On the value of Elongation factor-1α for reconstructing pterygote insect phylogeny

Increasing 28 mitogenomes of Ephemeroptera, Odonata and Plecoptera support the Chiastomyaria hypothesis with three different outgroup combinations

BACKGROUND

The phylogenetic relationships of Odonata (dragonflies and damselflies) and Ephemeroptera (mayflies) remain unresolved. Different researchers have supported one of three hypotheses (Palaeoptera, Chiastomyaria or Metapterygota) based on data from different morphological characters and molecular markers, sometimes even re-assessing the same transcriptomes or mitochondrial genomes. The appropriate choice of outgroups and more taxon sampling is thought to eliminate artificial phylogenetic relationships and obtain an accurate phylogeny. Hence, in the current study, we sequenced 28 mt genomes from Ephemeroptera, Odonata and Plecoptera to further investigate phylogenetic relationships, the probability of each of the three hypotheses, and to examine mt gene arrangements in these species. We selected three different combinations of outgroups to analyze how outgroup choice affected the phylogenetic relationships of Odonata and Ephemeroptera.

METHODS

Mitochondrial genomes from 28 species of mayflies, dragonflies, damselflies and stoneflies were sequenced. We used Bayesian inference (BI) and Maximum likelihood (ML) analyses for each dataset to reconstruct an accurate phylogeny of these winged insect orders. The effect of outgroup choice was assessed by separate analyses using three outgroups combinations: (a) four bristletails and three silverfish as outgroups, (b) five bristletails and three silverfish as outgroups, or (c) five diplurans as outgroups.

RESULTS

Among these sequenced mitogenomes we found the gene arrangement IMQM in Heptageniidae (Ephemeroptera), and an inverted and translocated tRNA-Ile between the 12S RNA gene and the control region in Ephemerellidae (Ephemeroptera). The IMQM gene arrangement in Heptageniidae (Ephemeroptera) can be explained via the tandem-duplication and random loss model, and the transposition and inversion of tRNA-Ile genes in Ephemerellidae can be explained through the recombination and tandem duplication-random loss (TDRL) model. Our phylogenetic analysis strongly supported the Chiastomyaria hypothesis in three different outgroup combinations in BI analyses. The results also show that suitable outgroups are very important to determining phylogenetic relationships in the rapid evolution of insects especially among Ephemeroptera and Odonata. The mt genome is a suitable marker to investigate the phylogeny of inter-order and inter-family relationships of insects but outgroup choice is very important for deriving these relationships among winged insects. Hence, we must carefully choose the correct outgroup in order to discuss the relationships of Ephemeroptera and Odonata.

The mitochondrial genomes of palaeopteran insects and insights into the early insect relationships

Phylogenetic relationships of basal insects remain a matter of discussion. In particular, the relationships among Ephemeroptera, Odonata and Neoptera are the focus of debate. In this study, we used a next-generation sequencing approach to reconstruct new mitochondrial genomes (mitogenomes) from 18 species of basal insects, including six representatives of Ephemeroptera and 11 of Odonata, plus one species belonging to Zygentoma. We then compared the structures of the newly sequenced mitogenomes. A tRNA gene cluster of IMQM was found in three ephemeropteran species, which may serve as a potential synapomorphy for the family Heptageniidae. Combined with published insect mitogenome sequences, we constructed a data matrix with all 37 mitochondrial genes of 85 taxa, which had a sampling concentrating on the palaeopteran lineages. Phylogenetic analyses were performed based on various data coding schemes, using maximum likelihood and Bayesian inferences under different models of sequence evolution. Our results generally recovered Zygentoma as a monophyletic group, which formed a sister group to Pterygota. This confirmed the relatively primitive position of Zygentoma to Ephemeroptera, Odonata and Neoptera. Analyses using site-heterogeneous CAT-GTR model strongly supported the Palaeoptera clade, with the monophyletic Ephemeroptera being sister to the monophyletic Odonata. In addition, a sister group relationship between Palaeoptera and Neoptera was supported by the current mitogenomic data.

Elongation Factor-1α Accurately Reconstructs Relationships Amongst Psyllid Families (Hemiptera: Psylloidea), with Possible Diagnostic Implications

The superfamily Psylloidea (Hemiptera: Sternorrhyncha) lacks a robust multigene phylogeny. This impedes our understanding of the evolution of this group of insects and, consequently, an accurate identification of individuals, of their plant host associations, and their roles as vectors of economically important plant pathogens. The conserved nuclear gene elongation factor-1 alpha (EF-1α) has been valuable as a higher-level phylogenetic marker in insects and it has also been widely used to investigate the evolution of intron/exon structure. To explore evolutionary relationships among Psylloidea, polymerase chain reaction amplification and nucleotide sequencing of a 250-bp EF-1α gene fragment was applied to psyllids belonging to five different families. Introns were detected in three individuals belonging to two families. The nine genera belonging to the family Aphalaridae all lacked introns, highlighting the possibility of using intron presence/absence as a diagnostic tool at a family level. When paired with cytochrome oxidase I gene sequences, the 250 bp EF-1α sequence appeared to be a very promising higher-level phylogenetic marker for psyllids.

