The ecological tale of Gonyleptidae (Arachnida,Opiliones) evolution: phylogeny of a Neotropical lineage of armoured harvestmen using ecological,behavioural and chemical characters

The large Neotropical family Gonyleptidae comprises nearly 820 species divided into 16 subfamilies. The majority of publications on harvestman ecology, behaviour and scent gland secretion chemistry have focused on this family. We used the information available in the literature and combined it with an intensive search for ecological, behavioural and chemical data to infer the phylogeny of the Gonyleptidae. We included 28 species belonging to 14 of the 16 gonyleptid subfamilies in the ingroup and four species belonging to the families Cosmetidae, Stygnidae and Manaosbiidae in the outgroup. We performed the analyses using equally weighted characters and coded 63 characters comprising 153 states, which makes this the largest non‐morphological, non‐molecular phylogenetic data matrix published to date. We obtained five most parsimonious trees, and the strict consensus resulted in six collapsed nodes. The results show that the monophyly of Gonyleptidae is equivocal because Metasarcinae is placed at a basal polytomy with the outgroups Cosmetidae and Stygnidae. Gonyleptinae, Pachylinae and Progonyleptoidellinae are polyphyletic groups, but the remaining subfamilies are monophyletic and have several synapomorphies. Based on the resulting topology, we discuss the performance of ecological, behavioural and chemical characters, and map a selected set of characters to discuss their evolutionary patterns in the family.     

Molecular phylogeny of the fungus gnat family Mycetophilidae (Diptera,Mycetophiliformia)

Abstract A molecular phylogeny of the fungus gnat family Mycetophilidae based on the nuclear 18S, 28S, and the mitochondrial 16S rRNA genes is presented. The total alignment included 58 taxa and 1704 bp. The family was recovered as monophyletic in parsimony and Bayesian analyses. In the Bayesian analysis, Mycetophilinae and its two tribes, Mycetophilini and Exechiini, were monophyletic with good statistical support. The subfamily Mycomyinae was found consistently in a sister‐group relationship to Mycetophilinae. Gnoristinae was rendered paraphyletic, subtending Mycomyinae and Mycetophilinae. Within Gnoristinae, the genera Coelosia Winnertz, Boletina Staeger, Gnoriste Meigen group with Docosia Winnertz, usually considered to be a member of Leiinae. No support was found for the monophyly of the subfamilies Sciophilinae and Leiinae.     

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.     

Molecular phylogenetics of Erebidae (Lepidoptera,Noctuoidea)

As a step towards understanding the higher‐level phylogeny and evolutionary affinities of quadrifid noctuoid moths, we have undertaken the first large‐scale molecular phylogenetic analysis of the moth family Erebidae, including almost all subfamilies, as well as most tribes and subtribes. DNA sequence data for one mitochondrial gene (COI) and seven nuclear genes (EF‐1α, wingless, RpS5, IDH, MDH, GAPDH and CAD) were analysed for a total of 237 taxa, principally type genera of higher taxa. Data matrices (6407 bp in total) were analysed by parsimony with equal weighting and model‐based evolutionary methods (maximum likelihood), which revealed a well‐resolved skeleton phylogenetic hypothesis with 18 major lineages, which we treat here as subfamilies of Erebidae. We thus present a new phylogeny for Erebidae consisting of 18 moderate to strongly supported subfamilies: Scoliopteryginae, Rivulinae, Anobinae, Hypeninae, Lymantriinae, Pangraptinae, Herminiinae, Aganainae, Arctiinae, Calpinae, Hypocalinae, Eulepidotinae, Toxocampinae, Tinoliinae, Scolecocampinae, Hypenodinae, Boletobiinae and Erebinae. Where possible, each monophyletic lineage is diagnosed by autapomorphic morphological character states, and within each subfamily, monophyletic tribes and subtribes can be circumscribed, most of which can also be diagnosed by morphological apomorphies. All additional taxa sampled fell within one of the four previously recognized quadrifid families (mostly into Erebidae), which are now found to include two unusual monobasic taxa from New Guinea: Cocytiinae (now in Erebidae: Erebinae) and Eucocytiinae (now in Noctuidae: Pantheinae).     

