The Mitochondrial Genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the Evolutionary Timescale of Tachinid Flies

Tachinid flies are natural enemies of many lepidopteran and coleopteran pests of forests, crops, and fruit trees. In order to address the lack of genetic data in this economically important group, we sequenced the complete mitochondrial genome of the Palaearctic tachinid fly Elodia flavipalpis Aldrich, 1933. Usually found in Northern China and Japan, this species is one of the primary natural enemies of the leaf-roller moths (Tortricidae), which are major pests of various fruit trees. The 14,932-bp mitochondrial genome was typical of Diptera, with 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. However, its control region is only 105 bp in length, which is the shortest found so far in flies. In order to estimate dipteran evolutionary relationships, we conducted a phylogenetic analysis of 58 mitochondrial genomes from 23 families. Maximum-likelihood and Bayesian methods supported the monophyly of both Tachinidae and superfamily Oestroidea. Within the subsection Calyptratae, Muscidae was inferred as the sister group to Oestroidea. Within Oestroidea, Calliphoridae and Sarcophagidae formed a sister clade to Oestridae and Tachinidae. Using a Bayesian relaxed clock calibrated with fossil data, we estimated that Tachinidae originated in the middle Eocene.     

Phylogenomic analysis of the beetle suborder Adephaga with comparison of tailored and generalized ultraconserved element probe performance

Adephaga is the second largest suborder of beetles (Coleoptera) and they serve as important arthropod predators in both aquatic and terrestrial ecosystems. The suborder is divided into Geadephaga comprising terrestrial families and Hydradephaga for aquatic lineages. Despite numerous studies, phylogenetic relationships among the adephagan families and monophyly of the Hydradephaga itself remain in question. Here we conduct a comprehensive phylogenomic analysis of the suborder using ultraconserved elements (UCEs). This study presents the first in vitro test of a newly developed UCE probe set customized for use within Adephaga that includes both probes tailored specifically for the suborder, alongside generalized Coleoptera probes previously found to work in adephagan taxa. We assess the utility of the entire probe set, as well as comparing the tailored and generalized probes alone for reconstructing evolutionary relationships. Our analyses recovered strong support for the paraphyly of Hydradephaga with whirligig beetles (Gyrinidae) placed as sister to all other adephagan families. Geadephaga was strongly supported as monophyletic and placed sister to a clade composed of Haliplidae + Dytiscoidea. Monophyly of Dytiscoidea was strongly supported with relationships among the dytiscoid families resolved and strongly supported. Relationships among the subfamilies of Dytiscidae were strongly supported but largely incongruent with prior phylogenetic estimates for the family. The results of our UCE probe comparison showed that tailored probes alone outperformed generalized probes alone, as well as the full combined probe set (containing both types of probes), under decreased taxon sampling. When taxon sampling was increased, the full combined probe set outperformed both tailored probes and generalized probes alone. This study provides further evidence that UCE probe sets customized for a focal group result in a greater number of recovered loci and substantially improve phylogenomic analysis.     

Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of ‘Hydradephaga’

The beetle suborder Adephaga has been the subject of many phylogenetic reconstructions utilizing a variety of data sources and inference methods. However, no strong consensus has yet emerged on the relationships among major adephagan lineages. Ultraconserved elements (UCEs) have proved useful for inferring difficult or unresolved phylogenies at varying timescales in vertebrates, arachnids and Hymenoptera. Recently, a UCE bait set was developed for Coleoptera using polyphagan genomes and a member of the order Strepsiptera as an outgroup. Here, we examine the utility of UCEs for reconstructing the phylogeny of adephagan families, in the first in vitro application a UCE bait set in Coleoptera. Our final dataset included 305 UCE loci for 18 representatives of all adephagan families except Aspidytidae, and two polyphagan outgroups, with a total concatenated length of 83 547 bp. We inferred trees using maximum likelihood analyses of the concatenated UCE alignment and coalescent species tree methods (astral ii , ASTRID, svdquartets ). Although the coalescent species tree methods had poor resolution and weak support, concatenated analyses produced well‐resolved, highly supported trees. Hydradephaga was recovered as paraphyletic, with Gyrinidae sister to Geadephaga and all other adephagans. Haliplidae was recovered as sister to Dytiscoidea, with Hygrobiidae and Amphizoidae successive sisters to Dytiscidae. Finally, Noteridae was recovered as monophyletic and sister to Meruidae. Given the success of UCE data for resolving phylogenetic relationships within Adephaga, we suggest the potential for further resolution of relationships within Adephaga using UCEs with improved taxon sampling, and by developing Adephaga‐specific probes.     

