A secondary structural model of the 28S rRNA expansion segments D2 and D3 from rootworms and related leaf beetles (Coleoptera: Chrysomelidae; Galerucinae)

Phylogenetic Signal Dissection of Heterogeneous 28S and 16S rRNA Genes in Spinicaudata (Branchiopoda, Diplostraca)

It is still a challenge to reconstruct the deep phylogenetic relationships within spinicaudatans, and there are several different competing hypotheses regarding the interrelationships among Eocyzicidae, Cyzicidae s. s., Leptestheriidae, and Limnadiidae of the Suborder Spinicaudata. In order to explore the source of the inconsistencies, we focus on the sequence variation and the structure model of two rRNA genes based on extensive taxa sampling. The comparative sequence analysis revealed heterogeneity across species and the existence of conserved motifs in all spinicaudatan species. The level of intraspecific heterogeneity differed among species, which suggested that some species might have undergone a relaxed concerted evolution with respect to the 28S rRNA gene. The Bayesian analyses were performed on nuclear (28S rRNA, EF1α) and mitochondrial (16S rRNA, COI) genes. Further, we investigated compositional heterogeneity between lineages and assessed the potential for phylogenetic noise compared to signal in the combined data set. Reducing the non-phylogenetic signals and application of optimal rRNA model recovered a topology congruent with inference from the transcriptome data, whereby Limnadiidae was placed as a sister group to Leptestheriidae + Eocyzicidae with high support (topology I). Tests of alternative hypotheses provided implicit support for four competing topologies, and topology I was the best.

Molecular phylogenetic assessment of the tribal classification of Lamiinae (Coleoptera: Cerambycidae)

Lamiinae is the most diverse subfamily of longhorned beetles, with about 20,000 described species classified into 80 tribes. Most of the tribes of Lamiinae were proposed during the 19th century and the suprageneric classification of the subfamily has never been assessed under phylogenetic criteria. In this study, we present the first tribal-level phylogeny of Lamiinae, inferred from 130 terminals (representing 46 tribes, prioritizing generic type species of the tribes) and fragments of two mitochondrial and three nuclear markers (cox1, rrnL, Wg, CPS and LSU; 5,024 aligned positions in total). Analyses were performed under Maximum Likelihood and Bayesian methods based on two datasets: a dataset including all taxa available for the study, and a reduced dataset with 111 terminals where taxa only contributing with mitochondrial markers were excluded from the matrix. The monophyly of Lamiinae was corroborated in three of the four analyses and 11 of the 35 tribes with more than one species represented in the analyses were consistently recovered as monophyletic. However, 15 tribes were not retrieved as monophyletic, requiring a revision of their boundaries: Acanthocinini, Acanthoderini, Agapanthiini, Apomecynini, Desmiphorini, Dorcaschematini, Enicodini, Hemilophini, Monochamini, Onciderini, Parmenini, Phytoeciini, Pogonocherini, Pteropliini and Saperdini. Based on these results, when strong support values for paraphyly were recovered, we argue a number of tribe synonymies, including Moneilemini as synonym of Acanthocinini; Onocephalini of Onciderini; Dorcadionini, Gnomini, Monochamini and Rhodopinini of Lamiini; and Obereini and Phytoeciini of Saperdini. Other taxonomic changes proposed in this study based on the criterion of monophyly and supported by morphological characters include the transfer of Tricondyloides and Stenellipsis to Enicodini, and of Dylobolus stat. rest., which is removed as subgenus of Mecas and restituted as genus, to Hemilophini. Furthermore, our analyses suggest that Ostedes and Neohoplonotus should be removed from Acanthocinini and Parmenini, respectively, and Colobotheini should be redefined to encompass several genera currently placed in Acanthocinini.

The life aquatic with spiders (Araneae): repeated evolution of aquatic habitat association in Dictynidae and allied taxa

Despite the dominance of terrestriality in spiders, species across a diverse array of families are associated with aquatic habitats. Many species in the spider family Dictynidae are associated with water, either living near it or, in the case of Argyroneta aquatica, in it. Previous studies have indicated that this association arose once within the family. Here we test the hypothesis of a single origin via the broadest phylogeny of dictynids and related ‘marronoids’ to date, using several taxa that were not previously sampled in molecular analyses to provide the first quantitative test of the hypothesis put forth by Wheeler et al. (2016). We sampled 281 terminal taxa from 14 families, assembling a matrix with 4380 total base pairs of data from most taxa. We also assembled an atlas of morphological traits with potential significance for both ecology and taxonomy. Our resulting trees indicate that an aquatic habitat association has arisen multiple times within dictynids. Dictynidae and the genus Dictyna are polyphyletic and the genera Lathys and Cicurina remain unplaced. A review of aquatic habitat associations in spiders indicates that it occurs in members of at least 21 families. With our morphological atlas, we explore characters that have been implicated in aiding an aquatic lifestyle, which in the past may have caused confusion regarding taxon placement. Our results indicate that not all spiders with traits thought to be useful for aquatic habitat associations occupy such habitats, and that some spider taxa lacking these traits are nonetheless associated with water.

