Systematics and biology of the iconic Australian scribbly gum moths Ogmograptis Meyrick (Lepidoptera: Bucculatricidae) and their unique insect-plant interaction

The larvae of particular Ogmograptis spp. produce distinctive scribbles on some smooth-barked Eucalyptus spp. which are a common feature on many ornamental and forest trees in Australia. However, although they are conspicuous in the environment the systematics and biology of the genus has been poorly studied. This has been addressed through detailed field and laboratory studies of their biology of three species (O. racemosa Horak sp. nov., O. fraxinoides Horak sp. nov., O. scribula Meyrick), in conjunction with a comprehensive taxonomic revision support by a molecular phylogeny utilising the mitochondrial Cox1 and nuclear 18S genes. In brief, eggs are laid in bark depressions and the first instar larvae bore into the bark to the level where the future cork cambium forms (the phellegen). Early instar larvae bore wide, arcing tracks in this layer before forming a tighter zig-zag shaped pattern. The second last instar turns and bores either closely parallel to the initial mine or doubles its width, along the zig-zag shaped mine. The final instar possesses legs and a spinneret (unlike the earlier instars) and feeds exclusively on callus tissue which forms within the zig-zag shaped mine formed by the previous instar, before emerging from the bark to pupate at the base of the tree. The scars of mines them become visible scribble following the shedding of bark. Sequence data confirm the placement of Ogmograptis within the Bucculatricidae, suggest that the larvae responsible for the ‘ghost scribbles’ (unpigmented, raised scars found on smooth-barked eucalypts) are members of the genus Tritymba, and support the morphology-based species groups proposed for Ogmograptis. The formerly monotypic genus Ogmograptis Meyrick is revised and divided into three species groups. Eleven new species are described: Ogmograptis fraxinoides Horak sp. nov., Ogmograptis racemosa Horak sp. nov. and Ogmograptis pilularis Horak sp. nov. forming the scribula group with Ogmograptis scribula Meyrick; Ogmograptis maxdayi Horak sp. nov., Ogmograptis barloworum Horak sp. nov., Ogmograptis paucidentatus Horak sp. nov., Ogmograptis rodens Horak sp. nov., Ogmograptis bignathifer Horak sp. nov. and Ogmograptis inornatus Horak sp. nov. as the maxdayi group; Ogmograptis bipunctatus Horak sp. nov., Ogmograptis pulcher Horak sp. nov., Ogmograptis triradiata (Turner) comb. nov. and Ogmograptis centrospila (Turner) comb. nov. as the triradiata group. Ogmograptis notosema (Meyrick) cannot be assigned to a species group as the holotype has not been located. Three unique synapomorphies, all derived from immatures, redefine the family Bucculatricidae, uniting Ogmograptis, Tritymba Meyrick (both Australian) and Leucoedemia Scoble & Scholtz (African) with Bucculatrix Zeller, which is the sister group of the southern hemisphere genera. The systematic history of Ogmograptis and the Bucculatricidae is discussed.

Read classification for next generation sequencing

Next Generation Sequencing (NGS) has revolutionised molec- ular biology, allowing routine clinical sequencing. NGS data consists of short sequence reads, given context through downstream assembly and annotation, a process requiring reads consistent with the assumed species or species group. The common bacterium Staphylococcus aureus may cause severe and life-threatening infections in humans, with some strains exhibiting antibiotic resistance. Here we apply an SVM classifier to the important problem of distinguishing S. aureus sequencing projects from other pathogens, including closely related Staphylococci. Using a sequence k-mer representation, we achieve precision and recall above 95%, implicating features with important functional associations.

Supplementary material : large scale read classification for next generation sequencing

Next Generation Sequencing (NGS) has revolutionised molecular biology, resulting in an explosion of data sets and an increasing role in clinical practice. Such applications necessarily require rapid identification of the organism as a prelude to annotation and further analysis. NGS data consist of a substantial number of short sequence reads, given context through downstream assembly and annotation, a process requiring reads consistent with the assumed species or species group. Highly accurate results have been obtained for restricted sets using SVM classifiers, but such methods are difficult to parallelise and success depends on careful attention to feature selection. This work examines the problem at very large scale, using a mix of synthetic and real data with a view to determining the overall structure of the problem and the effectiveness of parallel ensembles of simpler classifiers (principally random forests) in addressing the challenges of large scale genomics.

