Reanalyzing the Palaeoptera problem – The origin of insect flight remains obscure
Introduction
The phylogenetic relationships between the three lineages mayflies (Ephemeroptera), damselflies and dragonflies (Odonata), and all other winged insects (Neoptera), subsumed as the “Palaeoptera Problem” (Hovmöller et al., 2002), are a matter of debate now for decades. Resolving these early branching events within pterygote evolution has been a persisting challenge using molecular data (Whiting et al., 1997, Wheeler, 2001, Hovmöller et al., 2002). Also a wealth of morphological arguments have been brought forward in support of the three different hypotheses on phylogenetic relationships. Here, we only briefly state these morphological arguments, detailed overviews have been given in Klass (2007) and Klass (2009), and highlight various molecular studies.
The morphological arguments in favor of the Chiastomyaria hypothesis (Ephemeroptera + Neoptera; Fig. 1a) are based on the direct sperm transfer in Ephemeroptera and all neopteran insects. Compared to Chiastomyaria, Odonata have a male secondary copulatory apparatus which functions as a temporary sperm reservoir, sperm removal, and sperm transfer system (Tillyard, 1917, Boudreaux, 1979, Corbet, 1980, Pfau, 1991, Pfau, 2011). Also, the similar functioning of the flight apparatus of Ephemeroptera and Neoptera with thoracic muscle groups attached to the tergum and thus moving the wings indirectly during the upstroke was proposed as a potential synapomorphy (Matsuda, 1970, Pfau, 1986, Pfau, 1991).
Molecular support for Chiastomyaria was mainly provided by analyses of nuclear rRNA data (18S and/or 28S) based on improved alignment procedures (Kjer, 2004, Yoshizawa and Johnson, 2005, Misof et al., 2007) and biologically more realistic alignments based on RNA secondary structures (Mallatt and Giribet, 2006, von Reumont et al., 2009). Also analyses of large-scale datasets e.g. within mitogenomic studies (Wan et al., 2012, Li et al., 2014) and ‘phylogenomic’ studies – multi-gene approaches based on whole genome and/or transcriptomic data (Simon et al., 2009, Letsch and Simon, 2013) supported Chiastomyaria.
Metapterygota (Odonata + Neoptera; Fig. 1b) was proposed based on features of the mandibular food uptake system, the respiratory system, the imaginal molts and the circulatory system (Staniczek, 2000, Staniczek, 2001, Beutel and Pohl, 2006, Pass, 2006). In Odonata and Neoptera, the mandibles are anteriorly connected to the head with a ball-and-socket joint whereas in Ephemeroptera an anterior articulation complex is present which is in fact composed of two joints, an anterolateral and a paratentorial part (Staniczek, 2000, Staniczek, 2001). A homologous anterior articulation complex is also present in Zygentoma, the sistergroup of all winged insects (Staniczek, 2000, Staniczek, 2001, Blanke et al., 2014, Blanke et al., 2015). Concerning the respiratory system, the meso- and metathoracic legs and wings are supplied by two tracheal stems each originating from the spiraculi of the same and the following segment in Odonata and Neoptera (Kristensen, 1975, Kristensen, 1981). Moreover, Ephemeroptera are the only winged insects, which undergo an additional molt during the winged stage.
Molecular support for Metapterygota is comparably low (e.g., Whiting et al., 1997, Wheeler et al., 2001, Hovmöller et al., 2002, Ogden and Whiting, 2003) and mainly driven by mitogenomic approaches (Ma et al., 2014, Song et al., 2016). Simon et al. (2012) recovered Metapterygota based on a phylogenomic approach but it was also highlighted that phylogenomic data matrices have more complex phylogenetic signal, thus recovering different branching scenarios.
Palaeoptera (Odonata + Ephemeroptera; Fig. 1c) was proposed based on similarities in the antennae, maxillae, and wings (Brauckmann and Zessin, 1989, Bechly et al., 2001, Kukalová-Peck, 2008). In Odonata and Ephemeroptera the pedicellus is longer than the scapus, and both taxa lack antennal circulatory organs in the adult stage. The maxillae in both taxa are characterized by the presence of mesally directed dentisetae, and strengthened setae-like structures at the lacinia (Staniczek, 2000, Staniczek, 2001, Blanke et al., 2012). However, it has to be emphasized that subapical rows of setae superficially resembling dentiseta-like structures were also shown for Blattodea (Zhuzhikov, 2007), but at present it is unclear from the published data, whether the depicted mesal rows of setae really constitute dentisetae. Further investigation on a larger taxon sampling with more detailed documentation of the lacinial morphology is necessary in order to derive a well-informed conclusion about the identity of these structures.
