Spatial Phylogenetics































Spatial phylogenetics: methods for exploring phylogenetic diversity, endemism, and turnover on the landscape

            Biodiversity is usually measured by examining changes in the number of species across a region to identify areas of particularly high species diversity and endemism. Beta-diversity, or turn-over on the landscape, is likewise usually measured by comparing proportions of species shared among subareas. However, investigations based on species distributions alone lack the depth of analyses that take a phylogenetic approach. Our approach combines two main elements, a phylogeny and a spatial dataset representing the terminals in the phylogeny, hence the term Spatial Phylogenetics. These two elements can be applied to any taxonomic group at any level, and also, at any geographic level (e.g. nature reserve, state, country, continent). These methods are rank-free since it does not matter what taxonomic levels the terminals represent, as long as they are monophyletic and their geographic distribution can be characterized, and are thus relatively robust to lumping and splitting decisions by taxonomists.


            Our international research group is developing and applying a novel suite of phylogenetic tools including two new metrics, Relative Phylogenetic Diversity and Relative Phylogenetic Endemism, and new methods called Categorical Analysis of Neo- And Paleo-Endemism (CANAPE), Range Weighted Branch Length Difference (RWiBaLD), and phylogenetic range-weighted turnover (PhyloRWT).


            CANAPE searches for centers of endemism, and classifies them by the branch lengths of the rare taxa within them, allowing, for the first time, a clear, quantitative distinction between centers of neo- and paleo-endemism across an area.  RWiBaLD complements CANAPE and makes a close-up examination of the statistical distribution of branch lengths within a single subarea, allowing a clear understanding of which braches on the tree are responsible for the patterns seen in CANAPE.  Both CANAPE and RWiBaLD are tested statistically with the same spatial randomization of terminal taxa on the map.


            PhyloRWT examines turnover in amount of the tree shared among subareas, while emphasizing the branches that are range-restricted.  It serves as a particularly useful measure of phylobetadiversity for purposes of understanding changes in phylogenetic assemblages across the landscape. PhyloRWT can be applied for a variety of purposes including bioregionalization, ecological studies of causes for beta-diversity, and complementarity analyses for applied conservation studies.  Understanding such patterns of biodiversity on the landscape is important for conservation planning, given the need to prioritize efforts in the face of rapid habitat loss and human-induced climate change.  These new phylogenetic methods allow assessments of protected lands that are not limited by reliance on species distribution alone and can identify complementary areas of biodiversity that have unique evolutionary histories in need of conservation.


Spatial Phylogenetic Software


Biodiverse blog

Biodiverse R pipeline


 Foundational papers:
(click title to link to paper)

B.D. Mishler, N.J. Knerr, C.E. González-Orozco, A.H. Thornhill, S.W. Laffan, and J.T. Miller. 2014. Phylogenetic measures of biodiversity and neo- and paleo-endemism in Australian Acacia.Nature Communications  5: 4473 doi:10.1038/ncomms5473.  

N.S. Nagalingum, N. Knerr, S.W. Laffan, C.E. González-Orozco, A.H. Thornhill, J.T. Miller, and B.D. Mishler. 2015. Continental scale patterns and predictors of fern richness and phylogenetic diversity. Frontiers in Genetics  6:132. doi:10.3389/fgene.2015.00132. 

A.N. Schmidt-Lebuhn, N.J. Knerr, J.T. Miller, and B.D. Mishler.  2015. Phylogenetic diversity and endemism of Australian daisies (Asteraceae)Journal of Biogeography 42: 1114–1122.  doi: 10.1111/jbi.12488

C.E. González-Orozco, B.D. Mishler, J.T. Miller, S.W. Laffan, N. Knerr, P. Unmack, Arthur Georges, A.H. Thornhill, D.F. Rosauer, and B. Gruber. 2015. Assessing biodiversity and endemism using phylogenetic methods across multiple taxonomic groups. Ecology and Evolution 5: 5177–5192

S.W. Laffan, D.F. Rosauer, G. Di Virgilio, J. T. Miller, C.E. González-Orozco, N. J. Knerr, A.H. Thornhill, and B.D. Mishler. 2016. Range-weighted metrics of species and phylogenetic turnover can better resolve biogeographic breaks and boundaries. Methods in Ecology and Evolution 7: 580-588.

A.H. Thornhill, B.D. Mishler, N. J. Knerr, C.E. Gonzalez-Orozco, C.M. Costion, D.M. Crayn, S.W. Laffan, and J.T. Miller. 2016. Continental-scale spatial phylogenetics of Australian angiosperms provides insights into ecology, evolution and conservation. Journal of Biogeography. Early View