O R I G I N A L A R T I C L E doi:10.1111/j.1558-5646.2009.00927.x RECENT ECOLOGICAL DIVERGENCE DESPITE MIGRATION IN SOCKEYE SALMON (ONCORHYNCHUS NERKA) Scott A. Pavey,1,2,3 Jennifer L. Nielsen,4 and Troy R. Hamon2 1Biological Sciences Department, Simon Fraser University, Burnaby, British Columbia V5A 1S6 Canada 2National Park Service, P.O. Box 7, King Salmon, Alaska 99613 3E-mail: spavey@sfu.ca 4U.S. Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, Alaska 99508 Received December 18, 2008 Accepted December 1, 2009 Ecological divergence may result when populations experience different selection regimes, but there is considerable discussion about the role of migration at the beginning stages of divergence before reproductive isolating mechanisms have evolved. However, detection of past migration is difﬁcult in current populations and tools to differentiate genetic similarities due to migration versus recent common ancestry are only recently available. Using past volcanic eruption times as a framework, we combine morphological analyses of traits important to reproduction with a coalescent-based genetic analysis of two proximate sockeye salmon (Oncorhynchus nerka) populations. We ﬁnd that this is the most recent (∼500 years, 100 generations) natural ecological divergence recorded in a ﬁsh species, and report that this divergence is occurring despite migration. Although studies of ﬁsh divergence following the retreat of glaciers (10,000–15,000 years ago) have contributed extensively to our understanding of speciation, the Aniakchak system of sockeye salmon provides a rare example of the initial stages of ecological divergence following natural colonization. Our results show that even in the face of continued migration, populations may diverge in the absence of a physical barrier. K E Y W O R D S : Colonization, divergence with migration, ecological speciation, isolation with migration (IM), rapid evolution, sympatric speciation. Populations subjected to different selection regimes can evolve reproductive isolation (Mayr 1947). This divergence ultimately may result in speciation arising from ecological differences (Bush 1994; Schluter 1996a,b, 2000; Feder et al. 2005; Rundle and Nosil 2005; Funk et al. 2006). In many cases of ecological divergence, a physical barrier to migration separates the populations in the ini- tial stages (Schluter 2001; Schluter et al. 2001; Rundle and Nosil 2005). When the populations regain contact, isolating mecha- nisms (behavioral, morphological, etc.) have already evolved in the absence of migration. In populations that are currently sym- patric, this may have occurred via a double colonization event; after one colonization occurs and a population locally adapts to a habitat or resource then a second colonization occurs and adapts to an unoccupied niche (Schluter 2001; Schluter et al. 2001). Alternatively, colonization may have occurred from two differ- ent source populations that brought differences that evolved in allopatry (Schluter et al. 2001). However, in some cases, divergence may occur with gene flow in early stages (Johnson et al. 1996; Filchak et al. 2000; Johannesson 2001; Barluenga et al. 2006; Hey 2006; Savolainen et al. 2006; Bolnick and Fitzpatrick 2007; Nosil 2008). Recently colonized populations may provide ideal systems for the study of ecological divergence, as initial reproductive isolation has a dis- proportionate effect on divergence that may not be apparent at later stages (Coyne and Orr 2004). Very recent cases (<1000 years) of colonization and ecological divergence demonstrate that this 1 7 7 3 C 2010 The Author(s). Journal compilation C 2010 The Society for the Study of Evolution. Evolution 64-6: 1773–1783