The Effect of Phylogenetic Uncertainty and Imputation on EDGE Scores

Abstract

8Faced with the challenge of saving as much diversity as possible given financial and time constraints, conser-9 vation biologists are increasingly prioritizing species on the basis of their overall contribution to evolutionary 10 diversity. Metrics such as EDGE (Evolutionary Distinct and Globally Endangered) have been used to set 11 such evolutionarily-based conservation priorities for a number of taxa, such as mammals, birds, corals, am-12 phibians, and sharks. Each application of EDGE has required some form of correction to account for species 13 whose position within the tree of life are unknown. Perhaps the most advanced of these corrections is phy-14 logenetic imputation, but to date there has been no systematic assessment of both the sensitivity of EDGE 15 scores to a phylogeny missing species, and the impact of using imputation to correct for species missing from 16 the tree. Here we perform such an assessment, by simulating phylogenies, removing some species to make 17 the phylogeny incomplete, imputating the position of those species, and measuring (1) how robust ED scores 18 are for the species that are not removed and (2) how accurate the ED scores are for those removed and 19 then imputed. We find that the EDGE ranking for species on a tree is remarkably robust to missing species 20 from that tree, but that phylogenetic imputation for missing species, while unbiased, does not accurately 21 reconstruct species' evolutionary distinctiveness. On the basis of these results, we provide clear guidance for 22EDGE scoring in the face of phylogenetic uncertainty.

Global priorities for conservation of reptilian phylogenetic diversity in the face of human impacts

“…1) of any tetrapod group (14.1 MY; compared to 8.5 MY for amphibians, 8.3 MY for crocodilians, 4.9 MY for lepidosaurs, 3.9 MY for mammals and 3.1 MY for birds), and lepidosaurs have the greatest unique contribution to PD by a single species (median TBL = 238.7 MY-Sphenodon punctatus). As previously reported 45 , the calculation of species-level measures of PD is largely robust to the influence of missing species and our results remain largely unchanged when repeated on our rarefied phylogenetic trees (Supplementary Table 3).…”

“…Branch length data were extracted for all phylogenies prior to the removal of species with no spatial data to limit the impact of differing availability of spatial data across the different classes on our species-level analyses. Species-level PD metrics, which are predominantly composed of TBL scores of species, have been shown to be robust to the omission of species from the phylogeny 45 . However, to further control for differences in taxonomic completeness, we repeated these analyses using the rarefied trees outlined above for each clade and recalculated total PD and median TBL.…”

Preserving evolutionary history with improved confidence

“…Total phylogenetic branch length is indeed Faith's PD (Faith, 1992). Readers are welcome to bear Faith's PD in mind when reading Weedop et al (2019); we feel our results and arguments hold.…”

Apply our best model inferences now

“…Therefore, biologists must do what they can, including development of metrics for use in biodiversity management and loss mitigation. Weedop et al () provide a valuable phylogenetic simulation, evaluating the effects of missing species (missing data) on calculation of the EDGE (Evolutionary Distinct and Globally Endangered) metric. EDGE scores combine measures of evolutionary distinctiveness (ED) and conservation status for use in prioritizing species for conservation efforts.…”

“…This capacity for improvement of phylogenetic models via iterative testing, brings potential improvements in EDGE metrics as well. Weedop et al (2019) and many others note that we are currently losing the fight to conserve biological diversity. Therefore, although model evaluation and refinement are a continual priority, we should use our best available tools to prioritize our conservation efforts when necessary, and save as much as possible now.…”