Phylogeny and systematics of the subfamily Bryocorinae based on morphology with emphasis on the tribe Dicyphini sensu Schuh,

The classification of the hyperdiverse true bug family Miridae is far from settled, and is particularly contentious for the cosmopolitan subfamily Bryocorinae. The morphological diversity within the subfamily is pronounced, and a lack of explicit character formulation hampers stability in the classification. Molecular partitions are few and only a handful of taxa have been sequenced. In this study the phylogeny of the subfamily Bryocorinae has been analysed based on morphological data alone, with an emphasis on evaluating the tribe Dicyphina sensu Schuh, 1976, within which distinct groups of taxa exist. A broad sample of taxa was examined from each of the bryocorine tribes. A broad range of outgroup taxa from most of the other mirid subfamilies was also examined to test for bryocorine monophyly, ingroup relationships and to determine character polarity. In total a matrix comprising 44 ingroup, 15 outgroup taxa and 111 morphological characters was constructed. The phylogenetic analysis resulted in a monophyletic subfamily Bryocorinae sensu Schuh (1976, 1995), except for the genus Palaucoris, which is nested within Cylapinae. The tribe Dicyphini sensu Schuh (1976, 1995) has been rejected. The subtribe Odoniellina is synonymized with the subtribe Monaloniina and the subtribes Dicyphina, Monaloniina and Eccritotarsina are now elevated to tribal level, with the Dicyphini now restricted in composition and definition. The genus Felisacus is highly autapomorphic and a new tribe – the Felisacini – is erected for the included taxa. This phylogeny of the tribes of the Bryocorinae comprises the following sister‐group relationships: Dicyphini ((Bryocorini + Eccritotarsini)(Felisicini + Monaloniini)).     

Insights into the phylogenetic relationships within Cixiidae (Hemiptera: Fulgoromorpha): cladistic analysis of a morphological dataset

Abstract.  According to the most recent classifications proposed, the planthopper family Cixiidae comprises three subfamilies, namely Borystheninae, Bothriocerinae and Cixiinae, the latter with 16 tribes. Here we examine morphological characters to present the first phylogenetic reconstructions within Cixiidae derived from a cladistic analysis. We scored 85 characters of the head, thorax, and male and female genitalia for 50 taxa representative of all cixiid subfamilies and tribes and for six outgroup taxa. Analyses were based on maximum parsimony – using both equally weighted and successive weighting procedures – and Bayesian inferences. The monophyly of most currently accepted tribes and subfamilies was investigated through Templeton statistical tests of alternative phylogenetic hypotheses. The cladistic analyses recover the monophyly of Cixiidae, the subfamily Bothriocerinae, and the tribes Pentastirini, Mnemosynini, and Eucarpiini. Successive weighting and Bayesian inference recover the monophyly of the tribe Gelastocephalini, but only Bayesian inference supports the monophyly of Semoniini. The relationships recovered support the groups [Stenophlepsini (Borystheninae + Bothriocerinae)] arising from the tribe Oecleini, and [Andini + Brixiidini + Brixiini (polyphyletic) + Bennini]. Templeton tests reject the alternative hypothesis of a monophyletic condition for the tribe Pintaliini as presently defined.     

Total‐evidence phylogenetic analysis and reclassification of the Phylinae (Insecta: Heteroptera: Miridae), with the recognition of new tribes and subtribes and a redefinition of Phylini

The subfamily Phylinae (Heteroptera: Miridae) is one of the largest subfamilies of plant bugs and in the most recent classification comprised six tribes: Pilophorini, Hallodapini, Auricillocorini, Phylini, Pronotocrepini, and Leucophoropterini. Phylogenetic analyses of the subfamily using dynamic homology (POY), parsimony (TNT), and model‐based (RAxML) methods are presented. A dataset comprising both morphological and molecular characters (16S, 18S, 28S, and COI–COII) was assembled for taxon samples of 164 ingroup and nine outgroup taxa. A reclassification of the subfamily based on the POY analysis is presented, recognizing nine tribes and nine subtribes. The Auricillocorini is synonymized with the Hallodapini and the Pronotocrepini with the Cremnorrhini; the Phylini was found to be polyphyletic and is redefined; the Semiini and Nasocorini are resurrected and redefined; and the Decomiini and Coatonocapsiniare presented as new tribes. The Hallodapini, rather than the Pilophorini, was found to be the sister‐group to the remaining Phylinae.     