Molecular phylogeny of flat‐footed flies (Diptera: Platypezidae): main clades supported by new morphological evidence

The molecular phylogeny of flat‐footed flies is inferred from analysis of DNA sequence data from the five mitochondrial genes 12S, 16S, COI, COII and CytB, and the nuclear gene 28S and discussed with the recent systematics based on morphological features. The Bayesian inference, maximum likelihood and maximum parsimony analyses included 42 species of 18 genera, representing all four extant subfamilies (Microsaniinae, Melanderomyiinae, Callomyiinae and Platypezinae) and all known genera except one (Metaclythia). Representatives of the brachycerous taxa Lonchopteridae, Phoridae, Sciadocerinae (Phoridae) and Opetiidae are used as outgroups, and Lonchoptera was used to root the trees. Our results show Platypezidae consisting of two well‐supported clades, the first with the subfamilies Melanderomyiinae + Callomyiinae and the second formed by subfamily Platypezinae. Genus Microsania was resolved as a separate lineage distant from Platypezidae which clustered with Opetiidae as its sister group, both together forming a sister group to Platypezidae. At the generic level, the genus Agathomyia proved not to be monophyletic in any of the analyses. The species Chydaeopeza tibialis is sister to Agathomyia sexmaculata, and consequently, the genus Chydaeopeza Shatalkin, 1992 is a new junior synonym of Agathomyia Verrall, 1901. Bifurcated setae on legs of adult Platypezidae are documented as a new synapomorphy of the family, exclusive of Microsania. Outstretched wings and only a small overlap of their surfaces at resting position are considered a new synapomorphy for the subfamily Platypezinae. Other phylogenetically important characters defining main clades are documented, and their relevance/validity in phylogenetic studies is discussed. The current systematic concept of Platypezidae is discussed, and new phylogenetic hypotheses are proposed.     

Molecular phylogeny of Omaliinae (Coleoptera: Staphylinidae) and its implications for evolution of atypically long elytra in rove beetles

Staphylinidae, or rove beetles, are a megadiverse family known for their typically very short elytra exposing most of the abdomen, but the putatively early-derived subfamily Omaliinae and its relatives have been known to include multiple taxa with unusually long elytra. The ancestral elytral length of the family and of this subfamily have long been debated. We present a phylogenetic analysis of Omaliinae based on partial mitochondrial COI (1488 bp), COII (366 bp), 12S rDNA (353 bp), nuclear 18S rDNA (1814 bp), 28S rDNA (876 bp) and CAD (869 bp) data. In all, 51 species in 31 genera and four outgroup species were included. The concatenated sequences were analysed by both parsimony- and model-based (Bayesian and maximum likelihood) methods. The subfamily Omaliinae was not supported as a monophyletic group. The model-based analyses (Bayesian and maximum likelihood trees) showed Empelinae nested within Omaliinae (excluding Corneolabiini), whereas parsimony analysis found all three putative ingroup subfamilies, Empelinae, Glypholomatinae and Microsilphinae, grouped within Omaliinae. Within the Omaliinae, the tribes Coryphiini and Eusphalerini were each supported as monophyletic, whereas Anthophagini and Omaliini were each nonmonophyletic. We hypothesize that there have been at least four independent origins of long elytra from short elytra in the omaliine lineage.     

