Insufficient resolving power of mitogenome data in deciphering deep phylogeny of Holometabola

The mitochondrial genome (mitogenome) is one of the most widely used markers for phylogenetic analysis. Compared with whole-genome data, mitogenome data are less expensive to obtain and easier to manipulate. However, compositional bias and accelerated evolutionary rate reduce the effectiveness of the mitogenome in determining insect phylogeny. This study shows that mitogenome data are not suitable to reconstruct deep holometabolan evolution, even with a most comprehensive data coding scheme and the more realistic CAT model. For the deep levels of divergence within Holometabola, protein-coding genes only retain weak phylogenetic signals, leading to peculiar interordinal relationships. Consensus relationships in the Holometabola phylogeny, such as the monophyly of Holometabola, the most basal position of Hymenoptera, and the sister group relationship between the Strepsiptera and Coleoptera were rarely resolved in our analyses. The relationships of the holometabolan groups as inferred by mitogenomes are highly vulnerable to gene types, data coding regimes, model choice, and optimality criteria, and no consistent alternative hypothesis of Holometabola's relationships is supported. Thus, we suggest that the slowly evolving nuclear genes or genome-scale approaches may be better options for resolving deep-level phylogeny of Holometabola.     

A Unique Box in 28S rRNA Is Shared by the Enigmatic Insect Order Zoraptera and Dictyoptera

The position of the Zoraptera remains one of the most challenging and uncertain concerns in ordinal-level phylogenies of the insects. Zoraptera have been viewed as having a close relationship with five different groups of Polyneoptera, or as being allied to the Paraneoptera or even Holometabola. Although rDNAs have been widely used in phylogenetic studies of insects, the application of the complete 28S rDNA are still scattered in only a few orders. In this study, a secondary structure model of the complete 28S rRNAs of insects was reconstructed based on all orders of Insecta. It was found that one length-variable region, D3-4, is particularly distinctive. The length and/or sequence of D3-4 is conservative within each order of Polyneoptera, but it can be divided into two types between the different orders of the supercohort, of which the enigmatic order Zoraptera and Dictyoptera share one type, while the remaining orders of Polyneoptera share the other. Additionally, independent evidence from phylogenetic results support the clade (Zoraptera+Dictyoptera) as well. Thus, the similarity of D3-4 between Zoraptera and Dictyoptera can serve as potentially valuable autapomorphy or synapomorphy in phylogeny reconstruction. The clades of (Plecoptera+Dermaptera) and ((Grylloblattodea+Mantophasmatodea)+(Embiodea+Phasmatodea)) were also recovered in the phylogenetic study. In addition, considering the other studies based on rDNAs, this study reached the highest congruence with previous phylogenetic studies of Holometabola based on nuclear protein coding genes or morphology characters. Future comparative studies of secondary structures across deep divergences and additional taxa are likely to reveal conserved patterns, structures and motifs that can provide support for major phylogenetic lineages.     

18S rDNA sequences and the holometabolous insects

The Holometabola (insects with complete metamorphosis: beetles, wasps, flies, fleas, butterflies, lacewings, and others) is a monophyletic group that includes the majority of the world's animal species. Holometabolous orders are well defined by morphological characters, but relationships among orders are unclear. In a search for a region of DNA that will clarify the interordinal relationships we sequenced approximately 1080 nucleotides of the 5' end of the 18S ribosomal RNA gene from representatives of 14 families of insects in the orders Hymenoptera (sawflies and wasps), Neuroptera (lacewing and antlion), Siphonaptera (flea), and Mecoptera (scorpionfly). We aligned the sequences with the published sequences of insects from the orders Coleoptera (beetle) and Diptera (mosquito and Drosophila), and the outgroups aphid, shrimp, and spider. Unlike the other insects examined in this study, the neuropterans have A-T rich insertions or expansion regions: one in the antlion was approximately 260 bp long. The dipteran 18S rDNA evolved rapidly, with over 3 times as many substitutions among the aligned sequences, and 2-3 times more unalignable nucleotides than other Holometabola, in violation of an insect-wide molecular clock. When we excluded the long-branched taxa (Diptera, shrimp, and spider) from the analysis, the most parsimonious (minimum-length) trees placed the beetle basal to other holometabolous orders, and supported a morphologically monophyletic clade including the fleas+scorpionflies (96% bootstrap support). However, most interordinal relationships were not significantly supported when tested by maximum likelihood or bootstrapping and were sensitive to the taxa included in the analysis. The most parsimonious and maximum-likelihood trees both separated the Coleoptera and Neuroptera, but this separation was not statistically significant.(ABSTRACT TRUNCATED AT 250 WORDS)     

