title: Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era.
abstract: Estimating the rate of exchange of individuals among populations is a central concern to evolutionary ecology and its applications to conservation and management. For instance, the efficiency of protected areas in sustaining locally endangered populations and ecosystems depends on reserve network connectivity. The population genetics theory offers a powerful framework for estimating dispersal distances and migration rates from molecular data. In the marine realm, however, decades of molecular studies have met limited success in inferring genetic connectivity, due to the frequent lack of spatial genetic structure in species exhibiting high fecundity and dispersal capabilities. This is especially true within biogeographic regions bounded by well-known hotspots of genetic differentiation. Here, we provide an overview of the current methods for estimating genetic connectivity using molecular markers and propose several directions for improving existing approaches using large population genomic datasets. We highlight several issues that limit the effectiveness of methods based on neutral markers when there is virtually no genetic differentiation among samples. We then focus on alternative methods based on markers influenced by selection. Although some of these methodologies are still underexplored, our aim was to stimulate new research to test how broadly they are applicable to nonmodel marine species. We argue that the increased ability to apply the concepts of cline analyses will improve dispersal inferences across physical and ecological barriers that reduce connectivity locally. We finally present how neutral markers hitchhiking with selected loci can also provide information about connectivity patterns within apparently well-mixed biogeographic regions. We contend that one of the most promising applications of population genomics is the use of outlier loci to delineate relevant conservation units and related eco-geographic features across which connectivity can be measured.
authors.affiliation: Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France.
authors.forename: Pierre-Alexandre
authors.initials: PA
authors.lastname: Gagnaire
authors.affiliation: CNRS team Diversity and connectivity of coastal marine landscapes, Station Biologique de Roscoff Roscoff, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff Roscoff, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Broquet
authors.affiliation: Aix Marseille Université, CNRS-IRD-Avignon Université, IMBE UMR 7263 Marseille, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Aurelle
authors.affiliation: CNRS team Diversity and connectivity of coastal marine landscapes, Station Biologique de Roscoff Roscoff, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff Roscoff, France.
authors.forename: Frédérique
authors.initials: F
authors.lastname: Viard
authors.affiliation: Université de Montpellier Montpellier, France.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Souissi
authors.affiliation: Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France.
authors.forename: François
authors.initials: F
authors.lastname: Bonhomme
authors.affiliation: Université de Montpellier Montpellier, France ; Ifremer, UMR "Ecosystèmes Marins Exploités" Sète, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Arnaud-Haond
authors.affiliation: Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bierne
keywords: connectivity; gene flow; marine conservation; population genomics; population structure