Identification of net‐winged beetle larvae (Coleoptera: Lycidae) using three mtDNA fragments: a comparison of their utility

Abstract We investigated the effectiveness of short mitochondrial DNA fragments for the identification of lycid larvae. The rrnL, cox1 and nad5 mtDNA sequences from 17 specimens of immature stages of Lycidae and Lampyridae were combined with a previously published dataset of homologous fragments representing all major lineages of Lycidae and outgroups. Their relationships were analysed under parsimony criteria. We demonstrate that high‐density profiles are necessary for accurate identification of unknown samples to generic and tribal levels and that a multilocus approach is critical for obtaining reliable results. Although widely used, the cox1 mtDNA fragment showed the worst performance for identification at genus level when the query species was not present in the library. Stronger support for deeper branches came from rrnL mtDNA. The neotenic female larvae and male adult stages of Platerodrilus sp. and Macrolibnetis depressus Pic, 1938 were associated by mtDNA fragments. Based on the present identification, larvae of Dictyopterini (Dictyopterini gen. sp., Dictyoptera aurora Herbst, 1784), Sulabanus sp., Leptotrichalus sp. (Metriorrhynchini) and Macrolibnetis depressus Pic, 1938 (Platerodrilini) are described for the first time. Further species of Platycis Thomson, 1859, Plateros Bourgeois, 1979, Macrolycus Waterhouse, 1878, Cautires Waterhouse, 1879 and Lyponia Waterhouse, 1878 are identified by morphology and molecular markers. The data on larval morphology and their usefulness for classification are discussed.     

Phenetic and cladistic relationships among tenebrionid beetles (Coleoptera)

Abstract. The higher classification of Tenebrionidae is analysed using numerical phenetic, numerical cladistic and traditional Hennigian methods. In all, eighty characters are examined for about 335 taxa; definitive analyses are made on combinations of eighteen to seventy characters for thirty-three OTUs. At lower levels of relationship (genera and closely related tribes) phenetic and cladistic classifications are shown to be congruent, but at higher levels (tribes and subfamilies) there is marked discordance with phenetic results being more stable. A consensus classification is more similar to the Hennigian cladogram than is any single computer generated cladogram. Two main tribal groups – the Lagrioid and Tenebrionoid groups – are suggested which differ in defensive glands, female anatomy, wing and mouthpart morphology, larval characters and other features. The Tenebrionoid group consists of three main subdivisions – the tenebrionine, coelometopine and diaperine lineages. Changes in classificatory position are recommended for eighty-seven genera and tribes (listed in Appendix E) and implied for numerous others.     

Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the laurasiatherian mammals

Although great progress has been made in resolving the relationships of placental mammals, the position of several clades in Laurasiatheria remain controversial. In this study, we performed a phylogenetic analysis of 97 orthologs (46,152 bp) for 15 taxa, representing all laurasiatherian orders. Additionally, phylogenetic trees of laurasiatherian mammals with draft genome sequences were reconstructed based on 1608 exons (2,175,102 bp). Our reconstructions resolve the interordinal relationships within Laurasiatheria and corroborate the clades Scrotifera, Fereuungulata, and Cetartiodactyla. Furthermore, we tested alternative topologies within Laurasiatheria, and among alternatives for the phylogenetic position of Perissodactyla, a sister-group relationship with Cetartiodactyla receives the highest support. Thus, Pegasoferae (Perissodactyla + Carnivora + Pholidota + Chiroptera) does not appear to be a natural group. Divergence time estimates from these genes were compared with published estimates for splits within Laurasiatheria. Our estimates were similar to those of several studies and suggest that the divergences among these orders occurred within just a few million years.     

Phylogenetic relationships and convergent evolution of ocean‐shore ground beetles (Coleoptera: Carabidae: Trechinae: Bembidion and relatives)