Phylogeny of the higher Libelluloidea (Anisoptera: Odonata): an exploration of the most speciose superfamily of dragonflies

Although libelluloid dragonflies are diverse, numerous, and commonly observed and studied, their phylogenetic history is uncertain. Over 150 years of taxonomic study of Libelluloidea Rambur, 1842, beginning with Hagen (1840), [Rambur, M.P., 1842. Neuropteres. Histoire naturelle des Insectes, Paris, pp. 534; Hagen, H., 1840. Synonymia Libellularum Europaearum. Dissertation inaugularis quam consensu et auctoritate gratiosi medicorum ordinis in academia albertina ad summos in medicina et chirurgia honores.] and Selys (1850), [de Selys Longchamps, E., 1850. Revue des Odonates ou Libellules d'Europe [avec la collaboration de H.A. Hagen]. Muquardt, Bruxelles; Leipzig, 1-408.], has failed to produce a consensus about family and subfamily relationships. The present study provides a well-substantiated phylogeny of the Libelluloidea generated from gene fragments of two independent genes, the 16S and 28S ribosomal RNA (rRNA), and using models that take into account non-independence of correlated rRNA sites. Ninety-three ingroup taxa and six outgroup taxa were amplified for the 28S fragment; 78 ingroup taxa and five outgroup taxa were amplified for the 16S fragment. Bayesian, likelihood and parsimony analyses of the combined data produce well-resolved phylogenetic hypotheses and several previously suggested monophyletic groups were supported by each analysis. Macromiinae, Corduliidae s. s., and Libellulidae are each monophyletic. The corduliid (s.l.) subfamilies Synthemistinae, Gomphomacromiinae, and Idionychinae form a monophyletic group, separate from the Corduliinae. Libellulidae comprises three previously accepted subfamilies (Urothemistinae, a very restricted Tetrathemistinae, and a modified Libellulinae) and five additional consistently recovered groups. None of the other previously proposed subfamilies are supported. Bayesian analyses run with an additional 71 sequences obtained from GenBank did not alter our conclusions. The evolution of adult and larval morphological characters is discussed here to suggest areas for future focus. This study shows the inherent problems in using poorly defined and sometimes inaccurately scored characters, basing groups on symplesiomorphies, and failure to recognize the widespread effects of character correlation and convergence, especially in aspects of wing venation.     

Molecular phylogeny of the plant bugs (Heteroptera: Miridae) and the evolution of feeding habits

The first comprehensive cladistic analysis of Miridae, the plant bugs, is presented based on analysis of 3935 base pairs of mitochondrial (16S, COI) and nuclear (18S, 28SD3) DNA for 91 taxa in seven subfamilies. Data were analysed using maximum likelihood (ML), parsimony and Bayesian inference (BI) phylogenetic frameworks. The phylogenetic results are compared with previous hypotheses of higher relationships in the family using alternative hypothesis tests. A Bayesian relaxed molecular clock is used to examine divergence times, and ancestral feeding habits are reconstructed using parsimony and a Bayesian approach. Clades recovered in all analyses are as follows: Cimicomorpha, Miroidea and Miridae; Bryocorinae: Bryocorini; Stenodemini; Mirinae; Deraeocorinae (Clevinemini + Deraeocorini); Cylapinae; Isometopinae; Bryocorinae: Dicyphini; Orthotylini; Phylinae (Phylini + Pilophorini), and Phylinae as sister group to all the remaining mirid taxa. These results are largely congruent with former hypotheses based on morphological data with respect to the monophyly of various subfamilies and tribes; however, our results indicate that the subfamily Bryocorinae is not monophyletic, as the two tribes, Dicypini and Bryocorini, were separated in the phylogenetic results. Divergence time estimates indicate that the radiation of the Miridae began in the Permian; most genus‐level radiations within subfamilies began in the late Cretaceous, probably in response to the angiosperm radiation. Ancestral feeding state reconstructions based on Bayesian and parsimony inference were largely congruent and both reconstructed phytophagy as the ancestral state of the Miridae. Furthermore, the feeding habits of the common ancestors of Mirinae + Deraeocorinae, Bryocorinae + Cylapinae + Isometopinae + Orthotylinae, and the remaining taxa excluding Phylinae, were inferred as phytophagous. Therefore, at least three shifts from phytophagy or polyphagy to predation occurred within the Miridae. Additionally, based on the mirid host‐plant records, we discovered several trends, such as a strong relationship between host‐plant ranges and a facultative feeding habit. © The Willi Hennig Society 2011.     

