Phylogenetic Problems Research Articles

Partitioned Gene-Tree Analyses and Gene-Based Topology Testing Help Resolve Incongruence in a Phylogenomic Study of Host-Specialist Bees (Apidae: Eucerinae).

Incongruence among phylogenetic results has become a common occurrence in analyses of genome-scale data sets. Incongruence originates from uncertainty in underlying evolutionary processes (e.g., incomplete lineage sorting) and from difficulties in determining the best analytical approaches for each situation. To overcome these difficulties, more studies are needed that identify incongruences and demonstrate practical ways to confidently resolve them. Here, we present results of a phylogenomic study based on the analysis 197 taxa and 2,526 ultraconserved element (UCE) loci. We investigate evolutionary relationships of Eucerinae, a diverse subfamily of apid bees (relatives of honey bees and bumble bees) with >1,200 species. We sampled representatives of all tribes within the group and >80% of genera, including two mysterious South American genera, Chilimalopsis and Teratognatha. Initial analysis of the UCE data revealed two conflicting hypotheses for relationships among tribes. To resolve the incongruence, we tested concatenation and species tree approaches and used a variety of additional strategies including locus filtering, partitioned gene-trees searches, and gene-based topological tests. We show that within-locus partitioning improves gene tree and subsequent species-tree estimation, and that this approach, confidently resolves the incongruence observed in our data set. After exploring our proposed analytical strategy on eucerine bees, we validated its efficacy to resolve hard phylogenetic problems by implementing it on a published UCE data set of Adephaga (Insecta: Coleoptera). Our results provide a robust phylogenetic hypothesis for Eucerinae and demonstrate a practical strategy for resolving incongruence in other phylogenomic data sets.

Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos.

Rapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g., morphology and molecular) or genetic markers (e.g., nuclear and organelle) often yield inconsistent results. The tribe Arundinarieae, that is, the temperate bamboos, is a clade of tetraploid originated 22 Ma and subsequently radiated in East Asia. Previous studies of Arundinarieae have found conflicting relationships and/or low support. Here, we obtain nuclear markers from ddRAD data for 213 Arundinarieae taxa and parallel sampling of chloroplast genomes from genome skimming for 147 taxa. We first assess the feasibility of using ddRAD-seq data for phylogenetic estimates of paleopolyploid and rapidly radiated lineages, optimize clustering thresholds, and analysis workflow for orthology identification. Reference-based ddRAD data assembly approaches perform well and yield strongly supported relationships that are generally concordant with morphology-based taxonomy. We recover five major lineages, two of which are notable (the pachymorph and leptomorph lineages), in that they correspond with distinct rhizome morphologies. By contrast, the phylogeny from chloroplast genomes differed significantly. Based on multiple lines of evidence, the ddRAD tree is favored as the best species tree estimation for temperate bamboos. Using a time-calibrated ddRAD tree, we find that Arundinarieae diversified rapidly around the mid-Miocene corresponding with intensification of the East Asian monsoon and the evolution of key innovations including the leptomorph rhizomes. Our results provide a highly resolved phylogeny of Arundinarieae, shed new light on the radiation and reticulate evolutionary history of this tribe, and provide an empirical example for the study of recalcitrant plant radiations. [Arundinarieae; ddRAD; paleopolyploid; genome skimming; rapid diversification; incongruence.]

Protein‐encoding ultraconserved elements provide a new phylogenomic perspective of Oestroidea flies (Diptera: Calyptratae)

