Chao-Dong ZHU

A species of the tribe Synergini (Hymenoptera: Cynipidae) was reared from a gall collected in China on Castanea mollissima Blume and Castanea seguinii Dode. The morphological features of this gall wasp indicate that it is an undescribed species belonging to the genus Synergus and is herein described as a new species, Synergus castaneus PujadeÐVillar, Bernardo et Viggiani sp. nov. (Hymenoptera Cynipidae: Synergini). This is the Þrst known instance of a species of Synergus emerging from Castanea galls (Fagaceae). Data on the diagnosis, distribution, and biology of the new species are given. Morphological features of this species are discussed and illustrated. No other known gall-inducing species emerged from the collected galls, whereas tens of specimens of parasitoids and adults of the inquiline micromoth Andrioplecta pulverula Meyrick (Lepidoptera: Tortricidae) did. 28S-D2 and COI sequences conÞrmed that S. castaneus is a distinct species belonging to the genus Synergus.

1. Hierarchical clustering of molecular data is commonly used for estimation of species diversity in all forms of life. Parameters appropriate for species-level clustering are usually derived from reference data and applied for the delineation of sequences of unknown species membership, although it is not clear how this should be carried out in a multilocus scenario. 2. We introduce a novel means of concurrent clustering parameter optimization and delineation for multilocus data. A simulated annealing heuristic search is performed, whereby clustering thresholds are independently varied for each locus, but optimized according to the recovery of expected taxonomic species globally over loci. For each iteration of the search, one or more loci are randomly selected and a different threshold is separately proposed to cluster each, then the loci are linked to form global species units. Where the set of thresholds group the reference (species labelled) data with high taxonomic congruence, they are adopted for clustering of the subject (nonlabelled) sequences into global molecular operational taxonomic units (global MOTU). Four mined test data sets composed of both reference and subject sequences are combined with a newly sequenced three gene Apoidea data set, and subject to the proposed method. 3. Even optimizing four loci and thousands of sequences, the approach rapidly convergences on a set of parameters with maximal optimality score, although the method masks a high degree of incongruence, and does not always converge on a single set of thresholds. For example, of the 476 Apoidea sequences, 70 global MOTU were inferred over the heuristic search, although the number of single gene MOTU were much lower for the 28S RNA locus, and a range of equally optimal clustering thresholds were observed for the CytB gene. 4. We demonstrate the approach as a scalable species delineation solution for heterogeneous data sets composed of incompletely and inconsistently labelled data from public DNA data bases, for newly sequenced multilocus data, or both. The delineation over a heuristic search of clustering parameters facilitates the estimation of species diversity in multilocus data, giving species estimates that take into account uncertainty regarding choice of clustering thresholds.

Hepatitis B virus (HBV) has evolved into phylogenetically separable genotypes and subgenotypes. Accurately assigning the subgenotype for an HBV strain is of clinical and epidemiological significance. In this paper, we review the recommendations currently employed for HBV subgenotyping, the history of HBV subgenotyping, the effects of recombination on HBV subgenotyping, misclassifications in HBV subgeno-typing, and suggestions are made to correct the misclassifications. Finally, proposals are made to guide future HBV subgenotyping.

Mitogenomes can provide information for phylogenetic analyses and evolutionary biology. The complete mitochondrial genome of Amata emma (Lepidoptera: Erebidae) was sequenced and analyzed in the study. The circular genome is 15,463 bp in size, with the gene content, orientation and order identical to other ditrysian insects. The genome composition of the major strand shows highly A+T biased and exhibits negative AT-skew and GC-skew. The initial codons are the canonical putative start codons ATN with the exception of cox1 gene which uses CGA instead. Ten genes share complete termination codons TAA, and three genes use incomplete stop codons TA or T. Additionally, the codon distribution and Relative Synonymous Codon Usage of the 13 PCGs in the A. emma mitogenome are consistent with those in other Noctuid mitogenomes. All tRNA genes have typical cloverleaf secondary structures, except for the trnS1 (AGN) gene, in which the dihydrouridine (DHU) arm is simplified down to a loop. The secondary structures of two rRNA genes broadly conform with the models proposed for these genes of other Lepidopteran insects. Except for the A+T-rich region, there are three major intergenic spacers, spanning at least 10 bp and five overlapping regions. There are obvious differences in the A+T-rich region between A. emma and other Lepidopteran insects reported previously except that the A+T-rich region contains an 'ATAGA'-like motif followed by a 19 bp poly-T stretch and a (AT) 9 element preceded by the 'ATTTA' motif. It neither has a poly-A (in the a strand) upstream trnM nor potential stem-loop structures and just has some simple structures like (AT) n GTAT. The phylogenetic relationships based on nucleotide sequences of 13 PCGs using Bayesian inference and maximum likelihood methods provided a well-supported a broader outline of Lepidoptera and which agree with the traditional morphological classification and recently working, but with a much higher support.