Furthermore, a plethora of wing characters has been proposed as synapomorphic for Odonata and Ephemeroptera: the inability to fold the wings over the abdomen horizontally, similar wing-base sclerites and similarities in the intercalary veins, the proximate stem of the anterior radial vein (RA) and the posterior radial vein (RP) as well as the common stem of anterior medial vein (MA) and posterior medial vein (MP) (Riek and Kukalová-Peck, 1984, Willkommen and Hörnschemeyer, 2007, Yoshizawa and Ninomiya, 2007, Kukalová-Peck, 2008).
The Palaeoptera hypothesis was predominantly supported by earlier molecular studies and nuclear rRNA data analyses (18S and/or 28S). Ogden and Whiting (2003) demonstrated that the particular arrangement of Odonata and Ephemeroptera is extraordinarily sensitive to alignment methodology, the alignment parameters selected within a particular methodology, and the method of tree reconstruction. As a consequence support increased for Chiastomyaria (see above), or, alternatively, Palaeoptera was only weakly supported (Letsch et al., 2010). Alternative molecular markers, such as nuclear protein coding genes (DNA polymerase delta) and the two largest subunits of RNA polymerase II (Ishiwata et al., 2010, Sasaki et al., 2013) or a combination of nuclear rRNA data (18S and 28S) and nuclear protein coding genes (Histone 3 and Elongation factor-1α), again supported the Palaeoptera hypothesis (Kjer et al., 2006). The Palaeoptera hypothesis also gained increased support by several phylogenomic studies (e.g., Meusemann et al., 2010, von Reumont et al., 2012). However, Thomas et al. (2013) showed the impact of taxon sampling, outgroup choice and heterogeneous base composition across taxa on the retrieved relationships between Odonata, Ephemeroptera and Neoptera. Their analyses of datasets based on Sanger sequencing data including nuclear rRNA data (12S, 18S and 28S) and nuclear and mitochondrial protein coding genes (Histone 3, Elongation factor-1α and the mitochondrial gene cytochrome oxidase subunit II) consistently supported Palaeoptera. Moreover, they reanalyzed previously published mitogenomic and phylogenomic studies and highlighted potential sources of systematic error. A recent phylogenomic study addressing the relationships among all major insect lineages supported Palaeoptera in all tree reconstructions (Misof et al., 2014). However, analyses of alternative signal using Four-cluster Likelihood Quartet Mapping also revealed inherent phylogenetic signal for Chiastomyaria, which is not visible from simple tree reconstruction analyses alone.
To further shed light on the early branching events within pterygote evolution, we reanalyzed the Palaeoptera problem in an attempt to address potential alternative and/or confounding signal within phylogenomic data. We therefore compiled new datasets mainly based on transcriptomes published by Misof et al. (2014) and including data from whole genomes. In addition, we evaluated in-depth confounding and alternative signal using various methodological approaches. In addition, the morphological arguments brought forward since the reviews of Klass (2007) and Klass (2009) are discussed in the light of results we obtained from our molecular analyses.
