DOI: 10.5061/dryad.z08kprrgs
title: Supplementary material for: Phylogenetic biodiversity metrics should account for both accumulation and attrition of evolutionary heritage

description: Phylogenetic metrics are essential tools used in the study of ecology,
 evolution and conservation. Phylogenetic diversity (PD) in particular is
 one of the most prominent measures of biodiversity, and is based on the
 idea that biological features accumulate along the edges of phylogenetic
 trees that are summed. We argue that PD and many other phylogenetic
 biodiversity metrics fail to capture an essential process that we term
 attrition. Attrition is the gradual loss of features and other sources of
 variety through causes other than extinction. Here we introduce
 `EvoHeritage', a generalisation of PD that is founded on the joint
 processes of accumulation and attrition of features. We argue that whilst
 PD measures evolutionary history, EvoHeritage is required to capture a
 more pertinent subset of evolutionary history including only components
 that have survived attrition. We show that EvoHeritage is not the same as
 PD on a tree with scaled edges; instead, accumulation and attrition
 interact in a more complex non-monophyletic way that cannot be captured by
 edge lengths alone. This leads us to speculate that the one-dimensional
 edge lengths of classic trees may be insufficiently flexible to capture
 the nuances of evolutionary processes. We derive a measure of EvoHeritage
 and show that it elegantly reproduces species richness and PD at opposite
 ends of a continuum based on the intensity of attrition. We demonstrate
 the utility of EvoHeritage in ecology as a predictor of community
 productivity compared with species richness and PD. We also show how
 EvoHeritage can quantify living fossils and resolve their associated
 controversy. We suggest how the existing calculus of PD-based metrics and
 other phylogenetic biodiversity metrics can and should be recast in terms
 of EvoHeritage accumulation and attrition.
description: Data was reprocessed from published sources as described in the
 associated manuscript methods section There is no
 primary data included. Supplementary material and
 glossary contain mathematical details and proofs rather than any primary
 data sets.
description: R for use of code, otherwise PDF and CSV readers are needed to
 access the files.
description: # Title of Dataset *** This dataset contains 1. A glossary 2. Details and
 mathematical proofs 3. Data plotted in figure 9 ## Description of the data
 and file structure 1. The glossary is a single PDF file 2. The details and
 mathematical proofs are a single PDF file 3. Data plotted in figure 9 as a
 series of 4 .csv files a. Filenames correpond to Jurassic and Cretaceous
 cases as described in main text b. Column with name result.data.tip.label
 gives species names c. Columns with names LF.min, LF.lq, LF.median, LF.uq,
 LF.max give the living-fossil-ness values min, lower quartile, median,
 upper quartile and max respectively. ## Sharing/Access information Data
 was derived from the following sources (as described in the associated
 manuscript methods) * Upham, N. S., J. A. Esselstyn, and W. Jetz. 2019.
 Inferring the mammal tree: species-level sets of phylogenies for questions
 in ecology, evolution, and conservation. PLoS Biology 17(12):e3000494.
 https://datadryad.org/stash/dataset/doi:10.5061/dryad.tb03d03