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Title: Phylogenetic Distance Metrics for Studies of Focal Species in Communities: Quantiles and Cumulative Curves
The phylogenetic distance between species often predicts differences in ecologically important traits. The phylogenetic diversity and structure of biological communities can inform our understanding of the processes that shape those communities, and there is a well-developed framework for comparing phylogenetic structures of communities. However, particularly in studies of phylogenetic distances from one focal species to other members of its assemblage (a one-to-many framework), the standard metrics of community-wide studies encounter significant limitations due to the left-skewed distribution of pairwise phylogenetic distances in most biological communities. For studies that require estimating the degree of phylogenetic isolation of a focal taxon, the mean phylogenetic distance (MPD) usually provides little power to distinguish among taxa because it is heavily weighted by the many ways to be distantly related, whereas the nearest taxon distance (NTD) is highly idiosyncratic and ignores cases where multiple close relatives may contribute equally strongly to influence the focal species. Here we highlight the value of examining the cumulative distribution of phylogenetic distances in studies that take a focal-species approach. We describe and discuss the benefits of two new metrics. An integrated metric of phylogenetic distances (AUPhyDC) uses information from the whole cumulative distribution, whereas the tenth quantile (PD10) is an extremely simple metric that improves on NTD by capturing the influence of multiple close relatives on ecological interactions. Several recent examples found that PD10 did a better job of revealing ecological patterns than NTD or MPD. We provide R code to facilitate the use of these approaches and advocate for the inclusion of PD10 along with NTD and MPD in statistical packages for phylogenetic ecology.  more » « less
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    Mountains provide uniquely informative systems for examining how biodiversity is distributed and identifying the causes of those patterns. Elevational patterns of species richness are well‐documented for many taxa but comparatively few studies have investigated patterns in multiple dimensions of biodiversity along mountainsides, which can reveal the underlying processes at play. Here, we use trait‐based diversity patterns to determine the role of abiotic filters and competition in the assembly of communities of small mammals across elevation and evaluate the surrogacy of taxonomic, functional, and phylogenetic dimensions of diversity.


    Great Basin ecoregion, western North America.


    Rodents and shrews.


    The elevational distributions of 34 species were determined from comprehensive field surveys conducted in three arid, temperate mountain ranges. Elevation–diversity relationships and community assembly processes were inferred from phylogenetic (PD) and functional diversity (FD) patterns of mean pairwise and mean nearest‐neighbor distances while accounting for differences in species richness. FD indices were calculated separately for traits related to either abiotic filtering (β‐niche traits) or biotic interactions (α‐niche traits) to test explicit predictions of the role of each across elevation.


    Trait‐based tests of processes indicated that abiotic filtering tied to a strong aridity gradient drives the assembly of both low‐ and high‐elevation communities. Support for competition was not consistent with theoretical expectations under the stress‐dominance hypothesis, species interactions‐abiotic stress hypothesis, or guild assembly rule. Mid‐elevation peaks in species richness contrasted with overall FD and PD, which generally increased with elevation. PD and total FD were correlated on two of three mountains.

    Main conclusions

    The functional diversity of small mammal communities in these arid, temperate mountains is most consistent with abiotic filters, whereas support for competition is weak. Decomposing FD into traits related to separate assembly processes and examining ecoregional variation in diversity were critical for uncovering the generality of mechanisms. Divergent patterns among dimensions revealed species richness to be a poor surrogate for PD and FD across elevation and reflect the effect of biogeographic and evolutionary history. This first analysis of elevational multidimensional diversity gradients for temperate mammals provides a versatile framework for future comparative studies.

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    The GCFR centred in south‐western and western South Africa.

    Time period

    All data were collected between 1978–2014.

    Major taxa studied

    Vascular plants within the GCFR.


    Spectral diversity was calculated using leaf reflectance spectra (450–950 nm) and was related to other dimensions of biodiversity via linear models. The accuracy of different spectral diversity metrics was compared using 10‐fold cross‐validation.


    We found that a distance‐based spectral diversity metric was a robust predictor of species, functional and phylogenetic biodiversity. This result serves as a proof‐of‐concept that spectral diversity is a potential surrogate of biodiversity across a hyper‐diverse biogeographic region. While our results support the generality of spectral diversity as a biodiversity surrogate, we also find that relationships vary between different geographic subregions and biomes, suggesting that differences in broad‐scale community composition can affect these relationships.

    Main conclusions

    Spectral diversity was shown to be a robust surrogate of multiple dimensions of biodiversity across biomes and a widely varying biogeographic region. We also extend these surrogacy relationships to ecological redundancy to demonstrate the potential for additional insights into community structure based on spectral reflectance.

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