Section snippets
Data set generation
We compiled two different datasets (Supplementary Material Table S1). Dataset A comprised 41 taxa, including sequence data from five Odonata and five Ephemeroptera species, seven primarily wingless Hexapoda (two Diplura, two Archaeognatha and three Zygentoma), and one representative each for the 24 currently recognized neopteran insect orders. Data were derived from transcriptomes or genomes. In dataset B, we included only neopteran taxa for which (draft) genomes were available, leading to 26
The early branching events of winged insects
Palaeoptera was inferred in all analyses with 100% bootstrap support in both datasets (Fig. 2 and Supplementary Material Fig. S3). Other relationships, except for a few clades within polyneopteran and paraneopteran insects in the tree derived from dataset A, were maximally supported. Zygentoma was inferred as sistergroup to Pterygota in all trees with maximal support (Fig. 2, Supplementary Material Fig. S3). The high support for Palaeoptera is in agreement with most molecular multi-gene or
Conclusion
In contrast to earlier molecular studies, which also supported Metapterygota, the present study excludes this hypothesis as a possible evolutionary scenario of early winged insects. However, ambiguities still exist concerning the Palaeoptera and Chiastomyaria hypotheses. Besides methodological considerations concerning systematic bias, the comparatively low coverage of Ephemeroptera and primarily wingless Hexapoda might affect current phylogenetic reconstructions. However, simply adding more
Acknowledgements
The authors thank Panagiotis Provataris (ZMB, ZFMK Bonn, Germany), Bernhard Misof (ZMB, ZFMK Bonn, Germany) and Stephen Richards (Baylor, Houston, USA) in the frame of the i5K consortium for granting us permission to use and analyze the unpublished genome sequence and preliminary official gene sets of the dragonfly Ladona fulva and the mayfly Ephemera danica. The authors also especially thank the 1KITE Odonata group (www.1kite.org/subprojects.html), Ryuichiro Machida (University of Tsukuba,
References (112)
- et al.
Basic local alignment search tool
J. Mol. Biol.
(1990) - et al.
The palaeoptera problem: basal pterygote phylogeny inferred from 18S and 28S rDNA sequences
Cladistics
(2002) - et al.
Phylogenomics: the beginning of incongruence?
Trends Genet.
(2006) - et al.
The phylogeny of Ephemeroptera in Pterygota revealed by the mitochondrial genome of Siphluriscus chinensis (Hexapoda: Insecta)
Gene
(2014) - et al.
Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch
Mol. Phylogenet. Evol.
(2006) - et al.
Characterizing positive and negative selection and their phylogenetic effects
Gene
(2008) - et al.
Towards an 18S phylogeny of hexapods: accounting for group-specific character covariance in optimized mixed nucleotide/doublet models
Zoology (Jena)
(2007) - et al.
Genomic and morphological evidence converge to resolve the enigma of strepsiptera
Curr. Biol.
(2012) - et al.
The problem with “the Paleoptera Problem:” sense and sensitivity
Cladistics
(2003) Homology and the optimization of DNA sequence data
Cladistics
(2001)
Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice
Syst. Biol.
New results concerning the morphology of the most ancient dragonflies (Insecta: odonatoptera) from the Namurian of Hagen-Vorhalle (Germany)
J. Zool. Syst. Evol. Res.
Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes)
Syst. Biol.
Endopterygote systematics – where do we stand and what is the goal (Hexapoda, Arthropoda)?
Syst. Entomol.
The identification of concerted convergence in insect heads corroborates Palaeoptera
Syst. Biol.
Head morphology of Tricholepidion gertschi indicates monophyletic Zygentoma
Front. Zool.
Mandibles with two joints evolved much earlier in the history of insects: dicondyly is a synapomorphy of bristletails, silverfish and winged insects
Syst. Entomol.
Computational biomechanics changes our view on insect head evolution
Proc. Biol. Sci.
Revival of Palaeoptera—head characters support a monophyletic origin of Odonata and Ephemeroptera (Insecta)
Cladistics
A site- and time-heterogeneous model of amino acid replacement
Mol. Biol. Evol.
Arthropod Phylogeny with Special Reference to Insects, 99 Edition
Neue Meganeuridae aus dem Namurium von Hagen-Vorhalle (BRD) und die Phylogenie der Meganisoptera (Insecta, Odonata)
Deutsche Entomologische Zeitschrift
An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics
Syst. Biol.
BLAST plus : architecture and applications
BMC Bioinf.
Terrace aware data structure for phylogenomic inference from supermatrices
Syst. Biol.
Biology of Odonata
Annu. Rev. Entomol.
Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects
Mol. Biol. Evol.
Phylogenomics and the reconstruction of the tree of life
Nat. Rev. Genet.
Phylogenetic analysis of gene expression
Integr. Comp. Biol.
Pairwise comparisons across species are problematic when analyzing functional genomic data
Proc. Natl. Acad. Sci. U. S. A.
New light shed on the oldest insect
Nature
Improved modeling of compositional heterogeneity supports sponges as sister to all other animals
Curr. Biol.
SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building
Mol Biol Evol
Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites
Mol. Biol. Evol.
