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.     

Molecular evolution and radiation of dung beetles in Madagascar

Madagascar is the world's fourth largest island and has a wide range of climates and ecosystems. Environmental diversity combined with long history of isolation (160 Myr) has generated a high level of endemism at different taxonomic levels, making Madagascar one of the hotspots of global biodiversity. Dung beetles, represented by the two tribes of Canthonini and Helictopleurini, exemplify a large insect taxon. Helictopleurini are completely endemic to Madagascar while Canthonini are endemic at generic level. Using data from mitochondrial and nuclear genes, phylogenetic relationships were investigated in a sample of 44 species. The phylogeny for Canthonini consists of several distinct clades, possibly reflecting multiple colonization of Madagascar. The phylogeny does not support the current taxonomy for all genera. The phylogeny for Helictopleurini lacks statistical support at supra‐specific level, and genetic divergence among the Helictopleurini species is comparable with that among species within genera in Canthonini. These results suggest that Helictopleurini has undergone rapid speciation and most likely more recently than Canthonini, consistent with the estimated radiation time based on mtDNA mutation rates in insects and with knowledge about the systematics and geographic distribution of dung beetles worldwide. A detailed analysis of sequence composition identified common patterns in Malagasy dung beetles and other insects. © The Willi Hennig Society 2007.     

Molecular phylogeny of rootworms and related galerucine beetles (Coleoptera: Chrysomelidae)

The Galerucinae (Coleoptera: Chrysomelidae) sensu stricto (true galerucines) comprise a large assemblage of diverse phytophagous beetles containing over 5000 described species. Together with their sister taxon, the flea beetles, which differ from true galerucines by having the hind femora usually modified for jumping, the Galerucinae sensu lato comprises over 13 000 described species and is the largest natural group within the Chrysomelidae. Unlike the flea beetles, for which robust hierarchical classification schemes have not been erected, an existing taxonomic structure exists for the true galerucines, based mostly on the works of the late John Wilcox. In the most recent taxonomic list of the Galerucinae sensu stricto, five tribes were established comprising 29 sections housing 488 genera. The majority of the diversity within these tribes is found within the tribe Luperini, in which two genera, Monolepta and Diabrotica, are known to contain over 500 described species. Here, we extend the work from previous phylogenetic studies of the Galerucinae by analysing four amplicons from three gene regions (18S and 28S rRNA; COI) representing 249 taxa, providing the largest phylogenetic analysis of this taxon to date. Using two seven‐state RNA models, we combine five maximum likelihood models (RNA + DNA for the rRNAs; three separate DNA models for the COI codon positions) for these partitions and analyse the data under likelihood using Bayesian inference. The results of these two analyses are compared with those from equally weighted parsimony. Instead of choosing the results from one optimality criterion over another, either based on statistical support, tree topology or philosophical predisposition, we elect to draw attention to the similar results produced by all three analyses, illustrating the robustness of the data to these different analytical methods. In general, the results from all three analyses are consistent with each other and previous molecular phylogenetic reconstructions for Galerucinae, except that increased taxon sampling for several groups, namely the tribes Hylaspini and Oidini, has improved the phylogenetic position of these taxa. As with previous analyses, under‐sampled taxa, such as the Old World Metacyclini and all sections of the subtribe Luperina, continue to be unstable, with the few taxa representing these groups fluctuating in their positions based on the implemented optimality criterion. Nonetheless, we report here the most comprehensive phylogenetic estimation for the Galerucinae to date.     

DNA based cladograms augment the discovery of a new Ips species from China (Coleoptera: Curculionidae: Scolytinae)

The implementation of DNA in taxonomic study is in its infancy because the association of the amount and type of nucleotide change with species boundaries has not been fully examined for most taxa. Mitochondrial cytochrome c oxidase I (COI) nucleotide data is currently the most popular molecular marker for delimiting species boundaries and a standard pair‐wise nucleotide divergence between groups of individuals has been suggested for the recognition of new species. It is unlikely that such a standard would be applicable across animal species, but the association of the amount and type of nucleotide change with species boundaries could help with the establishment of a taxon‐specific DNA taxonomy. This study utilizes DNA data from nuclear and mitochondrial genes to improve the taxonomy of an important forest beetle pest, Ips. Amount and type of nucleotide difference are associated with monophyletic species based on a cladistic analysis of these data. As a result, a new species from China is described for a clade of beetles whose nucleotide differences exceeded the amount of evolutionary change observed within currently recognized species. The COI data are analyzed independently with an expanded taxon data set, including pair‐wise nucleotide differences between recognized sister species. The wide range of average intraspecific pair‐wise nucleotide difference (0–10.0%) suggests limitations to the application of a standard percent nucleotide difference as a means to identify species boundaries. At most, average COI nucleotide intraspecific difference provides an informal guide to identify potential clades that may warrant further systematic investigation. © The Willi Hennig Society 2007.     