Large scale read classification for next generation sequencing

Next Generation Sequencing (NGS) has revolutionised molecular biology, resulting in an explosion of data sets and an increasing role in clinical practice. Such applications necessarily require rapid identification of the organism as a prelude to annotation and further analysis. NGS data consist of a substantial number of short sequence reads, given context through downstream assembly and annotation, a process requiring reads consistent with the assumed species or species group. Highly accurate results have been obtained for restricted sets using SVM classifiers, but such methods are difficult to parallelise and success depends on careful attention to feature selection. This work examines the problem at very large scale, using a mix of synthetic and real data with a view to determining the overall structure of the problem and the effectiveness of parallel ensembles of simpler classifiers (principally random forests) in addressing the challenges of large scale genomics.

Molecular phylogeny and biogeography of langurs and leaf monkeys of South Asia (Primates: Colobinae)

The two recently proposed taxonomies of the langurs and leaf monkeys (Subfamily Colobinae) provide different implications to our understanding of the evolution of Nilgiri and purple-faced langurs. Groves (2001) [Groves, C.P., 2001. Primate Taxonomy. Smithsonian Institute Press, Washington], placed Nilgiri and purple-faced langurs in the genus Trachypithecus, thereby suggesting disjunct distribution of the genus Trachypithecus. [Brandon-Jones, D., Eudey, A.A., Geissmann, T., Groves, C.P., Melnick, D.J., Morales, J.C., Shekelle, M., Stewart, C.-B., 2003. Asian primate classification. Int. J. Primatol. 25, 97–162] placed these langurs in the genus Semnopithecus, which suggests convergence of morphological characters in Nilgiri and purple-faced langurs with Trachypithecus. To test these scenarios, we sequenced and analyzed the mitochondrial cytochrome b gene and two nuclear DNA-encoded genes, lysozyme and protamine P1, from a variety of colobine species. All three markers support the clustering of Nilgiri and purple-faced langurs with Hanuman langur (Semnopithecus), while leaf monkeys of Southeast Asian (Trachypithecus) form a distinct clade. The phylogenetic position of capped and golden leaf monkeys is still unresolved. It is likely that this species group might have evolved due to past hybridization between Semnopithecus and Trachypithecus clades.

Techno-economic considerations of shark driftnet fishery, off Lagos coast, Nigeria

Experimental fishing operations with driftnets were conducted in Lagos coastal waters with a view to finding out appropriate gear for effective exploitation of sharks and other pelagic fish species that are not normally caught in trawls. The design and fabrication of the driftnets as well as the fishing trials were undertaken between May, 1977 and April, 1978. Six baited driftnet sets of equal panels with three stretched mesh sizes of 190.5mm; 228.6mm and 241.3mm were used. Analysis were carried out on species composition of catches, weight and number of species/group of fish, catch efficiency of the driftnets as well as on operating costs and financial returns

Seafood consumption and supply sources in Hawaii, 2000-2009

Measures of consumption and supply sources of seafood can provide valuable input to research and policy planning of a viable food system. This article fills a gap in the existing literature by mapping the existing seafood supply flows from various sources (local, domestic U.S., and foreign) in Hawaii. The authors trace the seafood transshipment of foreign origin via the continental United States to Hawaii and update total and per capita consumption of seafood more accurately by including noncommercial catches into the analysis. Per capita seafood consumption in Hawaii from all commercial sources is estimated at an annual average of 29 edible pounds during the 10-year period from 2000 to 2009. This is significantly more than the 16 edible pounds for all U.S consumption in 2009. Including noncommercial catch, the same measure increases to 37 edible pounds. The eight-pound differential suggests that noncommercial fishing is an important source of seafood supply in Hawaii. Overall, fresh tuna (Thunnus spp.) is the single largest species group consumed, followed by Pacific and Atlantic salmon (Salmonidae). By edible weight, the majority of Hawaii’s commercial seafood supply comes from foreign sources (57%) vs. local sources (37%), and U.S. domestic sources (6%). The leading sources for Hawaii’s direct seafood imports from 2000 to 2009, were Taiwan, Japan, New Zealand, the Philippines, and the Marshall Islands. Local supply becomes the majority source once noncommercial catch is included with 51% of the total supply.