AbstractThe diverse superfamily Oestroidea with more than 15 000 known species includes among others blow flies, flesh flies, bot flies and the diverse tachinid flies. Oestroidea exhibit strikingly divergent morphological and ecological traits, but even with a variety of data sources and inferences there is no consensus on the relationships among major Oestroidea lineages. Phylogenomic inferences derived from targeted enrichment of ultraconserved elements or UCEs have emerged as a promising method for resolving difficult phylogenetic problems at varying timescales. To reconstruct phylogenetic relationships among families of Oestroidea, we obtained UCE loci exclusively derived from the transcribed portion of the genome, making them suitable for larger and more integrative phylogenomic studies using other genomic and transcriptomic resources. We analysed datasets containing 37–2077 UCE loci from 98 representatives of all oestroid families (except Ulurumyiidae and Mystacinobiidae) and seven calyptrate outgroups, with a total concatenated aligned length between 10 and 550 Mb. About 35% of the sampled taxa consisted of museum specimens (2–92 years old), of which 85% resulted in successful UCE enrichment. Our maximum likelihood and coalescent‐based analyses produced well‐resolved and highly supported topologies. With the exception of Calliphoridae and Oestridae all included families were recovered as monophyletic with the following conclusions: Oestroidea is monophyletic with Mesembrinellidae as sister to the remaining oestroid families; Oestridae is paraphyletic with respect to Sarcophagidae; Polleniidae is sister to Tachinidae; Rhinophoridae sister to (Luciliinae (Toxotarsinae (Melanomyinae + Calliphorinae))); Phumosiinae is sister to Chrysomyinae and Bengaliinae is sister to Rhiniidae. These results support the ranking of most calliphorid subfamilies as separate families.

Phylogenetic double placement of mixed samples.

MotivationConsider a simple computational problem. The inputs are (i) the set of mixed reads generated from a sample that combines two organisms and (ii) separate sets of reads for several reference genomes of known origins. The goal is to find the two organisms that constitute the mixed sample. When constituents are absent from the reference set, we seek to phylogenetically position them with respect to the underlying tree of the reference species. This simple yet fundamental problem (which we call phylogenetic double-placement) has enjoyed surprisingly little attention in the literature. As genome skimming (low-pass sequencing of genomes at low coverage, precluding assembly) becomes more prevalent, this problem finds wide-ranging applications in areas as varied as biodiversity research, food production and provenance, and evolutionary reconstruction.ResultsWe introduce a model that relates distances between a mixed sample and reference species to the distances between constituents and reference species. Our model is based on Jaccard indices computed between each sample represented as k-mer sets. The model, built on several assumptions and approximations, allows us to formalize the phylogenetic double-placement problem as a non-convex optimization problem that decomposes mixture distances and performs phylogenetic placement simultaneously. Using a variety of techniques, we are able to solve this optimization problem numerically. We test the resulting method, called MIxed Sample Analysis tool (MISA), on a varied set of simulated and biological datasets. Despite all the assumptions used, the method performs remarkably well in practice.Availability and implementationThe software and data are available at https://github.com/balabanmetin/misa and https://github.com/balabanmetin/misa-data.Supplementary information Supplementary data are available at Bioinformatics online.

The deep(er) roots of Eukaryotes and Akaryotes

Background: Locating the root node of the “tree of life” (ToL) is one of the hardest problems in phylogenetics, given the time depth. The root-node, or the universal common ancestor (UCA), groups descendants into organismal clades/domains. Two notable variants of the two-domains ToL (2D-ToL) have gained support recently. One 2D-ToL posits that eukaryotes (organisms with nuclei) and akaryotes (organisms without nuclei) are sister clades that diverged from the UCA, and that Asgard archaea are sister to other archaea. The other 2D-ToL proposes that eukaryotes emerged from within archaea and places Asgard archaea as sister to eukaryotes. Williams et al. ( Nature Ecol. Evol. 4: 138–147; 2020) re-evaluated the data and methods that support the competing two-domains proposals and concluded that eukaryotes are the closest relatives of Asgard archaea. Critique: The poor resolution of the archaea in their analysis, despite employing amino acid alignments from thousands of proteins and the best-fitting substitution models, contradicts their conclusions. We argue that they overlooked important aspects of estimating evolutionary relatedness and assessing phylogenetic signal in empirical data. Which 2D-ToL is better supported depends on which kind of molecular features are better for resolving common ancestors at the roots of clades – protein-domains or their component amino acids. We focus on phylogenetic character reconstructions necessary to describe the UCA or its closest descendants in the absence of reliable fossils. Clarifications: It is well known that different character types present different perspectives on evolutionary history that relate to different phylogenetic depths. We show that protein structural-domains support more reliable phylogenetic reconstructions of deep-diverging clades in the ToL. Accordingly, Eukaryotes and Akaryotes are better supported clades in a 2D-ToL.