有瓣蝇类分类、系统发育及演化

有瓣蝇类(Calyptratae)隶属于昆虫纲(Insecta)四大超适应辐射类群之一的双翅目(Diptera),占双翅目已知物种多样性的近20%。有瓣蝇类分布广泛,生物学习性极为多样,在维系生态系统稳定中发挥着重要作用,是媒介、法医、传粉和天敌昆虫学研究领域的热点类群,也是探究双翅目系统演化及其成功适应辐射的关键类群。为了还原有瓣蝇类的演化历史,许多著名昆虫学者先后对该类昆虫开展过不同层面的研究。有瓣蝇类的单系性得到了普遍支持,并被分为3个总科——虱蝇总科(Hippoboscoidea)、蝇总科(Muscoidea)和狂蝇总科(Oestroidea),其中单系的狂蝇总科与多系的蝇总科聚为一支,再与虱蝇总科成为姐妹群。在科级阶元水平,蝠蝇科(Streblidae)(虱蝇总科)、花蝇科(Anthomyiidae)(蝇总科)、丽蝇科(Calliphoridae)(狂蝇总科)、邻寄蝇科(Rhinophoridae)(狂蝇总科)等类群的单系性仍有待验证,且新的科仍在不断被建立［如粉蝇科(Polleniidae)、乌鲁鲁蝇科(Ulurumyiidae)］,因此,有瓣蝇类科级系统发育关系仍不十分明晰。已有研究对虱蝇总科虱蝇科(Hippoboscidae)、蝠蝇科、蛛蝇科(Nycteribiidae),蝇总科蝇科(Muscidae)、粪蝇科(Scathophagidae),狂蝇总科麻蝇科(Sarcophagidae)、狂蝇科(Oestridae)胃蝇亚科(Gasterophilinae)的演化历史进行研究,明确了起源与扩散、寄主转移、取食策略等关键生物学习性的演化历史。但由于部分关键类群生活史信息的缺失,以及尚未有效解决的系统发育关系,有瓣蝇类演化历史仍有许多待解之谜。本文综述了有瓣蝇类分类、系统发育及演化研究进展,是在系统学研究进入系统发育基因组学时代后对该类群相关研究进展的首次全面总结。     

Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly

The dipteran clade Calyptratae is comprised of approximately 18 000 described species (12% of the known dipteran diversity) and includes well‐known taxa such as houseflies, tsetse flies, blowflies and botflies, which have a close association with humans. However, the phylogenetic relationships within this insect radiation are very poorly understood and controversial. Here we propose a higher‐level phylogenetic hypothesis for the Calyptratae based on an extensive DNA sequence dataset for 11 noncalyptrate outgroups and 247 calyptrate species representing all commonly accepted families in the Oestroidea and Hippoboscoidea, as well as those of the muscoid grade. DNA sequences for genes in the mitochondrial (12S, 16S, cytochrome c oxidase subunit I and cytochrome b) and nuclear genome [18S, 28S, the carbamoyl phosphate synthetase region of CAD (rudimentary), Elongation factor one alpha] were used to reconstruct the relationships. We discuss problems relating to the alignment and analysis of large datasets and emphasize the advantages of utilizing a guide tree‐based approach for the alignment of the DNA sequences and using the leaf stability index to identify ‘wildcard’ taxa whose excessive instability obscures the phylogenetic signal. Our analyses support the monophyly of the Calyptratae and demonstrate that the superfamily Oestroidea is nested within the muscoid grade. We confirm that the monotypic family Mystacinobiidae is an oestroid and further revise the composition of the Oestroidea by demonstrating that the previously unplaced and still undescribed ‘McAlpine’s fly’ is nested within this superfamily as a probable sister group to Mystacinobiidae. Within the Oestroidea we confirm with molecular data that the Calliphoridae are a paraphyletic grade of lineages. The families Sarcophagidae and Rhiniidae are monophyletic, but support for the monophyly of Tachinidae and Rhinophoridae depends on analytical technique (e.g. parsimony or maximum likelihood). The superfamilies Hippoboscoidea and Oestroidea are consistently found to be monophyletic, and the paraphyly of the muscoid grade is confirmed. In the overall relationships for the calyptrates, the Hippoboscoidea are sister group to the remaining Calyptratae, and the Fanniidae are sister group to the nonhippoboscoid calyptrates, whose relationships can be summarized as (Muscidae (Oestroidea (Scathophagidae, Anthomyiidae))).     

