Analyses

content/01.abstract.md

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 ## Abstract {.page_break_before}
 
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+I have not yet written an abstract! 
+Basically, malaria is still bad, including in the Sahel. 
+We try to compare populations of Anopheles in the region and slightly farther away to try to detect population structure.
+In particular, we would like to see if populations aestivate or migrate in the most arid (during the dry season) regions.
+There is a some population structure with fairly distant locations but within the Sahel it is pretty weak.

content/02.introduction.md

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 # Introduction
 
-- Malaria is not good
-- Population structure affects behaviour, IR profile -> risk and response
-- Why Mali for this study
+Malaria remains one of the most infectious and deadliest diseases in the world. 
+There were an estimated 249 000 000 new cases and an estimated 608 000 deaths in 2022 [@WMR2023]. 
+Despite all the effort and investment in the last 20 years, progress in malaria prevention, treatment and elimination has largely stalled. 
+The malaria burden is overwhelmingly limited to the WHO African region. 
+Within the WHO African region, some countries are even more negatively affected than others. 
+While the Sahelian region of Africa is not the worst affected region in Africa, it includes countries such as Niger (9th in terms of cases), Mali (7th) and Burkina Faso (6th) as well as parts of Nigeria which is the worst affected country in the world. 
+It is also worth noting that the Sahelian region of Africa is one of the worst affected regions of the globe by climate change [@SCA2022] and that many countries in the region (Mali, Niger, Burkina Faso, Sudan, ...) have suffered through political instabilities and coups. 
+
+Anopheles gambiae s.l. is the main vector of malaria in Africa. 
+It is prevalent in the Sahelian region. 
+The complex is composed of several taxa with various resting and feeding behaviours as well as insecticide resistance profiles that lives in sympatry. [Add citation] 
+The complex contains Anopheles gambiae s.s., Anopheles coluzzii and Anopheles arabiensis which are known to be major vectors of malaria. 
+The complex also includes some minor vectors such as Anopheles melas and Anopheles merus as well as cryptic taxa whose status as vectors is yet to be investigated. 
+Anopheles funestus is another major vector complex present in the Sahelian region. 
+In this paper, we will focus our attention mostly on Anopheles coluzzii and Anopheles gambiae s.s.. 
+We are interested in observing population structure within taxa and gene flow between populations as these can affect and be affected by behavioural differences and changes and can offer opportunities or present hurdles to the implementation of various malaria control methods such as the use of bednets or the release of genetically modified vectors. 
+
+The Sahelian region of Africa is characterised by a wet season from June to September and a dry season (find estimate of precipitations during both periods and a citation). 
+Climatic conditions during the dry season are hostile to anopheles gambiae s.l. development (dry and hot weather, absence of water to lay eggs in and for larvae to develop, lower number of people on whom to feed, ...). 
+Furthermore, the dry season lasts for a significantly longer time than the estimated lifespan of an anopheles gambiae s.l. mosquito. 
+Yet, during the wet season, the anopheles gambiae s.l. numbers go back up and they continue to cause a heavy burden on human health. 
+Several different explanations exist for the this yearly return of the anopheles gambiae s.l. threat. 
+Succinctly, they may leave the Sahel for a more hospitable region for the duration of the dry season and come back at the start of the wet season using changing winds patterns to fly longer distances [@Huestis19], i.e., they perform long distance migration; the local population may be eradicated but replaced by the short-distance migration of mosquitoes from region where breeding can continue [@Charlwood00]; the local population may migrate short distances to locations that can sustain breeding [@Lehmann14]; or they may find a way to survive during the whole duration of the dry season with a much smaller and less active population that reactivates at the start of the wet season when conditions become more hospitable, i.e., they may aestivate [@Lehmann10].
+How these populations deal with the dry season has an obvious impact on population structure as aestivating populations are isolated whereas migrating ones can have significant gene flow with populations native to the region they migrate to.
+Several studies have been conducted to attempt to answer this question [@Mwima23].
+In this paper, we will try to use new whole genome data that has only recently become available.
+
+![Map of 2nd administrative regions used for An. gambiae and An. coluzzii](./images/admin2_map.png "Map of 2nd administrative regions used for An. gambiae and An. coluzzii")
+Our analysis will be centred around 3 main groups of mosquitoes: we will use samples collected by Lehmann et al. [@Huestis19], available samples coming from Mali that were collected through multiple partnerships [cite all Malian studies] as well as available samples from Burkina Faso [cite all Burkina studies]. 
+These data will also be compared to other data from the rest of Africa used as references. 
+The Sahelian region covers much more than just Mali and Burkina Faso but no data is yet available from most other Sahelian countries (Niger, Chad, Sudan, ...). 
+On the other hand, the Gambia is usually considered to be part of the Sahel but the distribution of malaria vectors in the Gambia is very different from what is observed in Mali or Burkina Faso [cite Gambian analysis] hence data from the Gambia will only be used as a source of comparison.