EF-1α DNA Sequences Indicate Multiple Origins of Introduced Populations of Essigella californica (Hemiptera: Aphididae)

Aphids in the pine-feeding Nearctic genus Essigella (Sternorrhyncha, Aphididae, Lachninae) have been introduced in Europe, North Africa, Oceania, and South America. Mitochondrial, nuclear, and endosymbiont DNA sequences of 12 introduced populations from three continents confirm they all belong to Essigella californica (Essig, 1909). Intron sequence variation of the nuclear gene EF-1α has revealed the existence of four distinct groups. Group I gathers one population from China, where the species is newly reported, and several from Europe (France and Italy); Group II is represented by one population from Argentina; Group III includes two populations from Southern Australia with one from New Zealand; and Group IV corresponds to five populations from Eastern and South-Eastern Australia. These results indicate that introduced populations of E. californica have at least four source populations. They also show that intron variation of EF-1α can be a method to discriminate populations of asexually reproducing aphids.

First Records of Culicoides sonorensis (Diptera: Ceratopogonidae), a Known Vector of Bluetongue Virus, in Southern Ontario

Ceratopogonidae (Diptera) were collected on sheep farms in southern Ontario to establish whether Culicoides spp. pose a threat to the livestock industry. Specimens were collected in modified CO2-baited Centers for Disease Control and Prevention light traps, returned to the laboratory, freeze-killed, and identified to species under a microscope. In addition to Culicoides variipennis (Coquillet), we found that Culicoides sonorensis Wirth & Jones occurred on a number of farms over a 2-yr period. These records represent a significant departure from C. sonorensis' previously known geographical distribution. We present spatial and temporal distribution data for both species, with an emphasis on C. sonorensis. DNA sequence information is presented so that researchers lacking the necessary taxonomic skills can determine whether C. sonorensis is present in their collections. To differentiate C. sonorensis from C. variipennis, taxonomically reliable and informative traits were found in EF1α and, to a lesser extent, in ITS1, whereas the universal barcode region of cytochrome oxidase subunit 1 (CO1) was unsuitable.

Convergent intron gains in hymenopteran elongation factor-1α

The eukaryotic translation elongation factor-1α gene (eEF1A) has been used extensively in higher level phylogenetics of insects and other groups, despite being present in two or more copies in several taxa. Orthology assessment has relied heavily on the position of introns, but the basic assumption of low rates of intron loss and absence of convergent intron gains has not been tested thoroughly. Here, we study the evolution of eEF1A based on a broad sample of taxa in the insect order Hymenoptera. The gene is universally present in two copies - F1 and F2 - both of which apparently originated before the emergence of the order. An elevated ratio of non-synonymous versus synonymous substitutions and differences in rates of amino acid replacements between the copies suggest that they evolve independently, and phylogenetic methods clearly cluster the copies separately. The F2 copy appears to be ancient; it is orthologous with the copy known as F1 in Diptera, and is likely present in most insect orders. The hymenopteran F1 copy, which may or may not be unique to this order, apparently originated through retroposition and was originally intron free. During the evolution of the Hymenoptera, it has successively accumulated introns, at least three of which have appeared at the same position as introns in the F2 copy or in eEF1A copies in other insects. The sites of convergent intron gain are characterized by highly conserved nucleotides that strongly resemble specific intron-associated sequence motifs, so-called proto-splice sites. The significant rate of convergent intron gain renders intron-exon structure unreliable as an indicator of orthology in eEF1A, and probably also in other protein-coding genes.

Colliding fragment islands transport independent lineages of endemic rock-crawlers (Grylloblattodea: Grylloblattidae) in the Japanese archipelago

Fragment islands, viewed from the paradigm of island biogeographic theory, depend on continual immigration from continental sources to maintain levels of species diversity, or otherwise undergo a period of relaxation where species diversity declines to a lower equilibrium. Japan is a recently derived fragment island with a rich endemic flora and fauna. These endemic species have been described as paleoendemics, and conversely as recently derived Pleistocene colonists. Geological events in the Miocene period, notably the fragmentation and collision of islands, and the subsequent uplift of mountains in central Japan, provided opportunities for genetic isolation. More recently, cyclical climatic change during the Pliocene and Pleistocene periods led to intermittent land bridge connections to continental Asia. Here we investigate the pattern and timing of diversification in a diverse endemic lineage in order to test whether ongoing migration has sustained species diversity, whether there is evidence of relaxation, and how geological and climatic events are associated with lineage diversification. Using multi-locus genetic data, we test these hypotheses in a poorly dispersing, cold-adapted terrestrial insect lineage (Grylloblattodea: Grylloblattidae) sampled from Japan, Korea, and Russia. In phylogenetic analyses of concatenated data and a species tree approach, we find evidence of three deeply divergent lineages of rock-crawlers in Japan consistent with the pattern of island fragmentation from continental Asia. Tests of lineage diversification rates suggest that relaxation has not occurred and instead endemism has increased in the Japanese Grylloblattidae following mountain-building events in the Miocene. Although the importance of climate change in generating species diversity is a commonly held paradigm in Japanese biogeography, our analyses, including analyses of demographic change and phylogeographic range shifts in putative species, suggests that Pleistocene climatic change has had a limited effect on the diversification of rock-crawlers.

