A genotyping array for the globally invasive vector mosquito, Aedes albopictus

BACKGROUND

Although whole-genome sequencing (WGS) is the preferred genotyping method for most genomic analyses, limitations are often experienced when studying genomes characterized by a high percentage of repetitive elements, high linkage, and recombination deserts. The Asian tiger mosquito (Aedes albopictus), for example, has a genome comprising up to 72% repetitive elements, and therefore we set out to develop a single-nucleotide polymorphism (SNP) chip to be more cost-effective. Aedes albopictus is an invasive species originating from Southeast Asia that has recently spread around the world and is a vector for many human diseases. Developing an accessible genotyping platform is essential in advancing biological control methods and understanding the population dynamics of this pest species, with significant implications for public health.

METHODS

We designed a SNP chip for Ae. albopictus (Aealbo chip) based on approximately 2.7 million SNPs identified using WGS data from 819 worldwide samples. We validated the chip using laboratory single-pair crosses, comparing technical replicates, and comparing genotypes of samples genotyped by WGS and the SNP chip. We then used the chip for a population genomic analysis of 237 samples from 28 sites in the native range to evaluate its usefulness in describing patterns of genomic variation and tracing the origins of invasions.

RESULTS

Probes on the Aealbo chip targeted 175,396 SNPs in coding and non-coding regions across all three chromosomes, with a density of 102 SNPs per 1 Mb window, and at least one SNP in each of the 17,461 protein-coding genes. Overall, 70% of the probes captured the genetic variation. Segregation analysis found that 98% of the SNPs followed expectations of single-copy Mendelian genes. Comparisons with WGS indicated that sites with genotype disagreements were mostly heterozygotes at loci with WGS read depth < 20, while there was near complete agreement with WGS read depths > 20, indicating that the chip more accurately detects heterozygotes than low-coverage WGS. Sample sizes did not affect the accuracy of the SNP chip genotype calls. Ancestry analyses identified four to five genetic clusters in the native range with various levels of admixture.

CONCLUSIONS

The Aealbo chip is highly accurate, is concordant with genotypes from WGS with high sequence coverage, and may be more accurate than low-coverage WGS.

Angular Correlations in the β Decay of ^{8}B: First Tensor-Current Limits from a Mirror-Nucleus Pair

We present the first measurement of the α-β-ν angular correlation in the Gamow-Teller β^{+} decay of ^{8}B. This was accomplished using the Beta-decay Paul Trap, expanding on our previous work on the β^{-} decay of ^{8}Li. The ^{8}B result is consistent with the V-A electroweak interaction of the standard model and, on its own, provides a limit on the exotic right-handed tensor current relative to the axial-vector current of |C_{T}/C_{A}|^{2}<0.013 at the 95.5% confidence level. This represents the first high-precision angular correlation measurements in mirror decays and was made possible through the use of an ion trap. By combining this ^{8}B result with our previous ^{8}Li results, we demonstrate a new pathway for increased precision in searches for exotic currents.

Dating the origin and spread of specialization on human hosts in Aedes aegypti mosquitoes

The globally invasive mosquito subspecies Aedes aegypti aegypti is an effective vector of human arboviruses, in part because it specializes in biting humans and breeding in human habitats. Recent work suggests that specialization first arose as an adaptation to long, hot dry seasons in the West African Sahel, where Ae. aegypti relies on human-stored water for breeding. Here, we use whole-genome cross-coalescent analysis to date the emergence of human-specialist populationsand thus further probe the climate hypothesis. Importantly, we take advantage of the known migration of specialists out of Africa during the Atlantic Slave Trade to calibrate the coalescent clock and thus obtain a more precise estimate of the older evolutionary event than would otherwise be possible. We find that human-specialist mosquitoes diverged rapidly from ecological generalists approximately 5000 years ago, at the end of the African Humid Period-a time when the Sahara dried and water stored by humans became a uniquely stable, aquatic niche in the Sahel. We also use population genomic analyses to date a previously observed influx of human-specialist alleles into major West African cities. The characteristic length of tracts of human-specialist ancestry present on a generalist genetic background in Kumasi and Ouagadougou suggests the change in behavior occurred during rapid urbanization over the last 20-40 years. Taken together, we show that the timing and ecological context of two previously observed shifts towards human biting in Ae. aegypti differ; climate was likely the original driver, but urbanization has become increasingly important in recent decades.

