Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era

Type Article
Date 2015-09
Language English
Author(s) Gagnaire Pierre-Alexandre1, 2, Broquet Thomas3, 4, Aurelle Didier5, Viard Frederique3, 4, Souissi Ahmed1, Bonhomme Francois1, 2, Arnaud-Haond SophieORCID1, 6, Bierne Nicolas1, 2
Affiliation(s) 1 : Univ Montpellier, F-34095 Montpellier, France.
2 : CNRS Inst Sci Evolut, Stn Mediterraneenne Environnm Littoral, UMR 5554, UM CNRS IRD EPHE, Sete, France.
3 : CNRS Team Divers & Connect Coastal Marine Landsca, Stn Biol Roscoff, Roscoff, France.
4 : UPMC Univ Paris 06, Univ Paris 04, UMR 7144, Stn Biol Roscoff, Roscoff, France.
5 : CNRS IRD Avignon Univ, Aix Marseille Univ, IMBE, UMR 7263, Marseille, France.
6 : IFREMER, UMR Ecosyst Marins Exploites, Sete, France.
Source Evolutionary Applications (1752-4571) (Wiley-blackwell), 2015-09 , Vol. 8 , N. 8 , P. 769-786
DOI 10.1111/eva.12288
WOS© Times Cited 99
Keyword(s) connectivity, gene flow, marine conservation, population genomics, population structure
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.
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Gagnaire Pierre-Alexandre, Broquet Thomas, Aurelle Didier, Viard Frederique, Souissi Ahmed, Bonhomme Francois, Arnaud-Haond Sophie, Bierne Nicolas (2015). Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era. Evolutionary Applications, 8(8), 769-786. Publisher's official version : https://doi.org/10.1111/eva.12288 , Open Access version : https://archimer.ifremer.fr/doc/00275/38592/