Austromonticola, a new genus of broad-nosed weevil (Coleoptera, Curculionidae, Entiminae) from montane areas of New Zealand

Austromonticolagen. n. is proposed for a group of eight New Zealand alpine broad-nosed weevil species, all of which are here described: A. atriariussp. n. (type locality: Umbrella Mountains, Central Otago), A. caelibatussp. n. (type locality: Ohau Range, Mackenzie), A. furcatussp. n. (type locality: Old Man Range, Central Otago), A. inflatussp. n. (type locality: Hawkdun Range, Central Otago), A. planulatussp. n. (type locality: St Marys Range, Central Otago), A. postinventussp. n. (type locality: Kirkliston Range, South Canterbury), A. mataurasp. n. (type locality: Mt Dick, Otago Lakes) and A. rotundussp. n. (type locality: Old Man Range, Central Otago). All species occur exclusively above 1000 m elevation in the mountains of Central Otago and South Canterbury in the South Island. A phylogeny of the genus, including six outgroups, was inferred from 33 morphological characters. It resolved the genus as monophyletic, and revealed two strongly supported clades within Austromonticola. DNA sequences of four gene regions were obtained from five species. Of these, the 3' end of COI proved to be the most suitable for the identification of specimens. Females of all species have diagnostic secondary sexual structures on the elytra and ventrites. These structures are hypothesised to have evolved to assist with oviposition in and beside cushion plants or by selection for structures to mitigate the costs to females of prolonged mating.

The nuclear 28S gene fragment D3 as species marker in oribatid mites (Acari, Oribatida) from German peatlands

To make oribatid mites an applicable tool in monitoring programs it is necessary to find a molecular species marker that allows distinct, rapid and easy species identification. In previous studies, the common barcoding sequence COI showed to be too variable to serve as species marker in oribatid mites. The aim of the present study is to evaluate the potential use of the D3 region of the nuclear 28S rDNA gene for species identification. Therefore, we generated a reference DNA library of 28S D3 to identify specimens of the Oribatida from Germany, with focus on species occurring in peatlands being one of the most endangered habitats in Europe. New DNA sequences were obtained from 325 individuals and 64 species (58 genera, 34 families). By adding 28S D3-sequences from GenBank we altogether analysed 385 sequences from 89 German species, 32 of them restricted to peatlands and further 42 occurring in peatlands occasionally, representing 46 and 33% of the oribatids in German peatlands, respectively. P-distances were measured between species within families as well as for intraspecific divergence. 28S D3 showed low intraspecific genetic p-distances between 0 and 0.5%, interspecific distances within families varied between 0 and 9.7%. Most species pairs within families were further separated by one to four indels in addition to substitutions. Altogether, 93% of all analysed species are clearly delineated by 28S D3. Our study emphasises that 28S D3 rDNA is a useful barcode for the identification of oribatid mite specimens and represents an important step in building-up a comprehensive barcode library to allow metabarcoding analyses of environmental peatland samples for Oribatida in Germany as well as in Central Europe.

Molecular Phylogeny of Cypridoid Freshwater Ostracods (Crustacea: Ostracoda), Inferred from 18S and 28S rDNA Sequences

With the aim of exploring phylogenetic relationships within Cypridoidea, the most species-rich superfamily among the podocopidan ostracods, we sequenced nearly the entire 18S rRNA gene (18S) and part of the 28S rRNA gene (28S) for 22 species in the order Podocopida, with representatives from all the major cypridoid families. We conducted phylogenetic analyses using the methods of maximum likelihood, minimum evolution, and Bayesian analysis. Our analyses showed monophyly for Cyprididae, one of the four families currently recognized in Cypridoidea. Candonidae turned out to be paraphyletic, and included three clades corresponding to the subfamilies Candoninae, Paracypridinae, and Cyclocypridinae. We propose restricting the name Candonidae s. str. to comprise what is now Candoninae, and raising Paracypridinae and Cyclocyprininae to family rank within the superfamily Cypridoidea.