Through phylogenetic analysis of seven genes, we show that there have been at least six independent entries into intertidal habitats in the history of bembidiine carabids, in the ancestors of: (i) Orzolina Machado, (ii) Bembidion (Desarmatocillenus Netolitzky), (iii) Bembidion laticeps (LeConte) + palosverdes Kavanaugh & Erwin, (iv) Bembidion laterale (Samouelle), (v) Bembidion umi Sasakawa and Bembidion quadriimpressum (Motschulsky) (which may represent two separate entries), and (vi) B. nigropiceum (Marsham). The following lineages are widely separated within the subtribe Bembidiina: Orzolina is sister to the genus Ocys Stephens; subgenus Desarmatocillenus appears to be sister to all Bembidion Latreille excluding subgenus Phyla Motschulsky; B. laticeps + B. palosverdes is a clade in the Bembidion series; B. laterale is a member of the Princidium Motschulsky complex; B. umi and B. quadriimpressum are related to the Nearctic Clade of the Ocydromus Clairville complex; B. nigropiceum is sister to B. praeustum Dejean among sampled species. There are three separate lineages of ocean‐shore bembidiines that are known to prey on amphipods, and adults of these lineages [Bembidion (Desarmatocillenus), B. laterale, and B. mandibulare Solier] have unusually wide heads with long mandibles. Also common among independent lineages restricted to ocean shores are prominent front angles of the prothorax, larger numbers of setae on the elytral disc, a notable sinuation in the margin of each elytron near its apex, and short, wide mesotarsi. The reasons for the repeated evolution of these features are not evident. Our results also suggest that inland species of the Nearctic Clade may have arisen from an ocean‐shore ancestor. The close genetic similarities between the gravel river shore dwelling B. praeustum and the intertidal specialist B. nigropiceum suggest that the striking morphological adaptations of B. nigropiceum to the intertidal zone arose rapidly. We make one nomenclatural change: we resurrect the subgenus Lymneops Casey to accommodate B. palosverdes and B. laticeps.     

Phylogenomic analysis of gene co‐expression networks reveals the evolution of functional modules

Molecular evolutionary studies correlate genomic and phylogenetic information with the emergence of new traits of organisms. These traits are, however, the consequence of dynamic gene networks composed of functional modules, which might not be captured by genomic analyses. Here, we established a method that combines large‐scale genomic and phylogenetic data with gene co‐expression networks to extensively study the evolutionary make‐up of modules in the moss Physcomitrella patens, and in the angiosperms Arabidopsis thaliana and Oryza sativa (rice). We first show that younger genes are less annotated than older genes. By mapping genomic data onto the co‐expression networks, we found that genes from the same evolutionary period tend to be connected, whereas old and young genes tend to be disconnected. Consequently, the analysis revealed modules that emerged at a specific time in plant evolution. To uncover the evolutionary relationships of the modules that are conserved across the plant kingdom, we added phylogenetic information that revealed duplication and speciation events on the module level. This combined analysis revealed an independent duplication of cell wall modules in bryophytes and angiosperms, suggesting a parallel evolution of cell wall pathways in land plants. We provide an online tool allowing plant researchers to perform these analyses at http://www.gene2function.de .     

Rapid radiation of Rheum (Polygonaceae) and parallel evolution of morphological traits

In this study, we examined diversification history of Rheum and tested the hypothesis that morphological traits related to plant 'body-plans' evolved in parallel in this genus. We sequenced eight chloroplast DNA fragments (representing more than 8000 bps of the sequence for each species) of 34 species from the genus and 13 species from closely related genera. Phylogenetic analyses indicate that all species of Rheum form a monophyletic lineage sister to the two-species genus Oxyria, indicating that radiative diversifications have occurred in its evolutionary history. Our dating analyses further suggest that these radiations largely coincided with the extensive uplifts of the Qinghai-Tibetan Plateau (QTP). Ancestral state reconstruction and likelihood sensitivity tests strongly indicate that both decumbent and 'glasshouse-like' body-plan traits evolved in parallel in different clades. Our findings highlight the importance of the uplift of the QTP in promoting species diversification and the parallel evolution of morphological traits that are putatively adaptive during such an evolutionary history.     

Phylogeny, classification and evolution of ladybird beetles (Coleoptera: Coccinellidae) based on simultaneous analysis of molecular and morphological data

Ladybird beetles (family Coccinellidae) are a species-rich, ecologically diverse group of substantial agricultural significance, yet have been consistently problematic to classify, with evolutionary relationships poorly understood. In order to identify major clades within Coccinellidae, evaluate the current classification system, and identify likely drivers of diversification in this polyphagous group, we conducted the first simultaneous Bayesian analysis of morphological and multi-locus molecular data for any beetle family. Addition of morphological data significantly improved phylogenetic resolution and support for early diverging lineages, thereby better resolving evolutionary relationships than either data type alone. On the basis of these results, we formally recognize the subfamilies Microweisinae and Coccinellinae sensu?lipiński (2007). No significant support was found for the subfamilies Coccidulinae, Scymninae, Sticholotidinae, or Ortaliinae. Our phylogenetic results suggest that the evolutionary success of Coccinellidae is in large part attributable to the exploitation of ant-tended sternorrhynchan insects as a food source, enabled by the key innovation of unusual defense mechanisms in larvae.     

