Phylogenomics and biogeography of sawflies and woodwasps (hymenoptera, symphyta).

Phylogenomic approaches have recently helped elucidate various insect relationships, but large-scale comprehensive analyses on relationships within sawflies and woodwasps are still lacking. Here, we infer the relationships and long-term biogeographic history of these hymenopteran groups using a large dataset of 354 UCE loci collected from 385 species that represent all major lineages. Early Hymenoptera started diversifying during the Early Triassic ∼249 Ma and spread all over the ancient supercontinent Pangaea. We recovered Xyeloidea as a monophyletic sister group to other Hymenoptera and Pamphilioidea as sister to Unicalcarida. Within the diverse family Tenthredinidae, our taxonomically and geographically expanded taxon sampling highlights the non-monophyly of several traditionally defined subfamilies. In addition, the recent removal of Athalia and related genera from the Tenthredinidae into the separate family Athaliidae is supported. The deep historical biogeography of the group is characterised by independent dispersals and re-colonisations between the northern (Laurasia) and southern (Gondwana) palaeocontinents. The breakup of these landmasses led to ancient vicariance in several Gondwanan lineages, while interchange across the Northern Hemisphere has continued until the Recent. The little-studied African sawfly fauna is likewise a diverse mixture of groups with varying routes of colonization. Our results reveal interesting parallels in the evolution and biogeography of early hymenopterans and other ancient insect groups.

Description of six new species of Oecetis (Trichoptera, Leptoceridae) from Vietnam.

The following six new Oecetis species have been described and illustrated: O. lata, O. gretae, O. malickyi, O. porntipae, O. olahi, and O. hageni. The following three Oecetis species are recorded for the first time from Vietnam: O. maron Malicky Chantaramongkol 2005 (in Malicky 2005), O. iakchos Malicky 2005, and O. jachin Malicky Mey 2010 (in Malicky 2010a). We present new records of the following six Oecetis species that are previously known from Vietnam: O. raghava Schmid 1995, O. biramosa Martynov 1936, O. tripunctata (Fabricius 1793), O. meleagros Malicky Thani 2005, O. asmada Malicky 1979, and O. empusa Malicky Chaibu 2000. A map presents the distribution of the Oecetis species included in this report.

Eighteen new species of Oecetis McLachlan 1877 (Trichoptera, Leptoceridae) from New Caledonia.

Eighteen new species of Oecetis are described, diagnosed, and illustrated from New Caledonia: Oecetis amphora sp. nov., Oecetis ovula sp. nov., Oecetis ramosa sp. nov., Oecetis loyolaensi sp. nov., Oecetis millei sp. nov., Oecetis christinae sp. nov., Oecetis rostrata sp. nov., Oecetis alicae sp. nov., Oecetis oxybelis sp. nov., Oecetis dorsospina sp. nov., Oecetis multidentata sp. nov., Oecetis gracilis sp. nov., Oecetis rostra sp. nov., Oecetis triramosa sp. nov., Oecetis flucta sp. nov., Oecetis nouvellecaledoniensis sp. nov., Oecetis variabilis sp. nov., and Oecetis ovata sp. nov. A diagnostic key is provided for males of Oecetis species of New Caledonia. The species display similarities in genitalic characteristics but also a high diversity of apomorphic features. The new species were collected from lotic habitats across most of Grande Terre.

A simple method for data partitioning based on relative evolutionary rates.