Contrasting evolutionary patterns of 28S and ITS rRNA genes reveal high intragenomic variation in Cephalenchus (Nematoda): Implications for species delimitation

Concerted evolution is often assumed to be the evolutionary force driving multi-family genes, including those from ribosomal DNA (rDNA) repeat, to complete homogenization within a species, although cases of non-concerted evolution have been also documented. In this study, sequence variation of 28S and ITS ribosomal RNA (rRNA) genes in the genus Cephalenchus is assessed at three different levels, intragenomic, intraspecific, and interspecific. The findings suggest that not all Cephalenchus species undergo concerted evolution. High levels of intraspecific polymorphism, mostly due to intragenomic variation, are found in Cephalenchus sp1 (BRA-01). Secondary structure analyses of both rRNA genes and across different species show a similar substitution pattern, including mostly compensatory (CBC) and semi-compensatory (SBC) base changes, thus suggesting the functionality of these rRNA copies despite the variation found in some species. This view is also supported by low sequence variation in the 5.8S gene in relation to the flanking ITS-1 and ITS-2 as well as by the existence of conserved motifs in the former gene. It is suggested that potential cross-fertilization in some Cephalenchus species, based on inspection of female reproductive system, might contribute to both intragenomic and intraspecific polymorphism of their rRNA genes. These results reinforce the potential implications of intragenomic and intraspecific genetic diversity on species delimitation, especially in biodiversity studies based solely on metagenetic approaches. Knowledge of sequence variation will be crucial for accurate species diversity estimation using molecular methods.

Tempo and mode of evolutionary radiation in Diabroticina beetles (genera Acalymma, Cerotoma, and Diabrotica)

Adaptive radiation is an aspect of evolutionary biology encompassing microevolution and macroevolution, for explaining the principles of lineage divergence. There are intrinsic as well as extrinsic factors that can be postulated to explain that adaptive radiation has taken place in specific lineages. The Diabroticina beetles are a prominent example of differential diversity that could be examined in detail to explain the diverse paradigms of adaptive radiation. Macroevolutionary analyses must present the differential diversity patterns in a chronological framework. The current study reviews the processes that shaped the differential diversity of some Diabroticina lineages (i.e. genera Acalymma, Cerotoma, and Diabrotica). These diversity patterns and the putative processes that produced them are discussed within a statistically reliable estimate of time. This was achieved by performing phylogenetic and coalescent analyses for 44 species of chrysomelid beetles. The data set encompassed a total of 2,718 nucleotide positions from three mitochondrial and two nuclear loci. Pharmacophagy, host plant coevolution, competitive exclusion, and geomorphological complexity are discussed as putative factors that might have influenced the observed diversity patterns. The coalescent analysis concluded that the main radiation within Diabroticina beetles occurred between middle Oligocene and middle Miocene. Therefore, the radiation observed in these beetles is not recent (i.e. post-Panamanian uplift, 4 Mya). Only a few speciation events in the genus Diabrotica might be the result of the Pleistocene climatic oscillations.

How old are the rove beetles (Insecta: Coleoptera: Staphylinidae) and their lineages? Seeking an answer with DNA

The phylogeny and related evolutionary history of rove beetles (Coleoptera, Staphylinidae) remain unclear. This study provides phylogenetic analyses for the family based on three genes (mitochondrial COI, nuclear protein-coding wingless and a portion of the ribosomal 28S rDNA) including 2413 bp for 104 taxa representing most major staphylinid lineages. The subfamilies Oxyporinae, Paederinae, Steninae, and Proteininae are all well-supported clades, as evidenced by all three inference methods, namely maximum parsimony, Bayesian inference, and maximum likelihood. From fossils available for calibration, the divergence time of the main lineages in the family is estimated based on an uncorrelated lognormal relaxed molecular clock analysis method. The molecular clock analysis suggests that the family Staphylinidae dates from approximately the Early Triassic epoch and the most lineages of the family started to radiate from the Late Jurassic to the Early Paleogene.