The Strepsiptera problem: phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology

Phylogenetic relationships among the holometabolous insect orders were inferred from cladistic analysis of nucleotide sequences of 18S ribosomal DNA (rDNA) (85 exemplars) and 28S rDNA (52 exemplars) and morphological characters. Exemplar outgroup taxa were Collembola (1 sequence), Archaeognatha (1), Ephemerida (1), Odonata (2), Plecoptera (2), Blattodea (1), Mantodea (1), Dermaptera (1), Orthoptera (1), Phasmatodea (1), Embioptera (1), Psocoptera (1), Phthiraptera (1), Hemiptera (4), and Thysanoptera (1). Exemplar ingroup taxa were Coleoptera: Archostemata (1), Adephaga (2), and Polyphaga (7); Megaloptera (1); Raphidioptera (1); Neuroptera (sensu stricto = Planipennia): Mantispoidea (2), Hemerobioidea (2), and Myrmeleontoidea (2); Hymenoptera: Symphyta (4) and Apocrita (19); Trichoptera: Hydropsychoidea (1) and Limnephiloidea (2); Lepidoptera: Ditrysia (3); Siphonaptera: Pulicoidea (1) and Ceratophylloidea (2); Mecoptera: Meropeidae (1), Boreidae (1), Panorpidae (1), and Bittacidae (2); Diptera: Nematocera (1), Brachycera (2), and Cyclorrhapha (1); and Strepsiptera: Corioxenidae (1), Myrmecolacidae (1), Elenchidae (1), and Stylopidae (3). We analyzed approximately 1 kilobase of 18S rDNA, starting 398 nucleotides downstream of the 5' end, and approximately 400 bp of 28S rDNA in expansion segment D3. Multiple alignment of the 18S and 28S sequences resulted in 1,116 nucleotide positions with 24 insert regions and 398 positions with 14 insert regions, respectively. All Strepsiptera and Neuroptera have large insert regions in 18S and 28S. The secondary structure of 18S insert 23 is composed of long stems that are GC rich in the basal Strepsiptera and AT rich in the more derived Strepsiptera. A matrix of 176 morphological characters was analyzed for holometabolous orders. Incongruence length difference tests indicate that the 28S + morphological data sets are incongruent but that 28S + 18S, 18S + morphology, and 28S + 18S + morphology fail to reject the hypothesis of congruence. Phylogenetic trees were generated by parsimony analysis, and clade robustness was evaluated by branch length, Bremer support, percentage of extra steps required to force paraphyly, and sensitivity analysis using the following parameters: gap weights, morphological character weights, methods of data set combination, removal of key taxa, and alignment region. The following are monophyletic under most or all combinations of parameter values: Holometabola, Polyphaga, Megaloptera + Raphidioptera, Neuroptera, Hymenoptera, Trichoptera, Lepidoptera, Amphiesmenoptera (Trichoptera + Lepidoptera), Siphonaptera, Siphonaptera + Mecoptera, Strepsiptera, Diptera, and Strepsiptera + Diptera (Halteria). Antliophora (Mecoptera + Diptera + Siphonaptera + Strepsiptera), Mecopterida (Antliophora + Amphiesmenoptera), and Hymenoptera + Mecopterida are supported in the majority of total evidence analyses. Mecoptera may be paraphyletic because Boreus is often placed as sister group to the fleas; hence, Siphonaptera may be subordinate within Mecoptera. The 18S sequences for Priacma (Coleoptera: Archostemata), Colpocaccus (Coleoptera: Adephaga), Agulla (Raphidioptera), and Corydalus (Megaloptera) are nearly identical, and Neuropterida are monophyletic only when those two beetle sequences are removed from the analysis. Coleoptera are therefore paraphyletic under almost all combinations of parameter values. Halteria and Amphiesmenoptera have high Bremer support values and long branch lengths. The data do not support placement of Strepsiptera outside of Holometabola nor as sister group to Coleoptera. We reject the notion that the monophyly of Halteria is due to long branch attraction because Strepsiptera and Diptera do not have the longest branches and there is phylogenetic congruence between molecules, across the entire parameter space, and between morphological and molecular data.     

