Genomic signatures of population decline in the malaria mosquito Anopheles gambiae

Population genomic features such as nucleotide diversity and linkage disequilibrium are expected to be strongly shaped by changes in population size, and might therefore be useful for monitoring the success of a control campaign. In the Kilifi district of Kenya, there has been a marked decline in the abundance of the malaria vector Anopheles gambiae subsequent to the rollout of insecticide-treated bed nets. To investigate whether this decline left a detectable population genomic signature, simulations were performed to compare the effect of population crashes on nucleotide diversity, Tajima's D, and linkage disequilibrium (as measured by the population recombination parameter ρ). Linkage disequilibrium and ρ were estimated for An. gambiae from Kilifi, and compared them to values for Anopheles arabiensis and Anopheles merus at the same location, and for An. gambiae in a location 200 km from Kilifi. In the first simulations ρ changed more rapidly after a population crash than the other statistics, and therefore is a more sensitive indicator of recent population decline. In the empirical data, linkage disequilibrium extends 100-1000 times further, and ρ is 100-1000 times smaller, for the Kilifi population of An. gambiae than for any of the other populations. There were also significant runs of homozygosity in many of the individual An. gambiae mosquitoes from Kilifi. These results support the hypothesis that the recent decline in An. gambiae was driven by the rollout of bed nets. Measuring population genomic parameters in a small sample of individuals before, during and after vector or pest control may be a valuable method of tracking the effectiveness of interventions

Ultra-conserved sequences in the genomes of highly diverse Anopheles mosquitoes, with implications for malaria vector control

DNA sequences that are exactly conserved over long evolutionary time scales have been observed in a variety of taxa. Such sequences are likely under strong functional constraint and they have been useful in the field of comparative genomics for identifying genome regions with regulatory function. A potential new application for these ultra-conserved elements has emerged in the development of gene drives to control mosquito populations. Many gene drives work by recognising and inserting at a specific target sequence in the genome, often imposing a reproductive load as a consequence. They can therefore select for target sequence variants that provide resistance to the drive. Focusing on highly conserved, highly constrained sequences lowers the probability that variant, gene drive-resistant alleles can be tolerated. Here we search for conserved sequences of 18bp and over in an alignment of 21 Anopheles genomes, spanning an evolutionary timescale of 100 million years, and characterise the resulting sequences according to their location and function. Over 8000 ultra-conserved elements were found across the alignment, with a maximum length of 164 bp. Length-corrected gene ontology analysis revealed that genes containing Anopheles ultra-conserved elements were over-represented in categories with structural or nucleotide binding functions. Known insect transcription factor binding sites were found in 48% of intergenic Anopheles ultra-conserved elements. When we looked at the genome sequences of 1142 wild-caught mosquitoes we found that 15% of the Anopheles ultra-conserved elements contained no polymorphisms. Our list of Anopheles ultra-conserved elements should provide a valuable starting point for the selection and testing of new targets for gene-drive modification in the mosquitoes that transmit malaria

Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus

Vector population control using insecticides is a key element of current strategies to prevent malaria transmission in Africa. The introduction of effective insecticides, such as the organophosphate pirimiphos-methyl, is essential to overcome the recurrent emergence of resistance driven by the highly diverse Anopheles genomes. Here, we use a population genomic approach to investigate the basis of pirimiphos-methyl resistance in the major malaria vectors Anopheles gambiae and A. coluzzii. A combination of copy number variation and a single non-synonymous substitution in the acetylcholinesterase gene, Ace1, provides the key resistance diagnostic in an A. coluzzii population from Coˆte d’Ivoire that we used for sequence-based association mapping, with replication in other West African populations. The Ace1 substitution and duplications occur on a unique resistance haplotype that evolved in A. gambiae and introgressed into A. coluzzii, and is now common in West Africa primarily due to selection imposed by other organophosphate or carbamate insecticides. Our findings highlight the predictive value of this complex resistance haplotype for phenotypic resistance and clarify its evolutionary history, providing tools to for molecular surveillance of the current and future effectiveness of pirimiphos-methyl based interventions