Is sparse taxon sampling a problem for phylogenetic inference?
Syst. Biol.
Tracing the decay of the historical signal in biological sequence data
Syst. Biol.
Regression and time-series model selection in small samples
Biometrika
Phylogenetic relationships among insect orders based on three nuclear protein-coding gene sequences
Mol. Phylogenet. Evol.
SymTest
The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated
Syst. Biol.
The rapid generation of mutation data matrices from protein sequences
Comput. Appl. Biosci.
ModelFinder: fast model selection for accurate phylogenetic estimates
Br. J. Pharmacol.
MAFFT multiple sequence alignment software version 7: improvements in performance and usability
Mol. Biol. Evol.
Aligned 18S and insect phylogeny
Syst. Biol.
A molecular phylogeny of hexapoda
Arthropod Systematic Phylogeny
A critical review of current data and hypotheses on hexapod phylogeny
Proc Arthropod. Embryol. Soc. Japan
Die Stammesgeschichte der Hexapoden: eine kritische Diskussion neuerer Daten und Hypothesen
Denisia
Different versions of the Dayhoff rate matrix
Mol. Biol. Evol.
The phylogeny of hexapod “orders”. A critical review of recent accounts
Zeitschrift für zoologische Systematik und Evolutionsforschung
Phylogeny of insect orders
Annu. Rev. Entomol.
Cited by (31)
The evolution of insect biodiversity
2021, Current BiologyCitation Excerpt :The insect orders Odonata (dragonflies and damselflies) and Ephemeroptera (mayflies) were placed into the clade Palaeoptera, characterised by their inability to fold their wings over their abdomen, which distinguishes them from the remaining winged insects (Neoptera)66. However, the monophyly of Odonata and Ephemeroptera has been the subject of much debate, with the results of some morphological4,67–69 and molecular analyses11,30,70 suggesting that Palaeoptera may be paraphyletic with respect to Neoptera, and that Ephemeroptera may be representing the sister group of Neoptera11. Furthermore, the phylogeny of one of the three major radiations of neopterous insects, Polyneoptera (grasshoppers, roaches, mantises, stick insects, and their kin), has similarly remained difficult to resolve.
A review of the hexapod tracheal system with a focus on the apterygote groups
2021, Arthropod Structure and DevelopmentCitation Excerpt :As the relationships at the base of the Hexapoda are unresolved, we cannot state whether hemocyanin was independently reduced in Protura and Diplura or lost in a last common ancestor. The same applies to Ephemeroptera and Odonata (Simon et al., 2018). Subunit 2 must have been reduced independently in Collembola and Archaeognatha.
Male postabdomen reveals ancestral traits of Megasecoptera among winged insects
2020, Arthropod Structure and DevelopmentData curation and modeling of compositional heterogeneity in insect phylogenomics: A case study of the phylogeny of Dytiscoidea (Coleoptera: Adephaga)
2020, Molecular Phylogenetics and EvolutionCitation Excerpt :However, despite the almost exponential increase in sequence data, this growth has not been matched by a growing consensus over insect phylogeny. Many old controversies in insect evolution remain unresolved, such as the relationships among the earliest-branching endognathous orders, early-branching winged insects (the ‘Palaeoptera problem’), and the phylogenetic position of highly specialized parasites such as fleas (Kjer et al., 2016b; Misof et al., 2014; Beutel et al., 2017; Johnson et al., 2018; Simon et al., 2018; Wipfler et al., 2019). Likewise, the monophyly and position of numerous traditionally well-defined taxa has been questioned by recent phylogenomic studies (Pauli et al., 2018; Ding et al., 2019; Hamilton et al., 2019; McKenna et al., 2019; Tang et al., 2019; Wang et al., 2019; Winterton et al., 2019).
Putting the genome in insect phylogenomics
2019, Current Opinion in Insect ScienceCitation Excerpt :This is facilitated by the fact that the most highly expressed genes are often ‘house-keeping’ genes (i.e. those involved in basic cell functions), which tend to be in a single copy more often than for other gene types. Recent phylogenomic studies using transcriptomes in insects have generally focused on higher level questions, such as the relationships among orders [10,38••,39,40••] or families [41••,42,43], but transcriptomes also appear to provide resolution within families as well [44]. Phylogenomic analyses using transcriptomes have several advantages.