Effect of BG-Lures on the Male Aedes (Diptera: Culicidae) Sound Trap Capture Rates

With global expansion of the two main vectors of dengue, Aedes aegypti (Linnaeus, Diptera: Culicidae) and Aedes albopictus (Skuse, Diptera: Culicidae), there is a need to further develop cost-effective and user-friendly surveillance tools to monitor the population dynamics of these species. The abundance of Ae. aegypti and Ae. Albopictus, and associated bycatch captured by Male Aedes Sound Traps (MASTs) and BG-Sentinel (BGS) traps that were unbaited or baited with BG-Lures were compared in Cairns, Australia and Madang, Papua New Guinea. Mean male Ae. aegypti and Ae. albopictus catch rates in MASTs did not significantly differ when deployed with BG-Lures. Similarly, males of both these species were not sampled at statistically different rates in BGS traps with or without BG-Lures. However, MASTs with BG-Lures caught significantly less male Ae. aegypti than BGS traps baited with BG-Lures in Cairns, and MASTs without BG-Lures caught significantly more male Ae. albopictus than BGS traps without BG-Lures in Madang. Additionally, BG-Lures significantly increased female Ae. aegypti catch rates in BGS traps in Cairns. Lastly, bycatch capture rates in BGS traps were not significantly influenced by the addition of the BG-Lures. While this study provides useful information regarding the surveillance of Ae. aegypti and Ae. albopictus in these locations, further development and investigation is required to successfully integrate an olfactory lure into the MAST system.

Outcomes from international field trials with Male Aedes Sound Traps: Frequency-dependent effectiveness in capturing target species in relation to bycatch abundance

Aedes aegypti and Aedes albopictus vector dengue, chikungunya and Zika viruses. With both species expanding their global distributions at alarming rates, developing effective surveillance equipment is a continuing priority for public health researchers. Sound traps have been shown, in limited testing, to be highly species-specific when emitting a frequency corresponding to a female mosquito wingbeat. Determining male mosquito capture rates in sound traps based on lure frequencies in endemic settings is the next step for informed deployment of these surveillance tools. We field-evaluated Male Aedes Sound Traps (MASTs) set to either 450 Hz, 500 Hz, 550 Hz or 600 Hz for sampling Aedes aegypti and/or Aedes albopictus and compared catch rates to BG-Sentinel traps within Pacific (Madang, Papua New Guinea) and Latin American (Molas, Mexico and Orange Walk Town, Belize) locations. MASTs set to 450-550 Hz consistently caught male Ae. aegypti at rates comparable to BG-Sentinel traps in all locations. A peak in male Ae. albopictus captures in MASTs set at 550 Hz was observed, with the lowest mean abundance recorded in MASTs set to 450 Hz. While significantly higher abundances of male Culex were sampled in MASTs emitting lower relative frequencies in Molas, overall male Culex were captured in significantly lower abundances in the MASTs, relative to BG-Sentinel traps within all locations. Finally, significant differences in rates at which male Aedes and Culex were positively detected in trap-types per weekly collections were broadly consistent with trends in abundance data per trap-type. MASTs at 550 Hz effectively captured both male Ae. aegypti and Ae. albopictus while greatly reducing bycatch, especially male Culex, in locations where dengue transmission has occurred. This high species-specificity of the MAST not only reduces staff-time required to sort samples, but can also be exploited to develop an accurate smart-trap system-both outcomes potentially reducing public health program expenses.

A Low-Powered and Highly Selective Trap for Male Aedes (Diptera: Culicidae) Surveillance: The Male Aedes Sound Trap

As Aedes aegypti (Linnaeus, Diptera: Culicidae) expands its global distribution and vectors a range of debilitating arboviruses there is an increased need for enhanced mosquito surveillance. Consequently, we developed a Male Aedes Sound Trap (MAST) that requires minimal power and is highly species-specific. Two different versions of the MAST were developed, one that uses synthetic pyrethroid to kill captured mosquitoes (MAST Spray) and another which has an internal divider to create a killing chamber in which a sticky panel can be placed to capture mosquitoes (MAST Sticky). We compared weekly capture rates of male Ae. aegypti and bycatch from the two MAST versions to those from BG-Sentinel (BGS) traps and Sound-producing BG-Gravid Aedes Traps (SGATs) throughout Cairns, northern Australia. Weekly mean male Ae. aegypti catches did not significantly differ between trap types. However, the rate of positive weekly detections of male Ae. aegypti was lower for the MAST Sticky than the other three trap types. The MASTs sampled significantly fewer mosquitoes other than male Ae. aegypti, than either the BGS trap or the SGAT. Also, the MASTs and SGATs all caught significantly less non-Culicidae bycatch than the BGS traps. Consequently, we have developed a versatile male Ae. aegypti trap which is potentially of great benefit to Ae. aegypti surveillance programs.