Multistate characters and diet shifts: evolution of Erotylidae (Coleoptera)

The dominance of angiosperms has played a direct role in the diversification of insects, especially Coleoptera. The shift to angiosperm feeding from other diets is likely to have increased the rate of speciation in Phytophaga. However, Phytophaga is only one of many hyperdiverse lineages of beetles and studies of host-shift proliferation have been somewhat limited to groups that primitively feed on plants. We have studied the diet-diverse beetle family Erotylidae (Cucujoidea) to determine if diet is correlated with high diversification rates and morphological evolution by first reconstructing ancestral diets and then testing for associations between diet and species number and diet and ovipositor type. A Bayesian phylogenetic analysis of morphological data that was previously published in Leschen (2003, Pages 1-108 in Fauna of New Zealand, 47; 53 terminal taxa and 1 outgroup, 120 adult characters and 1 diet character) yielded results that are similar to the parsimony analyses of Leschen (2003). Ancestral state reconstructions based on Bayesian and parsimony inference were largely congruent and both reconstructed microfungal feeding (the diet of the outgroup Biphyllidae) at the root of the Erotylidae tree. Shifts among microfungal, saprophagous, and phytophagous diets were most frequent. The largest numbers of species are contained in lineages that are macrofungal feeders (subfamily Erotylinae) and phytophagous (derived Languriinae), although the Bayesian posterior predictive tests of character state correlation were unable to detect any significant associations. Ovipositor morphology correlated with diet (i.e., acute forms were associated with phytophagy and unspecialized forms were associated with a mixture of diets). Although there is a general trend to increased species number associated with the shift from microfungal feeding to phytophagy (based on character mapping and mainly restricted to shifts in Languriinae), there is a large radiation of taxa feeding on macrofungi. Cycad feeding is scattered in more deeply diverged taxa and may have preceded the evolution of angiosperm feeding in some groups. Preliminary analysis of diet mapped onto higher beetle phylogenies suggests that about half of the major Coleoptera lineages may have had fungus-feeding ancestors. We discuss the roles of stochastic models and prior distributions of the reconstruction of ancestral character states in the context of the current data.     

Phylogeny of the mega-diverse Gelechioidea (Lepidoptera): adaptations and determinants of success

The Gelechioidea, with 18,000 described and many more unnamed species ranks among the most diverse lepidopteran superfamilies. Nevertheless, their taxonomy has remained largely unresolved, and phylogenetic affinities among gelechioid families and lower taxa have been insufficiently understood. We constructed, for the first time, a comprehensive molecular phylogeny for the Gelechioidea. We sampled seven genes, in total 5466 base pairs, of 109 gelechioid taxa representing 32 of 37 recognized subfamilies, and two outgroup taxa. We used maximum likelihood methods and Bayesian inference to construct phylogenetic trees. We found that the families Autostichidae, Lecithoceridae, Xyloryctidae, and Oecophoridae s. str., in this order, are the most basally arising clades. Elachistidae s. l. was found to be paraphyletic, with families such as Gelechiidae and Cosmopterigidae nested within it, and Parametriotinae associated with several families previously considered unrelated to them. Using the phylogenetic trees, we examined patterns of life history evolution and determinants of the success of different lineages. Gelechioids express unusually wide variability in life-history strategies, including herbivorous, saprophagous, fungivorous, and carnivorous lineages. Most species are highly specialized in diet and other life history traits. The results suggest that either saprophagy was the ancestral feeding strategy from which herbivory evolved independently on multiple occasions, or that the ancestor was herbivorous with repeated origins of saprophagy. External feeding is an ancestral trait from which internal feeding evolved independently several times. In terms of species number, saprophages are dominant in Australia, while elsewhere several phytophagous lineages have extensively specialized and diversified. Internal feeding has remained a somewhat less generally adopted feeding mode, although in a few lineages significant radiations of leaf mining species have occurred. We conclude that diverse feeding modes, specialization among saprophages, repeated shifts to phytophagy, and a generally high specialization rate on single plant species (monophagy) are the major factors behind the success of the Gelechioidea.     