A unique box in 28S rRNA is shared by the enigmatic insect order Zoraptera and Dictyoptera

The position of the Zoraptera remains one of the most challenging and uncertain concerns in ordinal-level phylogenies of the insects. Zoraptera have been viewed as having a close relationship with five different groups of Polyneoptera, or as being allied to the Paraneoptera or even Holometabola. Although rDNAs have been widely used in phylogenetic studies of insects, the application of the complete 28S rDNA are still scattered in only a few orders. In this study, a secondary structure model of the complete 28S rRNAs of insects was reconstructed based on all orders of Insecta. It was found that one length-variable region, D3-4, is particularly distinctive. The length and/or sequence of D3-4 is conservative within each order of Polyneoptera, but it can be divided into two types between the different orders of the supercohort, of which the enigmatic order Zoraptera and Dictyoptera share one type, while the remaining orders of Polyneoptera share the other. Additionally, independent evidence from phylogenetic results support the clade (Zoraptera+Dictyoptera) as well. Thus, the similarity of D3-4 between Zoraptera and Dictyoptera can serve as potentially valuable autapomorphy or synapomorphy in phylogeny reconstruction. The clades of (Plecoptera+Dermaptera) and ((Grylloblattodea+Mantophasmatodea)+(Embiodea+Phasmatodea)) were also recovered in the phylogenetic study. In addition, considering the other studies based on rDNAs, this study reached the highest congruence with previous phylogenetic studies of Holometabola based on nuclear protein coding genes or morphology characters. Future comparative studies of secondary structures across deep divergences and additional taxa are likely to reveal conserved patterns, structures and motifs that can provide support for major phylogenetic lineages.

Phylogeny and evolution of life-history strategies in the Sycophaginae non-pollinating fig wasps (Hymenoptera, Chalcidoidea)

BACKGROUND

Non-pollinating Sycophaginae (Hymenoptera, Chalcidoidea) form small communities within Urostigma and Sycomorus fig trees. The species show differences in galling habits and exhibit apterous, winged or dimorphic males. The large gall inducers oviposit early in syconium development and lay few eggs; the small gall inducers lay more eggs soon after pollination; the ostiolar gall-inducers enter the syconium to oviposit and the cleptoparasites oviposit in galls induced by other fig wasps. The systematics of the group remains unclear and only one phylogeny based on limited sampling has been published to date. Here we present an expanded phylogeny for sycophagine fig wasps including about 1.5 times the number of described species. We sequenced mitochondrial and nuclear markers (4.2 kb) on 73 species and 145 individuals and conducted maximum likelihood and Bayesian phylogenetic analyses. We then used this phylogeny to reconstruct the evolution of Sycophaginae life-history strategies and test if the presence of winged males and small brood size may be correlated.

RESULTS

The resulting trees are well resolved and strongly supported. With the exception of Apocrytophagus, which is paraphyletic with respect to Sycophaga, all genera are monophyletic. The Sycophaginae are divided into three clades: (i) Eukoebelea; (ii) Pseudidarnes, Anidarnes and Conidarnes and (iii) Apocryptophagus, Sycophaga and Idarnes. The ancestral states for galling habits and male morphology remain ambiguous and our reconstructions show that the two traits are evolutionary labile.

CONCLUSIONS

The three main clades could be considered as tribes and we list some morphological characters that define them. The same biologies re-evolved several times independently, which make Sycophaginae an interesting model to test predictions on what factors will canalize the evolution of a particular biology. The ostiolar gall-inducers are the only monophyletic group. In 15 Myr, they evolved several morphological adaptations to enter the syconia that make them strongly divergent from their sister taxa. Sycophaginae appears to be another example where sexual selection on male mating opportunities favored winged males in species with small broods and wingless males in species with large broods. However, some species are exceptional in that they lay few eggs but exhibit apterous males, which we hypothesize could be due to other selective pressures selecting against the re-appearance of winged morphs.

Marvaldi A. Systematic revision, cladistics and biogeography of the genus Neogutierrezia Martínez (Coleoptera:Scarabaeidae) and its phylogenetic placement in Rutelinae based on structural alignment of 28S rDNA sequences

The Argentinean endemic genus Neogutierrezia Martínez, 1953 (Scarabaeidae : Rutelinae) is revised and seven new species are described: N. bicolor Ocampo & Ruiz-Manzanos, sp. nov., N. chelii Ocampo & Ruiz-Manzanos, sp. nov., N. galileoi Ocampo & Ruiz-Manzanos, sp. nov., N. lagosae Ocampo & Ruiz-Manzanos, sp. nov., N. payuniensis Ocampo & Ruiz-Manzanos, sp. nov., N. scutata Ocampo & Ruiz-Manzanos, sp. nov. and N. variabilis Ocampo & Ruiz-Manzanos, sp. nov. Species status is proposed for N. affinis Martínez stat. nov., which was formerly considered as subspecies of N. mirabilis Martínez. The genus Neogutierrezia now includes 10 species distributed in the Monte biogeographic province in Argentina. In order to clarify the systematic placement of the genus Neogutierrezia, a molecular phylogenetic analysis was performed using structurally aligned 28S rDNA sequences (expansion segments D2 and D3) from 23 taxa in Scarabaeoidea, including two representative species of Neogutierrezia. This is the first report of an annotated secondary structure alignment of the D2 and D3 segments of 28S rRNA that spans a wide sample of scarabaeoids, providing a useful homology template for further phylogenetic reconstruction in these and closely related beetles. Results of the molecular parsimony analysis strongly indicate that the genus is closely related to members of the Rutelinae (Scarabaeidae), and thus Neogutierrezia Martínez is transferred from Melolonthinae: Pachydemini to Rutelinae, new placement. A morphological cladistic analysis of the genus was also undertaken, including all the 10 known species in the genus plus two outgroup taxa in Rutelinae, and based on 53 adult characters. The most-parsimonious cladogram provides evidence for the monophyly of the genus, which shows three main clades, distributed in Central Monte and Southern Monte. The adult morphology of the 10 species is described and a key is provided, along with illustrations of the diagnostic characters. The biogeography of species in the genus is discussed.

