Sampling properties of DNA sequence data in phylogenetic analysis

We inferred phylogenetic trees from individual genes and random samples of nucleotides from the mitochondrial genomes of 10 vertebrates and compared the results to those obtained by analyzing the whole genomes. Individual genes are poor samples in that they infrequently lead to the whole-genome tree. A large number of nucleotide sites is needed to exactly determine the whole-genome tree. A relatively small number of sites, however, often results in a tree close to the whole-genome tree. We found that blocks of contiguous sites were less likely to lead to the whole-genome tree than samples composed of sites drawn individually from throughout the genome. Samples of contiguous sites are not representative of the entire genome, a condition that violates a basic assumption of the bootstrap method as it is applied in phylogenetic studies.      

Some observations on the effect of Daflon (micronized purified flavonoid fraction of Rutaceae aurantiae) in bancroftian filarial lymphoedema

BACKGROUND: Morbidity management is a core component of the global programme for the elimination of lymphatic filariasis. In a double-blind clinical trial, the tolerability and efficacy of Daflon (500 mg) + DEC (25 mg) or DEC (25 mg) alone, twice daily for 90 days, was studied in 26 patients with bancroftian filarial lymphoedema. RESULTS: None of the patients in either drug group reported any adverse reaction throughout the treatment period (90 days). Haematological and biochemical parameters were within normal limits and there was no significant difference between the pre-treatment (day 0) and post-treatment (day 90) values. The group receiving Daflon showed significant reduction in oedema volume from day 90 (140.6 PlusMinus; 18.8 ml) to day 360 (71.8 PlusMinus; 20.7 ml) compared to the pre-treatment (day 0, 198.4 PlusMinus; 16.5 ml) value. This accounted for a 63.8% reduction in oedema volume by day 360 (considering the pre-treatment (day 0) as 100%). In the DEC group, the changes in oedema volume (between day 1 and day 360) were not significant when compared to the pre-treatment (day 0) value. The percentage reduction at day 360 was only 9%, which was not significant (P > 0.05). CONCLUSION: This study has shown that Daflon (500 mg, twice a day for 90 days) is both safe and efficacious in reducing oedema volume in bancroftian filarial lymphoedema. Further clinical trials are essential for strengthening the evidence base on the role of this drug in the morbidity management of lymphatic filariasis.     

Olfactory responses of western flower thrips (Frankliniella occidentalis) populations to a non‐pheromone lure

Western flower thrips (WFT), Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), is a major pest of horticultural crops worldwide. The search for alternative pest management techniques has resulted in increasing interest in the use of kairomones and other behaviour‐modifying chemicals to mitigate the impact of this pest. In this study, we determined whether the origin of populations, feeding history, and/or genotype influence the response of WFT to the thrips kairomone lure methyl isonicotinate (MI) in a Y‐tube olfactometer study. Four New Zealand thrips populations were tested: (1) from a commercial glasshouse capsicum crop, (2) from a long‐established laboratory colony (>222 generations) kept on chrysanthemums, (3) from a laboratory colony (6–9 generations) kept on French dwarf beans, and (4) thought to be a separate cryptic non‐pest species from outdoor yellow tree lupins, Lupinus arboreus Sims (Fabaceae). In the laboratory tests, significantly more WFT from all four populations chose the MI‐laden arm of a Y‐tube olfactometer when it contained 1 μl methyl isonicotinate (61.3–73.2%) compared with the blank no‐odour arm. No differences in response to MI were found between the two laboratory and the one glasshouse WFT populations. Both laboratory populations and the greenhouse population belonged to the ‘glasshouse pest’ genotype of WFT. However, the cryptic non‐pest WFT genotype responded more strongly to MI than any of the other populations, although the response was only significantly stronger than that of the long‐established laboratory population. Significant differences were also found among populations in the average time taken for thrips to make a choice to enter either arm of the Y‐tube olfactometer, with the cryptic non‐pest lupin genotype taking the shortest time, followed by thrips from the capsicum glasshouse. The results are discussed with respect to the variability in olfactory perception and olfactory behaviour within a species and the relevance to the use of such a kairomone lure in pest management programmes.     

Modeling the potential global distribution of light brown apple moth Epiphyas postvittana (Lepidoptera: Tortricidae) using CLIMEX

Light brown apple moth Epiphyas postvittana is a significant horticultural pest native to Australia that currently has a limited global distribution. However, this pest can tolerate very heterogeneous climates and has a wide host range. It has recently established in California with considerable consequences for US international and domestic trade. It has resulted in increasing calls for targeted risk assessment so that appropriate quarantine measures can be put in place to prevent its entry into new regions and further spread. Potential global distribution has been predicted by comparing the climatic conditions of its native (Australia) and long-established (New Zealand) ranges to the rest of the world using CLIMEX. It was suggested that E. postvittana has potential to establish mainly in countries in Central and South America, southern Africa, Western Europe and Southeast Asia. The study provides basic information for further assessment of the establishment capacity of this species in new habitats, and adds to the knowledge required to make science-based decisions in biosecurity.     