Isolation with Migration model (IM), which jointly estimates divergence times and migration rates between two populations from DNA sequence data, can capture many phenomena when one population splits into two. The parameters inferences for IM are based on Markov Chain Monte Carlo method (MCMC). Standard implementations of MCMC are prone to fall into local optima. Metropolis Coupled MCMC [(MC) 3 ] as a variant of MCMC can more readily explore multiple peaks in posterior distribution of trees. Expensive execution time has limited the application of (MC) 3. This paper proposes a Parallel Metropolis Coupled Markov Chain Monte Carlo for IM. The proposed parallel algorithm retains the ability of (MC) 3 and maintains a fast execution time. Performance results indicate nearly linear speed improvement. This paper provides researcher with rapider and more high-efficiency methods to study population genetics and molecular ecology problems aided with super computer.

Four species and one subspecies of the genus Monema Walker, 1855 are recognized from China, in which M. tanaognatha Wu & Pan sp. n. is described as new, M. coralina Dudgeon, 1895 and M. meyi Solovyev & Witt, 2009 are newly recorded for China. The female of M. meyi is reported for the first time. Monema ni-grans de Joannis, 1901 and M. melli Hering, 1931 are synonymized with M. flavescens Walker, 1855. Cni-docampa rubriceps Matsumura, 1931 is regarded here as a subspecies of Monema flavescens Walker, 1855. The photographs of moths and their genitalia are given. A key to the species of the genus is provided.

With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this. We investigated this approach by focusing on the Tibetan plateau, which is one of the world's top biodiversity hotspots. There have been few studies of its invertebrates, although they constitute the vast majority of the region's diversity. Here we investigated species diversity of the lepidopteran family Noctuidae, across different environmental gradients, using measurements based on traditional morphology as well as on DNA barcoding. The COI barcode showed an average interspecific K2P distance of 9:45+2:08%, which is about four times larger than the mean intraspecific distance (1:85+3:20%). Using six diversity indices, we did not detect any significant differences in estimated species diversity between measurements based on traditional morphology and on DNA barcoding. Furthermore, we found strong positive correlations between them, indicating that barcode-based measures of species diversity can serve as a good surrogate for morphology-based measures in most situations tested. Eastern communities were found to have significantly higher diversity than Western ones. Among 22 environmental factors tested, we found that three (precipitation of driest month, precipitation of driest quarter, and precipitation of coldest quarter) were significantly correlated with species diversity. Our results indicate that these factors could be the key ecological factors influencing the species diversity of the lepidopteran family Noctuidae on the Tibetan plateau.

Four species and one subspecies of the genus Monema Walker, 1855 are recognized from China, in which M. tanaognatha Wu & Pan sp. n. is described as new, M. coralina Dudgeon, 1895 and M. meyi Solovyev & Witt, 2009 are newly recorded for China. The female of M. meyi is reported for the first time. Monema ni-grans de Joannis, 1901 and M. melli Hering, 1931 are synonymized with M. flavescens Walker, 1855. Cni-docampa rubriceps Matsumura, 1931 is regarded here as a subspecies of Monema flavescens Walker, 1855. The photographs of moths and their genitalia are given. A key to the species of the genus is provided.

This paper reports the first record of the genus Homalictus from China. We describe and illustrate H. (H.) nabanensis sp. n. collected from the Naban River Watershed National Nature Reserve, Xishuangbanna, Yunnan, China. The type specimens are deposited in

With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this. We investigated this approach by focusing on the Tibetan plateau, which is one of the world's top biodiversity hotspots. There have been few studies of its invertebrates, although they constitute the vast majority of the region's diversity. Here we investigated species diversity of the lepidopteran family Noctuidae, across different environmental gradients, using measurements based on traditional morphology as well as on DNA barcoding. The COI barcode showed an average interspecific K2P distance of 9:45+2:08%, which is about four times larger than the mean intraspecific distance (1:85+3:20%). Using six diversity indices, we did not detect any significant differences in estimated species diversity between measurements based on traditional morphology and on DNA barcoding. Furthermore, we found strong positive correlations between them, indicating that barcode-based measures of species diversity can serve as a good surrogate for morphology-based measures in most situations tested. Eastern communities were found to have significantly higher diversity than Western ones. Among 22 environmental factors tested, we found that three (precipitation of driest month, precipitation of driest quarter, and precipitation of coldest quarter) were significantly correlated with species diversity. Our results indicate that these factors could be the key ecological factors influencing the species diversity of the lepidopteran family Noctuidae on the Tibetan plateau.