Patterns of habitat affinity and Austral/Holarctic parallelism in dictynoid spiders (Araneae:Entelegynae)

The ability to survive in a terrestrial environment was a major evolutionary hurdle for animals that, once passed, allowed the diversification of most arthropod and vertebrate lineages. Return to a truly aquatic lifestyle has occurred only rarely among terrestrial lineages, and is generally associated with modifications of the respiratory system to conserve oxygen and allow extended periods of apnea. Among chelicerates, in particular spiders, where the circulatory system also serves as a hydrostatic skeleton, very few taxa have exploited aquatic environments, though these environments are abundant and range from freshwater ponds to the marine intertidal and relictual (salt) lakes. The traditional systematic positions of the taxa inhabiting these environments are controversial. Partitioned Bayesian analysis using a doublet model for stems in the nearly complete 18S rRNA gene (~1800 nt) and in the D2 and D3 regions of the 28S rRNA gene (~690 nt), and standard models for loops and full protein-coding histone H3 (349 nt) partitions (totalling 3133 bp when aligned) of dictynoid spiders and related lineages revealed that the only truly aquatic spider species, Argyroneta aquatica (Clerck, 1767) (Cybaeidae Banks, 1892), belongs in a clade containing other taxa with unusual habitat affinities related to an aquatic existence, including occupation of semi-aquatic (intertidal) areas (Desidae Pocock, 1985: Paratheuma spp.) and highly alkaline salt-crusts (Dictynidae O. Pickard-Cambridge, 1871: Saltonia incerta (Banks, 1898)). In a contrasting pattern, other spiders that also occupy intertidal zones, including some other members of the family Desidae (Desis spp., Badumna longinqua (L. Koch, 1867)), are an independently derived clade found primarily in the southern hemisphere. Use of the doublet model reduced some branch-support values in the single-gene trees for rRNA data, but resulted in a robust combined-data phylogeny from 18S rRNA, 28S rRNA, and histone H3. This combination of results – reduction in support in single-gene trees and gain in support in combined-data trees –is consistent with use of the doublet model reducing problematic signal from non-independent base pairs in individual data partitions, resulting in improved resolution in the combined-data analyses.

Molecular phylogeny and Holarctic diversification of the subtribe Calathina (Coleoptera: Carabidae: Sphodrini)

A molecular phylogeny of the subtribe Calathina was inferred from DNA sequence data from the mitochondrial cox1-cox2 region and the nuclear genes 28S and EF-1alpha. All lineages within Calathina from the Holarctic region were represented except for the monotypic subgenus Tachalus. Maximum Parsimony and Bayesian analyses of the combined data set showed that the subtribe is a monophyletic lineage that includes a single genus Calathus, where other taxa currently ranked as independent genera (Lindrothius, Synuchidius, Thermoscelis and Acalathus) are nested within this genus.Neocalathus and Lauricalathus, both subgenera of Calathus, were found to be polyphyletic and in need of taxonomic revision. The subtribe appears to have originated in the Mediterranean Basin and thereafter expanded into most parts of the Palearctic region, the Macaronesian archipelagos (at least five independent colonisation events), the Ethiopian highlands and the Nearctic region (at least two independent events).

