AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa

Background Current tools for Co-phylogenetic analyses are not able to cope with the continuous accumulation of phylogenetic data. The sophisticated statistical test for host-parasite co-phylogenetic analyses implemented in Parafit does not allow it to handle large datasets in reasonable times. The Parafit and DistPCoA programs are the by far most compute-intensive components of the Parafit analysis pipeline. We present AxParafit and AxPcoords (Ax stands for Accelerated) which are highly optimized versions of Parafit and DistPCoA respectively. Results Both programs have been entirely re-written in C. Via optimization of the algorithm and the C code as well as integration of highly tuned BLAS and LAPACK methods AxParafit runs 5–61 times faster than Parafit with a lower memory footprint (up to 35% reduction) while the performance benefit increases with growing dataset size. The MPI-based parallel implementation of AxParafit shows good scalability on up to 128 processors, even on medium-sized datasets. The parallel analysis with AxParafit on 128 CPUs for a medium-sized dataset with an 512 by 512 association matrix is more than 1,200/128 times faster per processor than the sequential Parafit run. AxPcoords is 8–26 times faster than DistPCoA and numerically stable on large datasets. We outline the substantial benefits of using parallel AxParafit by example of a large-scale empirical study on smut fungi and their host plants. To the best of our knowledge, this study represents the largest co-phylogenetic analysis to date. Conclusion The highly efficient AxPcoords and AxParafit programs allow for large-scale co-phylogenetic analyses on several thousands of taxa for the first time. In addition, AxParafit and AxPcoords have been integrated into the easy-to-use CopyCat tool

Irradiated Male Tsetse from a 40-Year-Old Colony Are Still Competitive in a Riparian Forest in Burkina Faso

Background Tsetse flies are the cyclical vectors of African trypanosomosis that constitute a major constraint to development in Africa. Their control is an important component of the integrated management of these diseases, and among the techniques available, the sterile insect technique (SIT) is the sole that is efficient at low densities. The government of Burkina Faso has embarked on a tsetse eradication programme in the framework of the PATTEC, where SIT is an important component. The project plans to use flies from a Glossina palpalis gambiensis colony that has been maintained for about 40 years at the Centre International de Recherche-Développement sur l'Elevage en zone Subhumide (CIRDES). It was thus necessary to test the competitiveness of the sterile males originating from this colony. Methodology/Principal Findings During the period January-February 2010, 16,000 sterile male G. p. gambiensis were released along a tributary of the Mouhoun river. The study revealed that with a mean sterile to wild male ratio of 1.16 (s.d. 0.38), the abortion rate of the wild female flies was significantly higher than before (p = 0.026) and after (p = 0.019) the release period. The estimated competitiveness of the sterile males (Fried index) was 0.07 (s.d. 0.02), indicating that a sterile to wild male ratio of 14.4 would be necessary to obtain nearly complete induced sterility in the female population. The aggregation patterns of sterile and wild male flies were similar. The survival rate of the released sterile male flies was similar to that observed in 1983-1985 for the same colony. Conclusions/Significance We conclude that gamma sterilised male G. p. gambiensis derived from the CIRDES colony have a competitiveness that is comparable to their competitiveness obtained 35 years ago and can still be used for an area-wide integrated pest management campaign with a sterile insect component in Burkina Faso. (Résumé d'auteur

Tsetse Salivary Gland Hypertrophy Virus: Hope or Hindrance for Tsetse Control?

Many species of tsetse flies (Diptera: Glossinidae) are infected with a virus that causes salivary gland hypertrophy (SGH), and flies with SGH symptoms have a reduced fecundity and fertility. The prevalence of SGH in wild tsetse populations is usually very low (0.2%–5%), but higher prevalence rates (15.2%) have been observed occasionally. The successful eradication of a Glossina austeni population from Unguja Island (Zanzibar) using an area-wide integrated pest management approach with a sterile insect technique (SIT) component (1994–1997) encouraged several African countries, including Ethiopia, to incorporate the SIT in their national tsetse control programs. A large facility to produce tsetse flies for SIT application in Ethiopia was inaugurated in 2007. To support this project, a Glossina pallidipes colony originating from Ethiopia was successfully established in 1996, but later up to 85% of adult flies displayed symptoms of SGH. As a result, the colony declined and became extinct by 2002. The difficulties experienced with the rearing of G. pallidipes, epitomized by the collapse of the G. pallidipes colony originating from Ethiopia, prompted the urgent need to develop management strategies for the salivary gland hypertrophy virus (SGHV) for this species. As a first step to identify suitable management strategies, the virus isolated from G. pallidipes (GpSGHV) was recently sequenced and research was initiated on virus transmission and pathology. Different approaches to prevent virus replication and its horizontal transmission during blood feeding have been proposed. These include the use of antiviral drugs such as acyclovir and valacyclovir added to the blood for feeding or the use of antibodies against SGHV virion proteins. In addition, preliminary attempts to silence the expression of an essential viral protein using RNA interference will be discussed