Single-copy nuclear genes resolve the phylogeny of the holometabolous insects

Background  

Evolutionary relationships among the 11 extant orders of insects that undergo complete metamorphosis, called Holometabola, remain either unresolved or contentious, but are extremely important as a context for accurate comparative biology of insect model organisms. The most phylogenetically enigmatic holometabolan insects are Strepsiptera or twisted wing parasites, whose evolutionary relationship to any other insect order is unconfirmed. They have been controversially proposed as the closest relatives of the flies, based on rDNA, and a possible homeotic transformation in the common ancestor of both groups that would make the reduced forewings of Strepsiptera homologous to the reduced hindwings of Diptera. Here we present evidence from nucleotide sequences of six single-copy nuclear protein coding genes used to reconstruct phylogenetic relationships and estimate evolutionary divergence times for all holometabolan orders.     

A mitochondrial genome phylogeny of the Neuropterida (lace-wings, alderflies and snakeflies) and their relationship to the other holometabolous insect orders

We present a mitochondrial (mt) genome phylogeny inferring relationships within Neuropterida (lacewings, alderflies and camel flies) and between Neuropterida and other holometabolous insect orders. Whole mt genomes were sequenced for Sialis hamata (Megaloptera: Sialidae), Ditaxis latistyla (Neuroptera: Mantispidae), Mongoloraphidia harmandi (Raphidioptera: Raphidiidae), Macrogyrus oblongus (Coleoptera: Gyrinidae), Rhopaea magnicornis (Coleoptera: Scarabaeidae), and Mordella atrata (Coleoptera: Mordellidae) and compared against representatives of other holometabolous orders in phylogenetic analyses. Additionally, we test the sensitivity of phylogenetic inferences to four analytical approaches: inclusion vs. exclusion of RNA genes, manual vs. algorithmic alignments, arbitrary vs. algorithmic approaches to excluding variable gene regions and how each approach interacts with phylogenetic inference methods (parsimony vs. Bayesian inference). Of these factors, phylogenetic inference method had the most influence on interordinal relationships. Bayesian analyses inferred topologies largely congruent with morphologically‐based hypotheses of neuropterid relationships, a monophyletic Neuropterida whose sister group is Coleoptera. In contrast, parsimony analyses failed to support a monophyletic Neuropterida as Raphidioptera was the sister group of the entire Holometabola excluding Hymenoptera, and Neuroptera + Megaloptera is the sister group of Diptera, a relationship which has not previously been proposed based on either molecular or morphological data sets. These differences between analytical methods are due to the high among site rate heterogeneity found in insect mt genomes which is properly modelled by Bayesian methods but results in artifactual relationships under parsimony. Properly analysed, the mt genomic data set presented here is among the first molecular data to support traditional, morphology‐based interpretations of relationships between the three neuropterid orders and their grouping with Coleoptera.     

