Tournament ABC analysis of the western Palaearctic population history of an oak gall wasp, Synergus umbraculus.

Approximate Bayesian computation (ABC) is a powerful and widely used approach in inference of population history. However, the computational effort required to discriminate among alternative historical scenarios often limits the set that is compared to those considered more likely a priori. While often justifiable, this approach will fail to consider unexpected but well-supported population histories. We used a hierarchical tournament approach, in which subsets of scenarios are compared in a first round of ABC analyses and the winners are compared in a second analysis, to reconstruct the population history of an oak gall wasp, Synergus umbraculus (Hymenoptera, Cynipidae) across the Western Palaearctic. We used 4,233 bp of sequence data across seven loci to explore the relationships between four putative Pleistocene refuge populations in Iberia, Italy, the Balkans and Western Asia. We compared support for 148 alternative scenarios in eight pools, each pool comprising all possible rearrangements of four populations over a given topology of relationships, with or without founding of one population by admixture and with or without an unsampled "ghost" population. We found very little support for the directional "out of the east" scenario previously inferred for other gall wasp community members. Instead, the best-supported models identified Iberia as the first-regional population to diverge from the others in the late Pleistocene, followed by divergence between the Balkans and Western Asia, and founding of the Italian population through late Pleistocene admixture from Iberia and the Balkans. We compare these results with what is known for other members of the oak gall community, and consider the strengths and weaknesses of using a tournament approach to explore phylogeographic model space.

The description of Alloxysta chinensis, a new Charipinae species from China (Hymenoptera, Figitidae).

A new figitid species, Alloxysta chinensis Fülöp & Mikó sp nova, based on females, is described from China and South Korea. The functional morphology and the phylogenetic implication of some anatomical structures frequently used in Charipinae and the validity of the genus Carvercharips is discussed. This manuscript is the first of its kind linking descriptive terminology to Hymenoptera Anatomy Ontology classes, which provides persistent links to definitions for terms used within this manuscript.

Phylogeny and DNA barcoding of inquiline oak gallwasps (Hymenoptera: Cynipidae) of the Western Palaearctic.

We examine phylogenetic relationships within the Synergus complex of herbivorous inquiline gallwasps (Hymenoptera; Cynipidae; Synergini) associated with cynipid host galls on oak, a biologically diverse group whose genus-level morphological taxonomy has long been considered stable but whose species level taxonomy is problematic. We incorporate data for over 70% of recognised Western Palaearctic species in five morphology-based genera (Ceroptres, Saphonecrus, Synergus, Synophrus, Ufo), comprising sequence for two mitochondrial loci (coxI, cytb) and one nuclear locus (28S D2). In particular, we assess the evidence for monophyly of two long-established, morphology-defined sections within the genus Synergus that differ in a range of biological traits. To aid analyses of ecological interactions within oak cynipid communities, we also consider the utility of cytochrome oxidase I (coxI) DNA barcodes in the oak inquilines. In this assessment, we do not assume that species are delineated at a single threshold value of sequence divergence for a single gene, but examine concordance in the composition of molecular operational Taxonomic units (MOTUs) across a range of sequence divergences in each gene and across genes. We also assess the impact of sampling effort on MOTU stability. Phylogenetic reconstructions for all three loci support monophyly for Synergus and Synophrus, but reject monophyly for Saphonecrus and for the two sections within Synergus. The suites of traits associated with the two sections of the genus Synergus are thus homoplasious. All three loci also reject monophyly for three Synergus species (S. hayneanus, S. pallipes, S. umbraculus). Sequences for each locus identify robust MOTUs that are largely concordant across loci for a range of cut-off values. Though many MOTU's correspond to recognised Linnean species, there is significant, multigene disagreement between groupings supported by morphology and sequence data, with both allocation of different morphospecies to the same MOTU and allocation of the same morphospecies to multiple MOTUs, regardless of cut-off value. Our results imply that while DNA barcoding has considerable utility within this group, morphology-based identification needs major revision at both genus and species levels. Further, lifehistory traits currently attributed to single morphospecies probably confound attributes of multiple lineages. Revealing patterns of character state evolution in Synergus requires collection of new host association and life history data explicitly linked to DNA barcode data for the specimens concerned.