Molecular systematics of the Cactaceae

Bayesian, maximum‐likelihood, and maximum‐parsimony phylogenies, constructed using nucleotide sequences from the plastid gene region trnK‐matK, are employed to investigate relationships within the Cactaceae. These phylogenies sample 666 plants representing 532 of the 1438 species recognized in the family. All four subfamilies, all nine tribes, and 69% of currently recognized genera of Cactaceae are sampled. We found strong support for three of the four currently recognized subfamilies, although relationships between subfamilies were not well defined. Major clades recovered within the largest subfamilies, Opuntioideae and Cactoideae, are reviewed; only three of the nine currently accepted tribes delimited within these subfamilies, the Cacteae, Rhipsalideae, and Opuntieae, are monophyletic, although the Opuntieae were recovered in only the Bayesian and maximum‐likelihood analyses, not in the maximum‐parsimony analysis, and more data are needed to reveal the status of the Cylindropuntieae, which may yet be monophyletic. Of the 42 genera with more than one exemplar in our study, only 17 were monophyletic; 14 of these genera were from subfamily Cactoideae and three from subfamily Opuntioideae. We present a synopsis of the status of the currently recognized genera.
© The Willi Hennig Society 2011.     

Phylogenetic relationships among genera of Aphidiinae (Hymenoptera: Braconidae) based on DNA sequence of the mitochondrial 16S rRNA gene

Phylogenetic relationships among forty‐nine taxa representing twenty‐four genera of Aphidiinae (Hymenoptera: Braconidae) were investigated using DNA sequence of a portion of the mitochondrial 16S rRNA gene and parsimony analysis. Seven species in six other subfamilies of Braconidae were used as outgroup. The results suggested that members of Aphidiinae are monophyletic. The basal lineage of Aphidiinae was Aclitus in weighted and unweighted parsimony analyses and Praini was basal relative to Ephedrini. With the exception of Pauesia and Aphidius, all genera were monophyletic. The results support generic status for Euaphidius, but not for Lysaphidus. Diaeretus leucopterus was internal to a clade composed of three Pauesia species, suggesting that the latter genus may be paraphyletic. A combined analysis that included DNA sequence of 16S rRNA, NADH1 dehydrogenase and 28S rRNA resulted in more robust cladograms with topologies similar to those inferred from the 16S rRNA gene sequence alone. The results are compared to previously proposed phylogenies of Aphidiinae based on morphological and molecular characters.     

Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)

Phylogenetic relationships within the Pentatomoidea are investigated through the coding and analysis of character data derived from morphology and DNA sequences. In total, 135 terminal taxa were investigated, representing most of the major family groups; 84 ingroup taxa are coded for 57 characters in a morphological matrix. As many as 3500 bp of DNA data are adduced for each of 52 terminal taxa, including 44 ingroup taxa, comprising the 18S rRNA, 16S rRNA, 28S rRNA, and COI gene regions. Character data are analysed separately and in the form of a total evidence analysis. Major conclusions of the phylogenetic analysis include: the concept of Urostylididae is restricted to that of earlier authors; the Saileriolinae is raised to family rank and treated as the sister group of all Pentatomoidea exclusive of Urostylididae sensu stricto; a broadly conceived Cydnidae, as recognized by Dolling, 1981 , is not supported; the placement of Thaumastellidae within the Pentatomoidea is affirmed and the taxon is recognized at family rank rather than as a subfamily of Cydnidae, although its exact phylogenetic position within the Pentatomoidea remains equivocal; the Parastrachiinae is treated as also including Dismegistus Amyot & Serville and placed within a broadly conceived Corimelaenidae, the latter group being treated at family rank; the family‐group taxa Dinidoridae and Tessaratomidae probably represent a monophyletic group, but the recognition of monophyletic subgroups will benefit from additional representation in the sequence data set; and the Lestoniidae is treated as the sister group of the Acanthosomatidae. The Acanthosomatidae and Scutelleridae are consistently recovered as monophyletic. The monophyly of the Pentatomidae appears unequivocal, inclusive of the Aphylinae and Cyrtocorinae, on the basis of morphology, the latter two taxa not being represented in the molecular data set. © The Willi Hennig Society 2008.     