Mantophasmatodea and phylogeny of the lower neopterous insects

Polyneoptera is a name sometimes applied to an assemblage of 11 insect orders comprising the lower neopterous or “orthopteroid” insects. These orders include familiar insects such as Orthoptera (grasshoppers), Blattodea (roaches), Isoptera (termites) (Mantodea) praying mantises, Dermaptera (earwigs), Phasmatodea (stick insects), Plecoptera (stoneflies), as well as the more obscure, Embiidina (web‐spinners), Zoraptera (angel insects) and Grylloblattodea (ice‐crawlers). Many of these insect orders exhibit a high degree of morphological specialization, a condition that has led to multiple phylogenetic hypotheses and little consensus among investigators. We present a phylogenetic analysis of the polyneopteran orders representing a broad range of their phylogenetic diversity and including the recently described Mantophasmatodea. These analyses are based on complete 18S rDNA, 28S rDNA, Histone 3 DNA sequences, and a previously published morphology matrix coded at the ordinal level. Extensive analyses utilizing different alignment methodologies and parameter values across a majority of possible ranges were employed to test for sensitivity of the results to ribosomal alignment and to explore patterns across the theoretical alignment landscape. Multiple methodologies support the paraphyly of Polyneoptera, the monophyly of Dictyoptera, Orthopteroidea (sensu Kukalova‐Peck; i.e. Orthoptera + Phasmatodea + Embiidina), and a group composed of Plecoptera + Dermaptera + Zoraptera. Sister taxon relationships between Embiidina + Phasmatodea in a group called “Eukinolabia”, and Dermaptera + Zoraptera (“Haplocercata”) are also supported by multiple analyses. This analysis also supports a sister taxon relationship between the newly described Mantophasmatodea, which are endemic to arid portions of southern Africa, and Grylloblattodea, a small order of cryophilic insects confined to the north‐western Americas and north‐eastern Asia, in a group termed “Xenonomia”. This placement, coupled with the morphological disparity of the two groups, validates the ordinal status of Mantophasmatodea. © The Willi Hennig Society 2005.     

9-Genes Reinforce the Phylogeny of Holometabola and Yield Alternate Views on the Phylogenetic Placement of Strepsiptera

Background

The extraordinary morphology, reproductive and developmental biology, and behavioral ecology of twisted wing parasites (order Strepsiptera) have puzzled biologists for centuries. Even today, the phylogenetic position of these enigmatic “insects from outer space” [1] remains uncertain and contentious. Recent authors have argued for the placement of Strepsiptera within or as a close relative of beetles (order Coleoptera), as sister group of flies (order Diptera), or even outside of Holometabola.

Methodology/Principal Findings

Here, we combine data from several recent studies with new data (for a total of 9 nuclear genes and ∼13 kb of aligned data for 34 taxa), to help clarify the phylogenetic placement of Strepsiptera. Our results unequivocally support the monophyly of Neuropteroidea ( = Neuropterida + Coleoptera) + Strepsiptera, but recover Strepsiptera either derived from within polyphagan beetles (order Coleoptera), or in a position sister to Neuropterida. All other supra-ordinal- and ordinal-level relationships recovered with strong nodal support were consistent with most other recent studies.

Conclusions/Significance

These results, coupled with the recent proposed placement of Strepsiptera sister to Coleoptera, suggest that while the phylogenetic neighborhood of Strepsiptera has been identified, unequivocal placement to a specific branch within Neuropteroidea will require additional study.     

Molecular Phylogenetics at the Felsenstein Zone: Approaching the Strepsiptera Problem Using 5.8S and 28S rDNA Sequences

Recent efforts to reconstruct the phylogenetic position of the insect order Strepsiptera have elicited a major controversy in molecular phylogenetics. We sequenced the 5.8S rDNA and major parts of the 28S rDNA 5′ region of the strepsipteran speciesStylops melittae.Their evolutionary dynamics were analyzed together with previously published insect rDNA sequences to identify tree estimation bias risks and to explore additional sources of phylogenetic information. Several major secondary structure changes were found as being autapomorphic for the Diptera, the Strepsiptera, or the Archaeognatha. Besides elevated substitution rates a significant AT bias was present in dipteran and strepsipteran 28S rDNA which, however, was restricted to stem sites in the Diptera while also affecting single-stranded sites in the Strepsiptera. When dipteran taxa were excluded from tree estimation all methods consistently supported the placement of Strepsiptera to within the Holometabola. When dipteran taxa were included maximum likelihood continued to favor a sister-group relationship of Strepsiptera with Mecoptera while remaining methods strongly supported a sister-group relationship with Diptera. Parametric bootstrap analysis revealed maximum likelihood as a consistent estimator if rate heterogeneity across sites was taken into account. Though the position of Strepsiptera within Holometabola remains elusive, we conclude that the evolution of dipteran and strepsipteran rDNA involved similar yet independent changes of substitution parameters.     

