Phylogenetic Measures of Biodiversity

Abstract

We developed a theoretical framework based on phylogenetic comparative methods to integrate phylogeny into three measures of biodiversity: species variability, richness, and evenness. These metrics can be used in conjunction with permutation procedures to test for phylogenetic community structure. As an illustration, we analyzed data on the composition of 58 lake fish communities in Wisconsin. The fish communities showed phylogenetic underdispersion, with communities more likely to contain closely related species. Using information about differences in environmental characteristics among lakes, we demonstrated that phylogenetic underdispersion in fish communities was associated with environmental factors. For example, lakes with low pH were more likely to contain species in the same clade of acid-tolerant species. Our metrics differ from existing metrics used to calculate phylogenetic community structure, such as net relatedness index and Faith's phylogenetic diversity. Our metrics have the advantage of providing an integrated and easy-to-understand package of phylogenetic measures of species variability, richness, and evenness with well-defined statistical properties. Furthermore, they allow the easy evaluation of contributions of individual species to different aspects of the phylogenetic organization of communities. Therefore, these metrics should aid with the incorporation of phylogenetic information into strategies for understanding biodiversity and its conservation.

Phylogenetic fields of species: cross-species patterns of phylogenetic structure and geographical coexistence

“…species are, on average, more distantly related than expected by chance) or randomness in the phylogenetic structure of an assemblage [13]. We used here the phylogenetic species variability (PSV) and phylogenetic species clustering (PSC) indices [26] that summarize the degree of phylogenetic relatedness among species in an assemblage, considering all species (i.e. deep phylogenetic level) or closest relatives only (i.e.…”

“…In addition, these indices are not affected by species richness and abundance, allowing the estimation of pure phylogenetic structure [26]. We used both PSV and PSC to statistically describe and compare the phylogenetic fields of species.…”

Phenotypic diversity, population structure and stress protein-based capacitoring in populations of Xeropicta derbentina, a heat-tolerant land snail species

“…The first parameter was nucleotide diversity π (average number of nucleotide differences within populations based on the K2P model of sequence evolution), estimated in Arlequin 3.5. For the former index, we used the adegenet package (version 1.3-6, Jombart 2008); for the latter, we treated haplotypes as species (Helmus et al 2007;Schrader et al 2013) and estimated the dissimilarity between the haplotype structures of two groups with the vegan package (version 2.0-5, Oksanen et al 2012). To detect differences in constitutive Hsp70 levels at 25°C and maximum induction levels among populations, we conducted analyses of variance (Welch-ANOVA) subsequent to checking data for normal distribution (visual inspection of histograms in addition to Shapiro-Wilk tests with α=0.05) and for homoscedasticity (Levene's test).…”

Global patterns in the phylogenetic structure of island mammal assemblages

“…So far, the analysis of phylogenetic emergent properties has been applied mostly at the scale of local communities, where both phylogenetically clustered and overdispersed communities have been found (Webb 2000;Anderson et al 2004;Cavender-Bares et al 2004, 2006Kembel & Hubbell 2006;Slingsby & Verboom 2006;Swenson et al 2006;Helmus et al 2007). At local scales, the main predictions are that (i) habitat filtering (where close relatives are brought together by shared habitat preferences) should give rise to phylogenetically clustered assemblages or (ii) competitive exclusion among close relatives should give rise to phylogenetically overdispersed assemblages (Haydon et al 1993;Webb 2000;Webb et al 2002).…”