"Phylogenetic endemism" is the amount of evolutionary history uniquely represented in a given area or region.
Calculations of phylogenetic endemism based on PD calculations go back to Faith (1992), but good example calculations can be found in Faith et al (2004).
Faith DP, Reid CAM, Hunter J. Integrating Phylogenetic Diversity, Complementarity, and Endemism. Conserv Biol. 2004;18:255–261.
Faith et al (2004) describe a measure of phylogenetic endemism, or PD-endemism, this way:
The PD measure uses phylogenetic patterns of evolutionary diversification to predict feature diversity of sets of species. The total PD of a given set is the total phylogenetic branch length spanned (represented) by its member species. The PD complementarity of a species is measured by the additional branch length it represents that is not spanned by a reference set of species (Faith 1992a). When the reference set is all other species, the PD complementarity value is the unique PD contribution of that species; it can be thought of as “endemism” at the level of features-within-species (rather than species-within-areas).
A PD-based measure of endemism of areas (Faith 1992a; 1994b) results when the reference set corresponds to the set of species found in all other areas. It is the amount of branch length (PD) or “evolutionary history” (Faith 1994a) uniquely represented by the area. For example, the PD unique to northwest Tasmania has been estimated for a phylogeny of amphipods. PD-endemism, more than conventional species-level endemism, highlighted the potential conservation importance of that area (Faith 1994b; for another example, see Moritz & Faith, 1998).
Because PD implicitly counts unit features among sets of objects, it provides straight-forward notions of complementarity (number of additional units gained) and endemism (number of units uniquely contained) in the context of objects and sets. These sets may be defined by the species themselves, or by areas as collections of species. Indeed, PD complementarity and endemism can be applied when sets are defined in other ways. For example, we can talk about the PD-endemism of an ecotype (rather than area), as for Acidobacterium lineages that are found globally but may represent bacterial evolutionary history that is unique to an acidic ecotype (Wise et al. 1997; see also Radajewski et al. 2000).
At a large geographic scale, PD-endemism may highlight different areas compared to species-endemism, because divergence corresponding to, say, complete genera may be restricted to one area (as for orchids in Australia, Faith 1994b; for related discussion on PD, see Sechrest et al. 2002; Polasky et al. 2001; Rogrigues & Gaston 2002).
PD endemism also may apply to samples or to habitats, as in applications in microbial ecology. See link at right and Biedermann L, Zeitz J, Mwinyi J, Sutter-Minder E, Rehman A, et al. (2013) Smoking Cessation Induces Profound Changes in the Composition of the Intestinal Microbiota in Humans. PLoS ONE 8(3): e59260. doi:10.1371/journal.pone.0059260
Faith, D. P. 1992a. Conservation evaluation and phylogenetic diversity. Biological Conservation 61:1-10.
Faith, D. P. 1992b. Systematics and conservation: on predicting the feature diversity of subsets of taxa. Cladistics 8:361-373.
Faith, D. P. 1994a. Phylogenetic pattern and the quantification of organismal biodiversity. Philosophical Transactions of the Royal Society of London, Series B. 345: 45-58.
Faith, D. P. 1994b. Phylogenetic diversity: a general framework for the prediction of feature diversity. Pages 251-268 in: Systematics and Conservation Evaluation. Forey, P. L., Humphries, C. J. and Vane-Wright, R. I (eds). Clarendon Press, Oxford.
Faith, D. P. 2002. Quantifying biodiversity: a phylogenetic perspective. Conservation Biology 16:248-252.
Faith, D. P. 2003. Biodiversity conservation and the tree-of-life. Science published online 28 July 2003 . http://www.sciencemag.org/content/300/5626/1707.abstract/reply#sci_el_726
Faith D. P. and P. A. Walker. 1996a. How do indicator groups provide information about the relative biodiversity of different sets of areas?: on hotspots, complementarity and pattern-based approaches. Biodiversity Letters 3:18-25.
Faith D. P. and P. A. Walker. 1996b. Environmental diversity: On the best-possible use of surrogate data for assessing the relative biodiversity of sets of areas. Biodiversity and Conservation 5:399-415.
Faith, D. P., P. A. Walker, and C. R. Margules. 2001. Some future prospects for systematic biodiversity planning in Papua New Guinea — and for biodiversity planning in general. Pacific Conservation Biology. 6:325-343.
Moritz, C. and D. P Faith. 1998. Comparative phylogeography and the identification of genetically divergent areas for conservation. Molecular Ecology 7:419-430.
Polasky, S., B. Csuti, C. Vossler, and S. M. Meyers. 2001. A comparison of taxonomic
distinctness versus richness as criteria for setting conservation priorities for North American birds. Biological Conservation 97:99-105.
Radajewski, S., P. Ineson, N. R. Parekh, and J. C. Murrell. 2000. Stable-isotope probing as a tool in microbial ecology. Nature 403:646-649.
Rodrigues, A. S. L. and K. J. Gaston. 2002. Maximising phylogenetic diversity in the selection of networks of conservation areas. Biological Conservation. 105:103-111.
Sechrest, W., T. M. Brooks, G. A. B. da Fonseca, W. R. Konstant, R. A. Mittermeier, A. Purvis, A. B. Rylands, and J. L. Gittleman. 2002. Hotspots and the conservation of evolutionary history. Proceedings of the National Academy of Science. 99:2067-2071.
Wise, M. G., J. V. McArthur, and L. J. Shimkets. 1997. Bacterial diversity of a Carolina bay as determined by 16S rRNA gene analysis: confirmation of novel taxa. Applied and Environmental Microbiology 63:1505–1514.
Dr Dan Faith , Principal Research Scientist