A DNA barcode library for Germany′s mayflies,stoneflies and caddisflies (Ephemeroptera,Plecoptera and Trichoptera)

Mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) are prominent representatives of aquatic macroinvertebrates, commonly used as indicator organisms for water quality and ecosystem assessments. However, unambiguous morphological identification of EPT species, especially their immature life stages, is a challenging, yet fundamental task. A comprehensive DNA barcode library based upon taxonomically well‐curated specimens is needed to overcome the problematic identification. Once available, this library will support the implementation of fast, cost‐efficient and reliable DNA‐based identifications and assessments of ecological status. This study represents a major step towards a DNA barcode reference library as it covers for two‐thirds of Germany's EPT species including 2,613 individuals belonging to 363 identified species. As such, it provides coverage for 38 of 44 families (86%) and practically all major bioindicator species. DNA barcode compliant sequences (≥500 bp) were recovered from 98.74% of the analysed specimens. Whereas most species (325, i.e., 89.53%) were unambiguously assigned to a single Barcode Index Number (BIN) by its COI sequence, 38 species (18 Ephemeroptera, nine Plecoptera and 11 Trichoptera) were assigned to a total of 89 BINs. Most of these additional BINs formed nearest neighbour clusters, reflecting the discrimination of geographical subclades of a currently recognized species. BIN sharing was uncommon, involving only two species pairs of Ephemeroptera. Interestingly, both maximum pairwise and nearest neighbour distances were substantially higher for Ephemeroptera compared to Plecoptera and Trichoptera, possibly indicating older speciation events, stronger positive selection or faster rate of molecular evolution.     

青蟹线粒体COI假基因的分离和特征分析

线粒体DNA标记在遗传结构和系统进化研究中得到广泛应用,然而核假基因的存在对此有很大威胁。本文以中国东南沿海的青蟹(Scylla paramamosain)为研究对象,利用线粒体COI基因的通用引物和特异性引物进行扩增,分别得到34个假基因（nuclear mitochondrial pseudogenes, Numts）和5个线粒体COI基因序列。在所获得的34个假基因中共定义了29种单倍型,根据序列的相似度,这些假基因可以分为2类,每类假基因都有各自保守的核苷酸序列。第Ⅰ类假基因存在2处插入序列和1处8 bp的缺失序列,这些位点导致了整个阅读框的移位;在第Ⅱ类假基因和5个线粒体COI序列中只有碱基替换,未发现插入和缺失序列。实验结果分析表明,这两类假基因分别代表了2次核整合事件,即核转移事件的最低值。研究结果提示了     

Leaf gall polymorphism and molecular phylogeny of a new Bruggmanniella species (Diptera: Cecidomyiidae: Asphondyliini) associated with Litsea acuminata (Lauraceae) in Taiwan,with ecological comparisons and a species description

Two types of cecidomyiid leaf galls, cup‐shaped and umbrella‐shaped, occur on Litsea acuminata (Lauraceae) in Taiwan. Based on the concept of gall shapes as “extended phenotypes” of gall inducers, these two types could be induced by different gall midge species. However, galls with intermediate shapes between the two types were recently discovered, which implies that possible genetic exchanges occur between the gall inducers of both types. To clarify the taxonomic status of gall midges responsible for the two types of galls on L. acuminata, we undertook taxonomic, molecular phylogenetic and ecological studies. Our findings show that the two gall types are induced by the same Bruggmanniella species and the species is new to science. We describe the species forming this range of galls as Bruggmanniella litseae sp. n. , and compare their geographical distribution, galling position and morphometry. Based on our results, a possible evolutionary scenario of B. litseae sp. n. is discussed.     