BACKGROUND: Multiple studies have demonstrated that partitioning of molecular datasets is important in model-based phylogenetic analyses. Commonly, partitioning is done a priori based on some known properties of sequence evolution, e.g. differences in rate of evolution among codon positions of a protein-coding gene. Here we propose a new method for data partitioning based on relative evolutionary rates of the sites in the alignment of the dataset being analysed. The rates are inferred using the previously published Tree Independent Generation of Evolutionary Rates (TIGER), and the partitioning is conducted using our novel python script RatePartitions. We conducted simulations to assess the performance of our new method, and we applied it to eight published multi-locus phylogenetic datasets, representing different taxonomic ranks within the insect order Lepidoptera (butterflies and moths) and one phylogenomic dataset, which included ultra-conserved elements as well as introns. METHODS: We used TIGER-rates to generate relative evolutionary rates for all sites in the alignments. Then, using RatePartitions, we partitioned the data into partitions based on their relative evolutionary rate. RatePartitions applies a simple formula that ensures a distribution of sites into partitions following the distribution of rates of the characters from the full dataset. This ensures that the invariable sites are placed in a partition with slowly evolving sites, avoiding the pitfalls of previously used methods, such as k-means. Different partitioning strategies were evaluated using BIC scores as calculated by PartitionFinder. RESULTS: Simulations did not highlight any misbehaviour of our partitioning approach, even under difficult parameter conditions or missing data. In all eight phylogenetic datasets, partitioning using TIGER-rates and RatePartitions was significantly better as measured by the BIC scores than other partitioning strategies, such as the commonly used partitioning by gene and codon position. We compared the resulting topologies and node support for these eight datasets as well as for the phylogenomic dataset. DISCUSSION: We developed a new method of partitioning phylogenetic datasets without using any prior knowledge (e.g. DNA sequence evolution). This method is entirely based on the properties of the data being analysed and can be applied to DNA sequences (protein-coding, introns, ultra-conserved elements), protein sequences, as well as morphological characters. A likely explanation for why our method performs better than other tested partitioning strategies is that it accounts for the heterogeneity in the data to a much greater extent than when data are simply subdivided based on prior knowledge.

Identification of sawflies and horntails (Hymenoptera, 'Symphyta') through DNA barcodes: successes and caveats.

The 'Symphyta' is a paraphyletic assemblage at the base of the order Hymenoptera, comprising 14 families and about 8750 species. All have phytophagous larvae, except for the Orussidae, which are parasitoids. This study presents and evaluates the results of DNA barcoding of approximately 5360 specimens of 'Symphyta', mainly adults, and 4362 sequences covering 1037 species were deemed of suitable quality for inclusion in the analysis. All extant families are represented, except for the Anaxyelidae. The majority of species and specimens are from Europe, but approximately 38% of the species and 13% of the specimens are of non-European origin. The utility of barcoding for species identification and taxonomy of 'Symphyta' is discussed on the basis of examples from each of the included families. A significant level of cryptic species diversity was apparent in many groups. Other attractive applications include the identification of immature stages without the need to rear them, community analyses based on metabarcoding of bulk samples and association of the sexes of adults.

Phylogeny of the symphytan grade of Hymenoptera: new pieces into the old jigsaw(fly) puzzle.

The Hymenoptera constitutes one of the largest, and ecologically and economically most important, insect orders. During the past decade, a number of hypotheses on the phylogenetic relationships among hymenopteran families and superfamilies have been presented, based on analyses of molecular and/or morphological data. Nevertheless, many questions still remain, particularly concerning relationships within the hyperdiverse suborder Apocrita, but also when it comes to the evolutionary history of the ancestrally herbivorous "sawfly" lineages that form the basal, paraphyletic grade Symphyta. Because a large part of the uncertainty appears to stem from limited molecular and taxonomic sampling, we set out to investigate the phylogeny of Hymenoptera using nine protein-coding genes, of which five are new to analyses of the order. In addition, we more than tripled the taxon coverage across the symphytan grade, introducing representatives for many previously unsampled lineages. We recover a well supported phylogenetic structure for these early herbivorous hymenopteran clades, with new information regarding the monophyly of Xyelidae, the placement of the superfamily Pamphilioidea as sister to Tenthredinoidea + Unicalcarida, as well as the interrelationships among the tenthredinoid families Tenthredinidae, Cimbicidae, and Diprionidae. Based on the obtained phylogenies, and to prevent paraphyly of Tenthredinidae, we propose erection of the tribe Heptamelini to family status (Heptamelidae). In particular, our results give new insights into subfamilial relationships within the Tenthredinidae and other species-rich sawfly families. The expanded gene set provides a useful toolbox for future detailed analyses of symphytan subgroups, especially within the diverse superfamily Tenthredinoidea.

A comparative analysis of genetic differentiation across six shared willow host species in leaf- and bud-galling sawflies.

