Phylogeny in Echinocereus (Cactaceae) based on combined morphological and molecular evidence: taxonomic implications

Echinocereus is a morphologically diverse genus that includes 64 species grouped into eight taxonomic sections based on morphological traits. In previous molecular phylogenetic analyses, the relationships amongst Echinocereus species were not entirely revealed and useful characters to recognize clades were not provided. The inclusion of several sources of evidence in a phylogenetic analysis is likely to produce more supported hypotheses. Therefore, we performed a combined phylogenetic analysis with a set of 44 morphological characters and six chloroplast DNA sequences. Topologies from parsimony and Bayesian analyses were mostly congruent. However, the relationships of E. poselgeri were not consistent between analyses. A second Bayesian analysis using a long-branch extraction test resulted in a topology with the morphological position of E. poselgeri congruent with that in parsimony analysis. Parsimony and Bayesian analyses corroborated the monophyly of Echinocereus, which included eight monophyletic groups. The combined phylogeny integrated into different clades those taxa that were not determined in previous analyses and changed the relationships of some recognized clades. The clades did not recover the recent infrageneric classification. In the present study, a new sectional classification for Echinocereus is proposed based on the eight recovered clades, which is supported by a combination of morphological and molecular characters. An identification key for sections in the genus is included.     

Phylogeny and reclassification of the Caucasigenini radiation from the Caucasus region (Gastropoda,Hygromiidae)

The Caucasigenini is an endemic radiation of hygromiid land snails from the Caucasus region. A phylogenetic analysis of morphological characters of the genitalia and the shell showed that the morphological characters are insufficient for resolving the relationships within the Caucasigenini. Convergences of the few parsimony informative characters in other groups of the Hygromiidae demonstrate that these characters are not reliable indicators of phylogenetic relationships. Phylogenetic analyses of sequences of cox1, 16S rDNA, 5.8S rDNA, ITS2 and 28S rDNA revealed several well‐supported groups. The relationships among these groups could not be resolved. It is likely that these groups originated in a rapid radiation during the uplift of the Caucasus. Based on the molecular phylogeny, we propose a new classification of the species of the Caucasigenini and establish a new genus, Lazicana gen. n.     

Phylogenetic and systematic study of Korean <Emphasis Type="Italic">Orius</Emphasis> species (Heteroptera: Anthocoridae) on the basis of molecular and morphological data

A phylogenetic and systematic study of Orius species (Heteroptera: Anthocoridae) from Korea has been conducted using both morphological and molecular characters. Thirty morphological character states were coded for 10 strains of 9 species. Five molecular markers, partial cytochrome c oxidase I (COI), cytochrome b (CytB), 16S rRNA (16S), 18S rRNA (18S), and 28S rRNA (28S), from mitochondrial and nuclear genes, were tested. Phylogenetic analyses based on molecular data were conducted by minimum evolution, maximum parsimony, maximum likelihood, and Bayesian phylogenetic (BP) analyses. Analysis of morphological data was performed using the parsimony programs NONA, and the combined dataset of morphological and molecular data was analyzed using BP analyses. The results of this study indicate that use of COI and CytB enabled relatively effective identification of species, whereas the sequences of 16S, 18S and 28S did not enable identification of closely related species such as Orius minutus and O. strigicollis. We discuss the usefulness of the five molecular markers for determining phylogenetic relationships and identifying the species.     

Exploring myrmecophily based on the phylogenetic interrelationships of Falagonia Sharp, 1883 (Coleoptera: Staphylinidae: Aleocharinae) and allied genera