Climate and Urbanization Drive Mosquito Preference for Humans

The majority of mosquito-borne illness is spread by a few mosquito species that have evolved to specialize in biting humans, yet the precise causes of this behavioral shift are poorly understood. We address this gap in the arboviral vector Aedes aegypti. We first collect and characterize the behavior of mosquitoes from 27 sites scattered across the species' ancestral range in sub-Saharan Africa, revealing previously unrecognized variation in preference for human versus animal odor. We then use modeling to show that over 80% of this variation can be predicted by two ecological factors-dry season intensity and human population density. Finally, we integrate this information with whole-genome sequence data from 375 individual mosquitoes to identify a single underlying ancestry component linked to human preference. Genetic changes associated with human specialist ancestry were concentrated in a few chromosomal regions. Our findings suggest that human-biting in this important disease vector originally evolved as a by-product of breeding in human-stored water in areas where doing so provided the only means to survive the long, hot dry season. Our model also predicts that the rapid urbanization currently taking place in Africa will drive further mosquito evolution, causing a shift toward human-biting in many large cities by 2050.

Improved reference genome of the arboviral vector Aedes albopictus

BACKGROUND

The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes.

RESULTS

We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes.

CONCLUSION

The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.

Efficient production of male Wolbachia-infected Aedes aegypti mosquitoes enables large-scale suppression of wild populations

The range of the mosquito Aedes aegypti continues to expand, putting more than two billion people at risk of arboviral infection. The sterile insect technique (SIT) has been used to successfully combat agricultural pests at large scale, but not mosquitoes, mainly because of challenges with consistent production and distribution of high-quality male mosquitoes. We describe automated processes to rear and release millions of competitive, sterile male Wolbachia-infected mosquitoes, and use of these males in a large-scale suppression trial in Fresno County, California. In 2018, we released 14.4 million males across three replicate neighborhoods encompassing 293 hectares. At peak mosquito season, the number of female mosquitoes was 95.5% lower (95% CI, 93.6-96.9) in release areas compared to non-release areas, with the most geographically isolated neighborhood reaching a 99% reduction. This work demonstrates the high efficacy of mosquito SIT in an area ninefold larger than in previous similar trials, supporting the potential of this approach in public health and nuisance-mosquito eradication programs.

Polymorphism analyses and protein modelling inform on functional specialization of Piwi clade genes in the arboviral vector Aedes albopictus

Current knowledge of the piRNA pathway is based mainly on studies on Drosophila melanogaster where three proteins of the Piwi subclade of the Argonaute family interact with PIWI-interacting RNAs to silence transposable elements in gonadal tissues. In mosquito species that transmit epidemic arboviruses such as dengue and chikungunya viruses, Piwi clade genes underwent expansion, are also expressed in the soma and cross-talk with proteins of recognized antiviral function cannot be excluded for some Piwi proteins. These observations underscore the importance of expanding our knowledge of the piRNA pathway beyond the model organism D. melanogaster. Here we focus on the emerging arboviral vector Aedes albopictus and we couple traditional approaches of expression and adaptive evolution analyses with most current computational predictions of protein structure to study evolutionary divergence among Piwi clade proteins. Superposition of protein homology models indicate possible high structure similarity among all Piwi proteins, with high levels of amino acid conservation in the inner regions devoted to RNA binding. On the contrary, solvent-exposed surfaces showed low conservation, with several sites under positive selection. Analysis of the expression profiles of Piwi transcripts during mosquito development and following infection with dengue serotype 1 or chikungunya viruses showed a concerted elicitation of all Piwi transcripts during viral dissemination of dengue viruses while maintenance of infection relied on expression of primarily Piwi5. Opposite, establishment of persistent infection by chikungunya virus is accompanied by increased expression of all Piwi genes, particularly Piwi4 and, again, Piwi5. Overall these results are consistent with functional specialization and a general antiviral role for Piwi5. Experimental evidences of sites under positive selection in Piwi1/3, Piwi4 and Piwi6, that have complex expression profiles, provide useful knowledge to design tailored functional experiments.

Improved reference genome of Aedes aegypti informs arbovirus vector control

Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector.

An improved, fully re-annotated Aedes aegypti genome assembly (AaegL5) provides insights into the sex-determining M locus, chemosensory systems that help mosquitoes to hunt humans and loci involved in insecticide resistance and will help to generate intervention strategies to fight this deadly disease vector.

