Insect invaders analysis pipeline

Biological invasions, and more specifically those enhanced by anthropogenic activities, are becoming more and more frequent. They in turn have a huge impact on these activities, but also on biodiversity. During biological invasions, we generally observe a decrease in genetic diversity in the introduced populations compared to the native populations. This is basically explained by a reduced number of individuals at the origin of the settlement of the new population. To explain the success of an invasion despite low genetic diversity, one hypothesis proposes a purging of the genetic loading (i.e., a loss of deleterious mutations) in the introduced populations [1,2].
To study the evolution of the genetic load, we performed whole-genome pool-sequencing of native and invasive populations of a dozen insect species [3]. This large amount of genetic data and species diversity will provide one of the broadest overviews of what happens during a biological invasion, but will also require the development of a specific pipeline. Therefore, using the workflow manager Nextflow and Singularity containers, we developed a pipeline to analyze this specific poolseq data.
References
1. Glémin Sylvain. 2003. “How are deleterious mutations purged? Drift versus nonrandom mating.” Evolution 57:2678–2687, https://doi.org/10.1111/j.0014-3820.2003.tb01512.x
2. Daly, Ella Z., Olivier Chabrerie, Francois Massol, Benoit Facon, Manon C. M. Hess, Aurélie Tasiemski, Frédéric Grandjean, Matthieu Chauvat, Frédérique Viard, Estelle Forey, Laurent Folcher, Elise Buisson, Thomas Boivin, Sylvie Baltora-Rosset, Romain Ulmer, Patricia Gibert, Gabrielle Thiébaut, Jelena H. Pantel, Tina Heger, David M. Richardson, and David Renault. 2023. “A Synthesis of Biological Invasion Hypotheses Associated with the Introduction–Naturalisation–Invasion Continuum.” Oikos 1–29, https://doi.org/10.1111/oik.09645
3. Evolution of the genetic load during biological invasions. https://anr.fr/Projet-ANR-19-CE02-0010