Molecular phylogeny of the Drosophila virilis section (Diptera : Drosophilidae) based on mitochondrial and nuclear sequences

Regardless of the well-documented virilis species group, most groups of the Drosophila virilis section have not been completely studied at molecular level since it was suggested. Therefore, phylogenetic relationships among and within species groups of the

Genetic differentiation and cryptic speciation in natural populations of Drosophila lacertosa

Drosophila lacertosa, an Oriental member of the robusta species group in the virilis-repleta radiation, has a wide distribution from northern India throughout China to the Far East. Phylogenetic analyses of mitochondrial ND2 gene sequences revealed two ge

Phylogeny of east Asian bufonids inferred from mitochondrial DNA sequences (Anura : Amphibia)

We investigated the relationships of Asian bufonids using partial sequences of mitochondrial DNA genes. Twenty-six samples representing 14 species of Bufo from China and Vietnam and 2 species of Torrentophryne from China were examined. Three samples of Bufo viridis from Armenia and Georgia were also sequenced to make a comparison to its sibling tetraploid species B. danatensis. Bufo americanus, from Canada, was used as the outgroup. Sequences from the 12S ribosomal RNA, 16S ribosomal RNA, cytochrome b, and the control region were analyzed using parsimony. East Asian bufonids were grouped into two major clades. One clade included B. andrewsi, B. bankorensis, B. gargarizans, B. tibetanus, B. tuberculatus, its sister clade B. cryptotympanicus, and the 2 species of Torrentophryne. The second clade consisted of B. galeatus, B. himalayanus, B. melanostictus, and a new species from Vietnam. The placement of three taxa (B. raddei B. viridis, and its sister species, B. danatensis) was problematic. The genus Torrentophryne should be synonymized with Bufo to remove paraphyly. Because B. raddei does not belong to the clade that includes B. viridis and B. danatensis, it was removed from the viridis species group. The species status of B bankorensis from Taiwan is evaluated. (C) 2000 Academic Press.

Mandibular variation among Chinese macaques

In order to clarify the degree to which mandibular variation among Chinese macaques results from functional adaptation and phylogenetic inertia, 13 mandibular variables were analyzed by bivariate and multivariate techniques. The results indicate, not surprisingly, that the main differences in the mandible are associated with size. The study further implies that the variation between species is not closely associated with differences in functional adaptation even though the dietary and related differences are large compared to the situation in other macaques. The great variety in diet and related factors among Chinese macaques may not have yet resulted in a significant variation in the mandible. This may be because their radiation in Asia, though involving considerably greater differences in habitat, climate, and so on, has occurred more recently than for other macaque species in Southeast Asia. Mandibular variation between these species, therefore, is likely to be more closely tied to their immediate prior phylogenetic history. For example, the two stump-tailed macaques are closely similar and are also closely similar to the Assam species. Function in the mandible in these species is quite different. The results, therefore, seem to support the hypothesis that these three macaque species should be placed in a single species-group (sinica) as proposed by Delson [1980], Pan [1998], and Pan et al. [1998]. (C) 2002 Wiley-Liss, Inc.