Natural Selection on Genes Related to Cardiovascular Health in High-Altitude Adapted Andeans

The increase in red blood cell mass (polycythemia) due to the reduced oxygen availability (hypoxia) of residence at high altitude or other conditions is generally thought to be beneficial in terms of increasing tissue oxygen supply. However, the extreme polycythemia and accompanying increased mortality due to heart failure in chronic mountain sickness most likely reduces fitness. Tibetan highlanders have adapted to high altitude, possibly in part via the selection of genetic variants associated with reduced polycythemic response to hypoxia. In contrast, high-altitude-adapted Quechua- and Aymara-speaking inhabitants of the Andean Altiplano are not protected from high-altitude polycythemia in the same way, yet they exhibit other adaptive features for which the genetic underpinnings remain obscure. Here, we used whole-genome sequencing to scan high-altitude Andeans for signals of selection. The genes showing the strongest evidence of selection-including BRINP3, NOS2, and TBX5-are associated with cardiovascular development and function but are not in the response-to-hypoxia pathway. Using association mapping, we demonstrated that the haplotypes under selection are associated with phenotypic variations related to cardiovascular health. We hypothesize that selection in response to hypoxia in Andeans could have vascular effects and could serve to mitigate the deleterious effects of polycythemia rather than reduce polycythemia itself.

Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice

The domestication history of rice remains controversial, with multiple studies reaching different conclusions regarding its origin(s). These studies have generally assumed that populations of living wild rice, O. rufipogon, are descendants of the ancestral population that gave rise to domesticated rice, but relatively little attention has been paid to the origins and history of wild rice itself. Here, we investigate the genetic ancestry of wild rice by analyzing a diverse panel of rice genomes consisting of 203 domesticated and 435 wild rice accessions. We show that most modern wild rice is heavily admixed with domesticated rice through both pollen- and seed-mediated gene flow. In fact, much presumed wild rice may simply represent different stages of feralized domesticated rice. In line with this hypothesis, many presumed wild rice varieties show remnants of the effects of selective sweeps in previously identified domestication genes, as well as evidence of recent selection in flowering genes possibly associated with the feralization process. Furthermore, there is a distinct geographical pattern of gene flow from aus, indica, and japonica varieties into colocated wild rice. We also show that admixture from aus and indica is more recent than gene flow from japonica, possibly consistent with an earlier spread of japonica varieties. We argue that wild rice populations should be considered a hybrid swarm, connected to domesticated rice by continuous and extensive gene flow.

Population genomics reveals that an anthropophilic population of Aedes aegypti mosquitoes in West Africa recently gave rise to American and Asian populations of this major disease vector

BACKGROUND

The mosquito Aedes aegypti is the main vector of dengue, Zika, chikungunya and yellow fever viruses. This major disease vector is thought to have arisen when the African subspecies Ae. aegypti formosus evolved from being zoophilic and living in forest habitats into a form that specialises on humans and resides near human population centres. The resulting domestic subspecies, Ae. aegypti aegypti, is found throughout the tropics and largely blood-feeds on humans.

RESULTS

To understand this transition, we have sequenced the exomes of mosquitoes collected from five populations from around the world. We found that Ae. aegypti specimens from an urban population in Senegal in West Africa were more closely related to populations in Mexico and Sri Lanka than they were to a nearby forest population. We estimate that the populations in Senegal and Mexico split just a few hundred years ago, and we found no evidence of Ae. aegypti aegypti mosquitoes migrating back to Africa from elsewhere in the tropics. The out-of-Africa migration was accompanied by a dramatic reduction in effective population size, resulting in a loss of genetic diversity and rare genetic variants.

CONCLUSIONS

We conclude that a domestic population of Ae. aegypti in Senegal and domestic populations on other continents are more closely related to each other than to other African populations. This suggests that an ancestral population of Ae. aegypti evolved to become a human specialist in Africa, giving rise to the subspecies Ae. aegypti aegypti. The descendants of this population are still found in West Africa today, and the rest of the world was colonised when mosquitoes from this population migrated out of Africa. This is the first report of an African population of Ae. aegypti aegypti mosquitoes that is closely related to Asian and American populations. As the two subspecies differ in their ability to vector disease, their existence side by side in West Africa may have important implications for disease transmission.