Abstract Aprostocetus pinus sp. nov. (Chalcidoidea: Eulophidae) is newly described as a leaf bud and microstrobilus pest of Pinus massoniana (Pinales: Pinaceae), an important afforestation species in southeast China. Both sexes of the parasitoid are described and illustrated.

Two species of the Colletes flavicornis-group from China are treated in this paper. C. vestitus sp. n. from Xinjiang is illustrated and described, and C. popovi Noskiewicz, 1936 is illustrated and redescribed. Both sexes of the two species are in addition characterized by DNA barcodes. The type specimens of the new species are deposited in the

This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/authorsrights a b s t r a c t Entomobryidae is the largest family in Collembola but relationships within the family have never been subjected to rigorous phylogenetic analyses. Within the family, body scales are present in many species, and are fundamental in the classification at the subfamilial and tribal levels. A molecular phylogeny was reconstructed using the nuclear 18SrRNA and partial 28SrRNA and the mitochondrial 16SrRNA to examine the evolution of scales across Entomobryidae subfamilies. These datasets were analyzed separately and combined, with parsimony, likelihood and Bayesian algorithms. Monophyly of Orchesellinae was not recovered, and it was split into a scaled clade and an unscaled clade, contradicting to all recent tax-onomic conceptions. The monophyly of Entomobryinae, Seirinae and Lepidocyrtinae is well supported however within Entomobryinae, the polyphyly of Entomobryini and Willowsiini implies that classification using the presence/absence of scales is not valid. Analyses of ancestral character state reconstruction in Entomobryidae indicate that the presence of body scales have evolved independently at least five times, with a loss of scales occurring independently at least twice. A revision of the family Entomobryidae on molecular and morphological basis is clearly needed.

The genus Copidosoma (Hymenoptera: Chalcidoidea: Encyrtidae) is a diverse group of polyembryonic parasitoids of Lepidoptera, including species that have the potential to control agricultural and forestry pests. Moreover, some species of Copidosoma display polyembryony. Despite their economic and scientific importance, little is known about the phylogeny of Copidosoma and its relations to other groups of Encyrtidae. Here we infer the phylogenetic relationships of this genus from nucleotide sequences of two nuclear (18S and 28S) and one mitochondrial (COI) genes. Forty-four species of Copidosoma and three species of Copidosomopsis plus two outgroup species are included in Maximum Parsimony and Bayesian analyses. Copidosomopsis syn. n. is proposed as a junior synonym of Copidosoma based on phylogenetic analysis results. Each of nine identical clades, resulting from both analyses, is proposed as informal species group: cervius group (cervius, chalconotum and serricorne), recovered as the basal lineage of Copidosoma; nacoleiae group (nacoleaie, meridionalis and an undescribed species, formerly belonging to the genus Copidosomopsis); boucheanum group (boucheanum, terebrator, peticus, phaloniae, ancharus, tibiale and sosares); noyesi group (noyesi and probably undescribed related species); albipes group (albipes and coimbatorense); varicorne group (including varicorne and subalbicorne in one subclade, and aretas and fuscisquama in the other); thebe group (thebe and probably undescribed related species); exiguum group (exiguum and probably undescribed related species); floridanum group (floridanum, primulum, transversum, truncatellum and agrotis). Host associations of the genus and host specificity of recognized groups are discussed. The current work offers a foundation for a comprehensive phylogeny of Copidosoma and the possibility to reconstruct cophylogeny between Copidosoma and their lepidopteran hosts.