Extreme convergence in stick insect evolution: phylogenetic placement of the Lord Howe Island tree lobster

The 'tree lobsters' are an enigmatic group of robust, ground-dwelling stick insects (order Phasmatodea) from the subfamily Eurycanthinae, distributed in New Guinea, New Caledonia and associated islands. Its most famous member is the Lord Howe Island stick insect Dryococelus australis (Montrouzier), which was believed to have become extinct but was rediscovered in 2001 and is considered to be one of the rarest insects in the world. To resolve the evolutionary position of Dryococelus, we constructed a phylogeny from approximately 2.4 kb of mitochondrial and nuclear sequence data from representatives of all major phasmatodean lineages. Our data placed Dryococelus and the New Caledonian tree lobsters outside the New Guinean Eurycanthinae as members of an unrelated Australasian stick insect clade, the Lanceocercata. These results suggest a convergent origin of the 'tree lobster' body form. Our reanalysis of tree lobster characters provides additional support for our hypothesis of convergent evolution. We conclude that the phenotypic traits leading to the traditional classification are convergent adaptations to ground-living behaviour. Our molecular dating analyses indicate an ancient divergence (more than 22 Myr ago) between Dryococelus and its Australian relatives. Hence, Dryococelus represents a long-standing separate evolutionary lineage within the stick insects and must be regarded as a key taxon to protect with respect to phasmatodean diversity.

Phylogenetic relationships of tribes within Harpalinae (Coleoptera: Carabidae) as inferred from 28S ribosomal DNA and the wingless gene

Harpalinae is a large, monophyletic subfamily of carabid ground beetles containing more than 19,000 species in approximately 40 tribes. The higher level phylogenetic relationships within harpalines were investigated based on nucleotide data from two nuclear genes, wingless and 28S rDNA. Phylogenetic analyses of combined data indicate that many harpaline tribes are monophyletic, however the reconstructed trees showed little support for deeper nodes. In addition, our results suggest that the Lebiomorph Assemblage (tribes Lebiini, Cyclosomini, Graphipterini, Perigonini, Odacanthini, Lachnophorini, Pentagonicini, Catapiesini and Calophaenini), which is united by a morphological synapomorphy, is not monophyletic, and the tribe Lebiini is paraphyletic with respect to members of Cyclosomini. Two unexpected clades of tribes were supported: the Zuphiitae, comprised of Anthiini, Zuphiini, Helluonini, Dryptini, Galeritini, and Physocrotaphini; and a clade comprised of Orthogoniini, Pseudomorphini, and Graphipterini. The data presented in this study represent a dense sample of taxa to examine the molecular phylogeny of Harpalinae and provide a useful framework to examine the origin and evolution of morphological and ecological diversity in this group.

Molecular phylogeny and biogeography of an ancient Holarctic lineage of mygalomorph spiders (Araneae: Antrodiaetidae: Antrodiaetus)

The mygalomorph spider genera Antrodiaetus and Atypoides (Antrodiaetidae) belong to an ancient lineage that has persisted since at least the Cretaceous. These spiders display a classic disjunct Holarctic distribution with species in the eastern Palaearctic plus the western and eastern Nearctic. Prior phylogenetic analyses of this group have been proposed on the basis of morphology, but lack strong support and independent corroboration. Here we present the first phylogenetic analysis of species-level relationships based on molecular data obtained from the mitochondrial (cytochrome c oxidase subunit I) and nuclear (18S and 28S rRNA) genomes. Analyses corroborate earlier findings that Atypoides forms a paraphyletic grade with respect to Antrodiaetus, and consequently, that genus is formally synonymized under Antrodiaetus. In addition, our results support the relatively early divergence of Antrodiaetus roretzi. Antrodiaetus pacificus is "paraphyletic" with respect to the A. lincolnianus group and is likely an assemblage of numerous species. The final topology based on a combined molecular dataset, in conjunction with two different molecular dating techniques (penalized likelihood plus a Bayesian approach) and ancestral distribution reconstructions, was used to infer the historical biogeography of these spiders. Trans-Beringian and trans-Atlantic routes appear to account for the present-day distribution of Antrodiaetus in Japan and North America. Future studies on Antrodiaetus phylogeny will be used to address questions regarding morphological stasis and the evolution of quantitative morphological characters.

Phylogenetic relationships of click beetles (Coleoptera: Elateridae) inferred from 28S ribosomal DNA: Insights into the evolution of bioluminescence in Elateridae

Although the taxonomy of click beetles (family Elateridae) has been studied extensively, inconsistencies remain. We examine here the relationships between species of Elateridae based on partial sequences of nuclear 28S ribosomal DNA. Specimens were collected primarily from Japan, while luminous click beetles were also sampled from Central and South America to investigate the origins of bioluminescence in Elateridae. Neighbor-joining, maximum-parsimony, and maximum-likelihood analyses produced a consistent basal topology with high statistical support that is partially congruent with the results of previous investigations based on the morphological characteristics of larvae and adults. The most parsimonious reconstruction of the "luminous" and "nonluminous" states, based on the present molecular phylogeny, indicates that the ancestral state of Elateridae was nonluminous. This suggests that the bioluminescence in click beetle evolved independent of that of other luminous beetles, such as Lampyridae, despite their common mechanisms of bioluminescence.

