A phylogeny of anisopterous dragonflies (Insecta, Odonata) using mtRNA genes and mixed nucleotide/doublet models

Evolutionary history and divergence times of Odonata (dragonflies and damselflies) revealed through transcriptomics

Dragonflies and damselflies are among the earliest flying insects with extant representatives. However, unraveling details of their long evolutionary history, such as egg laying (oviposition) strategies, is impeded by unresolved phylogenetic relationships, particularly in damselflies. Here we present a transcriptome-based phylogenetic reconstruction of Odonata, analyzing 2,980 protein-coding genes in 105 species representing nearly all the order's families. All damselfly and most dragonfly families are recovered as monophyletic. Our data suggest a sister relationship between dragonfly families of Gomphidae and Petaluridae. According to our divergence time estimates, both crown-Zygoptera and -Anisoptera arose during the late Triassic. Egg-laying with a reduced ovipositor apparently evolved in dragonflies during the late Jurassic/early Cretaceous. Lastly, we also test the impact of fossil choice and placement, particularly, of the extinct fossil species, †Triassolestodes asiaticus, and †Proterogomphus renateae on divergence time estimates. We find placement of †Proterogomphus renateae to be much more impactful than †Triassolestodes asiaticus.

Phylogeny and classification of Odonata using targeted genomics

Dragonflies and damselflies are a charismatic, medium-sized insect order (~6300 species) with a unique potential to approach comparative research questions. Their taxonomy and many ecological traits for a large fraction of extant species are relatively well understood. However, until now, the lack of a large-scale phylogeny based on high throughput data with the potential to connect both perspectives has precluded comparative evolutionary questions for these insects. Here, we provide an ordinal hypothesis of classification based on anchored hybrid enrichment using a total of 136 species representing 46 of the 48 families or incertae sedis, and a total of 478 target loci. Our analyses recovered the monophyly for all three suborders: Anisoptera, Anisozygoptera and Zygoptera. Although the backbone of the topology was reinforced and showed the highest support values to date, our genomic data was unable to stronglyresolve portions of the topology. In addition, a quartet sampling approach highlights the potential evolutionary scenarios that may have shaped evolutionary phylogeny (e.g., incomplete lineage sorting and introgression) of this taxon. Finally, in light of our phylogenomic reconstruction and previous morphological and molecular information we proposed an updated odonate classification and define five new families (Amanipodagrionidae fam. nov., Mesagrionidae fam. nov., Mesopodagrionidae fam. nov., Priscagrionidae fam. nov., Protolestidae fam. nov.) and reinstate another two (Rhipidolestidae stat. res., Tatocnemididae stat. res.). Additionally, we feature the problematic taxonomic groupings for examination in future studies to improve our current phylogenetic hypothesis.

Quaternary Vicariance of Lotic Coeliccia in the Ryukyu-Taiwan Islands Contrasted with Lentic Copera

Lotic dragonflies and damselflies are expected to be more affected by vicariance than lentic sister species. We demonstrated that severe vicariant speciation acted on lotic Coeliccia in contrast to lentic Copera damselflies, which are both included in the family Platycnemididae. We constructed maximum likelihood and Bayesian inference trees of these Platycnemididae species from the continental islands of Ryukyu (Amami, Okinawa, and Yaeyama islands), Taiwan, and Japan relative to Chinese species using raxmlGUI and BEAST, based on the mitochondrial COI gene (682 bp), COII gene (494 bp), 16SrRNA (478 bp), and the nuclear 28SrRNA gene (807 bp). In BEAUti, we calibrated the splitting age of the MRCA of all the Coeliccia species as 1.55-0.15 million years ago (Ma), a date that corresponds to a geologic constraint: the Okinawa trough and associated straits, including the Yilan basin in Taiwan, began to rift at 1.55 Ma, isolating the Ryukyu-Taiwan islands from the Chinese continent. The vicariance split Coeliccia into the Ryukyu-side clade of Coeliccia ryukyuensis (Coe. r. ryukyuensis in Okinawa and Coe. r. amamii in Amami) and Coeliccia flavicauda (Coe. f. masakii in Yaeyama and Coe. f. flavicauda in southern Taiwan), and the Chinese-side clade of Coeliccia cyanomelas (northern Taiwan and China), separated by the Okinawa trough. These Coeliccia species were further deeply differentiated to form local populations on the major islands and some of the minor islands. The Copera clade constituted a sister of the lotic Coeliccia clade, but genetic differentiation was not recognizable in lentic Copera between China, Taiwan, and Japan. Base substitution rates applying a strict clock model were estimated for COI: 0.0783, COII: 0.0803, 18SrRNA: 0.0186, 28SrRNA: 0.00577, and combined: 0.0408 substitutions/site/myr, and these rates are relatively high.