Genetic divergence and speciation in plant-feeding insects could be driven by contrasting selection pressures imposed by different plant species and taxa. While numerous examples of host-associated differentiation (HAD) have been found, the overall importance of HAD in insect diversification remains unclear, as few studies have investigated its frequency in relation to all speciation events. One promising way to infer the prevalence and repeatability of HAD is to estimate genetic differentiation in multiple insect taxa that use the same set of hosts. To this end, we measured and compared variation in mitochondrial COI and nuclear ITS2 sequences in population samples of leaf-galling Pontania and bud-galling Euura sawflies (Hymenoptera: Tenthredinidae) collected from six Salix species in two replicate locations in northern Fennoscandia. We found evidence of frequent HAD in both species complexes, as individuals from the same willow species tended to cluster together on both mitochondrial and nuclear phylogenetic trees. Although few fixed differences among the putative species were found, hierarchical AMOVAs showed that most of the genetic variation in the samples was explained by host species rather than by sampling location. Nevertheless, the levels of HAD measured across specific pairs of host species were not correlated in the two focal galler groups. Hence, our results support the hypothesis of HAD as a central force in herbivore speciation, but also indicate that evolutionary trajectories are only weakly repeatable even in temporally overlapping radiations of related insect taxa.

Magadacerina, a new genus of Leptoceridae (Trichoptera) from Madagascar.

Magadacerina forcipata, new genus, new species (Trichoptera: Leptoceridae), is described from Madagascar. The monotypic genus is characterised by having the tibial spur formula 2,2,2; wings with sessile bifurcation of M; genitalia with preanal appendages fused with segment IX and greatly produced posterad, and a tergum X with an anteriorly extended ventral base articulating with a sclerotised spine-like process of the phallic shield. The new genus is most closely related to Blyzophilus in the tribe Blyzophilini.

Phylogeny of the Polycentropodidae (Insecta: Trichoptera) based on protein-coding genes reveal non-monophyletic genera.

We tested the previous hypotheses of the phylogenetic position and monophyly of the caddisfly family Polycentropodidae. We also tested previous hypotheses about the internal generic relationship within the family by including 15 ingroup genera, many of them also represented by the genotype. All families that were previously taxonomically associated with the polycentropodids were included in the analysis. The total data set of 2225 bp representing sequences of combined nuclear and mitochondrial genes and 171 taxa, was analyzed using Bayesian inference. We found strong support for a monophyletic Polycentropodidae with Ecnomidae as the closest sister group. The recently erected families Kambaitipsychidae and Pseudoneureclipsidae were monophyletic and distantly related to the Polycentropodidae. Within Polycentropodidae, monophyly and validity of the genera Neucentropus, Neureclipsis, Cyrnus, Holocentropus, Tasmanoplegas, Pahamunaya, Cernotina and Cyrnellus was strongly supported, while the genera Polycentropus, Polyplectropus, Plectrocnemia, Placocentropus and Nyctiophylax were all polyphyletic. The New Caledonian species were polyphyletic and represented three distinct clades. The sister group to the New Caledonian clades are from Australia, New Zealand and Chile, respectively. The Vanuatu species evolved after dispersal from the Fiji Islands. New internal primers for cytochrome oxidase I sequences of Trichoptera are introduced.

VoSeq: a voucher and DNA sequence web application.

There is an ever growing number of molecular phylogenetic studies published, due to, in part, the advent of new techniques that allow cheap and quick DNA sequencing. Hence, the demand for relational databases with which to manage and annotate the amassing DNA sequences, genes, voucher specimens and associated biological data is increasing. In addition, a user-friendly interface is necessary for easy integration and management of the data stored in the database back-end. Available databases allow management of a wide variety of biological data. However, most database systems are not specifically constructed with the aim of being an organizational tool for researchers working in phylogenetic inference. We here report a new software facilitating easy management of voucher and sequence data, consisting of a relational database as back-end for a graphic user interface accessed via a web browser. The application, VoSeq, includes tools for creating molecular datasets of DNA or amino acid sequences ready to be used in commonly used phylogenetic software such as RAxML, TNT, MrBayes and PAUP, as well as for creating tables ready for publishing. It also has inbuilt BLAST capabilities against all DNA sequences stored in VoSeq as well as sequences in NCBI GenBank. By using mash-ups and calls to web services, VoSeq allows easy integration with public services such as Yahoo! Maps, Flickr, Encyclopedia of Life (EOL) and GBIF (by generating data-dumps that can be processed with GBIF's Integrated Publishing Toolkit).