Phylogenetic relationships of Iberian dung beetles (Coleoptera: scarabaeinae): insights on the evolution of nesting behavior

A phylogeny of the main lineages of dung beetles (Coleoptera: Scarabaeinae) from the Iberian Peninsula was based on partial nucleotide sequences (about 1221 bp) of the mitochondrial cytochrome oxidase I and II genes of 33 taxa. Our phylogenetic analyses confirmed the validity and composition of most of the recognized tribes within the subfamily. Interestingly, the Onitini showed an evolutionary rate significantly higher than that of the other tribes. The molecular phylogeny supports a sister-group relationship of the tribes Onitini and Oniticellini + Onthophagini. A close relationship of Scarabaeini, Gymnopleurini, and Sisyphini is also suggested but lacks bootstrap support. Surprisingly, the Coprini, which had always been related to the Oniticellini and Onthophagini, were placed closer to the Scarabaeini, Gymnopleurini, and Sisyphini. The inferred molecular phylogeny was used to assess the main evolutionary trends of nesting behavior. Our results suggest tentative single origins for both the tunneling and the rolling behaviors, and the possibility that the rolling behavior could have been lost secondarily in Copris.     

The morphological evolution of the Adephaga (Coleoptera)

The evolution of the coleopteran suborder Adephaga is discussed based on a robust phylogenetic background. Analyses of morphological characters yield results nearly identical to recent molecular phylogenies, with the highly specialized Gyrinidae placed as sister to the remaining families, which form two large, reciprocally monophyletic subunits, the aquatic Haliplidae + Dytiscoidea (Meruidae, Noteridae, Aspidytidae, Amphizoidae, Hygrobiidae, Dytiscidae) on one hand, and the terrestrial Geadephaga (Trachypachidae + Carabidae) on the other. The ancestral habitat of Adephaga, either terrestrial or aquatic, remains ambiguous. The former option would imply two or three independent invasions of aquatic habitats, with very different structural adaptations in larvae of Gyrinidae, Haliplidae and Dytiscoidea.     

Evolutionary relationships among the Scarabaeini (Coleoptera: Scarabaeidae) based on combined molecular and morphological data

The Scarabaeini is an old world tribe of ball-rolling dung beetles that have origins dating back to at least the mid-upper Miocene (19-8 million years ago). The tribe has received little to no attention in morphological or molecular phylogenetics. We obtained sequence data from the mitochondrial cytochrome oxidase subunit I (1,197 bp) and 16S ribosomal RNA (461 bp) genes for 25 species of the Scarabaeini in an attempt to further resolve broad phylogenetic relationships within this tribe. Sequence data from both markers along with 216 morphological and 3 biological characters were analysed separately and combined. Independent analyses showed poorly resolved trees with many of the intermediate and basal nodes collapsed by low bootstrap values. Many sites in both genes exhibited strong A+T nucleotide bias and high interlineage divergences. The combined analysis revealed a number of well supported relationships such as the monophyly of the nocturnal species Scarabaeus satyrus, S. [Neateuchus] proboscideus, and S. zambesianus. Furthermore, the total evidence tree suggested to elevate S. (Pachysoma) to the status of an independent genus, Pachysoma, as a sister taxon to a clade containing Pachylomerus femoralis and Scarabaeus sensu lato. Within the latter, the following subgenera were maintained by the combination of data sets: S. (Scarabaeolus), S. (Sceliages), and S. (Kheper). Both, feeding specialisation and food relocation behaviour, were inferred to be polyphyletic in the Scarabaeini. Total evidence analysis found no support for common ancestry of Scarabaeini and Eucraniini.     

Evolutionary relationships among food habit, loss of flight, and reproductive traits: life-history evolution in the Silphinae (Coleoptera: Silphidae)

Flightlessness in insects is generally thought to have evolved due to changes in habitat environment or habitat isolation. Loss of flight may have changed reproductive traits in insects, but very few attempts have been made to assess evolutionary relationships between flight and reproductive traits in a group of related species. We elucidated the evolutionary history of flight loss and its relationship to evolution in food habit, relative reproductive investment, and egg size in the Silphinae (Coleoptera: Silphidae). Most flight-capable species in this group feed primarily on vertebrate carcasses, whereas flightless or flight-dimorphic species feed primarily on soil invertebrates. Ancestral state reconstruction based on our newly constructed molecular phylogenetic tree implied that flight muscle degeneration occurred twice in association with food habit changes from necrophagy to predatory, suggesting that flight loss could evolve independently from changes in the environmental circumstances per se. We found that total egg production increased with flight loss. We also found that egg size increased with decreased egg number following food habit changes in the lineage leading to predaceous species, suggesting that selection for larger larvae intensified with the food habit change. This correlated evolution has shaped diverse life-history patterns among extant species of Silphinae.     