Evolution of genes and repeats in the Nimrod superfamily.

The recently identified Nimrod superfamily is characterized by the presence of a special type of EGF repeat, the NIM repeat, located right after a typical CCXGY/W amino acid motif. On the basis of structural features, nimrod genes can be divided into three types. The proteins encoded by Draper-type genes have an EMI domain at the N-terminal part and only one copy of the NIM motif, followed by a variable number of EGF-like repeats. The products of Nimrod B-type and Nimrod C-type genes (including the eater gene) have different kinds of N-terminal domains, and lack EGF-like repeats but contain a variable number of NIM repeats. Draper and Nimrod C-type (but not Nimrod B-type) proteins carry a transmembrane domain. Several members of the superfamily were claimed to function as receptors in phagocytosis and/or binding of bacteria, which indicates an important role in the cellular immunity and the elimination of apoptotic cells. In this paper, the evolution of the Nimrod superfamily is studied with various methods on the level of genes and repeats. A hypothesis is presented in which the NIM repeat, along with the EMI domain, emerged by structural reorganizations at the end of an EGF-like repeat chain, suggesting a mechanism for the formation of novel types of repeats. The analyses revealed diverse evolutionary patterns in the sequences containing multiple NIM repeats. Although in the Nimrod B and Nimrod C proteins show characteristics of independent evolution, many internal NIM repeats in Eater sequences seem to have undergone concerted evolution. An analysis of the nimrod genes has been performed using phylogenetic and other methods and an evolutionary scenario of the origin and diversification of the Nimrod superfamily is proposed. Our study presents an intriguing example how the evolution of multigene families may contribute to the complexity of the innate immune response.

T2prhd: a tool to study the patterns of repeat evolution.

BACKGROUND: The models developed to characterize the evolution of multigene families (such as the birth-and-death and the concerted models) have also been applied on the level of sequence repeats inside a gene/protein. Phylogenetic reconstruction is the method of choice to study the evolution of gene families and also sequence repeats in the light of these models. The characterization of the gene family evolution in view of the evolutionary models is done by the evaluation of the clustering of the sequences with the originating loci in mind. As the locus represents positional information, it is straightforward that in the case of the repeats the exact position in the sequence should be used, as the simple numbering according to repeat order can be misleading. RESULTS: We have developed a novel rapid visual approach to study repeat evolution, that takes into account the exact repeat position in a sequence. The "pairwise repeat homology diagram" visualizes sequence repeats detected by a profile HMM in a pair of sequences and highlights their homology relations inferred by a phylogenetic tree. The method is implemented in a Perl script (t2prhd) available for downloading at http://t2prhd.sourceforge.net and is also accessible as an online tool at http://t2prhd.brc.hu. The power of the method is demonstrated on the EGF-like and fibronectin-III-like (Fn-III) domain repeats of three selected mammalian Tenascin sequences. CONCLUSION: Although pairwise repeat homology diagrams do not carry all the information provided by the phylogenetic tree, they allow a rapid and intuitive assessment of repeat evolution. We believe, that t2prhd is a helpful tool with which to study the pattern of repeat evolution. This method can be particularly useful in cases of large datasets (such as large gene families), as the command line interface makes it possible to automate the generation of pairwise repeat homology diagrams with the aid of scripts.

Current status of the oak gallwasp (Hymenoptera: Cynipidae: Cynipini) fauna of the Eastern Palaearctic and Oriental Regions.