Half of the European fruit fly species barcoded (Diptera,Tephritidae); a feasibility test for molecular?identification

A feasibility test of molecular identification of European fruit flies (Diptera: Tephritidae) based on COI barcode sequences has been executed. A dataset containing 555 sequences of 135 ingroup species from three subfamilies and 42 genera and one single outgroup species has been analysed. 73.3% of all included species could be identified based on their COI barcode gene, based on similarity and distances. The low success rate is caused by singletons as well as some problematic groups: several species groups within the genus Terellia and especially the genus Urophora. With slightly more than 100 sequences – almost 20% of the total – this genus alone constitutes the larger part of the failure for molecular identification for this dataset. Deleting the singletons and Urophora results in a success-rate of 87.1% of all queries and 93.23% of the not discarded queries as correctly identified. Urophora is of special interest due to its economic importance as beneficial species for weed control, therefore it is desirable to have alternative markers for molecular identification.We demonstrate that the success of DNA barcoding for identification purposes strongly depends on the contents of the database used to BLAST against. Especially the necessity of including multiple specimens per species of geographically distinct populations and different ecologies for the understanding of the intra- versus interspecific variation is demonstrated. Furthermore thresholds and the distinction between true and false positives and negatives should not only be used to increase the reliability of the success of molecular identification but also to point out problematic groups, which should then be flagged in the reference database suggesting alternative methods for identification.     

古尼虫草与亚香棒虫草亲缘关系初探

目的:用分子生物学方法,对古尼虫草和亚香棒虫草进行研究,对其寄主昆虫CO(Icytochrome oxidase subunit I,细胞色素氧化酶亚基I)和真菌ITS(Internal Transcribed Sequence,内转录间隔区)区的基因序列进行比较,以确定两者亲缘关系。方法:在古尼虫草和亚香棒虫草性状研究的基础上,对两者来源真菌ITS区和寄主昆虫COI基因进行了PCR扩增和序列测定,对序列进行比对分析,并与GenBank核酸序列数据库中的序列进行BLAST检索比对。结果:发现古尼虫草和亚香棒虫草的来源真菌ITS区和寄主昆虫COI基因序列均有较高相似度。结论:古尼虫草和亚香棒虫草有较近的亲缘关系。     

Integrative taxonomy and evolutionary history of a newly revealed spider Dysdera ninnii complex (Araneae: Dysderidae)

The spider genus Dysdera is a species‐rich clade of specialized woodlice predators, composed typically of complexes of sibling species. Here, we analyse the Dysdera ninnii complex, distinguishing three species that exhibit slight but constant differences in the morphology of their copulatory organs, and in their genetic background. We designate a neotype for D. ninnii and redescribe it. We consider Dysdera pavesii Thorell, 1873 to be a junior synonym of Dysdera ninnii Canestrini, 1868. In addition, we describe two new species ( D ysdera moravica sp. nov. and D ysdera microdonta sp. nov. ). All three species occur in the region of north‐eastern Italy, Slovenia, and north‐western Croatia. D ysdera moravica sp. nov. expanded to central Europe. The species occur allopatrically or parapatrically. All three species possess the same diploid number and X0 sex chromosome determination. In some individuals we found chromosome fusions, and such polymorphism is common in spiders with holokinetic chromosomes. The analysis of mitochondrial (cytochrome c oxidase subunit I, COI) and nuclear ribosomal (internal transcribed spacer 2, ITS2) DNA markers revealed two clades, one formed by D. ninnii and D . microdonta sp. nov. , and a second by D . moravica sp. nov. Species of the first clade are not well defined by DNA markers. We noticed only weak separation of maternally inherited COI, and even overlap of autosomally inherited ITS2 sequences. We suggest that either short speciation time, unfinished lineage sorting, or rare hybridization events caused this pattern. In one sample of D . microdonta sp. nov. we detected the coxA gene of a Rickettsia species, which is the first record of this parasitic bacteria from the spider family Dysderidae. D ysdera microdonta sp. nov. occurs at higher altitudes than D. ninnii, and their distribution ranges form a long contact zone. Remarkably, we did not record any overlap of the two distribution ranges, suggesting that the lack of a precopulatory interspecific barrier causes a loss of reproduction potential. We hypothesize that because of the unsolved interspecific barrier together with only tiny differences in morphology and COI sequences, and no differences in karyotypes and ITS2 sequences, the D. ninnii species complex is evolutionarily young. © 2014 The Linnean Society of London