Large‐scale molecular phylogeny of metallic wood‐boring beetles (Coleoptera: Buprestoidea) provides new insights into relationships and reveals multiple evolutionary origins of the larval leaf‐mining habit

The family Buprestidae (jewel beetles or metallic wood‐boring beetles), contains nearly 15 000 species in 522 genera. Together with the small family Schizopodidae (seven species, three genera), they form the superfamily Buprestoidea. Adult Buprestoidea feed on flowers or foliage, whereas larvae are mostly internal feeders, boring in roots or stems, or mining the leaves of woody or herbaceous plants. The subfamilial and tribal classification of Buprestoidea remains unsettled, with substantially different schemes proposed by different workers based on morphology. Here we report the first large‐scale molecular phylogenetic study of the superfamily Buprestoidea based on data from four genes for 141 ingroup species. We used these data to reconstruct higher‐level relationships and to assess the current classification and the origins of the larval leaf‐mining habit within Buprestoidea. In our analyses, the monophyly of Buprestoidea was strongly supported, as was the monophyly of Schizopodidae and its placement sister to Buprestidae. Our results are largely consistent with the generally accepted major lineages of buprestoids, including clearly‐defined agrilines, buprestines–chrysochroines and early‐branching julodines–polycestines. In addition to Schizopodidae, three of the six subfamilies were monophyletic in our study: Agrilinae, Julodinae and the monogeneric Galbellinae (Galbella). Polycestinae was monophyletic with the exception of the enigmatic Haplostethini. Chrysochroinae and Buprestinae were not monophyletic, but were recovered together in a large mixed clade along with Galbella. The interrelationships of Chrysochroinae and Buprestinae were not well resolved; however they were clearly polyphyletic, with chrysochroine genera falling into several different well‐supported clades otherwise comprising buprestine genera. All Agrilinae were contained in a single strongly supported clade. Coraebini were dispersed throughout Agrilinae, with strong nodal support for several clades representing subtribes. Neither Agrilini nor Tracheini were monophyletic. The leaf‐mining genus Paratrachys (Paratracheini) was recovered within the Acmaeoderioid clade, consistent with the current classification, and confirming the independent origins of leaf‐mining within Polycestinae and Agrilinae. Additionally, our results strongly suggest that the leaf‐mining agriline tribe Tracheini is polyphyletic, as are several of its constituent subtribes. External root feeding was likely the ancestral larval feeding habit in Buprestoidea. The apparent evolutionary transitions to internal feeding allowed access to a variety of additional plant tissues, including leaves. Interestingly, the several genera of leaf‐mining agrilines do not form a monophyletic group. Many of these genera are diverse and highly specialized, possibly indicating adaptive radiations.     

Absence asymmetry: the evolution of monorchid beetles (Insecta: Coleoptera: Carabidae)

Asymmetrical monorchy, or the complete absence of one testis coupled with the presence of its bilateral counterpart, is reported for 174 species of the carabid beetle tribes Abacetini, Harpalini, and Platynini (Insecta: Coleoptera: Carabidae) based on a survey of over 820 species from throughout the family. This condition was not found in examined individuals of any other carabid beetle tribes, or of other adephagan beetle families. One monorchid taxon within Platynini exhibits symmetrical vasa deferentia at the beginning of the pupal stadium, suggesting that developmental arrest of the underdeveloped vas deferens takes place in pupation. The point at which development of the testis is interrupted is unknown. Complete absence of one organ of a bilateral pair--absence asymmetry--is rarely found in any animal clade and among insects is otherwise only known for testes in the minute-sized beetles of the family Ptiliidae, ovaries in Scarabaeinae dung beetles, and ovaries of some aphids. Based on current phylogenetic hypotheses for Carabidae, testis loss has occurred independently at least three times, and up to five origins are possible, given the variation within Abacetini. Clear phylogenetic evidence for multiple independent origins suggests an adaptive or functional cause for this asymmetry. A previously posited taxon-specific hypothesis wherein herbivory in the tribe Harpalini led to testis loss is rejected. Optimal visceral packing of the beetle abdomen is suggested as a general explanation. Specifically, based on the function of various organ systems, we hypothesize that interaction of internal organs and pressure to optimize organ size and space usage in each system led to the multiple origins and maintenance of the monorchid condition. Testes are the only redundant and symmetrically paired structures not thought to be developmentally linked to other symmetrical structures in the abdomen. Among all possible organs, they are the most likely--although the observed frequency is very small--to bypass constraints that maintain bilateral symmetry, resulting in absence asymmetry. However, based solely on our observations of gross morphology of internal organs, no function conclusively explains the ontogenetic loss of one testis in these taxa. Unlike the analogous absence asymmetry of organs in other animal groups, no dramatic body-form constraint--e.g., snakes and lung loss, ptiliid beetles' small body-size and relatively giant sperm--or adaptive scenario of improved locomotory performance--e.g., birds and ovary loss due to flight constraints-applies to these carabid beetles. We tentatively suggest that testis loss is driven wholly by an interaction among the internal organs of these beetles, possibly due to selective pressure to maximize the comparatively large accessory glands found in these taxa. However, as the ordering of these evolutionary events of testis loss and accessory gland size increase is not known, large accessory glands might have secondarily evolved to compensate for a decreased testicular output.     