Sequencing Herbarium Specimens of a Common Detrimental Plant Disease (Powdery Mildew)

Powdery mildew (Erysiphaceae) is a detrimental plant disease that occurs on a variety of economically important crops. Powdery mildew consists of over 873 species of fungal pathogens that affect over 10,000 plant species. Genetic identification of powdery mildew is accomplished using the internal transcribed spacer (ITS) and large subunit (LSU) regions of the nuclear ribosomal RNA gene cluster. The ITS and LSU regions of powdery mildews can be useful in ecological, epidemiological, phylogenetic, and taxonomic investigations. However, sequencing these regions is not without its challenges. For example, powdery mildew sequences are often contaminated with plant and/or fungal DNA. Also, there tends to be a limited amount and older specimens' DNA can fragment over time. The success of sequencing powdery mildew often depends on the primers used for running polymerase chain reaction (PCR). The primers need to be broad enough that they match the majority of powdery mildew DNA yet specific enough that they do not align with other organisms. A review of the taxonomy and phylogeny of the powdery mildews is presented with an emphasis on sequencing the ITS + LSU genomic regions. Additionally, we introduce a new nested primer protocol for sequencing powdery mildew herbarium samples that includes six new powdery mildew-specific primers. The new sequencing protocol presented allows specimens up to 130 years old to be sequenced consistently. Sequencing herbarium specimens can be extremely useful for addressing many ecological, epidemiological, phylogenetic, and taxonomic problems in multiple plant pathogenic systems including the powdery mildews.

Finding Most Compatible Phylogenetic Trees over Multi-State Characters

The reconstruction of the evolutionary tree of a set of species based on qualitative attributes is a central problem in phylogenetics. In the NP-hard perfect phylogeny problem the input is a set of taxa (species) and characters (attributes) on them, and the task is to find an evolutionary tree that describes the evolution of the taxa so that each character state evolves only once. However, in practical situations a perfect phylogeny rarely exists, motivating the maximum compatibility problem of finding the largest subset of characters admitting a perfect phylogeny. Various declarative approaches, based on applying integer programming (IP), answer set programming (ASP) and pseudo-Boolean optimization (PBO) solvers, have been proposed for maximum compatibility. In this work we develop a new hybrid approach to solving maximum compatibility for multi-state characters, making use of both declarative optimization techniques (specifically maximum satisfiability, MaxSAT) and an adaptation of the Bouchitt'e-Todinca approach to triangulation-based graph optimization problems. Empirically our approach outperforms in scalability the earlier proposed approaches w.r.t. various parameters underlying the problem.

RNA consensus structures for inferring green algal phylogeny: A three-taxon analysis for Golenkinia/Jenufa, Sphaeropleales and Volvocales (Chlorophyta, Chlorophyceae)

Background and Aims: Order please! was a recently published, very nice and apt title for a persistent problem in green algae phylogenetics. The green algal class Chlorophyceae comprises two clades (SV and OCC) made up of five orders (Sphaeropleales, Volvocales, Oedogoniales, Chaetopeltidales and Chaetophorales). A variety of data and methods have shown that one further group (Golenkinia+Jenufa) cannot be unambiguously placed among the five orders. In addition, concerning Sphaeropleaceae and/or Treubarinia the monophyly of Sphaeropleales and Volvocales remain unresolved. Methods: IUPAC (International Union of Pure and Applied Chemistry) encoded consensus sequences for different 18S rDNA data sets as well as corresponding 18S rDNA consensus structures were assembled for Sphaeropleales, Volvocales (with or without Treubarinia) and a Golenkinia+Jenufa assemblage to independently infer phylogenetic relationships in a three-taxon analysis. Using a known template structure, individual 18S rDNA secondary structures were predicted by homology modelling. Sequences and their individual secondary structures, automatically encoded by a 12-letter alphabet (each nucleotide with its three structural states, paired left, paired right, or unpaired), were simultaneously aligned; consensus structures and IUPAC encoded consensus sequences were read out from the different sequence-structure alignments. Key Results: In contrast to previous studies using 18S rDNA data, results of this study corroborate chloroplast data and strongly support a sister group relationship between Golenkinia+Jenufa and the Sphaeropleales. The Golenkinia+Jenufa assemblage shows 330 matches to the Sphaeropleales (sequence-structure consensus) but only 214 matches to the Volvocales (sequence-structure consensus). Phylogenetically informative nucleotides are highlighted and visualized in their structural context taking into account structural domains (I-IV) and hypervariable regions (V2-V9). Rooting the three-taxon scenario remains difficult because the extremely long branches of Golenkinia and Jenufa are attracted to a chosen outgroup, reducing bootstrap support in any conceivable four-taxon tree obtained by parsimony or profile-neighbor-joining analysis. Conclusions: This algal case study of 18S rDNA consensus data (IUPAC encoded sequences and consensus structures) coupled with profile distances between groups of sequences, demonstrated that a phylogenetic problem can be reduced to a three-taxon analysis.