Phylogenomic analysis suggests Coreidae and Alydidae (Hemiptera: Heteroptera) are not monophyletic

Next‐generation sequencing technologies (NGS) allow systematists to amass a wealth of genomic data from non‐model species for phylogenetic resolution at various temporal scales. However, phylogenetic inference for many lineages dominated by non‐model species has not yet benefited from NGS, which can complement Sanger sequencing studies. One such lineage, whose phylogenetic relationships remain uncertain, is the diverse, agriculturally important and charismatic Coreoidea (Hemiptera: Heteroptera). Given the lack of consensus on higher‐level relationships and the importance of a robust phylogeny for evolutionary hypothesis testing, we use a large data set comprised of hundreds of ultraconserved element (UCE) loci to infer the phylogeny of Coreoidea (excluding Stenocephalidae and Hyocephalidae), with emphasis on the families Coreidae and Alydidae. We generated three data sets by including alignments that contained loci sampled for at least 50%, 60%, or 70% of the total taxa, and inferred phylogeny using maximum likelihood and summary coalescent methods. Twenty‐six external morphological features used in relatively comprehensive phylogenetic analyses of coreoids were also re‐evaluated within our molecular phylogenetic framework. We recovered 439–970 loci per species (16%–36% of loci targeted) and combined this with previously generated UCE data for 12 taxa. All data sets, regardless of analytical approach, yielded topologically similar and strongly supported trees, with the exception of outgroup relationships and the position of Hydarinae. We recovered a monophyletic Coreoidea, with Rhopalidae highly supported as the sister group to Alydidae + Coreidae. Neither Alydidae nor Coreidae were monophyletic; the coreid subfamilies Hydarinae and Pseudophloeinae were recovered as more closely related to Alydidae than to other coreid subfamilies. Coreinae were paraphyletic with respect to Meropachyinae. Most morphological traits were homoplastic with several clades defined by few, if any, synapomorphies. Our results demonstrate the utility of phylogenomic approaches in generating robust hypotheses for taxa with long‐standing phylogenetic problems and highlight that novel insights may come from such approaches.     

Anchored hybrid enrichment challenges the traditional classification of flesh flies (Diptera: Sarcophagidae)

Sarcophagidae is one of the most species-rich families within the superfamily Oestroidea. This diversity is usually represented by three lineages: Miltogramminae, Paramacronychiinae and Sarcophaginae. Historically, the phylogenetic relationships among these lineages have been elusive, due to poorly supported hypotheses or small taxon sets, or both. This study provides a dramatic increase in molecular data, more balanced sampling of all three lineages from all biogeographical regions and a reassessment of morphological characters using scanning electron microscopy in the most comprehensive assessment of subfamily-level phylogeny in Sarcophagidae to date. This analysis of the largest molecular dataset ever produced for a phylogenetic analysis of a fly lineage, with 950 loci from anchored hybrid enrichment comprising 435 930 bp from 101 species, revealed Paramacronychiinae as sister to Miltogramminae, not to Sarcophaginae, as suggested by adult morphology. Maximum likelihood analysis produced a well-supported topology, with 91% of the nodes receiving strong bootstrap proportions (> 97%). In contrast to the molecular data, three out of nine morphological characters studied point to a sister-group relationship of (Sarcophaginae + Paramacronychiinae) and the remaining six characters are either silent on subfamily relationships or in need of further study. Re-examination of morphological structures provides new insights into the evolution of male genitalic traits within Sarcophagidae and highlights their convergence producing conflicting phylogenetic signal. Our phylogeny reconciles older and widely used systems of classification with tree-based thinking and sets up a classification of flesh flies that is more aligned with their evolutionary history.     