Evolution of GOUNDRY, a cryptic subgroup of Anopheles gambiae s.l., and its impact on susceptibility to Plasmodium infection

The recent discovery of a previously unknown genetic subgroup of Anopheles gambiae sensu lato underscores our incomplete understanding of complexities of vector population demographics in Anopheles. This subgroup, named GOUNDRY, does not rest indoors as adults and is highly susceptible to Plasmodium infection in the laboratory. Initial description of GOUNDRY suggested it differed from other known Anopheles taxa in surprising and sometimes contradictory ways, raising a number of questions about its age, population size and relationship to known subgroups. To address these questions, we sequenced the complete genomes of 12 wild-caught GOUNDRY specimens and compared these genomes to a panel of Anopheles genomes. We show that GOUNDRY is most closely related to Anopheles coluzzii, and the timing of cladogenesis is not recent, substantially predating the advent of agriculture. We find a large region of the X chromosome that has swept to fixation in GOUNDRY within the last 100 years, which may be an inversion that serves as a partial barrier to contemporary gene flow. Interestingly, we show that GOUNDRY has a history of inbreeding that is significantly associated with susceptibility to Plasmodium infection in the laboratory. Our results illuminate the genomic evolution of one of probably several cryptic, ecologically specialized subgroups of Anopheles and provide a potent example of how vector population dynamics may complicate efforts to control or eradicate malaria.

Diabolical survival in Death Valley: recent pupfish colonization, gene flow and genetic assimilation in the smallest species range on earth

One of the most endangered vertebrates, the Devils Hole pupfish Cyprinodon diabolis, survives in a nearly impossible environment: a narrow subterranean fissure in the hottest desert on earth, Death Valley. This species became a conservation icon after a landmark 1976 US Supreme Court case affirming federal groundwater rights to its unique habitat. However, one outstanding question about this species remains unresolved: how long has diabolis persisted in this hellish environment? We used next-generation sequencing of over 13 000 loci to infer the demographic history of pupfishes in Death Valley. Instead of relicts isolated 2-3 Myr ago throughout repeated flooding of the entire region by inland seas as currently believed, we present evidence for frequent gene flow among Death Valley pupfish species and divergence after the most recent flooding 13 kyr ago. We estimate that Devils Hole was colonized by pupfish between 105 and 830 years ago, followed by genetic assimilation of pelvic fin loss and recent gene flow into neighbouring spring systems. Our results provide a new perspective on an iconic endangered species using the latest population genomic methods and support an emerging consensus that timescales for speciation are overestimated in many groups of rapidly evolving species.

Reticulate Speciation and Barriers to Introgression in the Anopheles gambiae Species Complex

Speciation as a process remains a central focus of evolutionary biology, but our understanding of the genomic architecture and prevalence of speciation in the face of gene flow remains incomplete. The Anopheles gambiae species complex of malaria mosquitoes is a radiation of ecologically diverse taxa. This complex is well-suited for testing for evidence of a speciation continuum and genomic barriers to introgression because its members exhibit partially overlapping geographic distributions as well as varying levels of divergence and reproductive isolation. We sequenced 20 genomes from wild A. gambiae s.s., Anopheles coluzzii, Anopheles arabiensis, and compared these with 12 genomes from the “GOUNDRY” subgroup of A. gambiae s.l. Amidst a backdrop of strong reproductive isolation, we find strong evidence for a speciation continuum with introgression of autosomal chromosomal regions among species and subgroups. The X chromosome, however, is strongly differentiated among all taxa, pointing to a disproportionately large effect of X chromosome genes in driving speciation among anophelines. Strikingly, we find that autosomal introgression has occurred from contemporary hybridization between A. gambiae and A. arabiensis despite strong divergence (∼5× higher than autosomal divergence) and isolation on the X chromosome. In addition to the X, we find strong evidence that lowly recombining autosomal regions, especially pericentromeric regions, serve as barriers to introgression secondarily to the X. We show that speciation with gene flow results in genomic mosaicism of divergence and introgression. Such a reticulate gene pool connecting vector taxa across the speciation continuum has important implications for malaria control efforts.

Limit on Tensor Currents from ^{8}Li β Decay

In the standard model, the weak interaction is formulated with a purely vector-axial-vector (V-A) structure. Without restriction on the chirality of the neutrino, the most general limits on tensor currents from nuclear β decay are dominated by a single measurement of the β-ν[over ¯] correlation in ^{6}He β decay dating back over a half century. In the present work, the β-ν[over ¯]-α correlation in the β decay of ^{8}Li and subsequent α-particle breakup of the ^{8}Be^{*} daughter was measured. The results are consistent with a purely V-A interaction and in the case of couplings to right-handed neutrinos (C_{T}=-C_{T}^{'}) limits the tensor fraction to |C_{T}/C_{A}|^{2}<0.011 (95.5% C.L.). The measurement confirms the ^{6}He result using a different nuclear system and employing modern ion-trapping techniques subject to different systematic uncertainties.

