Ge-Xia Qiao

Comparative analysis of mitochondrial genomes of five aphid species (Hemiptera: Aphididae) and phylogenetic implications.

Insect mitochondrial genomes (mitogenomes) are of great interest in exploring molecular evolution, phylogenetics and population genetics. Only two mitogenomes have been previously released in the insect group Aphididae, which consists of about 5,000 known species including some agricultural, forestry and horticultural pests. Here we report the complete 16,317 bp mitogenome of Cavariella salicicola and two nearly complete mitogenomes of Aphis glycines and Pterocomma pilosum. We also present a first comparative analysis of mitochondrial genomes of aphids. Results showed that aphid mitogenomes share conserved genomic organization, nucleotide and amino acid composition, and codon usage features. All 37 genes usually present in animal mitogenomes were sequenced and annotated. The analysis of gene evolutionary rate revealed the lowest and highest rates for COI and ATP8, respectively. A unique repeat region exclusively in aphid mitogenomes, which included variable numbers of tandem repeats in a lineage-specific manner, was highlighted for the first time. This region may have a function as another origin of replication. Phylogenetic reconstructions based on protein-coding genes and the stem-loop structures of control regions confirmed a sister relationship between Cavariella and pterocommatines. Current evidence suggest that pterocommatines could be formally transferred into Macrosiphini. Our paper also offers methodological instructions for obtaining other Aphididae mitochondrial genomes.

DNA barcoding of genus Toxoptera Koch (Hemiptera: Aphididae): Identification and molecular phylogeny inferred from mitochondrial COI sequences

Abstract  Identification of aphid species is always difficult due to the shortage of easily distinguishable morphological characters. Aphid genus Toxoptera consists of species with similar morphology and similar to Aphis in most morphological characters except the stridulatory apparatus. DNA barcodes with 1 145 bp sequences of partial mitochondrial cytochrome‐coxidase I (COI) genes were used for accurate identification of Toxoptera. Results indicated mean intraspecific sequence divergences were 1.33%, whereas mean interspecific divergences were greater at 8.29% (0.13% and 7.79% if T. aurantii 3 and T. aurantii 4 are cryptic species). Sixteen samples were distinguished to four species correctly by COI barcodes, which implied that DNA barcoding was successful in discrimination of aphid species with similar morphology. Phylogenetic relationships among species of this genus were tested based on this portion of COI sequences. Four species of Toxoptera assembled a clade with low support in maximum‐parsimony (MP) analysis, maximum‐likelihood (ML) analysis and Bayesian phylogenetic trees, the genus Toxoptera was not monophyletic, and there were two sister groups, such as T. citricidus and T. victoriae, and two clades of T. aurantii which probably presented cryptic species in the genus.

The Effectiveness of Three Regions in Mitochondrial Genome for Aphid DNA Barcoding: A Case in Lachininae

Background The mitochondrial gene COI has been widely used by taxonomists as a standard DNA barcode sequence for the identification of many animal species. However, the COI region is of limited use for identifying certain species and is not efficiently amplified by PCR in all animal taxa. To evaluate the utility of COI as a DNA barcode and to identify other barcode genes, we chose the aphid subfamily Lachninae (Hemiptera: Aphididae) as the focus of our study. We compared the results obtained using COI with two other mitochondrial genes, COII and Cytb. In addition, we propose a new method to improve the efficiency of species identification using DNA barcoding. Methodology/Principal Findings Three mitochondrial genes (COI, COII and Cytb) were sequenced and were used in the identification of over 80 species of Lachninae. The COI and COII genes demonstrated a greater PCR amplification efficiency than Cytb. Species identification using COII sequences had a higher frequency of success (96.9% in “best match” and 90.8% in “best close match”) and yielded lower intra- and higher interspecific genetic divergence values than the other two markers. The use of “tag barcodes” is a new approach that involves attaching a species-specific tag to the standard DNA barcode. With this method, the “barcoding overlap” can be nearly eliminated. As a result, we were able to increase the identification success rate from 83.9% to 95.2% by using COI and the “best close match” technique. Conclusions/Significance A COII-based identification system should be more effective in identifying lachnine species than COI or Cytb. However, the Cytb gene is an effective marker for the study of aphid population genetics due to its high sequence diversity. Furthermore, the use of “tag barcodes” can improve the accuracy of DNA barcoding identification by reducing or removing the overlap between intra- and inter-specific genetic divergence values.