The Muscoidea (Diptera: Calyptratae) are paraphyletic: Evidence from four mitochondrial and four nuclear genes

Approximately 5% of the known species-level diversity of Diptera belongs to the Muscoidea with its approximately 7000 described species. Despite including some of the most abundant and well known flies, the phylogenetic relationships within this superfamily are poorly understood. Previous attempts at reconstructing the relationships based on morphology and relatively small molecular data sets were only moderately successful. Here, we use molecular data for 127 exemplar species of the Muscoidea, two species from the Hippoboscoidea, ten species representing the Oestroidea and seven outgroup species from four acalyptrate superfamilies. Four mitochondrial genes 12S, 16S, COI, and Cytb, and four nuclear genes 18S, 28S, Ef1a, and CAD are used to reconstruct the relationships within the Muscoidea. The length-variable genes were aligned using a guide tree that was based on the protein-encoding genes and the indel-free sections of the ribosomal genes. We found that, based on topological considerations, this guide tree was a significant improvement over the default guide trees generated by ClustalX. The data matrix was analyzed using maximum parsimony (MP) and maximum likelihood (ML) and yielded very similar tree topologies. The Calyptratae are monophyletic and the Hippoboscoidea are the sister group to the remaining calyptrates (MP). The Muscoidea are paraphyletic with a monophyletic Oestroidea nested within the Muscoidea as sister group to Anthomyiidae+Scathophagidae. The monophyly of three of the four recognized families in the Muscoidea is confirmed: the Fanniidae, Muscidae, and Scathophagidae. However, the Anthomyiidae are possibly paraphyletic. Within the Oestroidea, the Sarcophagidae and Tachinidae are sister groups and the Calliphoridae are paraphyletic.     

Multi-gene analysis provides a well-supported phylogeny of Rosales

Despite many attempts to resolve evolutionary relationships among the major clades of Rosales, some nodes have been extremely problematic and have remained unresolved. In this study, we use two nuclear and 10 plastid loci to infer phylogenetic relationships among all nine families of Rosales. Rosales were strongly supported as monophyletic; within Rosales all family relationships are well-supported with Rosaceae sister to all other members of the order. Remaining Rosales can be divided into two subclades: (1) Ulmaceae are sister to Cannabaceae plus (Urticaceae+Moraceae); (2) Rhamnaceae are sister to Elaeagnaceae plus (Barbeyaceae+Dirachmaceae). One noteworthy result is that we recover the first strong support for a sister relationship between the enigmatic Dirachmaceae and Barbeyaceae. These two small families have distinct morphologies and potential synapomorphies remain unclear. Future studies should try to identify nonDNA synapomorphies uniting Barbeyaceae with Dirachmaceae.     

A molecular phylogeny of fleas (Insecta: Siphonaptera): origins and host associations