Tensor interaction limit derived from the α-β-ν[over ¯] correlation in trapped 8Li ions

A measurement of the α-β-ν[over ¯] angular correlation in the Gamow-Teller decay (8)Li→(8)Be(*)+ν[over ¯]+β, (8)Be(*)→α+α has been performed using ions confined in a linear Paul trap surrounded by silicon detectors. The energy difference spectrum of the α particles emitted along and opposite the direction of the β particle is consistent with the standard model prediction and places a limit of 3.1% (95.5% confidence level) on any tensor contribution to the decay. From this result, the amplitude of any tensor component C(T) relative to that of the dominant axial-vector component C(A) of the electroweak interaction is limited to |C(T)/C(A)|<0.18 (95.5% confidence level). This experimental approach is facilitated by several favorable features of the (8)Li β decay and has different systematic effects than the previous β-ν[over ¯] correlation results for a pure Gamow-Teller transition obtained from studying (6)He β decay.

No evidence for positive selection at two potential targets for malaria transmission-blocking vaccines in Anopheles gambiae s.s

Human malaria causes nearly a million deaths in sub-Saharan Africa each year. The evolution of drug-resistance in the parasite and insecticide resistance in the mosquito vector has complicated control measures and made the need for new control strategies more urgent. Anopheles gambiae s.s. is one of the primary vectors of human malaria in Africa, and parasite-transmission-blocking vaccines targeting Anopheles proteins have been proposed as a possible strategy to control the spread of the disease. However, the success of these hypothetical technologies would depend on the successful ability to broadly target mosquito populations that may be genetically heterogeneous. Understanding the evolutionary pressures shaping genetic variation among candidate target molecules offers a first step towards evaluating the prospects of successfully deploying such technologies. We studied the population genetics of genes encoding two candidate target proteins, the salivary gland protein saglin and the basal lamina structural protein laminin, in wild populations of the M and S molecular forms of A. gambiae in Mali. Through analysis of intraspecific genetic variation and interspecific comparisons, we found no evidence of positive natural selection at the genes encoding these proteins. On the contrary, we found evidence for particularly strong purifying selection at the laminin gene. These results provide insight into the patterns of genetic diversity of saglin and laminin, and we discuss these findings in relation to the potential development of these molecules as vaccine targets.

Assessing the accuracy and power of population genetic inference from low-pass next-generation sequencing data

Next-generation sequencing (NGS) technologies have made it possible to address population genetic questions in almost any system, but high error rates associated with such data can introduce significant biases into downstream analyses, necessitating careful experimental design and interpretation in studies based on short-read sequencing. Exploration of population genetic analyses based on NGS has revealed some of the potential biases, but previous work has emphasized parameters relevant to human population genetics and further examination of parameters relevant to other systems is necessary, including situations where sample sizes are small and genetic variation is high. To assess experimental power to address several principal objectives of population genetic studies under these conditions, we simulated population samples under selective sweep, population growth, and population subdivision models and tested the power to accurately infer population genetic parameters from sequence polymorphism data obtained through simulated 4×, 8×, and 15× read depth sequence data. We found that estimates of population genetic differentiation and population growth parameters were systematically biased when inference was based on 4× sequencing, but biases were markedly reduced at even 8× read depth. We also found that the power to identify footprints of positive selection depends on an interaction between read depth and the strength of selection, with strong selection being recovered consistently at all read depths, but weak selection requiring deeper read depths for reliable detection. Although we have explored only a small subset of the many possible experimental designs and population genetic models, using only one SNP-calling approach, our results reveal some general patterns and provide some assessment of what biases could be expected under similar experimental structures.

First experimental determination of the charge radius of 74Rb and its application in tests of the unitarity of the Cabibbo-Kobayashi-Maskawa matrix

Collinear-laser spectroscopy with the bunched-beams technique was used for the study of neutron deficient Rb isotopes, out to (74)Rb (N = Z = 37) at TRIUMF. The measured hyperfine coupling constants of (76,78m)Rb were in agreement with literature values. The nuclear spin of (75)Rb was confirmed to be I = 3/2, and its hyperfine coupling constants were measured for the first time. The mean-square charge radius of (74)Rb was determined for the first time. This result has improved the isospin symmetry breaking correction term used to calculate the Ft value, with implications for tests of the unitarity of the Cabibbo-Kobayashi-Maskawa matrix.