Use of a mitochondrial COI sequence to identify species of the subtribe Aphidina (Hemiptera, Aphididae)

Abstract Aphids of the subtribe Aphidina are found mainly in the North Temperate Zone. The relative lack of diagnostic morphological characteristics has hindered the identification of species in this group. However, DNA-based taxonomic methods can clarify species relationships within this group. Sequence variation in a partial segment of the mitochondrial COI gene was highly effective for identifying species within Aphidina. Thirty-six species of Aphidina were identified in a neighbor-joining tree. Mean intraspecific sequence divergence in Aphidina was 0.52%, with a range of 0.00% to 2.95%, and the divergences of most species were less than 1%. Mean interspecific divergence within previously recognized genera or morphologically similar species groups was 6.80%, with a range of 0.68% to 11.40%, with variation mainly in the range of 3.50% to 8.00%. Possible reasons for anomalous levels of mean nucleotide divergence within or between some taxa are discussed.

Predicting potential distribution of chestnut phylloxerid (Hemiptera: Phylloxeridae) based on GARP and Maxent ecological niche models

The chestnut phylloxerid, Moritziella castaneivora, has been recently recorded as a forest pest in China. It heavily damaged chestnut trees and has caused serious economic losses in some main chestnut production areas. In order to effectively monitor and manage this pest, it is necessary to investigate its potential geographical distribution worldwide. In this study, we used two ecological niche models, Genetic Algorithm for Rule‐set Production (GARP) and Maximum Entropy (Maxent), along with the geographical distribution of the host plants, Japanese chestnut (Castanea crenata) and Chinese chestnut (Castanea mollissima), to predict the potential geographical distribution of M. castaneivora. The results suggested that the suitable distribution areas based on GARP were general consistent with those based on Maxent, but GARP predicted distribution areas that extended more in size than did Maxent. The results also indicated that the suitable areas for chestnut phylloxerid infestations were mainly restricted to Northeast China (northern Liaoning), East China (southern Shandong, northern Jiangsu and western Anhui), North China (southern Hebei, Beijing and Tianjin), Central China (eastern Hubei and southern Henan), Japan (Kinki, Shikoku and Tohoku) and most parts of the Korean Peninsula. In addition, some provinces of central and western China were predicted to have low suitability or unsuitable areas (e.g. Xinjiang, Qinghai and Tibet). A jackknife test in Maxent showed that the average precipitation in July was the most important environmental variable affecting the distribution of this pest species. Consequently, the study suggests several reasonable regulations and management strategies for avoiding the introduction or invasion of this high‐risk chestnut pest to these potentially suitable areas.

Use of Parsimony Analysis to Identify Areas of Endemism of Chinese Birds: Implications for Conservation and Biogeography

Parsimony analysis of endemicity (PAE) was used to identify areas of endemism (AOEs) for Chinese birds at the subregional level. Four AOEs were identified based on a distribution database of 105 endemic species and using 18 avifaunal subregions as the operating geographical units (OGUs). The four AOEs are the Qinghai-Zangnan Subregion, the Southwest Mountainous Subregion, the Hainan Subregion and the Taiwan Subregion. Cladistic analysis of subregions generally supports the division of China’s avifauna into Palaearctic and Oriental realms. Two PAE area trees were produced from two different distribution datasets (year 1976 and 2007). The 1976 topology has four distinct subregional branches; however, the 2007 topology has three distinct branches. Moreover, three Palaearctic subregions in the 1976 tree clustered together with the Oriental subregions in the 2007 tree. Such topological differences may reflect changes in the distribution of bird species through circa three decades.

Widespread infection and diverse infection patterns of Wolbachia in Chinese aphids

