Phylogenetic measures of biodiversity and neo- and paleo-endemism in Australian Acacia

Abstract

Understanding spatial patterns of biodiversity is critical for conservation planning, particularly given rapid habitat loss and human-induced climatic change. Diversity and endemism are typically assessed by comparing species ranges across regions. However, investigation of patterns of species diversity alone misses out on the full richness of patterns that can be inferred using a phylogenetic approach. Here, using Australian Acacia as an example, we show that the application of phylogenetic methods, particularly two new measures, relative phylogenetic diversity and relative phylogenetic endemism, greatly enhances our knowledge of biodiversity across both space and time. We found that areas of high species richness and species endemism are not necessarily areas of high phylogenetic diversity or phylogenetic endemism. We propose a new method called categorical analysis of neo-and paleoendemism (CANAPE) that allows, for the first time, a clear, quantitative distinction between centres of neo-and paleo-endemism, useful to the conservation decision-making process.

Acacia (wattle) and Cananga (ylang-ylang): from spiral to whorled and irregular (chaotic) phyllotactic patterns – a pictorial report

“…Acacia baueri with its globular inflorescences is considered to belong to section Phyllodineae or section Plurinerves rather than section Lycopodiifoliae [24,25,[31][32][33] (also Murphy, personal communication, 2016). Its position in molecular trees, however, is not yet resolved.…”

Understanding spatial patterns of biodiversity: How sensitive is phylogenetic endemism to the randomisation model?

“…The CANAPE index was calculated for a data set of 506 Acacia species aggregated to 3037 cells at a 50 km resolution (Mishler et al 2014). Four randomisations were used: CSR, RW with 100 km radius windows, PA with 100 km radius windows, and PA with no window constraint.…”

“…A more recent development of PE is the CANAPE method (Categorical Analysis of Neoand Palaeo-Endemism; Mishler et al 2014). CANAPE uses PE with a randomisation test to identify regions of geographically restricted long or short branches.…”

The Hunting of the SNaRC: A Snarky Solution to the Species Problem

“…A related metric has appeared more recently called phylogenetic endemism (PE), which is a measure of how range-restricted lineages are (Rosauer, Laffan, et al 2009). There is a burgeoning school of research called "spatial phylogenetics" that takes advantage of the availability of large-scale phylogenies, and big distributional data sets derived from museum digitization efforts, to look at patterns of PD and PE on the landscape (Gonzalez-Orozco, Pollock, et al 2016;Mishler, Knerr, et al 2014;Nagalingum, Knerr, et al 2015;Schmidt-Lebuhn, Knerr, et al 2015;Thornhill, Baldwin, et al 2017;Thornhill, Mishler, et al 2016). The results from these studies enable rankless phylogenetic evaluations of conservation priorities, as well as studies of evolution, ecology, and biogeography.…”