The larval ontogeny of Coryphaeschna perrensi (McLachlan, 1887): Supporting monophyletic groups in Aeshnidae dragonflies (Insecta: Odonata: Anisoptera)

The development of the larval external morphology of Coryphaeschna perrensi is reported based primarily on a comparison of successive exuviae of reared specimens, with the second stadium larvae first described separately. Accentuated changes observable throughout successive moltings occur in some structures, such as the head capsule, labium, and anal appendages, allowing for the definition of characters with naturally ordered, polarized, and linear states (transformation series) by ontogenetic evidence. The terminal (less general) and nonterminal (more general) states of the described transformation series correspond by primary homology to the conditions found in larvae of other dragonfly species. Consequently, as the result of a parsimony analysis and subsequently ontogenetic rooting, the disposition of the states of 17 characters in a sample of final-stadium larvae of 23 species, representatives of the six Aeshnidae tribes (21) and Austropetaliidae (2), results in a hierarchical network comprising six distinct taxonomic levels of inclusion of C. perrensi. The levels correspond to Aeshnidae, Aeshninae, Aeshnini (part) + Gynacanthini, Coryphaeschna + Remartinia, Coryphaeschna, and Coryphaeschna except C. adnexa, which are groups previously recognized as monophyletic resulting from analyses considering adult morphology. Immature insect morphology coupled with ontogenetic observation presenting great potential to hypothesize phylogenetic relationships and investigate heterochronic events.

The complete mitochondrial genome of the emperor dragonfly Anax imperator LEACH, 1815 (Odonata : Aeshnidae) via NGS sequencing

Here we report the complete mitochondrial genome of the emperor dragonfly, Anax imperator (Odonata: Aeshnidae) as the first of its genus. Data were generated via next generation sequencing (NGS) and assembled using an iterative approach. The typical metazoan set of 37 genes (13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes) was detected in the same gene order as in other odonate mitogenomes. However, only three intergenic spacer regions are present in A. imperator lacking the distinct s5 spacer, which was regarded as informative feature of the odonate suborder Anisoptera (dragonflies) but absent in Zygoptera (damselflies). With 16,087 bp, it is the longest anisopteran mitogenome to date, mainly due to the long A + T-rich control region of 1291 bp.

Musculoskeletal modelling under an evolutionary perspective: deciphering the role of single muscle regions in closely related insects

Insects show a remarkable diversity of muscle configurations, yet the factors leading to this functional diversity are poorly understood. Here, we use musculoskeletal modelling to understand the spatio-temporal activity of an insect muscle in several dragonfly species and to reveal potential mechanical factors leading to a particular muscle configuration. Bite characteristics potentially show systematic signal, but absolute bite force is not correlated with size. Muscle configuration and inverse dynamics show that the wider relative area of muscle attachment and the higher activity of subapical muscle groups are responsible for this high bite force. This wider attachment area is, however, not an evolutionary trend within dragonflies. Our inverse dynamic data, furthermore, show that maximum bite forces most probably do not reflect maximal muscle force production capability in all studied species. The thin head capsule and the attachment areas of muscles most probably limit the maximum force output of the mandibular muscles.

Molecular phylogeny of Orthetrum dragonflies reveals cryptic species of Orthetrum pruinosum

Dragonflies of the genus Orthetrum are members of the suborder Anisoptera, family Libellulidae. There are species pairs whose members are not easily separated from each other by morphological characters. In the present study, the DNA nucleotide sequences of mitochondrial and nuclear genes were employed to elucidate the phylogeny and systematics of Orthetrum dragonflies. Phylogenetic analyses could not resolve the various subfamilies of the family Libellulidae unequivocally. The nuclear 28S rRNA gene is highly conserved and could not resolve congeneric species of Orthetrum. Individual mitochondrial genes (COI, COII, and 16S rRNA) and combination of these genes as well as the nuclear ITS1&2 genes clearly differentiate morphologically similar species, such as the reddish species pairs O. chrysis and O. testaceum, and the bluish-coloured species O. glaucum and O. luzonicum. This study also reveals distinct genetic lineages between O. pruinosum schneideri (occurring in Malaysia) and O. pruinosum neglectum (occurring north of Peninsular Malaysia from India to Japan), indicating these taxa are cryptic species.

The gonangulum: a reassessment of its morphology, homology, and phylogenetic significance

The gonangulum is a sclerite in the female genitalic region of insects. Its presence or full development has long been considered an apomorphy supporting Zygentoma + Pterygota. Recent studies of female genitalia in several insect orders (K.-D. Klass and co-workers) revealed many new data on the gonangulum and homologous sclerotisations (laterocoxa LC9). Herein the gonangulum area is described (including articulations, muscle attachments, sulci) and compared among Archaeognatha, Zygentoma, Odonata, Dermaptera, Dictyoptera, and Notoptera. A wider perspective is provided to the topic by addressing some novel issues: identification of LC9 sclerotisations in non-insect taxa and in insects that secondarily lack an ovipositor; occurrence of homonomous sclerotisations in other abdominal segments of both sexes; morphological interpretation of LC9; and the role of paedomorphosis in LC9 evolution. As a result, there is currently no support for any insect lineage from this character system. For gonangulum-related characters both a significant intra-ordinal variation and frequent homoplasy are demonstrated using various Odonata, Dermaptera, and Dictyoptera as examples. Divergent fates of LC9 in simplified genitalia are shown using a dermapteran and an odonatan. We view all this as a showcase of how a renewed and more detailed examination of a character system can dramatically change the phylogenetic evidence drawn from it.