The taxonomy of Lomechusini Fleming has a complex history. Recent studies have shown that this group is polyphyletic; however, little is known about the evolutionary interrelationships among its constituent genera. The goals of the present study are to infer the phylogenetic relationships of Falagonia Sharp and closely related genera; to define the boundaries of those genera based on synapomorphic characters; and to explore the evolution of myrmecophily within the lineage. The phylogenetic analyses are based exclusively on morphological characters of adults. A total of 36 operational taxonomic units were used for the analysis. The best trees were selected based on maximum parsimony and Bayesian inference. During the parsimony reconstruction, different weighting strategies were used to recover the most robust phylogenetic hypothesis. Although minor differences were observed in the results of the different analyses, the topologies were consistent throughout. Several groups of genera proposed by Seevers (1965), such as the ‘Tetradonia’ and ‘Ecitopora’ groups, were not recovered. Thus, these may represent nonmonophyletic groups that were based on nonsynapomorphic diagnostic characters. Our analyses consistently recovered the genera Asheidium Santiago‐Jiménez, Delgadoidium Santiago‐Jiménez, Falagonia, Newtonidium Santiago‐Jiménez, Pseudofalagonia Santiago‐Jiménez, Sharpidium Santiago‐Jiménez, Tetradonia Wasmann and Thayeridium Santiago‐Jiménez, forming a monophyletic group that we have called the ‘Asheidium complex’. Falagonia mexicana Sharp shows seven autapomorphies, none of which were used to establish the genus. Based on the phylogenetic results, myrmecophily has evolved independently at least three times within the lineage. This study, based on morphological characters, is one of the first approaches towards gaining an understanding of the phylogenetic relationships within the polyphyletic tribe Lomechusini.     

Monophyly and phylogenetic relationships of the catfish genus Glyptothorax (Teleostei: Sisoridae) inferred from nuclear and mitochondrial gene sequences

GlyptothoraxBlyth (1860) is the most species-diverse and widely-distributed genus in the Sisoridae, but few studies have examined monophyly of the genus and phylogenetic relations within it. We used the nuclear RAG2 gene and mitochondrial COI and Cyt b genes from 50 of the approximately 70 species to examine monophyly of Glyptothorax and phylogenetic relationships within the genus. Molecular phylogenetic trees were constructed using maximum parsimony, maximum likelihood and Bayesian inference methods. All methods strongly supported monophyly of Glyptothorax, with Bagarius as its sister group. Both analyses of two- and three-gene datasets recovered nine major subclades of Glyptothorax, but some internal nodes remained poorly resolved. The phylogenetic relationships within the genus and existing taxonomic problems are discussed.     

Phylogeny of Impatiens (Balsaminaceae): integrating molecular and morphological evidence into a new classification

Impatiens L. is one of the largest angiosperm genera, containing over 1000 species, and is notorious for its taxonomic difficulty. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total evidence approach. Forty‐six morphological characters, mainly obtained from our own investigations, are combined with sequence data from three genetic regions, including nuclear ribosomal ITS and plastid atpB‐rbcL and trnL‐F. We include 150 Impatiens species representing all clades recovered by previous phylogenetic analyses as well as three outgroups. Maximum‐parsimony and Bayesian inference methods were used to infer phylogenetic relationships. Our analyses concur with previous studies, but in most cases provide stronger support. Impatiens splits into two major clades. For the first time, we report that species with three‐colpate pollen and four carpels form a monophyletic group (clade I). Within clade II, seven well‐supported subclades are recognized. Within this phylogenetic framework, character evolution is reconstructed, and diagnostic morphological characters for different clades and subclades are identified and discussed. Based on both morphological and molecular evidence, a new classification outline is presented, in which Impatiens is divided into two subgenera, subgen. Clavicarpa and subgen. Impatiens; the latter is further subdivided into seven sections.     

Phylogenetic relationships of the genus Cheilosia and the tribe Rhingiini (Diptera, Syrphidae) based on morphological and molecular characters

The phylogenetic relationships of the tribe Rhingiini and the genus Cheilosia (Diptera, Syrphidae) were investigated using morphological and molecular characters. The genus Cheilosia is one of the most diverse lineages of hoverflies (Syrphidae). The mitochondrial protein coding gene cytochrome c oxidase subunit I (COI), and the D2‐3 region of the nuclear 28S rRNA gene were chosen for sequencing, and morphological characters were scored for both adults and immature stages. The combined dataset included 56 ingroup taxa. The datasets were analyzed separately and in conjunction, using both static and dynamic alignment under the parsimony criterion. The aim of the study was to assess the phylogenetic relationships of the tribe Rhingiini, and to explore if the subgenera of Cheilosia were supported as monophyletic clades. Results showed that the monophyly of subtribes of Rhingiini remained ambiguous, especially due to unstable phylogenetic placements of the genera Portevinia and Rhingia. We recovered most subgenera of Cheilosia as monophyletic clades. Dynamic alignment, using the optimization alignment program POY, always recovered more parsimonious topologies under all parameter weighting schemes, than did parsimony analyses using static alignment and analyzed with NONA.     