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.     

Molecular phylogeny of the higher taxa of Odonata (Insecta) inferred from COI, 16S rRNA, 28S rRNA,and EF1‐α sequences

In this study, we sequenced both two mitochondrial genes (COI and 16S rRNA) and nuclear genes (28S rRNA and elongation factor‐1α) from 71 species of Odonata that represent 7 superfamilies in 3 suborders. Phylogenetic testing for each two concatenated gene sequences based on function (ribosomal vs protein‐coding genes) and origin (mitochondrial vs nuclear genes) proved limited resolution. Thus, four concatenated sequences were utilized to test the previous phylogenetic hypotheses of higher taxa of Odonata via Bayesian inference (BI) and maximum likelihood (ML) algorithms, along with the data partition by the BI method. As a result, three slightly different topologies were obtained, but the BI tree without partition was slightly better supported by the topological test. This topology supported the suborders Anisoptera and Zygoptera each being a monophyly, and the close relationship of Anisozygoptera to Anisoptera. All the families represented by multiple taxa in both Anisoptera and Zygoptera were consistently revealed to each be a monophyly with the highest nodal support. Unlike consistent and robust familial relationships in Zygoptera those of Anisoptera were partially unresolved, presenting the following relationships: ((((Libellulidae + Corduliidae) + Macromiidae) + Gomphidae + Aeshnidae) + Anisozygoptera) + (((Coenagrionidae + Platycnemdidae) + Calopterygidae) + Lestidae). The subfamily Sympetrinae, represented by three genera in the anisopteran family Libellulidae, was not monophyletic, dividing Crocothemis and Deielia in one group together with other subfamilies and Sympetrum in another independent group.     

Major lineages of Nolidae (Lepidoptera,Noctuoidea) elucidated by molecular phylogenetics

To elucidate the evolutionary relationships of the major lineages within the moth family Nolidae, we analysed a molecular dataset comprising eight independent gene regions (6.4 kbp), cytochrome c oxidase subunit I (COI) from the mitochondrial genome, and elongation factor‐1α (EF‐1α), ribosomal protein S5 (RpS5), carbamoylphosphate synthase domain protein (CAD), cytosolic malate dehydrogenase (MDH), glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH), isocitrate dehydrogenase (IDH) and wingless genes from the nuclear genome, using parsimony and model‐based evolutionary methods (maximum likelihood and Bayesian inference). Our analyses revealed a well‐resolved phylogenetic hypothesis, again recovering the six previously recognized families within Noctuoidea (i.e. Oenosandridae, Notodontidae, Euteliidae, Erebidae, Nolidae and Noctuidae), and monophyly of the quadrifid Noctuoidea (i.e. Euteliidae, Erebidae, Nolidae and Noctuidae). The family Nolidae is diagnosed and characterized by two synapomorphies from morphology: construction of a ridged boat‐shaped cocoon that bears a vertical exit slit at one end; and two other morphological character states: elongation of the forewing retinaculum into a bar‐like or digitate condition and possession of a postpiracular counter‐tympanal hood. We present a new phylogenetic hypothesis for Nolidae consisting of eight strongly supported subfamilies, two of which are erected here: Diphtherinae, Risobinae, Collomeninae subfam. nov., Beaninae subfam. nov., Eligminae, Westermanniinae, Nolinae and Chloephorinae. Where we are able, each monophyletic lineage is diagnosed by morphological autapomorphies and within each subfamily, monophyletic tribes and subtribes are circumscribed, most of which are also diagnosable by morphological apomorphies. We also describe two new taxa: Gelastocerini trib. nov. and Etannina subtrib. nov. The Neotropical subfamily Diphtherinae, here newly circumscribed, is considered to be the plesiomorphic sister lineage to the rest of Nolidae. Diphtherinae are characterized by loss of the proximal pair of metatibial spurs in males and by the presence of a frontal tubercle, which is presumably associated with a derived strategy of emergence from the cocoon.     