Wolbachia are intracellular symbionts that infect a wide range of arthropods and filarial nematodes. Aphids are engaged in diverse and complex relationships with their endosymbionts. Four supergroups (A, B, M and N) of Wolbachia were previously detected in aphids and supergroups M and N were only found in aphids. In this study, we detected and described Wolbachia infections in natural populations of aphids in China. Three supergroups (A, B and M) were found in the examined aphid species. Supergroup M was preponderant, whereas supergroups A and B were only detected in certain species. Supergroup N was not found in this study. There were four infection patterns of Wolbachia in aphids, namely, infection with supergroup M alone, co‐infection with supergroups A and M, co‐infection with supergroups B and M, and co‐infection with supergroups A, B and M. The pattern of infection only with supergroup M was universal and was found in all evaluated subfamilies. Only two subfamilies, Aphidinae and Lachninae, manifested to present all four infection patterns. Three patterns were observed in Calaphidinae (M, A&M, B&M) and Eriosomatinae (M, B&M, A&B&M). Two patterns were observed in the Anoeciinae (M, A&M) and Greenideinae (M, B&M), and only one pattern (M) was observed in the remaining families and/or subfamilies of Aphidoidea. These results indicated that Wolbachia infections in Chinese aphids are widespread. Phylogenetic analyses suggest that Wolbachia supergroup M spread rapidly and recently among all host species of aphids in China. Reasons for this spread and its mechanisms are discussed along with the possible effects of Wolbachia on their aphid hosts.

Phylogenetic congruence between Mollitrichosiphum (Aphididae: Greenideinae) and Buchnera indicates insect-bacteria parallel evolution

We wanted to test whether Mollitrichosiphum, an aphid genus with life cycles on subtropical woody host plants, and Buchnera, the primary endosymbiont of aphids, evolve in parallel. We used three aphid genes (mitochondrial COI, cytochrome oxidase subunit I and Cytb, cytochrome b; nuclear EF1α, translation elongation factor 1 alpha) and two Buchnera genes (16S rDNA; gnd, gluconate‐6‐phosphate dehydrogenase) to reconstruct phylogenies. The congruence between the phylogenetic trees of aphids and Buchnera was then measured. The results present phylogenetic evidence for the parallel evolution of Mollitrichosiphum and Buchnera at the intraspecific as well as the interspecific levels. Our results support the possibility of using endosymbiont genes to study host evolutionary history and biogeographical patterns. We also investigated the usability of the Buchnera gnd gene as a barcoding marker for aphid identification.

The complete mitochondrial genome of Cervaphis quercus (Insecta: Hemiptera: Aphididae: Greenideinae)

The mitochondrial genome of Cervaphis quercus has been sequenced and annotated. The entire genome of 15 272 bp encodes two ribosomal RNA genes (rrnL and rrnS), 22 transfer RNA (tRNA) genes, 13 protein‐coding genes and a control region. The genome has the same gene order as that found in the inferred ancestral insect. Nucleotide composition is highly A+T biased. All protein‐coding genes use standard mitochondrial initiation codons. Secondary structure models of the two ribosomal RNA genes of C. quercus are similar to those proposed for other insects. All tRNAs have the classic clover‐leaf structure, except for the dihydrouridine (DHU) arm of trnS (AGN), which forms a simple loop. The presence of structural elements in the control region is also discussed, with an emphasis on the possible regulation of replication and/or transcription. Comparison with mitochondrial genomes of other aphid species shows their gene arrangements are conserved; however, the variety of repeat regions in species from a different aphid subfamily, Aphidinae, suggests that they resulted from independent evolutionary events.

Revision and New Taxa of Fossil Prophalangopsidae (Orthoptera: Ensifera)

Abstract Taxonomy is investigated and revised for some prophalangopsid insects, yielded by the Middle Jurassic Jiulongshan and Upper Jurassic-Lower Cretaceous Yixian formations in China. Flexaboilus retinervius Li, Ren & Meng, 2007 and Furcaboilus excelsus Li, Ren & Meng, 2007 are considered as synonyms of Allaboilus gigantus Ren & Meng, 2006. Protaboilus lini Ren & Meng, 2006 is considered a synonym of Aboilus stratosus Li, Ren & Wang, 2007. Hebeihagla Hong, 1982b, Habrohagla Ren, Lu, Guo & Ji, 1995, Grammohagla Meng & Ren, 2006, Trachohagla Meng, Ren & Li, 2006 are considered as synonyms of Parahagla Sharov, 1968; Athehagla Meng & Ren, 2006 is considered a synonym of Ashanga Zherichin 1985. Genera Allaboilus, Circulaboilus Li, Ren & Wang, 2007 and Ashangopsis Lin, Huang & Nel, 2008 are revised. In addition, one new genus Scalpellaboilus gen. nov. and four new species: Scalpellaboilus angustus sp. nov., Circulaboilus priscus sp. nov., Allaboilus robustus sp. nov. and A. hani sp. nov. are described. Some wing venation variability in Prophalangopsidae is briefly discussed.