similarity, defined as the fraction of branch lengths shared between two samples. By analogy with the well-established distance–decay relationship, which describes the decrease in compositional similarity between two communities with increasing geographic distance (or equivalently elevational separation) between them (Soininen et al., 2007), we described the decrease in phylogenetic similarity with distance (phylogenetic distance–decay). Our objective in exploring both measures of beta-diversity is to understand not only if there are shifts in compositional similarity with increasing elevational distance, as expected along an environmental gradient, but to quantify the phylogenetic nature of the shifts.
Phylogenetic similarity reflects the combined additive influence of: (i) lineages that are shared between two communities that lead to shared taxa, and (ii) lineages that are shared but ultimately lead to unshared taxa. One can test whether the phylogenetic similarity between two communities is solely a consequence of compositional similarity, or if it is also caused by a nonrandom structure of shared and unshared lineages. A significant phylogenetic distance–decay pattern (i.e., one that differs from that expected by taxa turnover alone; see Materials and Methods) reflects significant spatial variability in lineage composition across a landscape. Based on the assumption of phylogenetic niche conservatism described above, changes in lineage composition should correspond to changes in the traits of species. Under this model, a significant phylogenetic distance–decay relationship should reflect strong variability in the ecologically relevant traits of biological communities across a landscape.
Whereas bacterial richness decreased monotonically from the lowest to highest elevations, plant richness followed a unimodal pattern with a peak in species richness at midelevations (Fig. 7.1A). These contrasting diversity patterns emerged when richness values were calculated for bacterial and plant samples individually and also when the samples for each respective group were pooled together at every elevational band [following the protocol suggested by Whittaker (1960)]. To our knowledge, an altitudinal richness pattern has never been reported for microorganisms. The patterns observed here for microbes and plants are consistent, respectively, with the classical monotonically decreasing and hump-shaped patterns observed across most macroorganism groups (Stevens, 1992; McCain, 2005; Rahbek, 2005). It has been argued that these two contrasting richness patterns may emerge as a result of inconsistent sampling approaches among different studies, rather than an underlying ecological mechanism (Lomolino, 2001; Rahbek, 2005). By implementing a parallel sample design for the bacteria and plants, we controlled for two potential biases: varia-