Molecular phylogenetics of the melyrid lineage (Coleoptera: Cleroidea)

The melyrid lineage of beetles form a distinct group of the superfamily Cleroidea with a high level of soft‐bodiedness. Here we present the first molecular phylogenetic analysis of this group. The data matrix included partial sequences of the small and large subunits of rRNA, the mitochondrial large subunit rRNA, and cytochrome oxidase subunit I of 67 melyrid and eight outgroup taxa. The concatenated sequences were analysed using maximum‐parsimony (MP), maximum‐likelihood (ML) and Bayesian analysis (BA) approach. The results strongly supported the monophyly of the melyrid lineage splitting into six major clades: Rhadalidae, Mauroniscidae, Prionoceridae, Melyridae sensu stricto, Dasytidae and Malachiidae. The rhadalids were placed in the most basal position, followed by mauroniscids and prionocerids. Three terminal lineages—the true melyrids, dasytids, and malachiids—are well supported by all analyses, but their mutual relationships remain uncertain as MP analysis proposed alternative topologies to that of the ML and BA trees, with often low node support in the latter two methods. The monophyly of the subfamily Danacaeinae (Dasytidae) with respect to the danacaeine genera of the southern hemisphere (Hylodanacaea, Listrocerus, Amecocerus) was challenged as they were found to be polyphyletic. Similarly, the monophyly of Attalus was rejected by our analyses and shown to be polyphyletic. Based on the preferred phylogenetic hypothesis, the subfamilies Rhadalinae, Dasytinae and Malachiinae are elevated to family rank. © The Willi Hennig Society 2011.     

Phylogeny of subfamily Epidendroideae (Orchidaceae) inferred from ndhF chloroplast gene sequences

This project undertakes the first molecular-based phylogenetic study of subfamily Epidendroideae (Orchidaceae). Approximately 1200 nucleotides (from the 3' half of the chloroplast gene ndhF for 34 orchid taxa and a lilioid monocot, Clivia miniata (Amaryllidaceae), were subjected to phylogenetic analysis using parsimony and maximum likelihood methods. Oryza sativa (Poaceae), a nonlilioid monocot, was designated as outgroup. Trees from both parsimony and maximum likelihood methods suggest that subfamily Epidendroideae is monophyletic, with Listera (Neottieae) as sister. Although subtribal relationships are typically well resolved and have strong branch support, intertribal relationships are generally poorly resolved. Perhaps this general lack of resolution among tribes reflects a rapid species radiation that coincided with anatomical, physiological, and anatomical adaptations that initiated large-scale epiphytism in the ancestral Epidendroideae. Six taxa in this study exhibit deletions that are not evenly divisible by three and result in extensive sequence frameshifts. For example, one deletion is 227 bp in length and is flanked by the short direct repeat sequence; TCAATAGGAATTTCTTTT. Multiple deletions and frameshifts suggest that ndhF may be a pseudogene, in at least some orchid taxa.     

Phylogeny of thrips (Insecta: Thysanoptera) based on five molecular loci

The order Thysanoptera (Paraneoptera), commonly known as thrips, displays a wide range of behaviours, and includes several pest species. The classification and suggested relationships among these insects remain morphologically based, and have never been evaluated formally with a comprehensive molecular phylogenetic analysis. We tested the monophyly of the suborders, included families and the recognized subfamilies, and investigated their relationships. Phylogenies were reconstructed based upon 5299 bp from five genetic loci: 18S ribosomal DNA, 28S ribosomal DNA, Histone 3, Tubulin‐alpha I and cytochrome oxidase c subunit I. Ninety‐nine thrips species from seven of the nine families, all six subfamilies and 70 genera were sequenced. Maximum parsimony, maximum likelihood and Bayesian analyses all strongly support a monophyletic Tubulifera and Terebrantia. The families Phlaeothripidae, Aeolothripidae, Melanthripidae and Thripidae are recovered as monophyletic. The relationship of Aeolothripidae and Merothripidae to the rest of Terebrantia is equivocal. Molecular data support previous suggestions that Aeolothripidae or Merothripidae could be a sister to the rest of Terebrantia. Four of the six subfamilies are recovered as monophyletic. The two largest subfamilies, Phlaeothripinae and Thripinae, are paraphyletic and require further study to understand their internal relationships.     

