Phylogenetic resolution and metrics of biodiversity and signal in conservation

Abstract

Over the past two decades, biodiversity assessments have moved beyond simply measuring species diversity and toward the utilization of phylogenetic information. Despite these major advances toward holistically estimating the similarity of species, challenges remain. Specifically, the large phylogenies utilized for such analyses often contain multiple polytomous nodes indicating a lack of information regarding the true relatedness of lineages. Unfortunately, relatively little attention has been paid to what impact these polytomies may have on downstream analyses of biodiversity. Here we begin with describing how polytomies should impact phylogenetic metrics of biodiversity, which is then followed by a simulation study examining 3360 phylogenies with seven different levels of resolution. The simulations show that an increase in polytomies increases the total branch length of the phylogenies, which generally results in an increase in phylogenetic metrics of biodiversity. Further, we show that measures of phylogenetic signal in species abundance increase when polytomies are introduced. The results are clear and consistent across phylogenies and are based on unavoidable realities regarding branch lengths in resolved versus unresolved phylogenies indicating that such results should be expected in all systems. We recommend that future research and biodiversity assessments clearly discuss these directional biases and attempt to quantify sensitivity in metrics via randomly resolving polytomies. These solutions will be needed as our exploration and documentation of biodiversity to promote better phylogenetic resolution across the tree of life continues.