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.

Multilocus genetic characterization of two ant vectors (Group II "Dirty 22" species) known to contaminate food and food products and spread foodborne pathogens

The U.S. Food and Drug Administration utilizes the presence of filth and extraneous materials as one of the criteria for implementing regulatory actions and assessing adulteration of food products of public health importance. Twenty-two prevalent pest species (also known as the ''Dirty 22'' species) have been considered by this agency as possible vehicles for the spread of foodborne diseases, and the presence of these species is considered an indicator of unsanitary conditions in food processing and storage facilities. In a previous study, we further categorized the Dirty 22 species into four groups: group I includes four cockroach species, group II includes two ant species, group III includes 12 fly species, and group IV includes four rodent species. Here, we describe the development of three nested PCR primer sets and multilocus genetic characterization by amplifying the small subunit rRNA, elongation factor 1-alpha, and wingless (WNT-1) genes of group II Dirty 22 ant species Monomorium pharaonis and Solenopsis molesta. These novel group II Dirty 22 species-specific nested PCR primer sets can be used when the specimens cannot be identified using conventional microscopic methods. These newly developed assays will provide correct identification of group II Dirty 22 ant species, and the information can be used in the control of foodborne pathogens.

A new species of Rhopalosiphum (Hemiptera, Aphididae) on Chusquea tomentosa (Poaceae, Bambusoideae) from Costa Rica

The new species Rhopalosiphum chusqueae Pérez Hidalgo & Villalobos Muller, is described from apterous viviparous females caught on Chusquea tomentosa in Cerro de la Muerte (Costa Rica). The identity of the species is supported both by the morphological features and by a molecular phylogenetic analysis based on a fragment of the mitochondrial DNA containing the 5' region of the cytochrome c oxidase 1 (COI) and on the nuclear gene coding for the Elongation factor-1 alpha (EF1α). The taxonomic position of the new species is discussed. An identification key to the Aphidinae species living on plants of Bambusoideae (Poaceae) is presented.

Advances in insect phylogeny at the dawn of the postgenomic era

Most species on Earth are insects and thus, understanding their evolutionary relationships is key to understanding the evolution of life. Insect relationships are increasingly well supported, due largely to technological advances in molecular sequencing and phylogenetic computational analysis. In this postgenomic era, insect systematics will be furthered best by integrative methods aimed at hypothesis corroboration from molecular, morphological, and paleontological evidence. This review of the current consensus of insect relationships provides a foundation for comparative study and offers a framework to evaluate incoming genomic evidence. Notable recent phylogenetic successes include the resolution of Holometabola, including the identification of the enigmatic Strepsiptera as a beetle relative and the early divergence of Hymenoptera; the recognition of hexapods as a crustacean lineage within Pancrustacea; and the elucidation of Dictyoptera orders, with termites placed as social cockroaches. Regions of the tree that require further investigation include the earliest winged insects (Palaeoptera) and Polyneoptera (orthopteroid lineages).

Insect phylogenomics: exploring the source of incongruence using new transcriptomic data

The evolution of the diverse insect lineages is one of the most fascinating issues in evolutionary biology. Despite extensive research in this area, the resolution of insect phylogeny especially of interordinal relationships has turned out to be still a great challenge. One of the challenges for insect systematics is the radiation of the polyneopteran lineages with several contradictory and/or unresolved relationships. Here, we provide the first transcriptomic data for three enigmatic polyneopteran orders (Dermaptera, Plecoptera, and Zoraptera) to clarify one of the most debated issues among higher insect systematics. We applied different approaches to generate 3 data sets comprising 78 species and 1,579 clusters of orthologous genes. Using these three matrices, we explored several key mechanistic problems of phylogenetic reconstruction including missing data, matrix selection, gene and taxa number/choice, and the biological function of the genes. Based on the first phylogenomic approach including these three ambiguous polyneopteran orders, we provide here conclusive support for monophyletic Polyneoptera, contesting the hypothesis of Zoraptera + Paraneoptera and Plecoptera + remaining Neoptera. In addition, we employ various approaches to evaluate data quality and highlight problematic nodes within the Insect Tree that still exist despite our phylogenomic approach. We further show how the support for these nodes or alternative hypotheses might depend on the taxon- and/or gene-sampling.