Taxonomic Review of the Family Lycidae (Coleoptera) in Korea

We reviewed the family Lycidae in Korea. The Korean Lycidae was recorded to fourteen species under eight genera until now. However, the taxonomy of Korean species was conducted without comparative analysis. We revised the Korean Lycidae to eleven species under seven genera of two subfamilies. Also, we provided the key to subfamilies, gernera, and species including illustrations of pronotum and aedeagus, the photos of adult habitus.     

Phylogenomic analysis of the hemp family (Cannabaceae) reveals deep cyto-nuclear discordance and provides new insights into generic relationships

Cannabaceae are a relatively small family of angiosperms, but they include several species of huge economic and cultural significance: marijuana or hemp (Cannabis sativa) and hops (Humulus lupulus). Previous phylogenetic studies have clarified the most deep relationships in Cannabaceae, but relationships remain ambiguous among several major lineages. Here, we sampled 82 species representing all genera of Cannabaceae and utilized a new dataset of 90 nuclear genes and 82 chloroplast loci from Hyb-Seq to investigate the phylogenomics of Cannabaceae. Nuclear phylogenetic analyses revealed a robust and consistent backbone for Cannabaceae. We observed nuclear gene-tree conflict at several deep nodes in inferred species trees, also cyto-nuclear discordance concerning the relationship between Gironniera and Lozanella and the relationships among Trema s.l. (including Parasponia), Cannabis + Humulus, and Chaetachme + Pteroceltis. Coalescent simulations and network analyses suggest that observed deep cyto-nuclear discordances were most likely to stem from incomplete lineage sorting (ILS); nuclear gene-tree conflict might be caused by both ILS and gene flow between species. All genera of Cannabaceae were recovered as monophyletic, except for Celtis, which consisted of two distinct clades: Celtis I (including most Celtis species) and Celtis II (including Celtis gomphophylla and Celtis schippii). We suggest that Celtis II should be recognized as the independent genus Sparrea based on both molecular and morphological evidence. Our work provides the most comprehensive and reliable phylogeny to date for Cannabaceae, enabling further exploration of evolutionary patterns across this family and highlighting the necessity of comparing nuclear with chloroplast data to examine the evolutionary history of plant groups.     

The phylogeny of diving beetles (Coleoptera: Dytiscidae) and the evolution of sexual conflict

A model of evolution based on conflicts of interest between the sexes over mating decisions is examined in relation to diving beetles (Dytiscidae). The model predicts the following evolutionary sequence: (1) cost to females of mating increases, (2) females evolve behavioural resistance to male mating attempts, (3) males evolve devices to overcome female resistance, and (4) females evolve morphological counter-adaptations to the male devices. This model is tested using species of Dytiscidae, in which (1) some species have a very long mating duration while others mate quickly, (2) females of some species resist male mating attempts by swift and erratic swimming when seized by a male, (3) males of some species possess a grasping device in the form of sucker-shaped setae on the legs used to adhere to the pronota or elytra of females prior to mating, and (4) females of some species have a modified dorsal cuticle with irregular sculpturing which appears to interfere with the male adhesive setae. The predicted order of evolution of some of these features was tested in a cladistic analysis of 52 taxa in Dytiscidae and Hygrobiidae using characters from adult and larval morphology and a portion of the gene wingless . The combined analysis resulted in nine most parsimonious cladograms. The consensus cladogram of these indicates that male sucker setae arose a single time in a clade of Dytiscinae. Nested within this clade are five groups with an independently derived, modified dorsal cuticle in females. This pattern of characters in Dytiscinae is consistent with the prediction implied by the model of sexual selection. The utility of wingless as a marker for phylogenetic analysis of diving beetles is discussed, and the resulting phylogeny is compared with previous analyses and current classification.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79 , 359–388.