De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology

BACKGROUND

Anopheles funestus is one of the primary vectors of human malaria, which causes a million deaths each year in sub-Saharan Africa. Few scientific resources are available to facilitate studies of this mosquito species and relatively little is known about its basic biology and evolution, making development and implementation of novel disease control efforts more difficult. The An. funestus genome has not been sequenced, so in order to facilitate genome-scale experimental biology, we have sequenced the adult female transcriptome of An. funestus from a newly founded colony in Burkina Faso, West Africa, using the Illumina GAIIx next generation sequencing platform.

METHODOLOGY/PRINCIPAL FINDINGS

We assembled short Illumina reads de novo using a novel approach involving iterative de novo assemblies and "target-based" contig clustering. We then selected a conservative set of 15,527 contigs through comparisons to four Dipteran transcriptomes as well as multiple functional and conserved protein domain databases. Comparison to the Anopheles gambiae immune system identified 339 contigs as putative immune genes, thus identifying a large portion of the immune system that can form the basis for subsequent studies of this important malaria vector. We identified 5,434 1:1 orthologues between An. funestus and An. gambiae and found that among these 1:1 orthologues, the protein sequence of those with putative immune function were significantly more diverged than the transcriptome as a whole. Short read alignments to the contig set revealed almost 367,000 genetic polymorphisms segregating in the An. funestus colony and demonstrated the utility of the assembled transcriptome for use in RNA-seq based measurements of gene expression.

CONCLUSIONS/SIGNIFICANCE

We developed a pipeline that makes de novo transcriptome sequencing possible in virtually any organism at a very reasonable cost ($6,300 in sequencing costs in our case). We anticipate that our approach could be used to develop genomic resources in a diversity of systems for which full genome sequence is currently unavailable. Our An. funestus contig set and analytical results provide a valuable resource for future studies in this non-model, but epidemiologically critical, vector insect.

The demographic histories of the M and S molecular forms of Anopheles gambiae s.s

Anopheles gambiae is a primary vector of Plasmodium falciparum, a human malaria parasite that causes over a million deaths each year in sub-Saharan Africa. Population genetic tests have been employed to detect natural selection at suspected A. gambiae antimalaria genes, but these tests have generally been compromised by the lack of demographically correct null models. Here, we used a coalescent simulation approach within a maximum likelihood framework to fit population growth, bottleneck, and migration models to polymorphism data from Cameroonian A. gambiae. The best-fit models for both the "M" and the "S" molecular forms of A. gambiae included ancient population growth and a high rate of migration from an unsampled subpopulation. After correcting for differences in effective population size, our models suggest that the molecular forms expanded at different times and both expansions significantly predate the advent of agriculture. We show that correcting null models for demography increases the power to detect natural selection in A. gambiae.

Reproductive output of female Anopheles gambiae (Diptera: Culicidae): comparison of molecular forms

Knowledge of ecological differences between the molecular forms of Anopheles gambiae Giles (Diptera: Culicidae) might lead to understanding of their unique contribution to disease transmission, to better vector control, and to identification of the forces that have separated them. We compared female fecundity measured as egg batch size in relation to body size between the molecular forms in Mali and contrasted them with their sibling species, Anopheles arabiensis Patton. To determine whether eggs of different egg batches are of similar "quality," we compared the total protein content of first-stage larvae (L1s), collected < 2 h after hatching in deionized water. Egg batch size significantly varied between An. gambiae and An. arabiensis and between the molecular forms of An. gambiae (mean batch size was 186.3, 182.5, and 162.0 eggs in An. arabiensis and the M and the S molecular form of An. gambiae, respectively). After accommodating female body size, however, the difference in batch size was not significant. In the S molecular form, egg protein content was not correlated with egg batch size (r = -0.08, P > 0.7) nor with female body size (r = -0.18, P > 0.4), suggesting that females with more resources invest in more eggs rather than in higher quality eggs. The mean total protein in eggs of the M form (0.407 microg per L1) was 6% higher than that of the S form (0.384 microg per L1), indicating that the M form invests a greater portion of her resources into current (rather than future) reproduction. A greater investment per offspring coupled with larger egg batch size may reflect an adaptation of the M form to low productivity larval sites as independent evidence suggests.