Morphological phylogeny of the variable fly family Stratiomyidae (Insecta,Diptera)

Brammer, C. A. & von Dohlen, C. D. (2010). Morphological phylogeny of the variable fly family Stratiomyidae (Insecta, Diptera). —Zoologica Scripta, 39, 363–377. Stratiomyidae is a dipteran family distributed worldwide and containing 2800 species classified into 12 subfamilies. Previous phylogenetic work on the Stratiomyidae consisted of a 20‐character morphological analysis of the subfamilies [ World Catalog of the Stratiomyidae (Insect: Diptera). Leiden: Backhuys Publishers, 2001 ], and a molecular study using 69 taxa and two gene regions [ Molecular Phylogenetics and Evolution, 43, 2007, 660 ]. In this study, we present an expanded morphological cladistic analysis using 92 characters and 80 taxa, representing 36 of 39 described genera and all 12 Stratiomyidae subfamilies, as well as Xylomyidae and Pantophthalmidae outgroups. Data are analysed under maximum parsimony with all characters unordered and weighted equally; nodal support is assessed with the bootstrap and Bremer index. The strict consensus of all shortest trees is well resolved, and many of the deeper nodes are supported, although the root is ambiguous. Antissinae, Stratiomyinae, Sarginae and the diverse Clitellariinae are not monophyletic. Clitellariinae are positioned across several lineages, with most species grouped into a single, unsupported clade. Many of the well‐supported relationships are consistent with several aspects of the previous studies. The position of Exodontha remains elusive. Character support for subfamilies and other major clades is discussed.     

Laying the foundations of evolutionary and systematic studies in crickets (Insecta,Orthoptera): a multilocus phylogenetic analysis

Orthoptera have been used for decades for numerous evolutionary questions but several of its constituent groups, notably crickets, still suffer from a lack of a robust phylogenetic hypothesis. We propose the first phylogenetic hypothesis for the evolution of crickets sensu lato, based on analysis of 205 species, representing 88% of the subfamilies and 71% tribes currently listed in the database Orthoptera Species File (OSF). We reconstructed parsimony, maximum likelihood and Bayesian phylogenies using fragments of 18S, 28SA, 28SD, H3, 12S, 16S, and cytb (~3600 bp). Our results support the monophyly of the cricket clade, and its subdivision into two clades: mole crickets and ant‐loving crickets on the one hand, and all the other crickets on the other (i.e. crickets sensu stricto). Crickets sensu stricto form seven monophyletic clades, which support part of the OSF families, “subfamily groups”, or subfamilies: the mole crickets (OSF Gryllotalpidae), the scaly crickets (OSF Mogoplistidae), and the true crickets (OSF Gryllidae) are recovered as monophyletic. Among the 22 sampled subfamilies, only six are monophyletic: Gryllotalpinae, Trigonidiinae, Pteroplistinae, Euscyrtinae, Oecanthinae, and Phaloriinae. Most of the 37 tribes sampled are para‐ or polyphyletic. We propose the best‐supported clades as backbones for future definitions of familial groups, validating some taxonomic hypotheses proposed in the past. These clades fit variously with the morphological characters used today to identify crickets. Our study emphasizes the utility of a classificatory system that accommodates diagnostic characters and monophyletic units of evolution. Moreover, the phylogenetic hypotheses proposed by the present study open new perspectives for further evolutionary research, especially on acoustic communication and biogeography.