Siphonaptera (fleas) is a highly specialized order of holometabolous insects comprising ～2500 species placed in 16 families. Despite a long history of extensive work on flea classification and biology, phylogenetic relationships among fleas are virtually unknown. We present the first formal analysis of flea relationships based on a molecular matrix of four loci (18S ribosomal DNA, 28S ribosomal DNA, Cytochrome Oxidase II, and Elongation Factor 1‐alpha) for 128 flea taxa from around the world representing 16 families, 25 subfamilies, 26 tribes, and 83 flea genera with eight outgroups. Trees were reconstructed using direct optimization and maximum likelihood techniques. Our analysis supports Tungidae as the most basal flea lineage, sister group to the remainder of the extant fleas. Pygiopsyllomorpha is monophyletic, as are the constituent families Lycopsyllidae, Pygiopsyllidae, and Stivaliidae, with a sister group relationship between the latter two families. Macropsyllidae is resolved as sister group to Coptopsyllidae with moderate nodal support. Stephanociricidae is monophyletic, as are the two constituent subfamilies Stephanocircinae and Craneopsyllinae. Vermipsyllidae is placed as sister group to Jordanopsylla. Rhopalopsyllidae is monophyletic as are the two constituent subfamilies Rhopalopsyllinae and Parapsyllinae. Hystrichopsyllidae is paraphyletic with Hystrichopsyllini placed as sister to some species of Anomiopsyllini and Ctenopariini placed as sister to Carterettini. Ctenophthalmidae is grossly paraphyletic with the family broken into seven lineages dispersed on the tree. Most notably, Anomiopsyllini is paraphyletic. Pulicidae and Chimaeropsyllidae are both monophyletic and these families are sister groups. Ceratophyllomorpha is monophyletic and includes Ischnopsyllidae, Ceratophyllidae, and Leptopsyllidae. Leptopsyllidae is paraphyletic as are its constituent subfamilies Amphipsyllinae and Leptopsyllinae and the tribes Amphipsyllini and Leptopsyllini. Ischnopsyllidae is monophyletic. Ceratophyllidae is monophyletic, with a monophyletic Dactypsyllinae nested within Ceratophyllinae, rendering the latter group paraphyletic. Mapping of general host associations on our topology reveals an early association with mammals with four independent shifts to birds. © The Willi Hennig Society 2008.     

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.     

Molecular phylogeny of the brachyuran crab superfamily Majoidea indicates close congruence with trees based on larval morphology

In this study, we constructed the first molecular phylogeny of the diverse crab superfamily Majoidea (Decapoda: Pleocyemata: Brachyura), using three loci (16S, COI, and 28S) from 37 majoid species. We used this molecular phylogeny to evaluate evidence for phylogenetic hypotheses based on larval and adult morphology. Our study supports several relationships predicted from larval morphology. These include a monophyletic Oregoniidae family branching close to the base of the tree; a close phylogenetic association among the Epialtidae, Pisidae, Tychidae, and Mithracidae families; and some support for the monophyly of the Inachidae and Majidae families. However, not all majoid families were monophyletic in our molecular tree, providing weaker support for phylogenetic hypotheses inferred strictly from adult morphology (i.e., monophyly of individual families). This suggests the adult morphological characters traditionally used to classify majoids into different families may be subject to convergence. Furthermore, trees constructed with data from any single locus were more poorly resolved than trees constructed from the combined dataset, suggesting that utilization of multiple loci are necessary to reconstruct relationships in this group.     

Using phylogenomics to resolve mega-families: An example from Compositae

Next-generation sequencing and phylogenomics hold great promise for elucidating complex relationships among large plant families. Here, we performed targeted capture of low copy sequences followed by next-generation sequencing on the Illumina platform in the large and diverse angiosperm family Compositae (Asteraceae). The family is monophyletic, based on morphology and molecular data, yet many areas of the phylogeny have unresolved polytomies and interpreting phylogenetic patterns has been historically difficult. In order to outline a method and provide a framework and for future phylogenetic studies in the Compositae, we sequenced 23 taxa from across the family in which the relationships were well established as well as a member of the sister family Calyceraceae. We generated nuclear data from 795 loci and assembled chloroplast genomes from off-target capture reads enabling the comparison of nuclear and chloroplast genomes for phylogenetic analyses. We also analyzed multi-copy nuclear genes in our data set using a clustering method during orthology detection, and we applied a network approach to these clusters—analyzing all related locus copies. Using these data, we produced hypotheses of phylogenetic relationships employing both a conservative (restricted to only loci with one copy per targeted locus) and a multigene approach (including all copies per targeted locus). The methods and bioinformatics workflow presented here provide a solid foundation for future work aimed at understanding gene family evolution in the Compositae as well as providing a model for phylogenomic analyses in other plant mega-families.     