鰋鮡鱼类(Glyptosternoid fishes)的系统进化和动物地理学研究

鰋鮡鱼类共包括9 属43 种（亚种），隶属于鲇形目（Siluriformes）鮡科 （Sisoridae）鰋鮡亚科（Glyptosternae）中鰋鮡族（Tribe Glyptosternini）的鰋鮡 亚族（Subtribe Glyptosternina）。鰋鮡鱼类形态上的共同特征为：无胸吸着器，胸、 腹鳍水平展开，第一根鳍条完全分节或在外缘生出许多软骨细条，被外表皮所裹， 在腹面看到的是许多与分节或软骨细条大致对应的横纹皱褶。鰋鮡鱼类集中分布 于青藏高原周边的水系中，部分属种向西分布到了中亚地区的阿姆河上游，是适 应山区急流环境的一群鱼类。近年来一系列的研究表明，鰋鮡鱼类为一单系类群， 它的起源和演化与青藏高原的隆升有着直接的关系。鰋鮡鱼类的系统发育研究， 可以为青藏高原隆升的年代、幅度和形式提供间接的证据，其系统发育树的拓扑 结构也直接反映了东喜马拉雅地区诸水系的形成与演变。 本研究对鰋鮡鱼类9 属进行了系统整理。1. 发现并描述了异齿鰋属 （Oreoglanis）两新种，分别为分布于景东无量山（澜沧江水系）的景东异齿鰋 （O. jingdongensis）和分布于怒江水系南景河和南滚河的无斑异齿鰋（O. immaculatus）。认为分布于中国的异齿鰋属鱼类均属于尖须异齿鰋种组（O. siamensis species group）。指出区分异齿鰋属两个种组：尖须异齿鰋种组和细尾 异齿鰋种组（O. delacouri species group）的特征是下唇中部是否具有中央缺刻， 尾型的差别（新月型尾或凹型尾）不能用来区分两个种组，给出了异齿鰋属的检 索表，并绘制了异齿鰋属鱼类分布图。2. 对鮡属（Pareuchiloglanis）鱼类进行了 系统整理，通过外部形态度量性状的比较，认为分布于澜沧江水系的，曾经被鉴 定为扁头鮡（P. kamengensis）的标本，应属于大鳍鮡（P. macropterus），扁头鮡 和大鳍鮡之间的最明显的差别在于腹鳍前长的不同。前者的腹鳍前长为体长的 53.2-64.9%，后者的腹鳍前长均不达体长的50%。3. 通过比较金沙江水系分布的 5 种鮡属鱼类，中华鮡（P. sinensis）、前臀鮡（P. anteanalis）、壮体鮡（P. robusta）、 四川鮡（P. sichuanensis）和天全鮡（P. tianquanensis），认为天全鮡和四川鮡之 间分布水系重叠，外部形态亦无差别，天全鮡很可能为四川鮡的同物异名。给出 了鮡属鱼类的系统检索表，并绘制了鮡属鱼类分布图。利用分子系统学的原理和方法对鰋鮡鱼类进行系统发育研究。测定了6 属 15 种鰋鮡鱼类和鮡科中非鰋鮡鱼类4 属7 种共28 个体的线粒体Cyt b 基因部分 片段和全序列（1138 bp），结合从GenBank 下载的相关类群相同的基因序列，以 魾属（Bagarius）的巨魾（B. yarrelli），纹胸鮡属（Glyptothorax）的穴形纹胸鮡 （G. cavia）、亮背纹胸鮡（G. dorsalis）、扎那纹胸鮡（G. zainaensis），福建纹胸 鮡（G. fukiensis fukiensis）、海南纹胸鮡（G. fukiensis hainanensis），黑鮡属（Gagata） 的长丝黑鮡（G. dolichonema）以及褶鮡属（Pseudecheneis）的黄斑褶鮡（P. sulcatus） 和无斑褶鮡（P. immaculatus）作为外类群，采用贝叶斯法（Bayesian）、最简约 法（maximum pasimony, MP）和邻接法（neighbour-joining, NJ）构建系统发育树。 结果显示： 1. 鰋鮡鱼类为一单系类群，并且与褶鮡属互为姐妹群关系； 2. 原鮡属、鰋属和凿齿鮡属是鰋鮡鱼类的三个基部类群； 3. 异齿鰋属构成为一个单系群，大鳍异齿鰋最早从该属的基部分化出来； 4. 石爬鮡属构成一个单系，并与分布于金沙江水系的中华鮡＋前臀鮡构成姐妹 群，黄石爬鮡和青石爬鮡的单倍型相互交错；显示两个物种的分类是不合适的， 而是同一水系不同支流种群之间梯度变异的例子，依据本次研究所得出的三个分 支图，结合青石爬鮡自西至东分布于金沙江、雅砻江、大渡河、青衣江、岷江等 的分布格局以及形态特征的分布，显示形态特征的分布变化有以下趋势：自西至 东，腹鳍位置逐渐前移；颌须渐趋缩短；胸鳍趋向发达、伸达腹鳍起点。这些变 化趋势是同一水系不同支流种群之间梯度变异的极好例子； 5. 分布于澜沧江以西（包括澜沧江）水系的鮡属鱼类（扁头鮡、细尾鮡、短鳍 鮡）与分布于怒江和伊洛瓦底江水系的拟鰋属鱼类构成为一支，并且二者共同与 分布于元江上游（红河水系）的大孔鮡构成为单系。其中，短体拟鰋和拟鰋互为 姐妹种；而扁头鮡和短鳍鮡也互为姐妹种；细尾鮡的系统地位则尚不能确定； 6. 无论在MP 树、贝叶斯树还是NJ 树中，石爬鮡属、鮡属、拟鰋属和异齿鰋属 构成一个单系，并且支持率达到了100％。 7. 鰋属位于鰋鮡鱼类的基部，是较早就从鰋鮡鱼类祖先中演化出来的一个类群， 鰋类的口吸盘是一个趋同性状，是在急流环境条件下形成的一种适应性性状，在 鰋类各属中不是同源特征； 8. 鮡属鱼类不是一个单系类群，分布于金沙江流域的鮡属鱼类与同流域分布的石爬鮡属鱼类聚成一支；澜沧江及其以西水系分布的鮡属鱼类与同流域分布的拟 鰋属鱼类聚成一支，之后这两支又同异齿鰋属共同构成为一个大支。 结合鰋鮡鱼类的系统发育分支图对其动物地理学进行研究。鰋鮡鱼类是由类 似纹胸鮡属（Glyptothorax）鱼类的祖先演化而来，鰋属（Exostoma）和凿齿鮡 属（Glaridoglanis）是较早就从从类似原鮡的祖先中演化出来，鮡属、石爬鮡属、 拟鰋属和异齿鰋属这一大支由类似原鮡的祖先演化而来。在青藏高原强烈隆起等 重大地理隔离事件发生之前，类似于现生的原鮡属鱼类已经广布喜马拉雅山脉东 西两侧。在青藏高原强烈隆起等重大地理隔离事件发生后，鰋鮡鱼类在相同的地 理隔离下独自演化为现在的分布格局。

