The Problem and Promise of Scale Dependency in Community Phylogenetics

Abstract

The problem of scale dependency is widespread in investigations of ecological communities. Null model investigations of community assembly exemplify the challenges involved because they typically include subjectively defined "regional species pools." The burgeoning field of community phylogenetics appears poised to face similar challenges. Our objective is to quantify the scope of the problem of scale dependency by comparing the phylogenetic structure of assemblages across contrasting geographic and taxonomic scales. We conduct phylogenetic analyses on communities within three tropical forests, and perform a sensitivity analysis with respect to two scaleable inputs: taxonomy and species pool size. We show that (1) estimates of phylogenetic overdispersion within local assemblages depend strongly on the taxonomic makeup of the local assemblage and (2) comparing the phylogenetic structure of a local assemblage to a species pool drawn from increasingly larger geographic scales results in an increased signal of phylogenetic clustering. We argue that, rather than posing a problem, "scale sensitivities" are likely to reveal general patterns of diversity that could help identify critical scales at which local or regional influences gain primacy for the structuring of communities. In this way, community phylogenetics promises to fill an important gap in community ecology and biogeography research.

Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

“…A comprehensive understanding of biodiversity requires investigation at multiple scales, including scales of space, time and organization (Levin, 1992;Swenson et al, 2006;Cavender-Bares et al, 2009). Community studies have devoted considerable attention to issues of spatial and temporal scales, whereas similar examination and discussion of the organizational scale is limited.…”

“…Second, and perhaps more importantly, as certain processes are only apparent and drive ecosystem variation at a particular spatiotemporal scale (Levin, 1992), their effects may only be evident by examining communities at a particular taxonomic resolution. Following previous notions of scale dependency in plant communities (Levin, 1992;Cavender-Bares et al, 2006Swenson et al, 2006Swenson et al, , 2007 and the idea of beta-versus alpha-niche (Silvertown et al, 2006a, b), we might postulate that large-scale processes such as climatic tolerances (beta-niche) may be better evidenced by broadly resolved community profiles ( Figures 1a and b); whereas, small-scale processes such as biotic interactions and microhabitat differentiation (alpha-niche) may only be evident with fine-level classification data (Figure 1c). With respect to prokaryotes with small cell size and short generation time (as considered in this study), a typical sampling setup probably emphasizes the effect of β-niche (evidenced by broadly resolved taxonomic data), whereas the effect of α-niche may be underestimated because of measurement limitations for biotic properties and microhabitat conditions (Ranjard and Richaume, 2001;Armitage et al, 2012).…”

“…With respect to the scale-dependency issue (Levin, 1992;Cavender-Bares et al, 2006Swenson et al, 2006Swenson et al, , 2007, we acknowledge that the detected patterns can vary according to phylogenetic combinations or target groups of communities. For example, the best taxonomic resolution and key environmental factor might differ when considering whole prokaryotic communities versus focusing on a particular taxonomic group (Johnson et al, 2006;Martiny et al, 2009).…”

“…In addition, we calculated the phylogeny-based UniFrac metric (Lozupone and Knight, 2005) as a standard to contrast our multi-level taxonomy-based composition analyses, as this metric has recently gained popularity in microbial community analyses and believed to be more informative than taxonomy-based estimates (Lozupone and Knight, 2005;Swenson, 2014). Moreover, given the potential scale dependency (Levin, 1992;Cavender-Bares et al, 2006Swenson et al, 2006Swenson et al, , 2007 in community-environment relationships, we considered case studies covering sampling sites from either global or local scales (Table 1) and which may provide insight into the scale dependency of microbial community assembly. Previous studies on plant communities (focused on within-community phylogenetic structure) have identified concerns about spatiotemporal and taxonomic scales on the detected pattern.…”

“…Previous studies on plant communities (focused on within-community phylogenetic structure) have identified concerns about spatiotemporal and taxonomic scales on the detected pattern. For example, the signal of phylogenetic clustering (that is, taxa within a given community contain lower mean phylogenetic distances than expected from random; as evidence for habitat filtering) has been found to be relatively evident when considering samples from a larger geographic region and/or a broader span of taxonomy (Cavender-Bares et al, 2006Swenson et al, 2006Swenson et al, , 2007. In this study, rather than detecting the within-community structure, we concentrated our analyses on the inter-community pattern (that is, how taxonomic compositions differ across sites in response to environmental factors) to assess whether changing taxonomic resolution affects the explained variance of community-environment relationships (Figure 1).…”