Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history

Abstract

We present a new, broadly applicable measure of the spatial restriction of phylogenetic diversity, termed phylogenetic endemism (PE). PE combines the widely used phylogenetic diversity and weighted endemism measures to identify areas where substantial components of phylogenetic diversity are restricted. Such areas are likely to be of considerable importance for conservation. PE has a number of desirable properties not combined in previous approaches. It assesses endemism consistently, independent of taxonomic status or level, and independent of previously defined political or biological regions. The results can be directly compared between areas because they are based on equivalent spatial units. PE builds on previous phylogenetic analyses of endemism, but provides a more general solution for mapping endemism of lineages. We illustrate the broad applicability of PE using examples of Australian organisms having contrasting life histories: pea-flowered shrubs of the genus Daviesia (Fabaceae) and the Australian species of the Australo-Papuan tree frog radiation within the family Hylidae.

Prediction of phylogeographic endemism in an environmentally complex biome

“…To calculate phylogeographic endemism, the length of each branch on the genealogy is divided equally across the grid cells in which it or its descendant lineages occur. These adjusted branch lengths are then summed for each cell, as described in [3]. High scores therefore are allocated to regions where a large component of phylogenetic variation is restricted to a small area.…”

“…To understand how the distribution of genetic variation has been impacted by recent history, we develop a new measure of endemism that is based on the tips of the Tree of Life-phylogeographic lineages. Differently from previous usages of higher rank phylogenies in studies of PE and genetic diversity [3,11], the metric is not affected by branch lengths and tree topology at deep phylogenetic levels (e.g. genera or higher), which may reflect processes older than those of interest [12].…”

“…Spatial measures of phylogenetic diversity [1] and weighted endemism [2] have been combined to map phylogenetic endemism (PE): the degree to which units of phylogenetic diversity are spatially restricted [3]. While these analyses portray the concentration of evolutionary history in geographical space and improve biodiversity studies and conservation strategy, relatively little is known about the biological processes that underscore PE and related metrics.…”

Incorporating phylogenetic information for the definition of floristic districts in hyperdiverse Amazon forests: Implications for conservation

“…(2010), respectively. Weighted phylogenetic endemism (WPE) is defined as the sum of branch lengths divided by the clade range for each branch on the spanning path linking a set of taxa to the root of the tree (Rosauer et al., 2009). AED measures the evolutionary distinctiveness of species based on abundance and phylogenetic distances according to the following formula: $\text{AED}=\underset{e\in s(T,i,r)}{false\sum }\frac{{\mathrm{\lambda }}_e}{n_e}$ …”

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

“…Faith (1992) pioneered a concept of phylogenetic diversity (PD) that can be used to characterize biodiversity much more accurately than species number. 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).…”