Eight Argentinean species of Dung-Inhabiting Philonthus Stephens (Coleoptera: Staphylinidae)

This review presents a detailed account and synthesis of studies of the family of tiger beetles (Cicindelidae) from the Neotropical region and their usefulness as a surrogate taxon. Information is included on their taxonomy, phylogeny, physiology, ecology, behavior and conservation. Using a model of historical development, this information is put into a context of what has been studied and what studies are most needed in the future to better understand, conserve and manage biodiversity in the Neotropics.     

Molecular phylogeny of beetle associated diplogastrid nematodes suggests host switching rather than nematode-beetle coevolution

Background  

Nematodes are putatively the most species-rich animal phylum. They have various life styles and occur in a variety of habitats, ranging from free-living nematodes in aquatic or terrestrial environments to parasites of animals and plants. The rhabditid nematode Caenorhabditis elegans is one of the most important model organisms in modern biology. Pristionchus pacificus of the family of the Diplogastridae has been developed as a satellite model for comparison to C. elegans. The Diplogastridae, a monophyletic clade within the rhabditid nematodes, are frequently associated with beetles. How this beetle-association evolved and whether beetle-nematode coevolution occurred is still elusive. As a prerequisite to answering this question a robust phylogeny of beetle-associated Diplogastridae is needed.     

Effective bacterial insecticidal proteins against coleopteran pests: A review

Coleoptera, the order of insects commonly referred to as beetles, are able to survive in various environments, and thus, comprise the largest order in the animal kingdom. Coleopterans mainly include coprophagous and phytophagous lineages, and many species of the latter lineage are serious pests. In addition to traditional chemical methods, biocontrol measures using various bacterial insecticidal proteins have also gradually been developed to control these insect pests. In this review, we summarized the possible coleopteran‐pest‐specific bacteria and insecticidal proteins that have been reported in the literature thus far and have provided a comprehensive overview and long‐term guidance for the control of coleopteran pests in the future.     

Pervasive gene flow across critical habitat for four narrowly endemic,sympatric taxa

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Several steps of lateral gene transfer followed by events of ‘birth-and-death’ evolution shaped a fungal sorbicillinoid biosynthetic gene cluster

Dung beetles (subfamily Scarabaeinae) are popular model organisms in ecology and developmental biology, and for the last two decades they have experienced a systematics renaissance with the adoption of modern phylogenetic approaches. Within this period 16 key phylogenies and numerous additional studies with limited scope have been published, but higher-level relationships of this pivotal group of beetles remain contentious and current classifications contain many unnatural groupings. The present study provides a robust phylogenetic framework and a revised classification of dung beetles. We assembled the so far largest molecular dataset for dung beetles using sequences of 8 gene regions and 547 terminals including the outgroup taxa. This dataset was analyzed using Bayesian, maximum likelihood and parsimony approaches. In order to test the sensitivity of results to different analytical treatments, we evaluated alternative partitioning schemes based on secondary structure, domains and codon position. We assessed substitution models adequacy using Bayesian framework and used these results to exclude partitions where substitution models did not adequately depict the processes that generated the data. We show that exclusion of partitions that failed the model adequacy evaluation has a potential to improve phylogenetic inference, but efficient implementation of this approach on large datasets is problematic and awaits development of new computationally advanced software. In the class Insecta it is uncommon for the results of molecular phylogenetic analysis to lead to substantial changes in classification. However, the results presented here are congruent with recent morphological studies and support the largest change in dung beetle systematics for the last 50 years. Here we propose the revision of the concepts for the tribes Deltochilini (Canthonini), Dichotomiini and Coprini; additionally, we redefine the tribe Sisyphini. We provide and illustrate synapomorphies and diagnostic characters supporting the new concepts to facilitate diagnosability of the redefined tribes. As a result of the proposed changes a large number of genera previously assigned to these tribes are now left outside the redefined tribes and are treated as incertae sedis. The present study redefines dung beetles classification and gives new insight into their phylogeny. It has broad implications for the systematics as well as for various ecological and evolutionary analyses in dung beetles.     