Phylogeny and evolution of Cervidae based on complete mitochondrial genomes

Mitochondrial DNA sequences can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We made phylogenetic analyses of 19 species of Cervidae, with Bos taurus as the outgroup. We used neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods on whole mitochondrial genome sequences. The consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Plesiometacarpalia and Telemetacarpalia, and four tribes, Cervinae, Muntiacinae, Hydropotinae, and Odocoileinae. The divergence times in these families were estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock method; the results were consistent with those of previous studies. We concluded that the evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; this method could be used broadly in phylogenetic evolutionary analysis of animal taxa.     

Systematics and morphological evolution within the moss family Bryaceae: a comparison between parsimony and Bayesian methods for reconstruction of ancestral character states

The Bryaceae are a large cosmopolitan moss family including genera of significant morphological and taxonomic complexity. Phylogenetic relationships within the Bryaceae were reconstructed based on DNA sequence data from all three genomic compartments. In addition, maximum parsimony and Bayesian inference were employed to reconstruct ancestral character states of 38 morphological plus four habitat characters and eight insertion/deletion events. The recovered phylogenetic patterns are generally in accord with previous phylogenies based on chloroplast DNA sequence data and three major clades are identified. The first clade comprises Bryum bornholmense, B. rubens, B. caespiticium, and Plagiobryum. This corroborates the hypothesis suggested by previous studies that several Bryum species are more closely related to Plagiobryum than to the core Bryum species. The second clade includes Acidodontium, Anomobryum, and Haplodontium, while the third clade contains the core Bryum species plus Imbribryum. Within the latter clade, B. subapiculatum and B. tenuisetum form the sister clade to Imbribryum. Reconstructions of ancestral character states under maximum parsimony and Bayesian inference suggest fourteen morphological synapomorphies for the ingroup and synapomorphies are detected for most clades within the ingroup. Maximum parsimony and Bayesian reconstructions of ancestral character states are mostly congruent although Bayesian inference shows that the posterior probability of ancestral character states may decrease dramatically when node support is taken into account. Bayesian inference also indicates that reconstructions may be ambiguous at internal nodes for highly polymorphic characters.     

Molecular systematics of the Jacks (Perciformes: Carangidae) based on mitochondrial cytochrome b sequences using parsimony,likelihood, and Bayesian approaches

The Carangidae represent a diverse family of marine fishes that include both ecologically and economically important species. Currently, there are four recognized tribes within the family, but phylogenetic relationships among them based on morphology are not resolved. In addition, the tribe Carangini contains species with a variety of body forms and no study has tried to interpret the evolution of this diversity. We used DNA sequences from the mitochondrial cytochrome b gene to reconstruct the phylogenetic history of 50 species from each of the four tribes of Carangidae and four carangoid outgroup taxa. We found support for the monophyly of three tribes within the Carangidae (Carangini, Naucratini, and Trachinotini); however, monophyly of the fourth tribe (Scomberoidini) remains questionable. A sister group relationship between the Carangini and the Naucratini is well supported. This clade is apparently sister to the Trachinotini plus Scomberoidini but there is uncertain support for this relationship. Additionally, we examined the evolution of body form within the tribe Carangini and determined that each of the predominant clades has a distinct evolutionary trend in body form. We tested three methods of phylogenetic inference, parsimony, maximum-likelihood, and Bayesian inference. Whereas the three analyses produced largely congruent hypotheses, they differed in several important relationships. Maximum-likelihood and Bayesian methods produced hypotheses with higher support values for deep branches. The Bayesian analysis was computationally much faster and yet produced phylogenetic hypotheses that were very similar to those of the maximum-likelihood analysis.     

Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei: Cypriniformes)

The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A>T, C>G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA.     