The 21st century sonographer: Role ambiguity in communicating an adverse outcome in obstetric ultrasound

Introduction: Ultrasound plays an integral role in pregnancy management in Australia. The role of a sonographer as the frontline practitioner is to scan the patient and identify any possible abnormalities, including foetal demise. This study sought the views, experiences and practices of Australian sonographers in communicating an adverse outcome to pregnant patients in different departmental settings in public and private sector practice. Method: Ten individual semi-structured interviews were conducted with 9 sonographers from metropolitan Sydney and 1 rural based sonographer. Results: The key themes emerging from the interview data were of ambiguity and inconsistency both in understanding the sonographer role and with practice protocols around communication when delivering “bad news” to pregnant patients. Most of the participants had not received any formal training in communication techniques. Conclusion: The sonographers wanted more autonomy, but with support and an agreed and consistent approach from their radiologists or sonologists. Practice sites that achieved the best results were those that had the greatest direct collaboration between the sonographer and the sonologist, which was demonstrated in the obstetrician-sonologist-run practices. Policy reform, improved clarity and standardised protocols are needed to improve practice guidelines for sonographers in communicating adverse outcomes to an expectant mother

Supplementary data

This file contains sampling localities. Mitochondrial sequence data has been deposited in GenBank with accession numbers HQ403680-HQ404165

Data from: Comparative phylogeography reveals a shared impact of Pleistocene environmental change in shaping genetic diversity within nine Anopheles mosquito species across the Indo-Burma biodiversity hotspot

Southeast Asia is one of the world’s richest regions in terms of biodiversity. An understanding of the distribution of diversity and the factors shaping it is lacking, yet essential for identifying conservation priorities for the region’s highly threatened biodiversity. Here we take a large scale comparative approach, combining data from nine forest associated Anopheles mosquito species and using statistical phylogeographic methods to disentangle the effects of environmental history, species specific ecology, and random coalescent effects. Spatially explicit modelling of Pleistocene demographic history supports a common influence of environmental events in shaping the genetic diversity of all species examined, despite differences in species' mtDNA gene trees. Populations were periodically restricted to allopatric northeastern and northwestern refugia, most likely due to Pleistocene forest fragmentation. Subsequent southwards post-glacial recolonisation is supported by a north-south gradient of decreasing genetic diversity. Repeated allopatric fragmentation and recolonisation has led to the formation of deeply divergent geographical lineages within four species and a suture zone where these intraspecific lineages meet along the Thai-Myanmar border. A common environmental influence for this divergence was further indicated by strong support for simultaneous divergence within the same four species, dating to approximately 900 kya. Differences in the geographical structuring of genetic diversity between species are likely the result of varying species’ biology. The findings have important implications for conservation planning; if the refugial regions and suture zone identified here are shared by other forest taxa, the unique and high levels of genetic diversity they house will make these areas conservation priorities

Predicting the equilibrium solubility of solid polycyclic aromatic hydrocarbons and dibenzothiophene using a combination of MOSCED plus molecular simulation or electronic structure calculations

<p>Methods to predict the equilibrium solubility of non-electrolyte solids are important for the design of novel separation processes. Here we demonstrate how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here SMD or SM8, can be used to predict parameters for the <u>MO</u>dified <u>S</u>eparation of <u>C</u>ohesive <u>E</u>nergy <u>D</u>ensity (MOSCED) method. The method is applied to the solutes naphthalene, anthracene, phenanthrene, pyrene and dibenzothiophene, compounds of interested to the petroleum industry and for environmental remediation. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. Comparing to a total of 422 non-aqueous and 193 aqueous experimental solubilities, we find the proposed method is able to well correlate the data. The use of MOSCED is additionally advantageous as it is a solubility parameter-based method useful for intuitive solvent selection and formulation.</p