ABC & the eighth plague of Egypt [locusts in forests]

“If you refuse to let them go, I will bring locusts into your country tomorrow. They will cover the face of the ground so that it cannot be seen. They will devour what little you have left after the hail, including every tree that is growing in your fields. They will fill your houses and those of all your officials and all the Egyptians.” Exodus 10:3-6

Marie-Pierre Chapuis, Louis Raynal, and co-authors, mostly from Montpellier, published last year a paper on the evolutionary history of the African arid-adapted pest locust, Schistocerca gregaria, called the eighth plague of Egypt in the Bible. And a cause for a major food disaster in East Africa over the past months. The analysis was run with ABC-RF techniques. The paper was first reviewed in PCI Evolutionary Biology, with the following points:

The present-day distribution of extant species is the result of the interplay between their past population demography (e.g., expansion, contraction, isolation, and migration) and adaptation to the environment (…) The understanding of the key factors driving species evolution gives important insights into how the species may respond to changing conditions, which can be particularly relevant for the management of harmful species, such as agricultural pests.

Meaningful demographic inferences present major challenges. These include formulating evolutionary scenarios fitting species biology and the eco-geographical context and choosing informative molecular markers and accurate quantitative approaches to statistically compare multiple demographic scenarios and estimate the parameters of interest. A further issue comes with result interpretation. Accurately dating the inferred events is far from straightforward since reliable calibration points are necessary to translate the molecular estimates of the evolutionary time into absolute time units (i.e. years). This can be attempted in different ways (…) Nonetheless, most experimental systems rarely meet these conditions, hindering the comprehensive interpretation of results.

The contribution of Chapuis et al. addresses these issues to investigate the recent history of the (…) desert locust (…) Owing to their fast mutation rate microsatellite markers offer at least two advantages: i) suitability for analyzing recently diverged populations, and ii) direct estimate of the germline mutation rate in pedigree samples (…) The main aim of the study is to infer the history of divergence of the two subspecies of the desert locust, which have spatially disjoint distribution corresponding to the dry regions of North and West-South Africa. They first use paleo-vegetation maps to formulate hypotheses about changes in species range since the last glacial maximum. Based on them, they generate 12 divergence models. For the selection of the demographic model and parameter estimation, they apply the recently developed ABC-RF approach (…) Some methodological novelties are also introduced in this work, such as the computation of the error associated with the posterior parameter estimates under the best scenario (…) The best-supported model suggests a recent divergence event of the subspecies of S. gregaria (around 2.6 kya) and a reduction of populations size in one of the subspecies (S. g. flaviventris) that colonized the southern distribution area. As such, results did not support the hypothesis that the southward colonization was driven by the expansion of African dry environments associated with the last glacial maximum (…) The estimated time of divergence points at a much more recent origin for the two subspecies, during the late Holocene, in a period corresponding to fairly stable arid conditions similar to current ones. Although the authors cannot exclude that their microsatellite data bear limited information on older colonization events than the last one, they bring arguments in favour of alternative explanations. The hypothesis privileged does not involve climatic drivers, but the particularly efficient dispersal behaviour of the species, whose individuals are able to fly over long distances (up to thousands of kilometers) under favourable windy conditions (…)

There is a growing number of studies in phylogeography in arid regions in the Southern hemisphere, but the impact of past climate changes on the species distribution in this region remains understudied relative to the Northern hemisphere. The study presented by Chapuis et al. offers several important insights into demographic changes and the evolutionary history of an agriculturally important pest species in Africa, which could also mirror the history of other organisms in the continent (…)

Microsatellite markers have been offering a useful tool in population genetics and phylogeography for decades (…) This study reaffirms the usefulness of these classic molecular markers to estimate past demographic events, especially when species- and locus-specific microsatellite mutation features are available and a powerful inferential approach is adopted. Nonetheless, there are still hurdles to overcome, such as the limitations in scenario choice associated with the simulation software used (e.g. not allowing for continuous gene flow in this particular case), which calls for further improvement of simulation tools allowing for more flexible modeling of demographic events and mutation patterns. In sum, this work not only contributes to our understanding of the makeup of the African biodiversity but also offers a useful statistical framework, which can be applied to a wide array of species and molecular markers.

 

 

non-uniform Laplace generation

This year, the French Statistical Society (SFDS) Prix Laplace has been granted to Luc Devroye, author of the Non-Uniform Random Generation bible. among many achievements!, prize that he will receive during the 2019 meeting in Nancy, this very week.

ASC 2012 (#3, also available by mind-reading)

This final morning at the ASC 2012 conference in Adelaide, I attended a keynote lecture by Sophia Rabe-Hesketh on GLMs that I particularly appreciated, as I am quite fond of those polymorphous and highly adaptable models (witness the rich variety of applications at the INLA conference in Trondheim last month). I then gave my talk on ABC model choice, trying to cover the three episodes in the series within the allocated 40 minutes (and got from Terry Speed the trivia information that Renfrey Potts, father to the Potts model, spent most of his life in Adelaide, where he died in 2005! Terry added that he used to run along the Torrens river, being a dedicated marathon runner. This makes Adelaide the death place of both R.A. Fisher and R. Potts.)

Later in the morning, Christl Donnelly  gave a fascinating talk on her experiences with government bodies during the BSE and foot-and-mouth epidemics in Britain in the past decades. It was followed by  a frankly puzzling [keynote Ozcots] talk delivered by Jessica Utts on the issue of parapsychology tests, i.e. the analysis of experiments testing for “psychic powers”. Nothing less. Actually, I first thought this was a pedagogical trick to capture the attention of students and debunk, however Utts’ focus on exhibiting such “powers” was definitely dead serious and she concluded that “psychic functioning appears to be a real effect”. So it came as a shock that she was truly believing in psychic paranormal abilities! I had been under the wrong impression that the 2005 Statistical Science paper of hers was demonstrating the opposite but it clearly belongs to the tradition of controversial Statistical Science that started with the Bible code paper… I also found it flabbergasting to learn that the U.S. Army is/was funding research in this area and is/was actually employing “psychics”, as well that the University of Edinburgh has a parapsychology unit within the department of psychology. (But, after all, UK universities also have long had schools of Divinity, so let the irrational in a while ago!)