1 Estimating connectivity in marine populations: an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios P. SAENZ-AGUDELO 1 , G. P. JONES 2 , S. R. THORROLD 3 and S. PLANES 1 1 Laboratoire Écosystèmes Aquatiques Tropicaux et Méditerranéens UMR 5244 CNRS-EPHE- UPVD, Université de Perpignan 66860 Perpignan Cedex, 2 School of Marine and Tropical Biology, and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia, 3 Biology Department MS # 50, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA Keywords: Assignment tests, coral-reef ecology, connectivity, larval dispersal, marine protected areas, metapopulation, microsatellites, parentage analysis, self-recruitment Correspondance: Serge Planes, Laboratoire Écosystèmes Aquatiques Tropicaux et Méditerranéens, UMR 5244 CNRS-EPHE-UPVD, Université de Perpignan, 66860 Perpignan Cedex, Fax: +33 4 68 50 36 86, E-Mail : planes@univ-perp.fr Running title: Estimating connectivity in marine populations