Phylogenetic significance of the wing-base of the Holometabola (Insecta)

The present knowledge of the wing-base morphology of the holometabolous insects is summarized, and the value of these structures for phylogenetic analysis is demonstrated. An autapomorphy of the Holometabola is a locking mechanism composed of a knob on the basalare and a corresponding cavity on the ventral wing-base. Two synapomorphic hindwing-base characters support a sister-group relationship of Coleoptera and Neuropterida. Only few data are available on the wing-base of the Hymenoptera. An autapomorphy of the taxon is a modification of the wing locking mechanism with reduced size of the basalare and its knob. It is demonstrated that wing-base characters are helpful for the analysis of the relationships between strepsipteran families. However, characters of the wing-base support neither a relationship of Strepsiptera and Coleoptera nor of Strepsiptera and Antliophora.     

Monophyletic Polyneoptera recovered by wing base structure

Phylogenetic relationships among the winged orders of Polyneoptera [Blattodea, Dermaptera, Embiodea (=Embioptera), Isoptera, Mantodea, Orthoptera, Phasmatodea, Plecoptera and Zoraptera] were estimated based on morphological data selected from the hindwing base structure. Cladistic analyses were carried out using hindwing base data alone and in combination with other, more general, morphological data. Both datasets resulted in similar trees and recovered the monophyly of Polyneoptera. Deepest phylogenetic relationships among the polyneopteran orders were not confidently estimated, but the monophyly of Mystroptera (= Embiodea + Zoraptera), Orthopterida (= Orthoptera + Phasmatodea) and Dictyoptera (= Blattodea + Mantodea + Isoptera) was supported consistently. In contrast, placements of Plecoptera and Dermaptera were unstable, although independent analysis of the wing base data supported their sister‐group relationship with two nonhomoplasious synapomorphies (unique conditions in the ventral basisubcostale, and in the articulation between the antemedian notal wing process and first axillary sclerite). Results from the combined wing base plus general morphology data were consistent, even if the wingless orders Grylloblattodea and Mantophasmatodea were included in the analysis. Generally, trees obtained from the present analyses were concordant with the results from other morphological and molecular analyses, but Isoptera were placed inappropriately to be the sister of Blattodea + Mantodea by the inclusion of the wing base data, probably as a result of morphological regressions of the order.     

Phylogenetic position of the Strepsiptera: Review of molecular and morphological evidence

Molecular evidence of the monophyly of the Halteria (Strepsiptera + Diptera) is reviewed. The majority of morphological characters, which have classically been used to establish a Strepsiptera + Coleoptera sister group, are rejected, because they are based on erroneous interpretations of strepsipteran morphology. The scorings of 31 morphological characters, which directly relate to the phylogenetic position of Strepsiptera, are provided, and their distribution and optimization on the molecular + morphological tree is discussed. Of these, 13 characters specifically support the placement of Strepsiptera within the Mecopterida; seven of which are based on the optimization of inapplicable or missing data, and six of which are based on states that can be scored for Strepsiptera. Only a single character (posteromotorism) suggests a sister group relationship with the Coleoptera. The morphological and molecular data are largely congruent, and suggest that the Strepsiptera are sister group to the Diptera.     