Phylogenetic relationships and molecular evolution in uropeltid snakes (Serpentes: Uropeltidae): allozymes and albumin immunology

Multilocus electrophoretic methods and microcomplement fixation comparisons of serum albumin are used to assess phylogenetic relationships among species of uropeltid snakes, to infer aspects of their population biology and biogeography, and to evaluate their relationships to other primitive snakes (Henophidia). There is very good agreement between phylogenetic inferences derived from the electrophoretic data and those derived from the albumin immunological data. Protein variation detected by electrophoresis is relatively high among 17 operational taxonomic units (OTUs) examined. The mean number of alleles per locus (5.1 across all OTUs), levels of polymorphism (25% of loci), and heterozygosity (4–6%), are typical of, or greater than, values reported for other snakes. Species of uropeltids are genetically highly differentiated, as measured by genetic distances (lowest interspecific Nei's unbiased genetic distances, 0.22-0.27 among several Sri Lankan species; 2.3 between Teretrurus of India and other uropeltines). The phylogenetic tree most consistent with both the immunological and electrophoretic data shows uropeltines from Sri Lanka to be monophyletic, but the Indian species are paraphyletic with respect to those from Sri Lanka. Rhinophis travancoricus of India is inferred to be the sister taxon to the Sri Lankan radiation. As the genera are presently understood, neither Rhinophis nor Uropeltis appears to be monophyletic. A biogeographic scenario derived from the phylogenetic hypothesis suggests an early diversification of uropeltids in India, followed by a single invasion into the lowlands of Sri Lanka. Subsequent evolution on Sri Lanka resulted in occupation of montane biotopes. Cylindrophis is the sister group to uropeltines and is considered a member of the Uropeltidae. The immunological data indicate no phylogenetic association between uropeltids and other ‘anilioid’ taxa, specifically Anilius, Loxocemus or Xenopeltis, although we cannot rule out a very remote relationship. We specifically reject the hypothesis that uropeltines and scolecophidians form a clade relative to henophidians. High levels of genetic variation and a trend toward negative F_IS values for polymorphic loci in three populations suggest generally large effective population sizes and outbreeding in these species. The niche-width variation hypothesis for allozyme loci is not supported by the uropeltid data. In comparison to other vertebrates, the relationship between Nei's genetic distance and albumin immunological distance in uropeltids suggests either conservative albumin evolution or strong differentiation at electrophoretic loci.     

Phylogeny of Myrmeleontiformia based on larval morphology (Neuropterida: Neuroptera)

The suborder Myrmeleontiformia is a derived lineage of lacewings (Insecta: Neuroptera) including the families Psychopsidae, Nemopteridae, Nymphidae, Ascalaphidae and Myrmeleontidae. In particular, Myrmeleontidae (antlions) are the most diverse neuropteran family, representing a conspicuous component of the insect fauna of xeric environments. We present the first detailed quantitative phylogenetic analysis of Myrmeleontiformia, based on 107 larval morphological and behavioural characters for 36 genera whose larvae are known (including at least one representative of all the subfamilies of the suborder). Four related families were used as outgroups to polarize character states. Phylogenetic analyses were conducted using both parsimony and Bayesian methods. The reconstructions resulting from our analyses corroborate the monophyly of Myrmeleontiformia. Within this clade, Psychopsidae are recovered as the sister family to all the remaining taxa. Nemopteridae (including both subfamilies Nemopterinae and Crocinae) are recovered as monophyletic and sister to the clade comprising Nymphidae + (Myrmeleontidae + Ascalaphidae). Nymphidae consist of two well‐supported clades corresponding to the subfamilies Nymphinae and Myiodactylinae. Our results suggest that Ascalaphidae may not be monophyletic, as they collapse into an unresolved polytomy under the Bayesian analysis. In addition, the recovered phylogenetic relationships diverge from the traditional classification scheme for ascalaphids. Myrmeleontidae are reconstructed as monophyletic, with the subfamilies Stilbopteryginae, Palparinae and Myrmeleontinae. We retrieved a strongly supported clade comprising taxa with a fossorial habit of the preimaginal instars, which represents a major antlion radiation, also including the monophyletic pit‐trap building species.