Phylogeny of the plant bug subfamily Mirinae (Hemiptera: Heteroptera: Cimicomorpha: Miridae) based on total evidence analysis

The first comprehensive phylogenetic analyses of the most diverse subfamily of plant bugs, Mirinae, is presented in this study, for 110 representative taxa based on total evidence analysis. A total of 85 morphological characters and 3898 bp of mitochondrial (16S, COI) and nuclear (18S, 28S) sequences were analysed for each partitioned and combined dataset based on parsimony, maximum likelihood and Bayesian inference. Major results obtained in this study include monophyly of the tribe Mecistoscelini. The largest tribe, Mirini, was recovered as polyphyletic, and Stenodemini was recovered as paraphyletic. The clade of Stenodemini + Mecistoscelini is the sister group of the remaining Mirinae. The monophyly of two complexes composed of superficially similar genera were tested; the Lygus complex was recovered as nonmonophyletic, and the Adelphocoris–Creontiades–Megacoelum complex was confirmed to be monophyletic. The generic relationships of the main clades within each tribe based on the phylogeny, as well as their supported morphological characters, are discussed.     

A phylogeny of Vetigastropoda and other “archaeogastropods”: re-organizing old gastropod clades

Abstract. The phylogenetic relationships among the “archaeogastropod” clades Patellogastropoda, Vetigastropoda, Neritimorpha, and Neomphalina are uncertain; the phylogenetic placement of these clades varies across different analyses, and particularly among those using morphological characteristics and those relying on molecular data. This study explores the relationships among these groups using a combined analysis with seven molecular loci (18S rRNA, 28S rRNA, histone H3, 16S rRNA, cytochrome c oxidase subunit I [COI], myosin heavy-chain type II, and elongation factor-1α [EF-1α]) sequenced for 31 ingroup taxa and eight outgroup taxa. The deep evolutionary splits among these groups have made resolution of stable relationships difficult, and so EF-1α and myosin are used in an attempt to re-examine these ancient radiation events. Three phylogenetic analyses were performed utilizing all seven genes: a single-step direct optimization analysis using parsimony, and two-step approaches using parsimony and maximum likelihood. A single-step direct optimization parsimony analysis was also performed using only five molecular loci (18S rRNA, 28S rRNA, histone H3, 16S rRNA, and COI) in order to determine the utility of EF-1α and myosin in resolving deep relationships. In the likelihood and POY optimal phylogenetic analyses, Gastropoda, Caenogastropoda, Neritimorpha, Neomphalina, and Patellogastropoda were monophyletic. Additionally, Neomphalina and Pleurotomariidae fell outside the remaining vetigastropods, indicating the need for further investigation into the relationship of these groups with other gastropods.     

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

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

New insights into polychaete phylogeny (Annelida) inferred from 18S rDNA sequences

Annelid systematics and the ingroup relationships of polychaete annelids are matter of ongoing debates in recent analyses. For the investigation of sedentary polychaete relationships a molecular phylogenetic analysis was conducted based on 94 sequences of 18S rDNA, including unpublished sequences of 13 polychaete species. The data set was analyzed with maximum parsimony and maximum likelihood methods, as wells as Bayesian inference. As in previous molecular analyses the monophyly of many traditional polychaete families is confirmed. No evidence has been found for a possible monophyly of Canalipalpata or Scolecida. In all analyses a placement of the Echiura as a derived polychaete ingroup with a close relationship to the Capitellidae is confirmed. The orbiniids appear paraphyletic with regard to Questa. Travisia is transferred from Opheliidae to Scalibregmatidae. The remaining opheliids include a yet undescribed ctenodrilid species from Elba, whereas the other investigated ctenodrilid Ctenodrilus serratus groups with the Cirratulidae and shows a close affinity to the cirratulid genus Dodecaceria. A common ancestry of Branchiomaldane and Arenicola, which has been predicted on morphological data, is confirmed by the analysis and a sistergroup relationship between Arenicolidae and Maldanidae is also recovered. These results support our assumption that on the basis of a broader taxon sampling the phylogenetic position of controversially discussed taxa can be inferred by using 18S rDNA sequence data.     