The Salivary Secretome of the Tsetse Fly Glossina pallidipes (Diptera: Glossinidae) Infected by Salivary Gland Hypertrophy Virus

Tsetse fly (Diptera; Glossinidae) transmits two devastating diseases to farmers (human African Trypanosomiasis; HAT) and their livestock (Animal African Trypanosomiasis; AAT) in 37 sub-Saharan African countries. During the rainy seasons, vast areas of fertile, arable land remain uncultivated as farmers flee their homes due to the presence of tsetse. Available drugs against trypanosomiasis are ineffective and difficult to administer. Control of the tsetse vector by Sterile Insect Technique (SIT) has been effective. This method involves repeated release of sterilized males into wild tsetse populations, which compete with wild type males for females. Upon mating, there is no offspring, leading to reduction in tsetse populations and thus relief from trypanosomiasis. The SIT method requires large-scale tsetse rearing to produce sterile males. However, tsetse colony productivity is hampered by infections with the salivary gland hypertrophy virus, which is transmitted via saliva as flies take blood meals during membrane feeding and often leads to colony collapse. Here, we investigated the salivary gland secretome proteins of virus-infected tsetse to broaden our understanding of virus infection, transmission and pathology. By this approach, we obtain insight in tsetse-hytrosavirus interactions and identified potential candidate proteins as targets for developing biotechnological strategies to control viral infections in tsetse colonies

The decline of the Serengeti Thomson's gazelle population

The population of Thomson's gazelles in the Serengeti National Park, Tanzania has declined by almost two thirds over a 13 year period. In the early 1970s, numbers stood at 0.66 million animals but had decreased to less than 0.25 million animals in 1985 as estimated by 5 different censuses using two different counting techniques. Predation, interspecific competition and disease are all factors that could have contributed to this decline, and at least one of these factors, predation, could now prevent the Thomson's gazelle population from increasing.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47770/1/442_2004_Article_BF00376974.pd

Plant chemicals and the sexual behavior of male tephritid fruit flies

Plant compounds affect insects in many different ways. In addition to being a food source, plants also contain secondary metabolites that may have positive and negative impacts on insects. The influence of these compounds on sexual behavior, in particular, has been the focus of many recent studies. Here, we review the existing literature on the effects of plant compounds on the sexual behavior of tephritid fruit fly males. We put special focus on polyphagous species whose males congregate in leks, where females exert strong mate selection. We first summarize the main findings related to plant compounds that increase male signaling behavior and attraction of females and consequently increase mating frequency, a phenomenon that has been recorded mainly for species of Anastrepha and Ceratitis. In other tephritid species, males are attracted to phenylpropanoids produced by plants (such as methyl eugenol or raspberry ketone) that, upon encounter, are consumed and sequestered by males. These compounds, or metabolic derivatives, which normally have negligible nutritional value, are included in the pheromone and also confer advantages in a sexual context: enhanced female attraction and improved male mating success. These phenomena have been reported for several Bactrocera species as well as for Zeugodacus cucurbitae. Because many tephritid species are serious pests, the effect of plant compounds on male behavior has been explored for potential incorporation into control strategies such as the sterile insect technique (SIT). We conclude noting several factors, such as age and nutrition during larval and adult stage, that modulate the effect of plant compounds on male mating behavior as well as some prominent gaps that preclude a thorough understanding of the plant-mediated enhancement of male sexual performance and hence limit our ability to effectively utilize phytochemicals in pest control strategies.Instituto de GenéticaFil: Segura, Diego Fernando. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética. Laboratorio de Genética de Insectos de Importancia Económica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Belliard, Silvina A. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética. Laboratorio de Genética de Insectos de Importancia Económica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Vera, María Teresa. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Tucumán. Facultad de Agronomía y Zootecnia; ArgentinaFil: Bachmann, Guillermo Enrique. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética. Laboratorio de Genética de Insectos de Importancia Económica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Ruiz, María Josefina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Tucumán. Facultad de Agronomía y Zootecnia; ArgentinaFil: Jofre-Barud, Flavia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Juan; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Fernández, Patricia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Delta del Paraná; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Lopez, M. Liza. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Juan; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Shelly, Todd E. United States Department of Agriculture. Animal and Plant Health Inspection Service; Estados Unido