Forty years of carabid beetle research in Europe - from taxonomy, biology, ecology and population studies to bioindication, habitat assessment and conservation

‘Carabidologists do it all’ (Niemelä 1996a) is a phrase with which most European carabidologists are familiar. Indeed, during the last half a century, professional and amateur entomologists have contributed enormously to our understanding of the basic biology of carabid beetles. The success of the field is in no small part due to regular European Carabidologists’ Meetings, which started in 1969 in Wijster, the Netherlands, with the 14th meeting again held in the Netherlands in 2009, celebrating the 40th anniversary of the first meeting and 50 years of long-term research in the Dwingelderveld. This paper offers a subjective summary of some of the major developments in carabidology since the 1960s. Taxonomy of the family Carabidae is now reasonably established, and the application of modern taxonomic tools has brought up several surprises like elsewhere in the animal kingdom. Progress has been made on the ultimate and proximate factors of seasonality and timing of reproduction, which only exceptionally show non-seasonality. Triggers can be linked to evolutionary events and plausibly explained by the “taxon cycle” theory. Fairly little is still known about certain feeding preferences, including granivory and ants, as well as unique life history strategies, such as ectoparasitism and predation on higher taxa. The study of carabids has been instrumental in developing metapopulation theory (even if it was termed differently). Dispersal is one of the areas intensively studied, and results show an intricate interaction between walking and flying as the major mechanisms. The ecological study of carabids is still hampered by some unresolved questions about sampling and data evaluation. It is recognised that knowledge is uneven, especially concerning larvae and species in tropical areas. By their abundance and wide distribution, carabid beetles can be useful in population studies, bioindication, conservation biology and landscape ecology. Indeed, 40 years of carabidological research have provided so much data and insights, that among insects - and arguably most other terrestrial organisms - carabid beetles are one of the most worthwhile model groups for biological studies.     

Use of insect rarity for biotope prioritisation: the tenebrionid beetles of the Central Apennines (Italy)

Insect conservation has been traditionally based mainly on the identification of priority biotopes. One of the most commonly used criteria for biotope prioritisation is the occurrence of priority species, hence the need for measures of species vulnerability. In this paper a two-step protocol for biotope prioritisation is proposed. Firstly, insect species vulnerability is estimated from rarity measures that can be easily derived from basic data. Then, these values of vulnerability are used to rank biotopes. The method was applied here to the tenebrionid beetles of the Central Apennines, a montane area of high conservation concern for South Europe. Their use in this paper is an example of the use of data hidden in museum collections for analyses dealing with traditionally overlooked insect groups. Most of conservation decisions for Mediterranean mountains are biased towards certain vertebrates. Although current management practices in the preserves of the study area are generally consistent with the conservation of tenebrionids (especially woodland protection, which is essential for arboreal species), results provided in this study stress the importance of preserving also open biotopes, which are crucial for many taxa, including several endemic forms. Moreover, there is indication that preservation of such kind of biotopes would be important also for vertebrates. The approach for biotope prioritisation based on species rarity was here applied to a single animal taxon, but it can be easily extended to other insect groups, in order to obtain a more general view of the relative importance of different biotope types for Apennine conservation.     

Climate change effects on animal and plant phylogenetic diversity in southern Africa

Much attention has been paid to the effects of climate change on species' range reductions and extinctions. There is however surprisingly little information on how climate change driven threat may impact the tree of life and result in loss of phylogenetic diversity (PD). Some plant families and mammalian orders reveal nonrandom extinction patterns, but many other plant families do not. Do these discrepancies reflect different speciation histories and does climate induced extinction result in the same discrepancies among different groups? Answers to these questions require representative taxon sampling. Here, we combine phylogenetic analyses, species distribution modeling, and climate change projections on two of the largest plant families in the Cape Floristic Region (Proteaceae and Restionaceae), as well as the second most diverse mammalian order in Southern Africa (Chiroptera), and an herbivorous insect genus (Platypleura) in the family Cicadidae to answer this question. We model current and future species distributions to assess species threat levels over the next 70 years, and then compare projected with random PD survival. Results for these animal and plant clades reveal congruence. PD losses are not significantly higher under predicted extinction than under random extinction simulations. So far the evidence suggests that focusing resources on climate threatened species alone may not result in disproportionate benefits for the preservation of evolutionary history.     