<Emphasis Type="Italic">Micronematobotrys</Emphasis>, a new genus and its phylogenetic placement based on rDNA sequence analyses

A new hyphomycetous fungus, Micronematobotrys verrucosus, isolated as an endophyte from Quercus liaotungensis and Ulmus macrocarpa in the Dongling Mountain of Beijing is described as a new monotypic genus represented by M. verrucosus. This new species differs morphologically from Botrytis-like fungi and other similar genera in possessing micronematous conidiophores and colored verrucose conidia. The phylogenetic relationships of Micronematobotrys among sexual ascomycetes are examined based on 18S and 28S rDNA sequence data using maximum parsimony and Bayesian methods. The phylogenetic analyses suggest that M. verrucosus is a member of Pyronemataceae in Pezizales.     

The past and the present through phylogenetic analysis: the rove beetle tribe Othiini now and 99 Ma

In order to classify and taxonomically describe the first two fossil Othiini (Coleoptera: Staphylinidae: Staphylininae) species from three well‐preserved specimens in Cretaceous Burmese amber, a phylogenetic analysis was conducted, combining extant and extinct taxa. A dataset of 76 morphological characters scored for 33 recent species across the subfamilies Staphylininae and Paederinae was analysed using maximum parsimony and Bayesian inference methods. The many differing phylogenetic hypotheses for higher‐level relationships in the large rove beetle subfamilies Staphylininae and Paederinae were summarized and their hitherto known fossil record was reviewed. Based on the analyses, the new extinct genus Vetatrecus gen.n. is described with two new species: V. adelfiae sp.n. and V. secretum sp.n. Both species share character states that easily distinguish them from all recent Othiini and demonstrate a missing morphological link between subfamilies Staphylininae and Paederinae. This is the first morphology‐based evidence for the paraphyly of Staphylininae with respect to Paederinae, suggested earlier by two independent molecular‐based phylogenies of recent taxa. Our newly discovered stem lineage of Othiini stresses the importance of fossils in phylogenetic analyses conducted with the aim of improving the natural classification of extant species. It also suggests that the definitions of Staphylininae and Paederinae, long‐established family‐group taxa, may have to be reconsidered. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:817F39C4-F36B-4FD9-96CD-5F8FB064C39E .     

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.     

A phylogenetic analysis of Myriapoda (Arthropoda) using two nuclear protein-encoding genes

Nucleotide and inferred amino acid sequences from two nuclear protein-encoding genes, elongation factor-aα and RNA polymerase II, were obtained from 34 myriapods and 14 other arthropods to determine phylogenetic relationships among and within the myriapod classes. Phylogenetic analyses using maximum parsimony and maximum likelihood methods recovered all three represented myriapod classes (Chilopoda, Diplopoda, Symphyla) and all multiply sampled chilopod and diplopod orders, often with high node support. In contrast, relationships between classes and between orders were recovered less consistently and node support was typically lower. The temporal structure of phylogenetic diversification in Myriapoda may explain this apparent pattern of the phylogenetic recovery.     