The position of the Hymenoptera within the Holometabola as inferred from the mitochondrial genome of Perga condei (Hymenoptera: Symphyta: Pergidae)

We sequenced most of the mitochondrial genome of the sawfly Perga condei (Insecta: Hymenoptera: Symphyta: Pergidae) and tested different models of phylogenetic reconstruction in order to resolve the position of the Hymenoptera within the Holometabola, using mitochondrial genomes. The mitochondrial genome sequenced for P. condei had less compositional bias and slower rates of molecular evolution than the honeybee, as well as a less rearranged genome organization. Phylogenetic analyses showed that, when using mitochondrial genomes, both adequate taxon sampling and more realistic models of analysis are necessary to resolve relationships among insect orders. Both parsimony and Bayesian analyses performed better when nucleotide instead of amino acid sequences were used. In particular, this study supports the placement of the Hymenoptera as sister group to the Mecopterida.     

Insect phylogenomics: results, problems and the impact of matrix composition

In this study, we investigated the relationships among insect orders with a main focus on Polyneoptera (lower Neoptera: roaches, mantids, earwigs, grasshoppers, etc.), and Paraneoptera (thrips, lice, bugs in the wide sense). The relationships between and within these groups of insects are difficult to resolve because only few informative molecular and morphological characters are available. Here, we provide the first phylogenomic expressed sequence tags data ('EST': short sub-sequences from a c(opy) DNA sequence encoding for proteins) for stick insects (Phasmatodea) and webspinners (Embioptera) to complete published EST data. As recent EST datasets are characterized by a heterogeneous distribution of available genes across taxa, we use different rationales to optimize the data matrix composition. Our results suggest a monophyletic origin of Polyneoptera and Eumetabola (Paraneoptera + Holometabola). However, we identified artefacts of tree reconstruction (human louse Pediculus humanus assigned to Odonata (damselflies and dragonflies) or Holometabola (insects with a complete metamorphosis); mayfly genus Baetis nested within Neoptera), which were most probably rooted in a data matrix composition bias due to the inclusion of sequence data of entire proteomes. Until entire proteomes are available for each species in phylogenomic analyses, this potential pitfall should be carefully considered.     

The mitochondrial genome of Bacillus stick insects (Phasmatodea) and the phylogeny of orthopteroid insects

The Order Phasmatodea (stick and leaf insects) includes many well-known species of cryptic phytophagous insects. In this work, we sequenced the almost complete mitochondrial genomes of two stick insect species of the genus Bacillus. Phasmatodea pertain to the Polyneoptera, and represent one of the major clades of heterometabolous insects. Orthopteroid insect lineages arose through rapid evolutionary radiation events, which likely blurred the phylogenetic reconstructions obtained so far; we therefore performed a phylogenetic analysis to resolve and date all major splits of orthopteroid phylogeny, including the relationships between Phasmatodea and other polyneopterans. We explored several molecular models, with special reference to data partitioning, to correctly detect any phylogenetic signal lying in rough data. Phylogenetic Informativeness analysis showed that the maximum resolving power on the orthopteroid mtDNA dataset is expected for the Upper Cretaceous, about 80millionyears ago (Mya), but at least 70% of the maximum informativeness is also expected for the 150-200 Mya timespan, which makes mtDNA a suitable marker to study orthopteroid splits. A complete chronological calibration has also been computed following a Penalized Likelihood method. In summary, our analysis confirmed the monophyly of Phasmatodea, Dictyoptera and Orthoptera, and retrieved Mantophasmatodea as sister group of Phasmatodea. The origin of orthopteroid insects was also estimated to be in the Middle Triassic, while the order Phasmatodea seems to appear in the Upper Jurassic. The obtained results evidenced that mtDNA is a suitable marker to unravel the ancient splits leading to the orthopteroid orders, given a proper methodological approach.     

Endopterygote systematics – where do we stand and what is the goal (Hexapoda,Arthropoda)?