Higher level molecular phylogeny of darkling beetles (Coleoptera: Tenebrionidae)

Insect diversity represents about 60% of the estimated million‐and‐a‐half described eukaryotic species worldwide, yet comprehensive and well‐resolved intra‐ordinal phylogenies are still lacking for the majority of insect groups. This is the case especially for the most species‐rich insect group, the beetles (Coleoptera), a group for which less than 4% of the known species have had their DNA sequenced. In this study, we reconstruct the first higher level phylogeny based on DNA sequence data for the species‐rich darkling beetles, a family comprising at least 20 000 species. Although amongst all families of beetles Tenebrionidae ranks seventh in terms of species diversity, the lack of knowledge on the phylogeny and systematics of the group is such that its monophyly has been questioned (not to mention those of the subfamilies and tribes contained within it). We investigate the evolutionary history of Tenebrionidae using multiple phylogenetic inference methods (Bayesian inference, maximum likelihood and parsimony) to analyse a dataset consisting of eight gene fragments across 404 taxa (including 250 tenebrionid species). Although the resulting phylogenetic framework only encompasses a fraction of the known tenebrionid diversity, it provides important information on their systematics and evolution. Whatever the methods used, our results provide strong support for the monophyly of the family, and highlight the likely paraphyletic or polyphyletic nature of several important tenebrionid subfamilies and tribes, notably the polyphyletic subfamilies Diaperinae and Tenebrioninae that clearly require substantial revision in the future. Some interesting associations in several groups are also revealed by the phylogenetic analyses, such as the pairing of Aphtora Bates with Phrenapatinae. Furthermore this study advances our knowledge of the evolution of the group, providing novel insights into much‐debated theories, such as the apparent relict distribution of the tribe Elenophorini.     

Molecular phylogeny of the sawfly subfamily Nematinae (Hymenoptera: Tenthredinidae)

Abstract.  Nematinae is one of the largest subfamilies in the sawfly family Tenthredinidae, but internal relationships are unknown in the absence of any formal phylogenetic analysis. To understand the internal phylogeny of Nematinae, we sequenced a portion of the mitochondrial cytochrome oxidase I gene and the nuclear elongation factor-1α gene from thirteen outgroup taxa and sixty-eight nematine species, the ingroup taxa of which represent all major genera and subgenera within the subfamily. Maximum parsimony and Bayesian phylogenetic analyses of the DNA sequence data show that: (1) Nematinae are monophyletic in a broad sense which includes Hoplocampa , Susana and the tribe Cladiini, which have been classified often into separate subfamilies; together with Craterocercus , these taxa form a paraphyletic basal grade with respect to the remaining Nematinae, but among-group relationships within the grade remain weakly resolved; (2) the remainder of the ingroup, Nematinae s. str, is monophyletic in all combined-data analyses; (3) within Nematinae s. str, the 'Higher' Nematinae is divided into three groups, Mesoneura and the large tribes Nematini and Pristiphorini; (4) although the traditional classifications at the tribal level are largely upheld, some of the largest tribes and genera are obviously para- or polyphyletic; (5) according to rate-smoothed phylogenies dated with two fossil calibration points, Nematinae originated 50–120 million years ago. In addition, the results from all Bayesian analyses provide strong and consistent support for the monophyly of Tenthredinidae, which has been difficult to demonstrate in previous parsimony analyses of morphological and molecular data.     

Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling

In this paper we included a very broad representation of grass family diversity (84% of tribes and 42% of genera). Phylogenetic inference was based on three plastid DNA regions rbcL, matK and trnL-F, using maximum parsimony and Bayesian methods. Our results resolved most of the subfamily relationships within the major clades (BEP and PACCMAD), which had previously been unclear, such as, among others the: (i) BEP and PACCMAD sister relationship, (ii) composition of clades and the sister-relationship of Ehrhartoideae and Bambusoideae + Pooideae, (iii) paraphyly of tribe Bambuseae, (iv) position of Gynerium as sister to Panicoideae, (v) phylogenetic position of Micrairoideae. With the presence of a relatively large amount of missing data, we were able to increase taxon sampling substantially in our analyses from 107 to 295 taxa. However, bootstrap support and to a lesser extent Bayesian inference posterior probabilities were generally lower in analyses involving missing data than those not including them. We produced a fully resolved phylogenetic summary tree for the grass family at subfamily level and indicated the most likely relationships of all included tribes in our analysis.     