Morphology and biology of the flower‐visiting water scavenger beetle genus Rygmodus (Coleoptera: Hydrophilidae)

Hydrophilidae (water scavenger beetles) is well known as an aquatic beetle family; however, it contains ca. 1,000 secondarily terrestrial species derived from aquatic ancestors. The New Zealand endemic genus Rygmodus White is a member of the hydrophilid subfamily Cylominae, which is the early‐diverging taxon of the largest terrestrial lineage (Cylominae + Sphaeridiinae) within the Hydrophilidae. In this paper we report that Rygmodus beetles are pollen‐feeding flower visitors as adults, but aquatic predators as larvae. Based on analyses of gut contents and a summary of collecting records reported on museum specimen labels, adult Rygmodus beetles are generalists feeding on pollen of at least 13 plant families. Rygmodus adult mouthparts differ from those of other (saprophagous) hydrophilid beetles in having the simple scoop‐like apex and mola with roughly denticulate surface, resembling the morphology found in pollen‐feeding staphylinid beetles. Larvae were found along the sides of streams, under stones and in algal mats and water‐soaked moss; one collected larval specimen was identified using DNA barcoding of two molecular markers, mitochondrial cytochrome oxidase 1 (cox1) and nuclear histone 3 (H3). Larvae of two species, Rygmodus modestus and Rygmodus sp., are described in detail and illustrated; they closely resemble ambush‐type predatory larvae of the hydrophilid tribe Hydrophilini in the head morphology. Rygmodus is the only known hydrophilid beetle with adults and larvae inhabiting different environments.     

Validation of tiger beetles as distinct family (Coleoptera: Cicindelidae), review and reclassification of tribal relationships

The higher-level taxonomy of tiger beetles is re-evaluated in light of recent publications based on large taxon sets and a large number of genetic loci. These studies have demonstrated that tiger beetles are a distinct family, Cicindelidae Latreille, sister to the Carabidae Latreille (ground beetles) or Trachypachidae Thomson (false ground beetles) + Carabidae. Recent phylogenies have also recovered consistent patterns in higher-level relationships within the tiger beetles that challenge the traditional taxonomic framework, most of which is more than a century old. These phylogenetic results are reviewed along with concordant morphological characters to create an updated higher-level classification. The subfamily Collyrinae Csiki is not supported by any modern data. We recognize six tribes, Manticorini Laporte (new sense), Megacephalini Laporte (new sense), Collyridini Brullé, Ctenostomatini Laporte, Cicindelini Latreille and the reinstated Oxycheilini Chaudoir (with emended spelling).     

Consumption by carabid beetles of three cereal aphid species relative to other prey types

The cereal aphidRhopalosiphum padi has previously been found to be a low quality prey for a range of generalist arthropod predators. The aim of this study was to reveal, using food consumption experiments whether this applies to other cereal aphids. The question of whether predator feeding capacity increased when several aphid species were offered relative to a single aphid species was also addressed by measuring food consumption on a mixed aphid diet relative to single aphid diets. Food consumption by five carabid beetles of the three cereal aphid speciesRhopalosiphum padi, Sitobion avenae andMetopolophium dirhodum was determined relative to fruit fliesDrosophila melanogaster and the collembolanIsotoma anglicana. Feeding rate was measured as food consumption over 24 hour both for previously satiated and beetles starved for 7 days. Generally the largest aphid consumption was ofM. dirhodum and the lowest ofR. padi, withS. avenae in between. The mixed aphid consumption experiments did not reveal a higher feeding rate on mixed aphid diets relative to single aphid diets. The results indicate low preference forR. padi andS. avenae.     