The relationship between agricultural intensification and biological control: experimental tests across Europe

Agricultural intensification can affect biodiversity and related ecosystem services such as biological control, but large-scale experimental evidence is missing. We examined aphid pest populations in cereal fields under experimentally reduced densities of (1) ground-dwelling predators (-G), (2) vegetation-dwelling predators and parasitoids (-V), (3) a combination of (1) and (2) (-G-V),compared with open-fields (control), in contrasting landscapes with low vs. high levels of agricultural intensification (AI), and in five European regions. Aphid populations were 28%, 97%, and 199% higher in -G, -V, and -G -V treatments, respectively, compared to the open fields, indicating synergistic effects of both natural-enemy groups. Enhanced parasitoid : host and predator : prey ratios were related to reduced aphid population density and population growth. The relative importance of parasitoids and vegetation-dwelling predators greatly differed among European regions, and agricultural intensification affected biological control and aphid density only in some regions. This shows a changing role of species group identity in diverse enemy communities and a need to consider region-specific landscape management.

Review of the genus Bursaphelenchus Fuchs, 1937 (Nematoda, Aphelenchida) with some conclusions on the host-parasite and vector-parasite evolution.

INTRODUCTION AND GOALS: Genus Bursaphelenchus includes several pests of the world importance for the rural economy, the most dangerous are the Bursaphelenchus xylophilus (the pinewood nematode caused decline of the pine trees in south Asia and in one spot area in Europe, Portugal, Peninsula de Setubal) and the Bursaphelenchus cocophilus, causing the decline of coco-palm plantations in Carribean and Latin American regions. The peculiarity of the host-parasite association of the genus that the nematode life cycle includes three trophic components: plant (mostly a tree), insect vector and a fungus. Goals of the presentation is to list all species of the world fauna and all efficient diagnostic characters, then create the identification tool and analyze the similarity of species and possible ways and causes of the host-parasite evolution of the group. RESULTS: Complete list of species with synonymy and a catalogue of all efficient diagnostic characters with their states, selected from papers of the most experienced taxonomists of the genus, are given for the genus Bursaphelenchus. List of known records of Bursaphelenchus species with names of natural vectors and plants and their families is given (for world pests the most important groups of trees and insects are listed). The tabular, traditional and computer-aided keys are presented. Dendrograms of species relationships (UPGMA, standard distance: mean character difference) based on all efficient taxonomic characters and separately on the spicule characters only, are given. Discussion whether the species groups are natural or purely diagnostic ones is based on the relationships dendrograms and the vector and associated plant ranges of Bursaphelenchus species; the xylophilus species group (B. xylophilus, B. abruptus, B. baujardi, B. conicaudatus, B. eroshenkii, B. fraudulentus, B. kolymensis, B. luxuriosae; B. mucronatus), the hunti group (B. hunti, B. seani, B. kevini and B. fungivorus) are probably the natural ones. CONCLUSIONS: The parasitic nematode association includes three trophic components: plant, insect vector and fungus. The initial insect-plant complex Scolytidae-Pinaceae is changeable and only in rare occasions the change of the preferred vector to Cerambycidae (the xylophilus group), Hymenoptera (the hunti group) led to formation of the natural species-groups. From the analysis it is clear that although the vector range is changeable it is comparatively more important for the evolution of the genus Bursaphelenchus than associations with plants at the family level. Data on the fungi species (3rd component in natural Bursaphelenchus associations) are insufficient for the detailed comparative analysis.