Documentation of a new hypotrich species in the family Amphisiellidae, Lamtostyla gui n. sp. (Protista, Ciliophora) using a multidisciplinary approach

An integrated approach considering both morphologic and molecular data is now required to improve biodiversity estimations and provide more robust systematics interpretations in hypotrichs, a highly differentiated group of ciliates. In present study, we document a new hypotrich species, Lamtostyla gui n. sp., collected from Chongming wetland, Shanghai, China, based on investigations using living observation, protargol staining, scanning and transmission electron microscopy, and gene sequencing. The new species is mainly recognized by having a short amphisiellid median cirral row composed of four cirri, three frontoventral cirri, three dorsal kinetids, four to eight macronuclear nodules, and small colorless cortical granules distributed as rosettes around dorsal bristles. Transmission electron microscope observation finds the associated microtubules of cirri and pharyngeal discs of L. gui are distinct from those in other hypotrichs. Morphogenesis of this species indicates that parental adoral membranelles retained intact or partial renewed is a potential feature to separate Lamtostyla granulifera-group and Lamtostyla lamottei-group. Phylogenetic analysis based on small subunit ribosomal RNA (rRNA) gene shows that this molecular marker is not useful to resolve phylogenetic relationships of the genus Lamtostyla, as well as many other hypotrichous taxa. We additionally characterize the internal transcribed spacers (ITS) region and the almost complete large subunit rRNA, which will be essential for future studies aimed at solving phylogenetic problems of Lamtostyla, or even the family Amphisiellidae. As a final remark, the critical screening of GenBank using ITS genes of our organism allows us to recognize a large amount of hypotrichous sequences have been misclassified as fungi. This observation suggests that hypotrichs could be frequently found in fungi-rich environment and overlooked by fungal specialists.

No background in biology is assumed

No background in biology is assumed

The deep(er) roots of Eukaryotes and Akaryotes

Background: Locating the root node of the "tree of life" (ToL) is one of the hardest problems in phylogenetics. The root-node or the universal common ancestor (UCA) divides descendants into organismal domains. Two notable variants of the two-domains ToL (2D-ToL) have gained support recently. One 2D-ToL posits that eukaryotes (organisms with nuclei) and akaryotes (organisms without nuclei) are sister clades that diverged from the UCA and that Asgard archaea are sister to other archaea, whereas the other proposes that eukaryotes emerged within archaea and places Asgard archaea sister to eukaryotes. Williams et al. ( Nature Ecol. Evol. 4: 138-147; 2020) re-evaluated the data and methods that support the competing two-domains proposals and concluded that eukaryotes are the closest relatives of Asgard archaea. Critique: We argue that important aspects of estimating evolutionary relatedness and assessing phylogenetic signal in empirical data were overlooked. We focus on phylogenetic character reconstructions necessary to describe the UCA or its closest descendants in the absence of reliable fossils. It is well known that different character types present different perspectives on evolutionary history that relate to different phylogenetic depths. Which 2D-ToL is better supported depends on which kind of molecular features - protein-domains or their component amino acids - are better for resolving common ancestors at the roots of clades. In practice, this involves reconstructing character compositions of the ancestral nodes all the way back to the UCA. We believe the criticisms of 2D-ToL focus on superficial aspects of the data and reflects common misunderstandings of phylogenetic reconstructions using protein domains (folds). Clarifications: Models of protein domain evolution support more reliable phylogenetic reconstructions. In contrast, even the best available amino acid substitution models fail to resolve the archaeal radiation, despite employing thousands of genes. Therefore, the primary domains Eukaryotes and Akaryotes are better supported in a 2D-ToL.

Improved Practical Algorithms for Rooted Subtree Prune and Regraft (rSPR) Distance and Hybridization Number.