Lehr's fields of campaniform sensilla in beetles (Coleoptera): Functional morphology. I. General part and allometry

In this first of three articles we show the construction of the articular part of the elytron, the root. The root bears a conspicuous field of campaniform sensilla. This field was studied using light and scanning electron microscopes. The diversity of shape of the field among beetles, types of orientation of elongated sensilla within the field, individual variability of their number among conspecifics are demonstrated. Elongated sensilla point to the junction of the elytron with the second axillary plate. Presumably, they monitor twist movement in this junction, which is possible if the elytron is open. The goal of the whole project is to reveal the effect of both structure and function of the hind wings and elytra on the morphology of this mechanosensory field. Our data on allometric relationships between the animal size and quantitative characteristics of the field in normally flying beetles provide an important background for further functional analysis of this sensory organ.We selected 14 series of several species belonging to the same taxon but differing in size from big to small. It is revealed that the area of the sensory field is directly proportional to the elytral area, whereas the number of sensilla is proportional to the square root of the elytral area. Despite the great range in the elytral area (1500 times) in series of selected species the area of an external pit or cap of a single sensillum varies only 25-fold. The density of sensilla per unit area of the sensory field increases with decrease of the elytral area.     

Phylogenetically informative rearrangements in mitochondrial genomes of Coleoptera, and monophyly of aquatic elateriform beetles (Dryopoidea)

Mitochondrial gene order in Coleoptera has been thought to be conservative but a survey of 60 complete or nearly complete genomes revealed a total of seven different gene rearrangements (deletions, gene order reversals), mainly affecting tRNA genes. All of these were found to be limited to a single taxon or a subclade of Coleoptera. The phylogenetic distribution of a translocation of tRNA(Pro) in three species of elateriform beetles was investigated further by sequencing three nearly complete mitochondrial genomes (Dascillidae, Byrrhidae, Limnichidae) and ten additional individuals for a ～1370 bp diagnostic fragment spanning the relevant region. Phylogenetic analysis consistently recovered the monophyly of families previously grouped in the contentious superfamily Dryopoidea, a group of approximately 10 beetle families with mainly aquatic lifestyles. The Byrrhidae (moss beetles) were not part of this lineage, although they may be its sister group, to recover the widely accepted Byrrhoidea. The tRNA(Pro) translocation was present in all members of Dryopoidea, but not in any other Elateriformia, providing independent support for this lineage and for a single origin of aquatic habits.     

Body size and biomass distributions of carrion visiting beetles: do cities host smaller species?

The question how animal body size changes along urban–rural gradients has received much attention from carabidologists, who noticed that cities harbour smaller species than natural sites. For Carabidae this pattern is frequently connected with increasing disturbance regimes towards cities, which favour smaller winged species of higher dispersal ability. However, whether changes in body size distributions can be generalised and whether common patterns exist are largely unknown. Here we report on body size distributions of carcass-visiting beetles along an urban–rural gradient in northern Poland. Based on samplings of 58 necrophages and 43 predatory beetle species, mainly of the families Catopidae, Silphidae, and Staphylinidae, we found contrary patterns of necrophages and predatory beetles. Body sizes of necrophages decreased towards the city centre and those of predators remained unchanged. Small necrophages and large predators dominated in abundance in the city centre. Necrophage body sizes appeared to be more regularly spaced in the city centre than expected from a random null model and in comparison to the rural pattern, pointing to increased competition.     

Female biased parasitism and the importance of host generation overlap in a sexually transmitted parasite of beetles

Sexual transmission is a widespread means of infection, but apart from those in humans, the ecology of sexually transmitted organisms is not well known. In this study, we present an ecological study of a sexually transmitted mite, Parobia husbandi Seeman and Nahrung (Acari: Podapolipidae), that lives beneath the elytra of Chrysophtharta agricola (Chapuis) (Coleoptera: Chrysomelidae). In each of 2 yr, prevalence of mites on beetles began each spring at about 10-20% but gradually increased to 80-100% by late summer. Overlap of adult beetle generations at this time (i.e., the parental generation mating with the F1 generation) is essential for the persistence of these mites. Mites exhibited temporal change in their spatial distribution on beetles; these changes were probably a response to beetle activity (e.g., emergence from diapause) and the need for dispersal from parental to F1 generation beetles. Prevalence and mean intensity of mites was higher on female beetles compared with male beetles. Female bias of sexually transmitted infection has been predicted in animals but hitherto observed only in primates. We speculate that variable male mate-finding success is the cause of these sex-based differences of mite infections, and that female bias in sexually transmitted disease (STD) infection will be widespread in the animal kingdom.