Cynipid gallwasps comprise 1364 species worldwide, predominantly in temperate regions of the Holarctic. The vast majority of recorded species are from the Nearctic and the Western Palaearctic, both of which are long-standing centers of research on the taxonomy and biology of this group. In contrast, the Eastern Palaearctic and the Oriental Region faunas are much less studied, but potentially extremely rich. Previously recorded species richness of cynipid groups in the Eastern Palaearctic and Oriental regions probably represents a significant underestimate. This is particularly marked for gallwasps associated with oaks (tribe Cynipini), as has been shown by recent works, which describe many new species galling oaks in the subgenera Quercus and Cyclobalanopsis and plants of the other Fagaceae genera (Castanopsis, Lithocarpus and Castanea). In the present paper, we summarise the current knowledge of oak gallwasps in the regions that extend from Pakistan, through Nepal and China to Japan and south to Indonesia, and list a total of 97 species of Cynipini from the area.

New species of cynipid inquilines of the genus Synergus (Hymenoptera: Cynipidae: Synergini) from the Eastern Palaearctic.

Eight new species of cynipid inquilines, Synergus abei Melika & Schwéger, S. belizinellus Schwéger & Melika, S. changtitangi Melika & Schwéger, S. formosanus Schwéger & Melika, S. ishikarii Melika & Schwéger, S. kawakamii Tang & Melika, S. khazani Melika & Schwéger and S. symbioticus Schwéger & Melika, from the Eastern Palaearctic are described. Descriptions, diagnoses, biology, and host associations for the new species and a key to all known Eastern Palaearctic Synergus species are given. All taxa are supported by morphological and molecular data. We discuss the status of all previously described Eastern Palaearctic Synergus species, and provide validation and synonymization of some species.

New species of cynipid inquilines of the genus Saphonecrus (Hymenoptera: Cynipidae: Synergini) from the Eastern Palaearctic, with a re-appraisal of known species world-wide.

Fifteen new species of cynipid inquilines, Saphonecrus chinensis Tang & Schwéger, S. gilvus Melika & Schwéger, S. globosus Schwéger & Tang, S. leleyi Melika & Schwéger, S. lithocarpii Schwéger & Melika, S. longinuxi Schwéger & Melika, S. morii Schwéger & Tang, S. nantoui Tang, Schwéger & Melika, S. nichollsi Schwéger & Melika, S. pachylomai Schwéger, Tang & Melika, S. robustus Schwéger & Melika, S. saliciniai Melika, Tang & Schwéger, S. shanzhukui Melika & Tang, S. symbioticus Melika & Schwéger, and S. taitungi Schwéger, Tang & Melika, from the Eastern Palaearctic are described. Descriptions, diagnoses, biology, and host associations for the new species, and a key to Palaearctic Saphonecrus species are given. All new taxa form distinct units as demonstrated by the molecular phylogenetic analyses of Palaearctic Saphonecrus species. The status of some earlier described Saphonecrus species is discussed also. The Synergini genus Lithonecrus Nieves-Aldrey & Butterill, 2014 is synonymized with Lithosaphonecrus Tang, Melika & Bozsó, 2013. Three Saphonecrus species are transferred to Synergus: Synergus brevis (Weld) comb. nova, Synergus hupingshanensis (Liu, Yang & Zhu) comb. nova, and Synergus yukawai (Wachi, Ide & Abe) comb. nova. Synophrus vietnamensis Abe, Ide, Konishi & Ueno is transferred to Lithosaphonecrus: Lithosaphonecrus vietnamensis Abe, Ide, Konishi & Ueno), comb. nova. The current number of valid Saphonecrus species worldwide is 36.

Short tandem repeat data analysis in a Mongolian population.

Fifteen somatic (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA) and five Y-chromosome (DYS19, DYS390, DYS391, DYS392, DYS393) short tandem repeat (STR) system analyses were carried out in a Mongolian population in order to define the possible relationship between Mongolians and old Hungarian population. For STR data analysis the Microsoft Excel-PowerStats program was used. Inter-population data analysis was performed with Arlequin Software ver. 2.000. The somatic markers showed meaningful difference between Mongolians and old Hungarians but the distribution of the Y-chromosome STR systems refers to a closer relationship between the old Hungarian and oriental populations.

Utilizing descriptive statements from the biodiversity heritage library to expand the Hymenoptera Anatomy Ontology.