—Public DNA databases are composed of data from many different taxa, although the taxonomic annotation on sequences is not always complete, which impedes the utilization of mined data for species-level applications. There is much ongoing work on species identification and delineation based on the molecular data itself, although applying species clustering to whole databases requires consolidation of results from numerous undefined gene regions, and introduces significant obstacles in data organization and computational load. In the current paper, we demonstrate an approach for species delineation of a sequence database. All DNA sequences for the insects were obtained and processed. After filtration of duplicated data, delineation of the database into species or molecular operational taxonomic units (MOTUs) followed a three-step process in which (i) the genetic loci L are partitioned, (ii) the species S are delineated within each locus, then (iii) species units are matched across loci to form the matrix L×S, a set of global (multilocus) species units. Partitioning the database into a set of homologous gene fragments was achieved by Markov clustering using edge weights calculated from the amount of overlap between pairs of sequences, then delineation of species units and assignment of species names were performed for the set of genes necessary to capture most of the species diversity. The complexity of computing pairwise similarities for species clustering was substantial at the cytochrome oxidase subunit I locus in particular, but made feasible through the development of software that performs pairwise alignments within the taxonomic framework, while accounting for the different ranks at which sequences are labeled with taxonomic information. Over 24 different homologs, the unidentified sequences numbered approximately 194,000, containing 41,525 species IDs (98.7% of all found in the insect database), and were grouped into 59,173 single-locus MOTUs by hierarchical clustering under parameters optimized independently for each locus. Species units from different loci were matched using a multipartite matching algorithm to form multilocus species units with minimal incongruence between loci. After matching, the insect database as represented by these 24 loci was found to be composed of 78,091 species units in total. 38,574 of these units contained only species labeled data, 34,891 contained only unlabeled data, leaving 4,626 units composed both of labeled and unlabeled sequences. In addition to giving estimates of species diversity of sequence repositories, the protocol developed here will facilitate species-level applications of modern-day sequence data sets. In particular, the L×S matrix represents a post-taxonomic framework that can be used for species-level organization of metagenomic data, and incorporation of these methods into phylogenetic pipelines will yield matrices more representative of species diversity.

An understanding of the global migration dynamics of highly pathogenic avian influenza A(H5N1) virus is helpful for surveillance and disease prevention. To characterize the migration network of this virus, we used genetic analysis, which supported a global persistence model in which each of 9 regions acts to some extent as a source. Siberia is the major hub for the dispersal of the virus. Southeast Asia and Africa are major sources of genetically and antigenically novel strains. We found evidence of local persistence of the virus in Southeast Asia and Africa, which is rare for human influenza A viruses. The differences in migration dynamics between avian and human influenza viruses might help with the design of region-specific surveillance efforts and the selection of vaccine candidates.

Two closely related new species of Aprostocetus Westwood (Hymenoptera: Eulophidae: Tetrastichinae) are described as fortuitous parasitoids of invasive gall inducers in two other genera of Tetrastichinae, Leptocybe Fisher & LaSalle and Qua-drastichus Girault. Aprostocetus causalis La Salle & Wu is a parasitoid of Leptocybe invasa Fisher & La Salle on Euca-lyptus spp. (Myrtaceae) in China and Thailand, and A. felix La Salle, Yang & Lin is a parasitoid of Quadrastichus erythrinae Kim on Erythrina spp. (Fabaceae) in Taiwan. Epitetrastichus nigriventris Girault, 1913 is removed from syn-onymy from Aprostocetus gala (Walker), and treated as the valid species A. nigriventris (Girault).

1. A number of systems have been developed for taxonomic identification of DNA sequence data. However, in eukaryotes, these systems are largely based on single predefined genes, and thus are vulnerable to biases from limited character sampling, and are not able to identify most sequences of genomic origin. 2. We here demonstrate an implementation for multigene DNA barcoding. First, a reference framework is built of frequently sequenced loci. Query sequence data are then organized by excising sequences homologous to references and assigning species names where the level of sequence similarity between query and reference falls within the (gene-appropriate) level of intraspecific variation usually observed. The approach is compared to some existing methods including 'bagpipe_phylo', a re-implementation for taxonomic assignment on phylogenies. 3. Seventy-eight per cent of the species and 94% of the genera known to be present in arthropod test queries were correctly inferred by the proposed multigene system. Most critically, the rate of species identification was increased over using a COI-only approach. Twenty-four per cent of species in the queries were found only in non-COI genes, with no clear reduction in the accuracy of species assignment at many of these other loci. Similarly , additional species assignments were made for a pooled metagenomic data set using non-COI columns. On a smaller query data set of 273 bee sequences, the accuracy of species assignment using modified calculation of distances was indistinguishable from phylogeny-based taxonomic identification. 4. Standardized single fragment DNA barcoding remains an invaluable tool in species identification for PCR-generated sequence data. The approach developed here supplements the established species-dense DNA barcode backbone with other genomic data, reducing error via integration of independent genetic loci and permitting additional identifications for non-barcode fragments. The latter will be particularly relevant in monitoring of community genomics using next-generation sequencing platforms.

