Introduction

Trait-mediated indirect interactions (TMIIs) are important mediators of community diversity and structure and associated ecosystem processes. Elucidating the genetic basis of ecologically important phenotypic traits is the first step toward understanding the complex interactions that occur among community members. Molecular markers routinely used in quantitative trait loci (QTL) analyses (e.g., amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs)) have provided researchers with a toolbox for investigating the genetic basis of heritable traits. A goal of this research is to link genetically based traits to community interactions and ecosystem function. Ultimately, this insight can open a window onto the evolutionary dynamics that shape community structure and associated ecosystem processes (e.g., nutrient cycling). Such an approach is important as it bears on the continued development of the field of community genetics, which seeks to understand the genetic interactions that occur between species and their abiotic environment in complex communities (e.g., Whitham et al. 2003, 2006; Johnson and Agrawal 2005; LeRoy et al. 2006; Bangert et al. 2006a, b; Schweitzer et al. 2008; Crutsinger et al. 2009; Bailey et al. 2009).

INTRODUCTION

The emerging field of community and ecosystem genetics has so far focused on how the genetic variation in one species can influence the composition of associated communities and ecosystem processes such as decomposition (see definitions in Table 3–1; reviews by Whitham et al. 2003, 2006; Johnson & Stinchcombe 2007; Hughes et al. 2008). A key component of this approach has been an emphasis on understanding how the genetics of foundation plant species influence a much larger community. It is reasoned that because foundation species structure their ecosystems by creating locally stable conditions and provide specific resources for diverse organisms (Dayton 1972; Ellison et al. 2005), the genetics of these species as “community drivers” are most important to understand and most likely to have cascading ecological and evolutionary effects throughout an ecosystem (Whitham et al. 2006). For example, when a foundation species’ genotype influences the relative fitness of other species, it constitutes an indirect genetic interaction (Shuster et al. 2006), and when these interactions change species composition and abundance among individual tree genotypes, they result in individual genotypes having distinct community and ecosystem phenotypes. Thus, in addition to an individual genotype having the “traditional” phenotype that population geneticists typically consider as the expression of a trait at the individual and population level, community geneticists must also consider higher-level phenotypes at the community and ecosystem level. The predictability of phenotypes at levels higher than the population can be quantified as community heritability (i.e., the tendency for related individuals to support similar communities of organisms and ecosystem processes; Whitham et al. 2003, 2006; Shuster et al. 2006).