The problem of computing the rooted subtree prune and regraft (rSPR) distance of two phylogenetic trees is computationally hard and so is the problem of computing the hybridization number of two phylogenetic trees (denoted by Hybridization Number Computation [HNC]). Since they are important problems in phylogenetics, they have been studied extensively in the literature. Indeed, quite a number of exact or approximation algorithms have been designed and implemented for them. In this article, we design and implement several approximation algorithms for them and one exact algorithm for HNC. Our experimental results show that the resulting exact program is much faster (namely, more than 80 times faster for the easiest dataset used in the experiments) than the previous best and its superiority in speed becomes even more significant for more difficult instances. Moreover, the resulting approximation program's output has much better results than the previous bests; indeed, the outputs are always nearly optimal and often optimal. Of particular interest is the usage of the Monte Carlo tree search (MCTS) method in the design of our approximation algorithms. Our experimental results show that with MCTS, we can often solve HNC exactly within short time.

Complete mitochondrial genome of Scincella modesta (Squamata: Scincidae)

The first complete mitochondrial genome sequence was determined for an oviparous lizard, Scincella modesta (Scincella, Scincidae). The total length of the complete mitochondrial genome was 17,511 bp, encodes 13 protein-coding genes, 22 tRNAs, 2 rRNA genes, and 2 non-coding regions. The overall base composition of S. modesta is A: 31.9%, T: 27.2%, G: 14.5%, and C: 26.5%. Most of the S. modesta mitochondrial genes are encoded on the H-strand except for the ND6 gene and eight tRNA genes, which are encoded on the L-strand. Mrbayes and ML tree based on 13 protein-coding genes indicated that S. vandenburghi is the sister group of the S. modesta within the genus Scincella. The complete mitogenome sequence of S. modesta provided fundamental data for resolving phylogenetic and genetic problems related to genus Scincella.

Parallel MOEA Based on Consensus and Membrane Structure for Inferring Phylogenetic Reconstruction

In recent years, inferring phylogenies has attracted lots of attention in both academic community and various application fields. Phylogenetic inference usually consists of a couple of evolutionary relationships, which can be represented as a phylogenetic tree. The phylogenetic reconstruction problem can be defined as an optimization problem, targeting at finding the most eligible tree among all possible topologies according to a selected criterion. Since the combinatorial number of possible topologies exceeds tolerance, various heuristic and metaheuristic methods have been proposed to find approximate solutions according to the selected criterion. However, different criterions are based on different principle and conflict with each other basically. In this line, scholars has proposed multi-objective evolutionary algorithm (MOEA) based on diverse criteria. Nevertheless, MOEA has suffered unbearable time consumption due to its inherent drawbacks of computational complexity and convergence. By studying the independence between the sub-populations in each time-consuming step of MOEA, the steps without global information can be designed to be executed in parallel, which can fundamentally address computational problems. Effective parallel algorithms designed with the characteristics of modern multicore clusters can solve such problems. In this sense, we propose a parallelized multi-objective evolutionary algorithm (MOEA-MC) by deploying on Spark, which added consensus into evolutionary algorithm to improve the quality of convergence and used membrane structure to keep equal solutions under different weights. In order to assess the performance achieved by the proposal, we have performed comparison among different methods on three real-world datasets separately. The results have certified that the solutions derived from MOEA-MC are superior to traditional methods in all studied datasets. And parallelized MOEA-MC can get dominant position and optimal Pareto-frontier simultaneously within minimal runtime.

MicroRNA evolution provides new evidence for a close relationship of Diplura to Insecta

AbstractThe phylogenetic interrelationships among four hexapod lineages (Protura, Collembola, Diplura and Insecta) are pivotal to understanding the origin of insects and the early diversification of Hexapoda, but they have been difficult to clarify based on the available data. In this study, we identified 91 conserved microRNA (miRNA) families from 36 panarthropod taxa, including seven newly sequenced non‐insect hexapods. We found major clade differentiation accompanied by the origin of novel miRNA families, and most miRNA clusters are conserved with a high degree of microsynteny. Importantly, we were able to identify two miRNA families unique to Hexapoda, and four miRNA families and a miRNA cluster that exist exclusively in Diplura and Insecta, suggesting a close relationship between Diplura and Insecta as well as the monophyly of Hexapoda. Combined with a phylogenetic analysis based on the presence/absence matrix of miRNA families, our study demonstrates the effectiveness of miRNA in resolving deep phylogenetic problems.

