The Anopheles gambiae complex includes the most efficient vectors of human malaria in sub-Saharan Africa, responsible for hundreds of millions of infections and hundreds of thousands of deaths (WHO, 2016). The two most recently diverged species - A. gambiae and A. coluzzii are recently diverged, having split no later than 540,000 years ago in association to human-made environmental changes. The strongest dependence of A. coluzzii from human-made environmental habitats allowed the expansion of the species range to dry and urban areas suboptimal for A. gambiae, changing malaria transmission patterns geographically, seasonally and ecologically in west-central Africa. The Anopheles gambiae 1000 genomes Consortium (Ag1000G) to which the proposer is associated is building a comprehensive catalogue of genetic variation in natural malaria vector populations. The first paper - including analyses on 765 specimens sampled from 14 locations across Africa and sequenced by Illumina high-throughput technology - highlighted an extraordinary nucleotide diversity. Although high-throughput sequencing technology implemented by the Ag1000G project will continue to produce big amount of data for fine scale genomic studies on A. gambiae and A. coluzzii, these big data will be of limited usage to study the population genetics and ecology, behaviour and vectorial role of these major malaria vectors at a fine geographic scale, which requires genotyping of several thousands of individuals per site. We aim to build on results of the Ag1000G project and to develop and validate novel easy-to-use tools to overcome the limitation of the current approaches in identifying signatures of introgression within A. gambiae and A. coluzzii genomes, and to apply them to shed light on two case studies of adaptive introgression on a trajectory towards hybrid speciation, thus providing novel details on ecological speciation of these organisms at the forefront of research on novel species formation.
While we expect that the MassArray iPlex platform (Task 1.1) will become the reference method for large scale studies on introgression between A. gambiae and A. coluzzii across Africa, the novel PCR methods developed in Task 1.2 will open the way to ecological and behavioral studies which require to process large numbers of samples and are presently impossible to carry out in areas of high hybridization, due to the lack of effective tools to identify the two species, as well as the "hybrid form". The two methods will be also very useful to rapidly gaining information from the several Afrotropical areas from where no data on genetic divergence and reproductive isolation between these two major malaria vector species are presently available. The finding of a population with admixed autosomes also in Kenya (where A. gambiae is the only species known to be present) thanks to the Ag1000G project (Miles et al. 2017), reveals that despite decades of studies the knowledge on the genetics of these two malaria vectors is still fragmentary and referred to relatively few areas across the African continent. We believe the tools we aim to develop will be widely applied, as happen with other protocol developed by our group in past years (Fanello et al. 2002, 246 citations; Santolamazza et al. 2008, 79 citations).
For malaria epidemiology. The synergy between this project and the above mentioned ExGenMal project will allow to clarify the epidemiological relevance of the novel "hybrid form2 in HHZ and beyond. The focus of Task 2.2 may highlight the potential of a radical change in malaria epidemiology in east Africa: if the situation observed in Kenya will turn out to be widespread, it would confer higher ecological flexibility to the local populations which will likely result in higher capacity to resist to insecticide, and possibly to different capacity to transmit malaria.
For the field of evolutionary biology. We expect our results provide novel details on this species pair, which are considered model organisms in the field ecological speciation, from the perspective of providing a window into what may represent contemporary adaptive introgression on a trajectory towards hybrid speciation.
For the research group. The funding of the proposed project will allow our group to continue working on our main and most scientifically rewarding research topic and, in particular, to take advantage from and contribute to the Ag1000G project, which provides huge genomic resources, but does not funds specific research projects. This is for us a major opportunity with high potential to lead to very high impact results and publications, as testified by the recent acceptance of the first consortium publication by Nature (Miles et al. 2017). Finally, we expect that results of the project will lead to the development of a future larger-scale research project to monitor the known regions of introgression between A. coluzzii and A. gambiae, identify other possible areas of high genetic exchange between the two species and assess the impact of this phenomenon on malaria transmission and on the possibility to effectively control these major vectors.
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