title: Deciphering the Routes of invasion of Drosophila suzukii by Means of ABC Random Forest.
abstract: Deciphering invasion routes from molecular data is crucial to understanding biological invasions, including identifying bottlenecks in population size and admixture among distinct populations. Here, we unravel the invasion routes of the invasive pest Drosophila suzukii using a multi-locus microsatellite dataset (25 loci on 23 worldwide sampling locations). To do this, we use approximate Bayesian computation (ABC), which has improved the reconstruction of invasion routes, but can be computationally expensive. We use our study to illustrate the use of a new, more efficient, ABC method, ABC random forest (ABC-RF) and compare it to a standard ABC method (ABC-LDA). We find that Japan emerges as the most probable source of the earliest recorded invasion into Hawaii. Southeast China and Hawaii together are the most probable sources of populations in western North America, which then in turn served as sources for those in eastern North America. European populations are genetically more homogeneous than North American populations, and their most probable source is northeast China, with evidence of limited gene flow from the eastern US as well. All introduced populations passed through bottlenecks, and analyses reveal five distinct admixture events. These findings can inform hypotheses concerning how this species evolved between different and independent source and invasive populations. Methodological comparisons indicate that ABC-RF and ABC-LDA show concordant results if ABC-LDA is based on a large number of simulated datasets but that ABC-RF out-performs ABC-LDA when using a comparable and more manageable number of simulated datasets, especially when analyzing complex introduction scenarios.
authors.affiliation: Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France.
authors.forename: Antoine
authors.initials: A
authors.lastname: Fraimout
authors.affiliation: Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Debat
authors.affiliation: INRA, Centre de Biologie et de Gestion des Populations (UMR INRA IRD Cirad Montpellier SupAgro), Montferrier-Sur-Lez, France.
authors.forename: Simon
authors.initials: S
authors.lastname: Fellous
authors.affiliation: INRA, Centre de Biologie et de Gestion des Populations (UMR INRA IRD Cirad Montpellier SupAgro), Montferrier-Sur-Lez, France.|Colorado State University, Fort Collins, CO.
authors.forename: Ruth A
authors.initials: RA
authors.lastname: Hufbauer
authors.affiliation: INRA, Centre de Biologie et de Gestion des Populations (UMR INRA IRD Cirad Montpellier SupAgro), Montferrier-Sur-Lez, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Foucaud
authors.affiliation: Centre de Mathématiques et Informatique, Aix-Marseille Université, Marseille, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Pudlo
authors.affiliation: Institut Montpelliérain Alexander Grothendieck, Université de Montpellier, Montpellier, France.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Marin
authors.affiliation: Tropical Conservation Biology & Environmental Science, University of Hawaii at Hilo, HI.
authors.forename: Donald K
authors.initials: DK
authors.lastname: Price
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard Lyon 1, Villeurbanne, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Cattel
authors.affiliation: College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan Province, People's Republic of China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Chen
authors.affiliation: Programa de Pós Graduação em Genética e Biologia Molecular, Programa de Pós Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
authors.forename: Marindia
authors.initials: M
authors.lastname: Deprá
authors.affiliation: CIRAD, UMR Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Paris, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: François Duyck
authors.affiliation: Department of Entomology, University of Wisconsin, Madison, WI.
authors.forename: Christelle
authors.initials: C
authors.lastname: Guedot
authors.affiliation: CABI, Delémont, Switzerland.
authors.forename: Marc
authors.initials: M
authors.lastname: Kenis
authors.affiliation: Graduate School of Environmental Earth Science, Hokkaido Daigaku University, Sapporo, Hokkaido Prefecture, Japan.
authors.forename: Masahito T
authors.initials: MT
authors.lastname: Kimura
authors.affiliation: Department of Entomology, Cornell University, Ithaca, NY.
authors.forename: Gregory
authors.initials: G
authors.lastname: Loeb
authors.affiliation: INRA, Centre de Biologie et de Gestion des Populations (UMR INRA IRD Cirad Montpellier SupAgro), Montferrier-Sur-Lez, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Loiseau
authors.affiliation: Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, Universita degli Studi di Padova, Padova, Italy.
authors.forename: Isabel
authors.initials: I
authors.lastname: Martinez-Sañudo
authors.affiliation: Departament de Genètica, Universitat de Barcelona, Barcelona, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Pascual
authors.affiliation: Division of Biological Sciences, University of California San Diego.
authors.forename: Maxi
authors.initials: M
authors.lastname: Polihronakis Richmond
authors.affiliation: Mid-Columbia Agricultural Research and Extension Center, Oregon State University, Hood River, OR.
authors.forename: Peter
authors.initials: P
authors.lastname: Shearer
authors.affiliation: Department of Genetics, North Carolina State University, Raleigh, NC.
authors.forename: Nadia
authors.initials: N
authors.lastname: Singh
authors.affiliation: Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan.
authors.forename: Koichiro
authors.initials: K
authors.lastname: Tamura
authors.affiliation: INRA, Centre de Biologie et de Gestion des Populations (UMR INRA IRD Cirad Montpellier SupAgro), Montferrier-Sur-Lez, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Xuéreb
authors.affiliation: MoA-CABI Joint Laboratory for Bio-safety, Chinese Academy of Agricultural Sciences, BeiXiaGuan, Haidian Qu, China.
authors.forename: Jinping
authors.initials: J
authors.lastname: Zhang
authors.affiliation: INRA, Centre de Biologie et de Gestion des Populations (UMR INRA IRD Cirad Montpellier SupAgro), Montferrier-Sur-Lez, France.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Estoup
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002681:China; D003198:Computer Simulation; D004330:Drosophila / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics; D005828:Genetics, Population / Q000379:methods*; D005838:Genotype; D006254:Hawaii; D058865:Introduced Species; D007564:Japan; D018895:Microsatellite Repeats / Q000235:genetics; D008957:Models, Genetic; D009656:North America; D058974:Phylogeography / Q000379:methods*
keywords: Drosophila suzukii; approximate Bayesian computation; invasion routes; population genetics; random forest