A Memetic Algorithm Based on an NSGA-II Scheme for Phylogenetic Tree Inference

Phylogenetic inference allows building a hypothesis about the evolutionary relationships between a group of species, which is usually represented as a tree. The phylogenetic inference problem can be seen as an optimization problem, searching for the most qualified tree among all the possible topologies according to a selected criterion. These criteria can be based on different principles. Due to the combinatorial number of possible topologies, diverse heuristics and meta-heuristics have been proposed to find approximated solutions according to one criterion. However, these methods may result in several phylogeny trees which could be in conflict with one another. In order to deal with this problem, models based on multiobjective optimization with different configurations have been used. In this paper, we propose an ad-hoc multiobjective memetic algorithm (MO-MA) to infer phylogeny using two objectives: 1) maximum parsimony and 2) likelihood. Several population operators and local search strategies are proposed and evaluated in order to measure their contribution to the algorithm. Additionally, we perform a comparison among different configurations and tree rearrangement strategies. The results show that the proposed MO-MA is able to identify a Pareto set of solutions that include new trees which were nondominated by solutions from the current state of the art single-objective optimization tools. Furthermore, the MO-MA improves the results presented in the literature for multiobjective approaches in all of the studied data sets. These results make our proposal a good alternative for phylogenetic inference.

Information Reconstruction on an Infinite Tree for a $$4\times 4$$-State Asymmetric Model with Community Effects

The information reconstruction problem on an infinite tree, is to collect and analyze massive data samples at the $n$th level of the tree to identify whether there is non-vanishing information of the root, as $n$ goes to infinity. This problem has wide applications in various fields such as biology, information theory and statistical physics, and its close connections to cluster learning, data mining and deep learning have been well established in recent years. Although it has been studied in numerous contexts, the existing literatures with rigorous reconstruction thresholds established are very limited. In this paper, motivated by a classical deoxyribonucleic acid (DNA) evolution model, the F$81$ model, and taking into consideration of the Chargaff's parity rule by allowing the existence of a guanine-cytosine content bias, we study the noise channel in terms of a $4\times 4$-state asymmetric probability transition matrix with community effects, for four nucleobases of DNA. The corresponding information reconstruction problem in molecular phylogenetics is explored, by means of refined analyses of moment recursion, in-depth concentration estimates, and thorough investigations on an asymptotic $4$-dimensional nonlinear second order dynamical system. We rigorously show that the reconstruction bound is not tight when the sum of the base frequencies of adenine and thymine falls in the interval $\left(0,1/2-\sqrt{3}/6\right)\bigcup \left(1/2+\sqrt{3}/6,1\right)$, which is the first rigorous result on asymmetric noisy channels with community effects.

Polynomial-Time Algorithms for Phylogenetic Inference Problems involving duplication and reticulation.

A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree based on a model with speciation and duplication where duplications are clustered in duplication episodes. The goal is to minimize the number of such episodes. The second variant, Parental Hybridization, aims at inferring a species network based on a model with speciation and reticulation. The goal is to minimize the number of reticulation events. It is a variant of the well-studied Hybridization Number problem with a more generous view on which gene trees are consistent with a given species network. We show that these seemingly different problems are in fact closely related and can, surprisingly, both be solved in polynomial time, using a structure we call "beaded trees". However, we also show that methods based on these problems have to be used with care because the optimal species phylogenies always have a restricted form. To mitigate this problem, we introduce a new variant of Unrestricted Minimal Episodes Inference that minimizes the duplication episode depth. We prove that this new variant of the problem can also be solved in polynomial time.

The complete mitochondrial genome of Athalia proxima (Hymenoptera: Tenthredinidae) and phylogenetic analysis

The nearly complete mitochondrial genome of Athalia proxima is 15852 bp in size, containing 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a partial control region. Compared to ancestral organization, seven tRNA genes were rearranged. Bayesian and maximum-likelihood trees recovered the monophyly of Tenthredinidae and A. proxima was the basal lineage. The mitogenome sequence provided fundamental data for resolving phylogenetic and genetic problems of Tenthredinidae.

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

AbstractNext‐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.