae to Syrphinae.     

Determination of phylogenetic position of Pipizini (Diptera: Syrphidae): based on molecular biological and morphological data

Based on the sequence analysis of 5.8S subunit and internal transcribed spacers (ITS ) of ribosomal RNA gene (rDNA), the molecular phylogenetic tree of representative species of Pipizini and three groups of Syrphidae with different feeding habits (seven species belong to six genera) was constructed. Meanwhile, the phylogenetic tree of tribes (including Pipizini and other 17 tribes of Syrphidae) was constructed using morphological characteristics of adults and larvae and the number of chromosomes. Both the results show that the relationship between Pipizini and predatory groups is closer than that between Pipizini and saprophagous groups. So it is suggested that Pipizini be transferred from Milesiinae to Syrphinae.     

The first phylogenetic study of Mesembrinellidae (Diptera: Oestroidea) based on molecular data: clades and congruence with morphological characters

The Mesembrinellidae (Diptera: Oestroidea) comprise a small group of strictly Neotropical calyptrate flies, with 36 described species. The group has often been treated as a subfamily of Calliphoridae, but there is growing evidence that it corresponds to a distinct Oestroidea lineage. Internal relationships have so far been addressed based only on morphology, with results lacking resolution and support. This is the first molecular phylogeny for the group, which is based on the analyses of 80 terminal taxa (22 mesembrinellid and 28 outgroup species) and 5 molecular markers (ITS2, 28S, COI, COII and 16S). Maximum‐parsimony, maximum‐likelihood and Bayesian inference methods were used, the latter two with partitioning strategies considering codon position and secondary structure information. Results corroborate the Mesembrinellidae as a monophyletic lineage inside Oestroidea. Three clades were consistently recovered: (1) (Laneella + Mesembrinella patriciae); (2) (Mesembrinella (excluding M. patriciae)  + Eumesembrinella); and (3) (Huascaromusca + Giovanella). Re‐examination of the female reproductive tract of M. patriciae revealed a Laneela‐type spermatheca, which corroborates the position of the species recovered in the molecular phylogenetic analyses. Mesembrinella and Huascaromusca are in all cases paraphyletic with regards to Eumesembrinella and Giovanella, respectively. These latter two genera should, thus, be seen as subjective junior synonyms.     

Identification and genetic relationships among nine Albizzia species based on morphological and molecular markers

Abstract

Identifying germplasm is an important component for efficient and effective management of plant genetic resources. This investigation was undertaken for the identification and analysis of genetic variation within 9 species of Albizzia through 33 morphological parameters, and 15 Random Amplified Polymorphic DNA (RAPD) and 17 Inter Simple Sequence Repeat (ISSR) primers. The use of selected RAPD and ISSR primers generated a total of 163 and 201 amplified DNA fragments, respectively. High frequencies of polymorphism, 95.05% for RAPD and 96.02% for ISSR, were detected. Statistical approaches were employed to construct genetic relationships by RAPD, ISSR and morphological analysis. Cluster analysis by the unweighted pair-group method (UPGMA) of Nei's similarity generated dendograms with similar topology that gave a better reflection of the diversity and affinities between species. These molecular results were comparable to main morphological characteristics. The correlation matrices generated by RAPD and ISSR markers were highly correlated (r = 0.843 at p = 1.0), thereby indicating congruence between these two marker systems. Both morphometric data and molecular markers have the potential to analyse genetic variation among the nine species of Albizzia, thus providing a major input for management strategy of plant genetic resources.