Relatively little is understood about the extent to which evolution in one species can result in changes to associated communities and ecosystems, the potential mechanisms responsible for those changes (genetic drift, gene flow or natural selection), the phenotypes or candidate genes that may link ecological and evolutionary dynamics, or the role of rapid evolution and feedbacks. However, linking genes and ecosystems in this manner is fundamental to placing community structure and ecosystem function in an evolutionary framework. This is not an easy endeavour as the field of community genetics is multi-disciplinary (Whitham et al., 2006), and ecological and evolutionary dynamics occur at different spatial and temporal scales. Recent reviews show that plant genetic variation can have extended consequences at the community and ecosystem level (extended phenotype; Whitham et al., 2003) affecting arthropod diversity, soil microbial communities, trophic interactions, carbon dynamics and soil nitrogen availability (Whitham et al., 2006; Johnson & Stinchcombe, 2007; Hughes et al., 2008; Bailey et al., 2009a). Its effects are not limited to single systems or even foundation species, but are common across broadly distributed plant and animal systems, and can have effects at the community and ecosystem level of similar magnitude to traditional ecological factors, such as differences among species (Bailey et al., 2009a, b).
Theory in the fields of community genetics (Shuster et al., 2006; Whitham et al., 2006) and co-evolution (Thompson, 2005) also supports the connection between evolutionary and ecological dynamics (Johnson et al., 2009). Multiple investigators argue that community and ecosystem phenotypes represent complex traits related to variation in the fitness consequences of inter-specific indirect genetic effects (IIGEs) (Thompson, 2005; Shuster et al., 2006; Whitham et al., 2006; Tetard-Jones et al., 2007). In their most basic form, IIGEs occur when the genotype of one individual affects the phenotype and fitness of an associated individual of a different species (Moore et al.,1997; Agrawal et al., 2001; Shuster et al., 2006; Wade, 2007). Such interactions are important in the geographic mosaic theory of co-evolution (Thompson, 2005), the development of community heritability (Shuster et al., 2006) and non-additive responses of community structure, biodiversity and ecosystem function (Bailey et al., 2009a). Empirical evidence for the effects of plant genetic variation on communities and ecosystems, paired with growing theoretical models explaining evolutionary mechanisms for these results, provides a solid foundation for understanding how evolutionary processes, such as drift and selection, may affect community structure and ecosystem function.