A single origin of gall association in a group of parasitic wasps with disparate morphologies

The braconid wasp subfamily Doryctinae mainly comprises idiobiont ectoparasitoids of other insect larvae. In recent years, however, members of a few genera have been discovered to be associated with galls from various unrelated host plant families, with some of these being gall inducers whereas others are suspected as being predators of gallers. Because of their considerable morphological differences, these gall-associated taxa traditionally have been placed in separate tribes or even in other subfamilies. In this study, we investigate the phylogenetic relationships among representatives of a number of different doryctine genera, including five of its seven gall-associated genera using two genetic markers. Here we analyzed the length-variable 28S sequence data based on secondary structure both excising the unalignable regions and recoding them according to indel length. In addition, multiple alignments were carried out with a range of gap-opening and extension parameters. The combined (28S+CO1) phylogenetic hypotheses obtained, both excluding and recoding the unalignable regions, recover a clade comprising the five gall-associated genera, and most of the analyses using multiple alignments also support this relationship. These results support a scenario in which secondary phytophagy evolves from initially attacking primary gall-forming hosts. The relationships recovered are also more congruent with a model that explains the macroevolution of insect plant association in the Doryctinae as reflecting geographic proximity rather than host plant relationships. Further, our phylogenetic hypotheses consistently show that one of the main morphological features employed in the higher level classification of the Doryctinae is actually highly homoplastic.     

Phylogeny and the colourful history of jewel bugs (Insecta: Hemiptera: Scutelleridae)

Members of the family Scutelleridae (Heteroptera: Pentatomomorpha: Pentatomoidea) are also called shield bugs because of the greatly enlarged scutellum, or jewel bugs because of the brilliant colours of many species. All scutellerids are phytophagous, feeding on various parts of their host plants. Due to lack of obvious synapomorphies and the failure to apply rigorous phylogenetic methods, the higher classification of Scutelleridae has been disputed for more than 150 years. Here we reconstructed a phylogeny of Scutelleridae based on complete sequences of 18S and 28S nuclear rDNAs and all 13 protein‐coding genes of the mitochondrial genome, with the sampled taxa covering all of the currently recognized subfamilies. The monophyly of Scutelleridae was confirmed by the congruence of the results of analyses conducted using Bayesian inference, maximum likelihood and maximum parsimony. The phylogenetic relationships among subfamilies were well resolved for the first time. Furthermore, time‐divergence studies estimated that the time of origin of Scutelleridae was in the Early Cretaceous (142.1–122.8 Ma), after the origin of the angiosperms. The diversification between the extant subfamilies of Scutelleridae and within the subfamilies occurred from the late Palaeocene to the late Miocene, simultaneously with the rise of the major groups of angiosperms and other phytophagous insects.     

Phylogeny of colletid bees (Hymenoptera: Colletidae) inferred from four nuclear genes

Colletidae comprise approximately 2500 species of bees primarily distributed in the southern continents (only two colletid genera are widely distributed: Colletes and Hylaeus). Previously published studies have failed to resolve phylogenetic relationships on a worldwide basis and this has been a major barrier to the progress of research regarding systematics and evolution of colletid bees. For this study, data from four nuclear gene loci: elongation factor-1alpha (F2 copy), opsin, wingless, and 28S rRNA were analyzed for 122 species of colletid bees, representing all subfamilies and tribes currently recognized; 22 species belonging to three other bee families were used as outgroups. Bayesian, maximum likelihood, and parsimony methods were employed to investigate the phylogenetic relationships within Colletidae and resulted in highly congruent and well-resolved trees. The phylogenetic results show that Colletidae are monophyletic and that all traditionally recognized subfamilies (except Paracolletinae) are also strongly supported as monophyletic. Our phylogenetic hypothesis provides a framework within which broad questions related to the taxonomy, biogeography, morphology, evolution, and ecology of colletid bees can be addressed.     

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.     

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 molecular phylogenetic and fruit evolutionary analysis of the major groups of the paleotropical woody bamboos (Gramineae: Bambusoideae) based on nuclear ITS, GBSSI gene and plastid trnL-F DNA sequences