Abstract. Impressive progress has been made recently in the systematics of holometabolous insects. Nevertheless, important questions remain controversial, and uncertainties concerning the relationships of major lineages may even have increased. New analytical techniques have been developed and an immense wealth of molecular data has accumulated. Although no decisive breakthrough has yet been achieved, recent analyses of large molecular datasets have contributed greatly to the reconstruction of the phylogeny of several holometabolous lineages. Extensive combined analyses with substantial morphological datasets and molecular data comprising several genes (‘total evidence’) are still required for a well‐founded phylogenetic hypothesis for the entire group. Endopterygota monophyly is supported mainly by the specific and derived mode of development, which may be considered as a new evolutionary level within Hexapoda. The basal branching pattern remains controversial. A division into two large clades comprising Coleoptera (+ Strepsiptera?) + Neuropterida, on the one hand, and Hymenoptera + [Amphiesmenoptera + Antliophora (including Strepsiptera?)], on the other, appears plausible. Alternative hypotheses have been proposed based on wing characters and molecular data. The position of Strepsiptera remains unsolved. Mecoptera almost certainly is not monophyletic, as Siphonaptera are probably sister to Boreidae. Immense progress has been made in the reconstruction of the intraordinal relationships of all orders, thanks to increasing studies based on combined datasets. Common efforts of morphologists and molecular systematists probably will lead to further rapid progress. Several discoveries of new higher ranking taxa during recent years have revealed that large‐scale habitat destruction will not only have disastrous effects on global biodiversity, but also on the study of insect phylogeny and evolution.     

Elongation factor-1 alpha occurs as two copies in bees: implications for phylogenetic analysis of EF-1 alpha sequences in insects

We report the complete sequence of a paralogous copy of elongation factor-1 alpha (EF-1 alpha) in the honeybee, Apis mellifera (Hymenoptera: Apidae). This copy differs from a previously described copy in the positions of five introns and in 25% of the nucleotide sites in the coding regions. The existence of two paralogous copies of EF-1 alpha in Drosophila and Apis suggests that two copies of EF-1 alpha may be widespread in the holometabolous insect orders. To distinguish between a single, ancient gene duplication and parallel, independent fly and bee gene duplications, we performed a phylogenetic analysis of hexapod EF-1 alpha sequences. Unweighted parsimony analysis of nucleotide sequences suggests an ancient gene duplication event, whereas weighted parsimony analysis of nucleotides and unweighted parsimony analysis of amino acids suggests the contrary: that EF-1 alpha underwent parallel gene duplications in the Diptera and the Hymenoptera. The hypothesis of parallel gene duplication is supported both by congruence among nucleotide and amino acid data sets and by topology-dependent permutation tail probability (T-PTP) tests. The resulting tree topologies are also congruent with current views on the relationships among the holometabolous orders included in this study (Diptera, Hymenoptera, and Lepidoptera). More sequences, from diverse orders of holometabolous insects, will be needed to more accurately assess the historical patterns of gene duplication in EF-1 alpha.      

Aligned 18S and insect phylogeny

The nuclear small subunit rRNA (18S) has played a dominant role in the estimation of relationships among insect orders from molecular data. In previous studies, 18S sequences have been aligned by unadjusted automated approaches (computer alignments that are not manually readjusted), most recently with direct optimization (simultaneous alignment and tree building using a program called "POY"). Parsimony has been the principal optimality criterion. Given the problems associated with the alignment of rRNA, and the recent availability of the doublet model for the analysis of covarying sites using Bayesian MCMC analysis, a different approach is called for in the analysis of these data. In this paper, nucleotide sequence data from the 18S small subunit rRNA gene of insects are aligned manually with reference to secondary structure, and analyzed under Bayesian phylogenetic methods with both GTR+I+G and doublet models in MrBayes. A credible phylogeny of Insecta is recovered that is independent of the morphological data and (unlike many other analyses of 18S in insects) not contradictory to traditional ideas of insect ordinal relationships based on morphology. Hexapoda, including Collembola, are monophyletic. Paraneoptera are the sister taxon to a monophyletic Holometabola but weakly supported. Ephemeroptera are supported as the sister taxon of Neoptera, and this result is interpreted with respect to the evolution of direct sperm transfer and the evolution of flight. Many other relationships are well-supported but several taxa remain problematic, e.g., there is virtually no support for relationships among orthopteroid orders. A website is made available that provides aligned 18S data in formats that include structural symbols and Nexus formats.