Foundation species represent excellent model systems for understanding the broad consequences of variation on community and ecosystem processes as they provide a focal resource upon which associated interacting species depend. As foundation species (Dayton 1972; Ellison et al. 2005), trees and other dominant plants often create stable conditions via plant traits that allow dependent communities to assemble regularly and influence ecosystem processes such as net primary productivity (NPP) and soil fertility (i.e., nutrient cycling, via accumulations of leaf or root organic matter or root exudates; Zinke 1962; Zak et al. 1986; Binkley and Giardina 1998; Bartelt-Ryser et al. 2005; Wardle 2006). Recent studies in both terrestrial and aquatic habitats have shown that intraspecific genetic variation (defined at multiple genetic scales, including introgression [movement of genes from one species to another], genotypic diversity [studies manipulating the number of genotypes in a population] and genotypic variation [variation among genotypes]) in foundation plants can have community-wide consequences. Intraspecific variation affects associated vertebrate, arthropod and microbial community composition or activity and ecosystem level processes (recently reviewed in Johnson and Stinchcombe 2007; Hughes et al. 2008; Whitham et al. 2008; Bailey et al. 2009). For example, genetic variation resulting from the introgression of genes from one species to another through the process of hybridization has been shown to have important consequences for associated species, communities and ecosystem processes in multiple hybridizing plant species, including Salix spp., Eucalyptus spp., Quercus spp. and Populus spp. (Fritz et al. 1994; Dungey et al. 2000; Hochwender and Fritz 2004; Ito and Ozaki 2005; Wimp et al. 2005; Tovar-Sanchez and Oyama 2006; Bangert et al. 2008). In the Populus system specifically, recent field and common garden studies have shown that genetic variation across a hybridizing system (P. fremontii, P. angustifolia and their natural F1 and backcross hybrids) results in shifts in plant traits, including secondary chemistry, plant water use and above- and belowground productivity (Fischer et al. 2004; Rehill et al. 2006; Schweitzer et al. 2008a; Lojewski et al. 2009). Whether due directly or indirectly to these plant traits, rates of leaf litter decomposition, total belowground carbon (C) allocation and pools of soil nitrogen (N) and rates of net N mineralization also shift along this genetic gradient (Schweitzer et al. 2004, 2008, b; LeRoy et al. 2006; Whitham et al. 2006; Lojewski et al. 2009; Fischer et al. 2007, 2010).
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.
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).
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