This study presented the first molecular phylogenetic analysis of the major clades of woody bamboos of the Old World tropics based on nuclear and chloroplast sequences (ITS, GBSSI and trnL-F). Sequence data from 53 species, representing 17 paleotropical woody bamboo genera, were analyzed using the maximum parsimony and Bayesian inference methods. All examined ingroup taxa were clustered into two clades, i.e., the Bambusinae+Dinochloa clade and the Melocanninae clade. The former clade included Bambusa, Bonia, Dendrocalamus, Dendrocalamopsis, Dinochloa, Gigantochloa, Molecalamus, Neomicrocalamus, Neosinocalamus, Oxytenanthera s. str. (sensu stricto), Racemobambos and Thyrsostachys. The Melocanninae clade consisted of Cephalostachyum, Leptocanna (better treated as part of Cephalostachyum), Melocanna, Pseudostachyum and Schizostachyum s. str. The subtribe Racemobambosinae and tribes Dendrocalameae and Oxytenanthereae were not supported and may be better placed in subtribe Bambusinae. The ovary characters seemed to be good criteria to distinguish these two clades. The reconstruction of ancestral fruit characters indicated that the bacoid caryopsis, namely, fleshy or berry-like fruits, was found to be scattered in three lineages of the examined paleotropical woody bamboos. Fruit characters are thus not reliable indicators of phylogeny and bacoid caryopsis likely represents a specialization for particular ecological conditions.     

Larval morphology and biology of oxycorynine weevils and the higher phylogeny of Belidae (Coleoptera, Curculionoidea)

Phylogenetic relationships among members of the family Belidae (Curculionoidea) were reconstructed through cladistic analysis using 58 characters and 17 terminals. The characters were from larval morphology (30), adult morphology (25) and biology regarding larval host-plants and feeding habits (three). They were scored for exemplar taxa in 17 genera, representing different belid subfamilies and tribes, plus two outgroup taxa in Megalopodidae and Nemonychidae. The sampled genera included all those for which larval and adult information is available, and two known only from adults. New information on the larvae and biology of two oxycorynines is provided. These are the Chilean Oxycraspedus cribricollis , whose larvae live in decayed female strobili of the gymnosperm Araucaria araucana , and Hydnorobius hydnorae from Argentina, whose larvae, described and illustrated in the present paper, develop inside the flower and fruit bodies of Prosopanche americana (Hydnoraceae), a root-parasitic angiosperm. The relationships proposed by the single optimal cladogram resulting from simultaneous analysis of all taxa and characters are recovered by one of three optimal cladograms based on the larval data set alone. The cladogram justifies a revised classification of Belidae in two sister subfamilies: Belinae (with tribes Pachyurini, Agnesiotidini and Belini) and Oxycoryninae (with tribes Oxycorynini and Aglycyderini). It summarizes larval and adult synapomorphies defining the family Belidae, subfamilies and tribes. Based on the phylogenetic tree, the evolution of biological traits is traced. Larval development in vegetative organs of conifers is ancestral in Belidae. A shift to reproductive structures characterizes the Oxycorynini, a habit which was conserved while several shifts to distantly related host-plant groups occurred.     

Bias and conflict in phylogenetic inference of myco-heterotrophic plants: a case study in Thismiaceae

Due to morphological reduction and absence of amplifiable plastid genes, the identification of photosynthetic relatives of heterotrophic plants is problematic. Although nuclear and mitochondrial gene sequences may offer a welcome alternative source of phylogenetic markers, the presence of rate heterogeneity in these genes may introduce bias/systematic error in phylogenetic analyses. We examine the phylogenetic position of Thismiaceae based on nuclear 18S rDNA and mitochondrial atpA DNA sequence data, as well as using parsimony, likelihood and Bayesian inference methods. Significant differences in evolutionary rates of these genes between closely related taxa lead to conflicting results: while parsimony analyses of 18S rDNA and combined data strongly support the monophyly of Thismiaceae, Bayesian inference, with and without a relaxed molecular clock, as well as the Swofford–Olsen–Waddell–Hillis (SOWH) test confidently reject this hypothesis. We show that rate heterogeneity in our data leads to long-branch attraction artifacts in parsimony analysis. However, using model-based inference methods the question of whether Thismiaceae are monophyletic remains elusive. On the one hand maximum likelihood nonparametric bootstrapping and parametric hypothesis tests fail to support a paraphyletic Thismiaceae, on the other hand Bayesian inference methods (both without and with a relaxed clock) significantly reject a monophyletic Thismiaceae. These results show that an adequate sampling, the use of rate homogeneous data, and the application of different inference methods are important factors for developing phylogenetic hypotheses of myco-heterotrophic plants. © The Willi Hennig Society 2009.