Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements

As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements

Ribosomal DNA phylogeny of the major extant arthropod classes and the evolution of myriapods

THE evolutionary relationships among arthropods are of particular interest because the best-studied model system for ontogenetic pattern formation, the insect Drosophila, is a member of this phylum. Evolutionary inferences about the developmental mechanisms that have led to the various designs of the arthropod body plan depend on a knowledge of the phylogenetic framework of arthropod evolution, Based on morphological evidence(1-3), but also on palaeontological considerations(4), the sister group of the insects is believed to be found among the myriapods. Using nuclear ribosomal gene sequences for constructing a molecular phylogeny, we provide strong evidence that the crustaceans and not the myriapods should be considered to be the sister group of the insects. Moreover, the degree of sequence divergence suggests that the diversification of the myriapods occurred during the Cambrian. Our findings have general implications for the course of land colonization by the different arthropod groups, as well as for the interpretation of primitive and derived features of arthropod morphology

An episodic change of rDNA nucleotide substitution rate has occurred during the emergence of the insect order Diptera

We have studied the potential reasons for a conspicuous deviation of substitution rates in Dipteran ribosomal genes. Systematic pairwise relative-rate tests reveal that a significant increase in substitution rate is characteristic for Diptera, but not for the other insects analyzed. Estimation of sequence change in specific lineages reveals that most of these substitutions took place during the evolution of the Dipteran stem lineage. When related to the paleontologically documented periods of absolute time, the substitution rate in the stem lineage of the Diptera underwent an at least 20-fold increase compared to other insect groups and subsequently dropped by a factor of 10 before the diversification of the major Dipteran subgroups. Systematic comparisons of nucleotide composition show that this episodic change in substitution rate was accompanied by a significant increase in A+T content of Dipteran rDNA. Our data suggest that the episodic evolution of the Dipteran rDNA has most probably been caused by a change of directional mutation pressure which must have occurred during the evolution of the stem lineage of the Diptera

Evolution and phylogeny of the diptera: A molecular phylogenetic analysis using 28S rDNA sequences

Portions of the large ribosomal subunit RNA gene (28S rDNA) encompassing the D1 and the D7 region were obtained from 16 dipteran species and families to reconstruct early phylogenetic events in the order Diptera. For outgroup comparison, the corresponding sequences were used from representative taxa of the Siphonaptera, Mecoptera, and Lepidoptera. A subset of 488 unambiguously alignable sites was analyzed with respect to important sequence evolution parameters. We found (1) sequence variability is significantly higher in double-stranded sites than in single-stranded sites, (2) transitions are close to saturation in most pairwise sequence comparisons, (3) significant substitution rate heterogeneity exists across sites, and (4) significant substitution rate heterogeneity exists among lineages. Tree reconstruction was carried out with the neighbor joining, maximum parsimony, and maximum likelihood methods. Four major subgroups are consistently and robustly supported: the Brachycera, the Culicomorpha, the Tipulomorpha sensu stricto, and the hitherto controversial Bibionomorpha sensu late, which includes the families Sciaridae, Mycetophilidae, Cecidomyiidae, Bibionidae, Scatopsidae, and Anisopodidae. The phylogenetic relationships within or among these subclades and the positions of the families Psychodidae and Trichoceridae were not robustly resolved. These results support the view that the mouthparts of extant dipteran larvae evolved from a derived sound state characterized by subdivided and obliquely moving mandibles. Furthermore sequence divergence and the paleontological record consistently indicate that a period of rapid cladogenesis gave rise to the major dipteran subgroups

Arthropod rDNA phylogeny revisited: A consistency analysis using Monte Carlo simulation

There has been a firm consent among traditional arthropod systematists that hexapods share a common most recent ancestor with myriapods. Molecular studies, however, question this view by supporting a closer relationship of hexapods with crustaceans. As there is only one evolutionary history, either molecular or morphological data must have been incorrectly interpreted. Morphology can be misleading when structural similarity results from convergent evolution. Molecular tree estimation can also be misleading when the underlying sequence evolution assumptions violate actual sequence evolution parameters. We therefore reexamined the validity of a previously published arthropod ribosomal DNA phylogeny using a new generation of molecular phylogenetic analysis tools. Attention was directed towards potential tree estimation bias arising from the combination of strong rate heterogeneity across sites in ribosomal sequences and elevated substitution rates of insect and crustacean sequences. Consistency analysis with the Monte Carlo simulation based parametric bootstrap method revealed that substitution rate differences in arthropod ribosomal DNA were large enough to cause tree estimation bias for methods that insufficiently correct for multiple substitutions. Maximum likelihood, however, proved immune against long-branch attraction when rate heterogeneity across sites was taken into account. When we estimated trees with maximum likelihood algorithms that take across-sites rate heterogeneity into account, the hexapod/crustacean sistergroup clade remained very strongly supported corroborating confidence in this clade. As recent analyses of protein coding genes and mitochondrial genome rearrangements also converge on uniting hexapods with crustaceans, a revision of the traditional ideas about the origin and evolution of hexapods seems inevitable

Insect embryogenesis - What is ancestral and what is derived?

The systematic genetic analysis of Drosophila development has provided us with a deep insight into the molecular pathways of early embryogenesis. The question arises now whether these insights can serve as a more general paradigm of early development, or whether they apply only to advanced insect orders. Though it is too early to give a definitive answer to this question, we suggest that there is currently no firm reason to believe that the molecular mechanisms that were elucidated in Drosophila may not also apply to other forms of insect embryogenesis. Thus, many of the Drosophila genes involved in early pattern formation may have comparable functions in other insects and possibly throughout the arthropods

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 species Stylops 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. (C) 1998 Academic Press

Mitochondrial protein phylogeny joins myriapods with chelicerates

The animal phylum Arthropoda is very useful for the study of body plan evolution given its abundance of morphologically diverse species and our profound understanding of Drosophila development(1). However, there is a lack of consistently resolved phylogenetic relationships between the four extant arthropod subphyla, Hexapoda, Myriapoda, Chelicerata and Crustacea. Recent molecular studies(2-4) have strongly supported a sister group relationship between Hexapoda and Crustacea, but have not resolved the phylogenetic position of Chelicerata and Myriapoda. Here we sequence the mitochondrial genome of the centipede species Lithobius forficatus and investigate its phylogenetic information content. Molecular phylogenetic analysis of conserved regions from the arthropod mitochondrial proteome yields highly resolved and congruent trees. We also rnd that a sister group relationship between Myriapoda and Chelicerata is strongly supported. We propose a model to explain the apparently parallel evolution of similar head morphologies in insects and myriapods