Abstract
The PD measure of phylogenetic diversity interprets branch lengths cladistically to make inferences about feature diversity. PD calculations extend conventional species-level ecological indices to the features level. The “phylogenetic beta diversity” framework developed by microbial ecologists calculates PD-dissimilarities between community localities. Interpretation of these PD-dissimilarities at the feature level explains the framework’s success in producing ordinations revealing environmental gradients. An example gradients space using PD-dissimilarities illustrates how evolutionary features form unimodal response patterns to gradients. This features model supports new application of existing species-level methods that are robust to unimodal responses, plus novel applications relating to climate change, commercial products discovery, and community assembly.
Highlights
Cladistic analyses are based on a well-known assumption about the relationship between features and phylogenetic pattern: shared ancestry can account for shared features among taxa
Our rationale is that: (1) based on the underlying cladistic model, PD-dissimilarities approximate the quantities we would get if we could directly calculate dissimilarities using evolutionary features, (2) evolutionary features in turn can be linked, by a simple “unimodal response” model, to environmental gradients, and (3) PDdissimilarities relate to unimodal response of features in the same way that conventional robust dissimilarities relate to unimodal response of species - allowing phylogenetic application of the existing robust analysis methods for inferring environmental gradients
This means that evolutionary features, including those represented by non-terminal phylogenetic branches, would have general unimodal responses to gradients (Figure 2b)
Summary
Cladistic analyses are based on a well-known assumption about the relationship between features (character states) and phylogenetic pattern: shared ancestry can account for shared features among taxa. That fundamental model is a basis for inference of phylogeny from observed character data for a set of taxa. Cladistic parsimony methods prefer trees that maximize this particular explanation of character variation; most-parsimonious trees equivalently minimize the sum of branch “lengths” that count character state changes. This inference of phylogenetic trees from characters is well-established, but this same cladistic model means that we can “work backwards”. We extend PD’s cladistic interpretation of phylogenetic branches as a proxy for evolutionary features. We will show how interpretation of these PD-dissimilarities at the level of features provides a model that justifies the microbial approach and points to new applications
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