Climate-driven diversity dynamics in plants and plant-feeding insects.

The origin of species-rich insect-plant food webs has traditionally been explained by diversifying antagonistic coevolution between plant defences and herbivore counter-defences. However, recent studies combining paleoclimatic reconstructions with time-calibrated phylogenies suggest that variation in global climate determines the distribution, abundance and diversity of plant clades and, hence, indirectly influences the balance between speciation and extinction in associated herbivore groups. Extant insect communities tend to be richest on common plant species that have many close relatives. This could be explained either by climate-driven diffuse cospeciation between plants and insects, or by elevated speciation and reduced extinction in herbivore lineages associated with expanding host taxa (resources). Progress in paleovegetation reconstructions in combination with the rapidly increasing availability of fossil-calibrated phylogenies provide means to discern between these alternative hypotheses. In particular, the 'Diffuse cospeciation' scenario predicts closely matching main diversification periods in plants and in the insects that feed upon them, while the 'Resource abundance-dependent diversification' hypothesis predicts that both positive and negative responses of insect diversity are lagged in relation to host-plant availability. The dramatic Cenozoic changes in global climate provide multiple possibilities for studying the mechanisms by which climatic shifts may drive diversity dynamics in plants and insect herbivores.

A new classification of the long-horned caddisflies (Trichoptera: Leptoceridae) based on molecular data.

BACKGROUND: Leptoceridae are among the three largest families of Trichoptera (caddisflies). The current classification is founded on a phylogenetic work from the 1980's, based on morphological characters from adult males, i.e. wing venation, tibial spur formula and genital morphology. In order to get a new opinion about the relationships within the family, we undertook a molecular study of the family based on sequences from five genes, mitochondrial COI and the four nuclear genes CAD, EF-1α, IDH and POL. RESULTS: The resulting phylogenetic hypotheses are more or less congruent with the morphologically based classification, with most genera and tribes recovered as monophyletic, but with some major differences. For monophyly of the two subfamilies Triplectidinae and Leptocerinae, one tribe of each was removed and elevated to subfamily status; however monophyly of some genera and tribes is in question. All clades except Leptocerinae, were stable across different analysis methods. CONCLUSIONS: We elevate the tribes Grumichellini and Leptorussini to subfamily status, Grumichellinae and Leptorussinae, respectively. We also propose the synonymies of Ptochoecetis with Oecetis and Condocerus with Hudsonema.

Testing the monophyly of Calocidae (Insecta: Trichoptera) based on multiple molecular data.

Calocidae constitute a hypothesised monophyletic group of caddisflies (Trichoptera) being geographically restricted to New Zealand (one genus) and Australia (five genera). This analysis tests the monophyly of the family based on sequences from five different molecular genes. The complete data set includes 29 species and covers a complete genus representation of the Calocidae as well as representatives of other families in which one or more calocid genera have been classified. Sequences from two mitochondrial (cytochrome oxidase I and 16S) and three nuclear (elongation factor 1-alpha, RNA polymerase-II, and Cadherin) genes were used, resulting in a 3958bp data set and 37.1% parsimony informative characters. The Cadherin (CAD) and RNA polymerase-II (POL-II) genes are used for the first time for revealing Trichoptera phylogenies. The character matrix was analyzed by using maximum parsimony (MP) and Bayesian criteria, the latter by applying three different partition strategies for comparison. Two most parsimonious trees were found, differing in the position of one clade within the sister-group to a monophyletic Calocidae. The Bayesian tree based on the maximum number of partitions differs from trees based on a reduced partition analysis with respect to taxa outside the current circumscription of Calocidae. Both the MP and Bayesian analyses left Calocidae monophyletic, with a monophyletic clade of all Australian genera being sister-group to the New Zealand genus. The results from the agreement subtree analysis demonstrates that CAD performs well both separately and in combination with other genes and adds substantial resolution to the calocid phylogeny in a combined MP analysis.