An ensemble model for predicting Rhopalosiphum padi abundance

A novel modeling method is proposed to predict the abundance of the main vector of barley yellow dwarf virus in autumn sown cereal crops. An ensemble model based on artificial neural networks (ANN) was developed to predict the number of Rhopalosiphum padi (L.) (Homoptera: Aphididae) caught in traps during the autumn flight period at Lincoln, Canterbury, New Zealand, over the period 1982–2003. Artificial neural networks were trained using historical weather data and aphid data collected from a suction trap. Model results were compared with those obtained using multiple regression (MR) models using the same independent variables. Both ANN and MR models were validated by leave‐one‐out validation, in other words, by sequentially jackknifing each year out of the data set, fitting a model to the remaining data, then using that model to predict the number of aphids for each jackknifed year. A linear ensemble of ANN models further improved the predictions and represented the trends in the number of aphids over the 22‐year period very well. The r² between the predicted and observed numbers of aphids for the ANN models changed from 0.68 to 0.83 using the linear ensemble model, but the ensemble approach did not change the prediction for the MR models. The absolute mean error (ABSME) of prediction was much lower for the ANN ensemble predictions compared to that for the MR models. The ABMSE for the ANN models dropped from 109 to 86 aphids compared to an ABMSE reduction from 245 to 220 aphids for the MR models. We discuss the potential for ensemble models for predicting insect abundance when long‐term historical data are available.     

The use of image analysis to study the effects of residues of esfenvalerate on the locomotory behaviour of Panonychus ulmi and Typhlodromus pyri (Acari: Tetranychidae, Phytoseiidae)

The influences of esfenvalerate on mite behaviour were investigated by image analysis. Video recordings of the locomotory behaviour of two mite species were converted into a series of x,y coordinates that, when joined, closely resembled their paths. These coordinates were used to calculate walking speed, direction of travel, turning frequency, turn bias and tortuosity. Two experimental arenas were used: (1) a leaf disc arena for the European red mite, Panonychus ulmi and (2) a glass coverslip arena for Typhlodromus pyri. The behavioural responses of P. ulmi and T. pyri to esfenvalerate (field rate) indicated that these mites did not show a preference for the unsprayed halves of the arenas during the first 48 min. However, significant differences between most of the behavioural parameters to esfenvalerate residues were found with P. ulmi when whole arenas were compared. © Rapid Science Ltd. 1998     

Mesozooplankton of the Kosi Bay lakes,South Africa

The Kosi coastal lake system, a chain of four interconnected basins, is located in the subtropical north-eastern corner of South Africa. Little information is available on zooplankton of the system and the main aim of this study is to report on zooplankton samples collected during 2002 and 2003. The set of samples consists of seasonal, subsurface mesozooplankton samples that were collected during nighttime in each of the lakes. A well-developed salinity gradient was evident along the interconnected lakes in the subsurface water during all seasons, ranging from freshwater in the upper lake Amanzamnyama to a maximum of 22 recorded in Lake Makhawulani. The zooplankton community structures of the lakes reflected the salinity gradient of the system, with some coastal marine taxa recorded in the lakes closer to the mouth and only freshwater taxa recorded in Lake Amanzamnyama. Mesozooplankton diversity and abundance were relatively low compared to other estuarine systems along the eastern coast of South Africa. The dominant taxa were calanoid copepods Acartiella natalensis and Pseudodiaptomus stuhlmanni and the mysid Mesopodopsis africana in the lower lakes, whereas cyclopoids Mesocyclops sp. and Thermocyclops sp. dominated the freshwater lake Amanzamnyama.     

Molecular phylogeny of Neotropical bioluminescent beetles (Coleoptera: Elateroidea) in southern and central Brazil

Bioluminescence in beetles is found mainly in the Elateroidea superfamily (Elateridae, Lampyridae and Phengodidae). The Neotropical region accounts for the richest diversity of bioluminescent species in the world with about 500 described species, most occurring in the Amazon, Atlantic rainforest and Cerrado (savanna) ecosystems in Brazil. The origin and evolution of bioluminescence, as well as the taxonomic status of several Neotropical taxa in these families remains unclear. In order to contribute to a better understanding of the phylogeny and evolution of bioluminescent Elateroidea we sequenced and analyzed sequences of mitochondrial NADH2 and the nuclear 28S genes and of the cloned luciferase sequences of Brazilian species belonging to the following genera: (Lampyridae) Macrolampis, Photuris, Amydetes, Bicellonycha, Aspisoma, Lucidota, Cratomorphus; (Elateridae) Conoderus, Pyrophorus, Hapsodrilus, Pyrearinus, Fulgeochlizus; and (Phengodidae) Pseudophengodes, Phrixothrix, Euryopa and Brasilocerus. Our study supports a closer phylogenetic relationship between Elateridae and Phengodidae as other molecular studies, in contrast with previous morphologic and molecular studies that clustered Lampyridae/Phengodidae. Molecular data also supported division of the Phengodinae subfamily into the tribes Phengodini and Mastinocerini. The position of the genus Amydetes supports the status of the Amydetinae as a subfamily. The genus Euryopa is included in the Mastinocerini tribe within the Phengodinae/Phengodidae. Copyright © 2013 John Wiley & Sons, Ltd.