The distribution of hatching time in Anopheles gambiae

Background

Knowledge of the ecological differences between the molecular forms of Anopheles gambiae and their sibling species, An. arabiensis might lead to understanding their unique contribution to disease transmission and to better vector control as well as to understanding the evolutionary forces that have separated them.

Methods

The distributions of hatching time of eggs of wild An. gambiae and An. arabiensis females were compared in different water types. Early and late hatchers of the S molecular form were compared with respect to their total protein content, sex ratio, development success, developmental time and adult body size.

Results

Overall, the distribution of hatching time was strongly skewed to the right, with 89% of the eggs hatching during the second and third day post oviposition, 10% hatching during the next four days and the remaining 1% hatching over the subsequent week. Slight, but significant differences were found between species and between the molecular forms in all water types. Differences in hatching time distribution were also found among water types (in each species and molecular form), suggesting that the eggs change their hatching time in response to chemical factors in the water. Early hatchers were similar to late hatchers except that they developed faster and produced smaller adults than late hatchers.

Conclusion

Differences in hatching time and speed of development among eggs of the same batch may be adaptive if catastrophic events such as larval site desiccation are not rare and the site's quality is unpredictable. The egg is not passive and its hatching time depends on water factors. Differences in hatching time between species and molecular forms were slight, probably reflecting that conditions in their larval sites are rather similar.

Q value of the superallowed decay of 46V and its influence on Vud and the unitarity of the Cabibbo-Kobayashi-Maskawa matrix

The masses of the radioactive nuclei (46)V and its decay daughter (46)Ti have been measured with the Canadian Penning Trap on-line Penning trap mass spectrometer to a precision of 1 x 10(-8). A Q(EC) value of 7052.90(40) keV for the superallowed beta decay of (46)V is obtained from the difference of these two masses. With this precise Q value, the Ft value for this decay is determined with improved precision. An investigation of an earlier Q-value measurement for (46)V uncovers a set of 7 measurements that cannot be reconciled with modern data and affects previous evaluations of V(ud) from superallowed Fermi decays. A new evaluation, adding our new data and removing the discredited subset, yields new values for G(V) and V(ud). When combined with recent results for V(us), this yields modified constraints for the unitarity of the Cabibbo-Kobayashi-Maskawa matrix and other extensions of the standard model.

Precise mass measurement of 68Se, a waiting-point nuclide along the rp process

Mass measurements of 68Ge, 68As, and 68Se have been obtained with the Canadian Penning Trap mass spectrometer. The results determine the mass excess of 68Se as -54 232(19) keV, the first measurement with a precision and reliability sufficient to address the light-curve and energy output of x-ray bursts as well as the abundances of the elements synthesized. Under typical conditions used for modeling x-ray bursts, 68Se is found to cause a significant delay in the rp process nucleosynthesis.

Development and Construct Validation of a Measure of Attitudes Toward Public Exposure to Sexual Stimuli

Developed a brief, reliable, and valid measure of attitudes toward public exposure to sexual stimuli. Both advocates and opponents of public exposure to such stimuli typically cite presumed effects upon children. Consequently many of the Likert format items in the several versions of the scale deal with prescriptive and prescriptive beliefs about the exposure of children to sex related stimuli. Over a three-year period five different groups of respondents participated in the study. Both the longer and the shorter versions of the scale administered to these groups appear to have acceptable reliabilities. In an attempt to provide construct validation information, the relationships between the Acceptance of Public Sexuality Scale and several measures of traditionalism were examined. As expected, scores on the scale were inversely related to measures of traditionalism and positively related to measures of modernity Possible uses of the scale were discussed.

The role of environmental ammonia in respiratory mycoplasmosis of rats

Young adult, pathogen-free rats of Sherman and Fischer (F344) substrains were inoculated intranasally with 10(8) colony-forming units (GFU) of M. pulmonis and housed for 4 to 6 weeks in environments with ammonia maintained at specific concentrations from 25 to 250 ppm. All levels of NH3--whether produced naturally from soiled bedding or derived from a purified source--significantly increased the severity of the rhinitis, otitis media, tracheitis, and pneumonia (including bronchiectasis) characteristic of murine respiratory mycoplasmosis (MRM). The prevalence of pneumonia, but not that of other respiratory lesions of MRM, showed a strong tendency to increase directly with environmental NH3 concentration. In contrast, NH3 exposure of rats not infected with M. pulmonis caused anatomic lesions that were unlike those of MRM and were limited to the nasal passages. It was concluded that environmental NH3, at concentrations commonly encountered in present day cage environments for rats, plays an important role in pathogenesis of MRM.