Phylogeographic analysis elucidates the influence of the ice ages on the disjunct distribution of relict dragonflies in Asia

Unusual biogeographic patterns of closely related groups reflect events in the past, and molecular analyses can help to elucidate these events. While ample research on the origin of disjunct distributions of different organism groups in the Western Paleartic has been conducted, such studies are rare for Eastern Palearctic organisms. In this paper we present a phylogeographic analysis of the disjunct distribution pattern of the extant species of the strongly cool-adapted Epiophlebia dragonflies from Asia. We investigated sequences of the usually more conserved 18 S rDNA and 28 S rDNA genes and the more variable sequences of ITS1, ITS2 and CO2 of all three currently recognised Epiophlebia species and of a sample of other odonatan species. In all genes investigated the degrees of similarity between species of Epiophlebia are very high and resemble those otherwise found between different populations of the same species in Odonata. This indicates that substantial gene transfer between these populations occurred in the comparatively recent past. Our analyses imply a wide distribution of the ancestor of extant Epiophlebia in Southeast Asia during the last ice age, when suitable habitats were more common. During the following warming phase, its range contracted, resulting in the current disjunct distribution. Given the strong sensitivity of these species to climatic parameters, the current trend to increasing global temperatures will further reduce acceptable habitats and seriously threaten the existences of these last representatives of an ancient group of Odonata.

Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: evidence from case studies in the Metazoa

Background

Failure to account for covariation patterns in helical regions of ribosomal RNA (rRNA) genes has the potential to misdirect the estimation of the phylogenetic signal of the data. Furthermore, the extremes of length variation among taxa, combined with regional substitution rate variation can mislead the alignment of rRNA sequences and thus distort subsequent tree reconstructions. However, recent developments in phylogenetic methodology now allow a comprehensive integration of secondary structures in alignment and tree reconstruction analyses based on rRNA sequences, which has been shown to correct some of these problems. Here, we explore the potentials of RNA substitution models and the interactions of specific model setups with the inherent pattern of covariation in rRNA stems and substitution rate variation among loop regions.

Results

We found an explicit impact of RNA substitution models on tree reconstruction analyses. The application of specific RNA models in tree reconstructions is hampered by interaction between the appropriate modelling of covarying sites in stem regions, and excessive homoplasy in some loop regions. RNA models often failed to recover reasonable trees when single-stranded regions are excessively homoplastic, because these regions contribute a greater proportion of the data when covarying sites are essentially downweighted. In this context, the RNA6A model outperformed all other models, including the more parametrized RNA7 and RNA16 models.

Conclusions

Our results depict a trade-off between increased accuracy in estimation of interdependencies in helical regions with the risk of magnifying positions lacking phylogenetic signal. We can therefore conclude that caution is warranted when applying rRNA covariation models, and suggest that loop regions be independently screened for phylogenetic signal, and eliminated when they are indistinguishable from random noise. In addition to covariation and homoplasy, other factors, like non-stationarity of substitution rates and base compositional heterogeneity, can disrupt the signal of ribosomal RNA data. All these factors dictate sophisticated estimation of evolutionary pattern in rRNA data, just as other molecular data require similarly complicated (but different) corrections.

Evolutionary relationships among scyphozoan jellyfish families based on complete taxon sampling and phylogenetic analyses of 18S and 28S ribosomal DNA

A stable phylogenetic hypothesis for families within jellyfish class Scyphozoa has been elusive. Reasons for the lack of resolution of scyphozoan familial relationships include a dearth of morphological characters that reliably distinguish taxa and incomplete taxonomic sampling in molecular studies. Here, we address the latter issue by using maximum likelihood and Bayesian methods to reconstruct the phylogenetic relationships among all 19 currently valid scyphozoan families, using sequence data from two nuclear genes: 18S and 28S rDNA. Consistent with prior morphological hypotheses, we find strong evidence for monophyly of subclass Discomedusae, order Coronatae, rhizostome suborder Kolpophorae and superfamilies Actinomyariae, Kampylomyariae, Krikomyariae, and Scapulatae. Eleven of the 19 currently recognized scyphozoan families are robustly monophyletic, and we suggest recognition of two new families pending further analyses. In contrast to long-standing morphological hypotheses, the phylogeny shows coronate family Nausithoidae, semaeostome family Cyaneidae, and rhizostome suborder Daktyliophorae to be nonmonophyletic. Our analyses neither strongly support nor strongly refute monophyly of order Rhizostomeae, superfamily Inscapulatae, and families Ulmaridae, Catostylidae, Lychnorhizidae, and Rhizostomatidae. These taxa, as well as familial relationships within Coronatae and within rhizostome superfamily Inscapulatae, remain unclear and may be resolved by additional genomic and taxonomic sampling. In addition to clarifying some historically difficult taxonomic questions and highlighting nodes in particular need of further attention, the molecular phylogeny presented here will facilitate more robust study of phenotypic evolution in the Scyphozoa, including the evolution characters associated with mass occurrences of jellyfish.