Hymenoptera, the insect order that includes sawflies, bees, wasps, and ants, exhibits an incredible diversity of phenotypes, with over 145,000 species described in a corpus of textual knowledge since Carolus Linnaeus. In the absence of specialized training, often spanning decades, however, these articles can be challenging to decipher. Much of the vocabulary is domain-specific (e.g., Hymenoptera biology), historically without a comprehensive glossary, and contains much homonymous and synonymous terminology. The Hymenoptera Anatomy Ontology was developed to surmount this challenge and to aid future communication related to hymenopteran anatomy, as well as provide support for domain experts so they may actively benefit from the anatomy ontology development. As part of HAO development, an active learning, dictionary-based, natural language recognition tool was implemented to facilitate Hymenoptera anatomy term discovery in literature. We present this tool, referred to as the 'Proofer', as part of an iterative approach to growing phenotype-relevant ontologies, regardless of domain. The process of ontology development results in a critical mass of terms that is applied as a filter to the source collection of articles in order to reveal term occurrence and biases in natural language species descriptions. Our results indicate that taxonomists use domain-specific terminology that follows taxonomic specialization, particularly at superfamily and family level groupings and that the developed Proofer tool is effective for term discovery, facilitating ontology construction.

A conserved gene cluster as a putative functional unit in insect innate immunity.

The Nimrod gene superfamily is an important component of the innate immune response. The majority of its member genes are located in close proximity within the Drosophila melanogaster genome and they lie in a larger conserved cluster ("Nimrod cluster"), made up of non-related groups (families, superfamilies) of genes. This cluster has been a part of the Arthropod genomes for about 300-350 million years. The available data suggest that the Nimrod cluster is a functional module of the insect innate immune response.

Whom do the sparrows follow? The effect of kinship on social preference in house sparrow flocks.

Non-aggressive social interactions between group-mates, e.g. maintenance of spatial proximity or activity synchrony are basic elements of a species' social structure, and were found to be associated with important fitness consequences in group-living animals. In the establishment of such affiliative relationships, kinship has often been identified as one of the key predictors, but this has rarely been studied in simple social groups such as flocks of gregarious birds. In this study we investigated whether kinship affects social preference, as measured by the tendency to associate with others during various social activities, in captive house sparrow (Passer domesticus) flocks where birds could interact with differently related flock-mates. We found that preference between flock-mates was correlated with familiarity from early nestling period: same-brood siblings followed their sib initiating new activities more often than non-sib birds. The strength of association between birds also tended to correlate with genetic relatedness, but this was mainly due to the effect of siblings' affiliation. Thus we concluded that house sparrows prefer the company of their siblings during social activities even well after fledging, which may facilitate kin-biased behaviours.

Molecular study of arbuscular mycorrhizal fungi colonizing the sporophyte of the eusporangiate rattlesnake fern (Botrychium virginianum, Ophioglossaceae).

The arbuscular mycorrhizal (AM) fungi colonizing the sporophytes of the eusporangiate rattlesnake fern (Botrychium virginianum, Ophioglossaceae) in its Hungarian population were investigated in the present study. Different regions of the nrRNA gene complex were analyzed using two different primer sets. These produced similar results for the detected AM fungi phylotypes. Several AM fungal lineages were associated with sporophytes of B. virginianum. Phylogenetic analyses of different partial small subunit datasets grouped one lineage into the Gigasporaceae, showing similarities with Scutellospora sequences. In addition to unidentified Scutellospora phylotypes, it is possible that S. gregaria also colonized the fern. Several AM fungal phylotypes colonizing the sporophytes grouped into Glomus group A. They did not form distinct clades but grouped with sequences of AM fungi with different geographic and host origins. One main lineage clustered into the widespread G. fasciculatum/G. intraradices group and one into the subgroup GlGrAc, while others had no affinity to the subgroups of Glomus group A. As AM fungal phylotypes associated with B. virginianum seem to belong to widespread AM fungal taxa and show no specificity to this fern, we suppose that the previously described special anatomy of AM of B. virginianum is determined by the plant.