Integration of geochemical and biological modifications in mining areas: waters, sediments and diatoms

The development of mining activities over thousands of years in the region of Aljustrel is nowadays visible as a vast area of ore tailings, slag and host rocks of sulphides mineralization. The generation of acidic waters by the alteration of pyritic minerals - Acid Mine Drainage (AMD) - causes a significant impact on the river system both in the south of the village (Rib ª. Água Forte) and in the north of it (Rib ª. Água Azeda and Barranco do Farrobo), which is reflected in extremely low pH values (< 3) and high concentrations of As, Cd, Cu, Fe, Mn, Pb, Zn and sulphates. This study aimed to assess the environmental impacts extent, integrating geochemical (surface waters and stream sediments) and biological (diatoms) parameters. Three groups of sites were defined, based on sediments and water analysis, which integration with diatom data showed the same association of groups: Group 1- impacted, with acidic pH (1.9-5.1), high metal contents (0.4-1975 mg L-1) and Fe-Mg-sulphate waters, being metals more bioavailable in waters in cationic form (Me2+); mineralogically the sediments were characterized by phyllosilicates and sulphates/oxy-hydroxysulphate phases, easily solubilized, retaining a high amount of metals when precipitated; dominant taxon was Pinnularia aljustrelica (a new species); Group 2- slightly impacted, weak acid to neutral pH (5.0-6.8), metal contents not so high (0.2-25 mg L-1) and Fe-Mg-sulphate to Mg-chloride waters; dominant taxa were Brachysira neglectissima and Achnanthidium minutissimum; Group 3- unimpacted, alkaline pH (7.0-8.4), low metal contents (0-7 mg L-1) with Mg-chloride waters. In this group, metals were associated to the primary phases (e.g. sulphides), not so easily available; the existence of high chloride contents explained the presence of typical taxa of brackish/marine (e.g. Entomoneis paludosa) waters. Taxonomical aspects of the diatoms were studied (discovery of a new species: Pinnularia aljustrelica Luis, Almeida et Ector sp. nov.), as well as morphometric (size decrease of diatoms valves, as well as the appearance of deformed valves of Eunotia exigua in Group 1 and A. minutissimum in Group 2) and physiological (effective to assess the effects of metals/acidity in the photosynthetic efficiency through PAM Fluorometry) aspects. A study was carried out in an artificial river system (microcosm) that aimed to mimic Aljustrel’s extreme conditions in controlled laboratory conditions. The chronic effects of Fe, SO42- and acidity in field biofilms, inoculated in the artificial rivers, were evaluated as well as their contribution to the communities’ tolerance to metal toxicity, through acute tests with two metals (Cu and Zn). In general, the effects caused by low pH values and high concentrations of Fe and SO42- were reflected at the community level by the decrease in diversity, the predominance of acidophilic species, the decrease in photosynthetic efficiency and the increase of enzymatic (e.g. catalase, superoxide dismutase) and non-enzymatic activities (e.g. total glutathione and total phytochelatins). However, it was possible to verify that acidity performed a protective effect in the communities, upon Cu and Zn addition. A comparative study between Aljustrel mining area and New Brunswick mining area was carried out, both with similar mining and geological conditions, reflected in similar diatom communities in both mines, but in very different geographic and climatic areas.