Defining the limits of taxonomic conservatism in host-plant use for phytophagous insects: molecular systematics and evolution of host-plant associations in the seed-beetle genus Bruchus Linnaeus (Coleoptera: Chrysomelidae: Bruchinae)

In this study, we have investigated the limits of taxonomic conservatism in host-plant use in the seed-beetle genus Bruchus. To reconstruct the insect phylogeny, parsimony and multiple partitioned Bayesian inference analyses were conducted on a combined data set of four genes. Permutation tests and both global and local maximum-likelihood optimizations of host preferences at distinct taxonomic levels revealed that host-fidelity is still discernible beyond the host-plant tribe level, suggesting the existence of more important than previously thought evolutionary constraints, which are further discussed in details. Our tree topologies are also mostly consistent with extant taxonomic groups. Through the analysis of this empirical data set we also provide meaningful insights on two methodological issues. First, Bayesian inference analyses suggest that partitioning by using codon positions greatly increase the accuracy of phylogenetical reconstructions. Regarding reconstruction of ancestral character states through maximum likelihood, the present study also highlights the usefulness of local optimizations. The issue of over-parameterization is also addressed, as the optimizations with the most parameter-rich models have returned the most counterintuitive results.

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements

As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements.

Higher phylogeny of zygaenid moths (Insecta: Lepidoptera) inferred from nuclear and mitochondrial sequence data and the evolution of larval cuticular cavities for chemical defence

Zygaenid moths are capable of releasing hydrogen cyanide in their defense by enzymatic break-down of cyanoglucosides, but only larvae of chalcosiine and zygaenine moths store cyanogenic compounds in cuticular cavities and thus are able to discharge defense droplets, which effectively deter potential predators. A previously proposed phylogeny of Zygaenidae hypothesized a sister group relationship of chalcosiine and zygaenine moths because of their similar larval defense system. Not all chalcosiine taxa possess cuticular cavities, however, and a comparable defense mechanism has been reported in larvae of the zygaenoid family Heterogynidae. Considering sequence data of seven molecular loci, the present study estimates the posterior probability of phylogenetic hypotheses explaining the occurrence of larval cuticular cavities. The molecular data confirm the previous exclusion of Himantopteridae from Zygaenidae and suggest their close affinity to Somabrachyidae. The sequence data also corroborate the recently proposed exclusion of the Phaudinae from the Zygaenidae, because this subfamily is recovered in a reasonably well supported species cluster consisting of members of the families Lacturidae, Limacodidae, Himantopteridae, and Somabrachyidae. We consequently agree to raise Phaudinae to family rank. Within Zygaenidae, the subfamilies Callizygaeninae, Chalcosiinae, and Procridinae most likely constitute a monophyletic group, which is sister to the Zygaeninae. Our results imply that cuticular cavities were probably present in the larvae of the most recent common ancestor of Zygaenidae. Heterogynidae cannot be confirmed as sister taxon to this family, but appear at the very first split of the Zygaenoidea, although with poor support. The specific pattern of taxa in the molecular phylogeny showing larval cuticular cavities opens the possibility that these structures could have been already present in the most recent common ancestor of the Zygaenoidea.

Parasite histories and novel phylogenetic tools: Alternative approaches to inferring parasite evolution from molecular markers

Parasitological research is often contingent on the knowledge of the phylogeny/genealogy of the studied group. Although molecular phylogenetics has proved to be a powerful tool in such investigations, its application in the traditional fashion, based on a tree inference from the primary nucleotide sequences may, in many cases, be insufficient or even improper. These limitations are due to a number of factors, such as a scarcity/ambiguity of phylogenetic information in the sequences, an intricacy of gene relationships at low phylogenetic levels, or a lack of criteria when deciding among several competing coevolutionary scenarios. With respect to the importance of a precise and reliable phylogenetic background in many biological studies, attempts are being made to extend molecular phylogenetics with a variety of new data sources and methodologies. In this review, selected approaches potentially applicable to parasitological research are presented and their advantages as well as drawbacks are discussed. These issues include the usage of idiosyncratic markers (unique features with presumably low probability of homoplasy), such as insertion of mobile elements, gene rearrangements and secondary structure features; the problem of ancestral polymorphism and reticulate relationships at low phylogenetic levels; and the utility of a molecular clock to facilitate discrimination among alternative scenarios in host-parasite coevolution.

Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted-wing parasites (Insecta: Strepsiptera)

We report the entire sequence (2864 nts) and secondary structure of the nuclear small subunit ribosomal RNA (SSU rRNA) gene (18S) from the twisted-wing parasite Caenocholax fenyesi texensis Kathirithamby & Johnston (Strepsiptera: Myrmecolacidae). The majority of the base pairings in this structural model map on to the SSU rRNA secondary and tertiary helices that were previously predicted with comparative analysis. These regions of the core rRNA were unambiguously aligned across all Arthropoda. In contrast, many of the variable regions, as previously characterized in other insect taxa, had very large insertions in C. f. texensis. The helical base pairs in these regions were predicted with a comparative analysis of a multiple sequence alignment (that contains C. f. texensis and 174 published arthropod 18S rRNA sequences, including eleven strepsipterans) and thermodynamic-based algorithms. Analysis of our structural alignment revealed four unusual insertions in the core rRNA structure that are unique to animal 18S rRNA and in general agreement with previously proposed insertion sites for strepsipterans. One curious result is the presence of a large insertion within a hairpin loop of a highly conserved pseudoknot helix in variable region 4. Despite the extraordinary variability in sequence length and composition, this insertion contains the conserved sequences 5'-AUUGGCUUAAA-3' and 5'-GAC-3' that immediately flank a putative helix at the 5'- and 3'-ends, respectively. The longer sequence has the potential to form a nine base pair helix with a sequence in the variable region 2, consistent with a recent study proposing this tertiary interaction. Our analysis of a larger set of arthropod 18S rRNA sequences has revealed possible errors in some of the previously published strepsipteran 18S rRNA sequences. Thus we find no support for the previously recovered heterogeneity in the 18S molecules of strepsipterans. Our findings lend insight to the evolution of RNA structure and function and the impact large insertions pose on genome size. We also provide a novel alignment template that will improve the phylogenetic placement of the Strepsiptera among other insect taxa.

Predicted Secondary Structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): Impact on Sequence Alignment and Phylogeny Estimation

We utilize the secondary structural properties of the 28S rRNA D2-D10 expansion segments to hypothesize a multiple sequence alignment for major lineages of the hymenopteran superfamily Ichneumonoidea (Braconidae, Ichneumonidae). The alignment consists of 290 sequences (originally analyzed in Belshaw and Quicke, Syst Biol 51:450-477, 2002) and provides the first global alignment template for this diverse group of insects. Predicted structures for these expansion segments as well as for over half of the 18S rRNA are given, with highly variable regions characterized and isolated within conserved structures. We demonstrate several pitfalls of optimization alignment and illustrate how these are potentially addressed with structure-based alignments. Our global alignment is presented online at (http://hymenoptera.tamu.edu/rna) with summary statistics, such as basepair frequency tables, along with novel tools for parsing structure-based alignments into input files for most commonly used phylogenetic software. These resources will be valuable for hymenopteran systematists, as well as researchers utilizing rRNA sequences for phylogeny estimation in any taxon. We explore the phylogenetic utility of our structure-based alignment by examining a subset of the data under a variety of optimality criteria using results from Belshaw and Quicke (2002) as a benchmark.

A Secondary Structural Model of the 28S rRNA Expansion Segments D2 and D3 for Chalcidoid Wasps (Hymenoptera: Chalcidoidea)

We analyze the secondary structure of two expansion segments (D2, D3) of the 28S ribosomal (rRNA)-encoding gene region from 527 chalcidoid wasp taxa (Hymenoptera: Chalcidoidea) representing 18 of the 19 extant families. The sequences are compared in a multiple sequence alignment, with secondary structure inferred primarily from the evidence of compensatory base changes in conserved helices of the rRNA molecules. This covariation analysis yielded 36 helices that are composed of base pairs exhibiting positional covariation. Several additional regions are also involved in hydrogen bonding, and they form highly variable base-pairing patterns across the alignment. These are identified as regions of expansion and contraction or regions of slipped-strand compensation. Additionally, 31 single-stranded locales are characterized as regions of ambiguous alignment based on the difficulty in assigning positional homology in the presence of multiple adjacent indels. Based on comparative analysis of these sequences, the largest genetic study on any hymenopteran group to date, we report an annotated secondary structural model for the D2, D3 expansion segments that will prove useful in assigning positional nucleotide homology for phylogeny reconstruction in these and closely related apocritan taxa.