Four fruit fly genera, Ichneumonosoma de Meijere, Pelmatops Enderlein, Pseudopelmatops Shiraki and Soita Walker, were studied and 19 species are recognized. Three new species, Soita infuscata Chen & Norrbom, Ichneumonosoma quad-ripunctata Chen & Freidberg, and I. triangularis Chen & Norrbom are described and illustrated. Ichneumonosoma and Soita are revised, and keys to all the species are provided. Ichneumonosoma imitans (de Meijere) is newly recorded from Thailand. One new synonym is established: Soita Walker = Xaniosternum Enderlein, and Xaniosternum ophioneum Enderlein is moved from Xaniosternum to Soita (n. comb.). In addition, new morphological, geographic and biological information for two stalk-eyed fruit fly genera, Pelmatops and Pseudopelmatops, are provided. Pelmatops fukienensis Zia & Chen is newly recorded from Burma, Pelmetops ichneumoneus (Westwood) is newly recorded from Thailand and Bur-ma, Pseudopelmatops angustifasciatus Zia & Chen is newly recorded from Vietnam, and the male of P. angustifasciatus is described and illustrated for the first time. The morphology of the compound eye and occipital protuberance of Pel-matops and Pseudopelmatops is described and illustrated for the first time. A cladistic analysis based on morphological characters of adults, a partial molecular analysis using the nuclear 28S rDNA (28S) and the mitochondrial cytochrome c oxidase I (COI) genes and a combined dataset were conducted to reconstruct the phylogeny of the four genera and their species. The results showed good support for monophyly of each of the four genera and the clade of the stalk-eyed fruit flies (Pelmatops + Pseudopelmatops). However, relationships of the stalk-eyed fruit flies with Soita and Ichneumonosoma are not clearly resolved, with the morphological analysis indicating that Ichneumonosoma is the sister group of the stalk-eyed fruit flies, but the 28S analysis and the combined analysis group Soita closer to the stalk-eyed fruit flies. Regarding relationships amongst congeners, Pelmatops was well resolved; Ichneumonosoma and Soita were partly resolved, and Pseudopelmatops was unresolved. In addition, a hypothesis about the biology of Pseudopelmatops and its relationship with Sesiidae (Lepidoptera) is discussed.

The yellow tortrix, Acleris fimbriana belongs to Tortricidae in Lepidoptera. We described the complete mitogenome of A. fimbriana, which is typical circular duplex molecules and 15,933 bp in length containing the standard metazoan set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and an A + T-rich region with macro-repeat sequences. All the inferred tRNA secondary structures show the common cloverleaf pattern, with the exception of trnS1(AGN) which lacks the DHU arm. The A. fimbriana mitochondrial genome has the same gene order with other lepidopterans.

The complete mitochondrial genome of the Colletes gigas (Hymenoptera: Colletidae) is determined to be 15,885 bp in length, containing 37 typical animal mitochondrial genes: 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a major non-coding AT-rich region. All PCGs initiate with typical ATN codons and end with the complete termination codon TAA, except for the cob gene, which harbors the stop codon of TAG. Twenty-four intergenic spacers (614 bp in total) and 7 overlapping regions (37 bp in total) are dispersed throughout the whole genome. The non-coding AT-rich region is 539 bp long and contains a tandem repeat region, which has also been reported in other insects. This is the first completely sequenced mitochondrial genome of the family Colletidae.

The peach fruit moth, Carposina sasakii belongs to Carposinidae in Lepidoptera. In this paper, we described the complete mitogenome of C. sasakii. It is 15,611 bp in length, including 13 PCGs, 2 rRNAs, 22 tRNAs and a major noncoding A + T-rich region, which revealed the typical gene content found in other metazoan mitogenomes. The overall base composition is 42.0% A, 39.5% T, 7.75% G and 10.75% C. The A + T-rich region is located between rrnS and trnM. There is a motif ATAGA in downstream of rrnS followed by a 19 bp Poly-T stretch. The Poly-A is not found in upstream of trnM, and the position of Poly-A is replaced by a stem-loop structure. There are eight mononucleotide repeat sequences (Tn/An) with the length of 7 bp-19bp, three dinucleotide repeat sequences (TA)n/(AT)n, and a longer repeat sequence (AATATATA)5 in A + T-rich region. The mononucleotide repeat sequences occur repeatedly in A + T-rich reigion of C. sasakii, which is special in insects sequenced of Lepidoptera.