Archive for ABC-RF

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

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , , on April 6, 2021 by xi'an

“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.



locusts in a random forest

Posted in pictures, Statistics, University life with tags , , , , , , , , , , , on July 19, 2019 by xi'an

My friends from Montpellier, where I am visiting today, Arnaud Estoup, Jean-Michel Marin, and Louis Raynal, along with their co-authors, have recently posted on biorXiv a paper using ABC-RF (Random Forests) to analyse the divergence of two populations of desert locusts in Africa. (I actually first heard of their paper by an unsolicited email from one of these self-declared research aggregates.)

“…the present study is the first one using recently developed ABC-RF algorithms to carry out inferences about both scenario choice and parameter estimation, on a real multi-locus microsatellite dataset. It includes and illustrates three novelties in statistical analyses (…): model grouping analyses based on several key evolutionary events, assessment of the quality of predictions to evaluate the robustness of our inferences, and incorporation of previous information on the mutational setting of the used microsatellite markers”.

The construction of the competing models (or scenarios) is built upon data of past precipitations and desert evolution spanning several interglacial periods, back to the middle Pleistocene, concluding at a probable separation in the middle-late stages of the Holocene, which corresponds to the last transition from humid to arid conditions in the African continent. The probability of choosing the wrong model is exploited to determine which model(s) lead(s) to a posterior [ABC] probability lower than the corresponding prior probability, and only one scenario stands this test. As in previous ABC-RF implementations, the summary statistics are complemented by pure noise statistics in order to determine a barrier in the collection of statistics, even though those just above the noise elements (which often cluster together) may achieve better Gini importance by mere chance. An aspect of the paper that I particularly like is the discussion of the various prior modellings one can derive from existing information (or lack thereof) and the evaluation of the impact of these modellings on the resulting inference based on simulated pseudo-data.