Molecular phylogenetics of cixiid planthoppers (Hemiptera: Fulgoromorpha): new insights from combined analyses of mitochondrial and nuclear genes

The planthopper family Cixiidae (Hemiptera: Fulgoromorpha) comprises approximately 160 genera and 2000 species divided in three subfamilies: Borystheninae, Bothriocerinae and Cixiinae, the later with 16 tribes. The current paper represents the first attempt to estimate phylogenetic relationships within Cixiidae based on molecular data. We use a total of 3652 bp sequence alignment of four genes: the mitochondrial coding genes Cytochrome c Oxidase subunit 1 (Cox1) and Cytochrome b (Cytb), a portion of the nuclear 18S rDNA and two non-contiguous portions of the nuclear 28S rDNA. The phylogenetic relationships of 72 terminal specimens were reconstructed using both maximum parsimony and Bayesian inference methods. Through the analysis of this empirical dataset, we also provide comparisons among different a priori partitioning strategies and the use of mixture models in a Bayesian framework. Our comparisons suggest that mixture models overcome the benefits obtained by partitioning the data according to codon position and gene identity, as they provide better accuracy in phylogenetic reconstructions. The recovered maximum parsimony and Bayesian inference phylogenies suggest that the family Cixiidae is paraphyletic in respect with Delphacidae. The paraphyly of the subfamily Cixiinae is also recovered by both approaches. In contrast to a morphological phylogeny recently proposed for cixiids, subfamilies Borystheninae and Bothriocerinae form a monophyletic group.     

Phylogenetic significance of morphological characters in the taxonomy of Pestalotiopsis species

There has been considerable disagreement regarding the relationships among Pestalotiopsis species and their delimitations. A molecular phylogenetic analysis was conducted on 32 species of Pestalotiopsis in order to evaluate the utility of morphological characters currently used in their taxonomy. Phylogenetic relationships were inferred from nucleotide sequences in the ITS regions and 5.8S gene of the rDNA under four optimality criteria: maximum parsimony, weighted parsimony, maximum likelihood, and neighbor joining. Phylogenies estimated from all analyses yielded trees of essentially similar topology and revealed 3 major groups that correspond with morphology-based classification systems. Molecular data indicated that the genus contains two distinct lineages based on pigmentation of median cells and four distinct groupings based on morphology of apical appendages. The analyses did not support reliability of other phenotypic characters of this genus, such as spore dimensions. Characters with particular phylogenetic significance are discussed in relation to the taxonomy of Pestalotiopsis.     

Phylogenetic relationships within the genus Desmothrips (Thysanoptera,Aeolothripidae), an Australian genus of facultative flower‐living predators

A phylogenetic analysis of the Australian Aeolothripidae genus Desmothrips Hood is presented. A data matrix with 27 species is analysed under parsimony criteria. The monophyly of Desmothrips is recovered. Continuous and discrete characters were analysed separately and in combination, and continuous characters were rescaled and analysed under equal weights. Three new species from the northwestern and one from the southeastern areas of Australia are described and illustrated. A key to the 18 species of Desmothrips is provided.     

The evolution of actinorhizal symbioses: Evidence for multiple origins of the symbiotic association

According to morphologically based classification systems, actinorhizal plants, engaged in nitrogen-fixing symbioses with Frankia bacteria, are considered to be only distantly related. However, recent phylogenetic analyses of seed plants based on chloroplast rbcL gene sequences have suggested closer relationships among actinorhizal plants. A more thorough sampling of chloroplast rbcL gene sequences from actinorhizal plants and their nonsymbiotic close relatives was conducted in an effort to better understand the phylogenetic relationships of these plants, and ultimately, to assess the homology of the different actinorhizal symbioses. Sequence data from 70 taxa were analyzed using parsimony analysis. Strict consensus trees based on 24 equally parsimonious trees revealed evolutionary divergence between groups of actinorhizal species suggesting that not all symbioses are homologous. The arrangement of actinorhizal species, interspersed with nonactinorhizal taxa, is suggestive of multiple origins of the actinorhizal symbiosis. Morphological and anatomical characteristics of nodules from different actinorhizal hosts were mapped onto the rbclL-based consensus tree to further assess homology among rbcL-based actinorhizal groups. The morphological and anatomical features provide additional support for the rbcL-based groupings, and thus, together, suggest that actinorhizal symbioses have originated more than once in evolutionary history.