Phylogenetic diversity

What is phylogenetic diversity (PD)?

Phylogenetic diversity (“PD”) is a measure of biodiversity, based on phylogeny (the tree of life).  Faith (1992) defined the phylogenetic diversity of a set of species as equal to the sum of the lengths of all those branches on the tree that span the  members of the set. The branch lengths on the tree are informative because they count the relative number of new features arising along that part of the tree. This means that PD indicates “feature diversity” and “option value” (see Faith 1992 for discussion and its Fig 1 to see how PD counts features).

Faith and Richards (2012) explored the loss of PD for corals, and presented a simple PD example:
FAITH RICHARDS 2012 PD biology-01-00906-g001

A hypothetical phylogenetic tree for species a through e. Branch lengths are shown above branches. The PD is 41 for this set of species (20 + 5 + 4 + 2 + 1 + 5 + 1 + 3). If species a was lost, 5 units of PD would be lost. Successive losses of species would imply PD losses of similar magnitude. However, the loss of the last species of the clade would imply that the deeper branch of 20 units is now lost as well.

This is a nice simple example because it not only highlights how PD can indicate some total amount of biodiversity (e.g. for a set of species) but also how the PD “calculus” can indicate gains and losses. Faith and Richards document cases within the coral phylogeny where the pattern of threats to species may produce a “tipping point”, where a series of small PD losses leads to a loss of a long deeper branch – and so a large loss of biodiversity.

Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 61:1–10.

Faith, D.P.; Richards, Z.T. (2012) Climate Change Impacts on the Tree of Life: Changes in Phylogenetic Diversity Illustrated for Acropora Corals. Biology, 1, 906-932. doi:10.3390/biology1030906

Faith (2018) Phylogenetic diversity and conservation evaluation: perspectives on multiple values, indices, and scales of application. In: (Scherson, R. and Faith, D.P. eds.) Phylogenetic Diversity. Applications and Challenges in Biodiversity Science (Springer, Cham, Switzerland) pp. 1-26.

Faith D. P. et al. (2018) Indicators for the Expected Loss of Phylogenetic Diversity. in Phylogenetic Diversity: Applications and Challenges in Biodiversity Science, R. A. Scherson, D. P. Faith, Eds. (Springer International Publishing, 2018), pp. 73–91;

author copy: Indicators for the Expected Loss of Phylogenetic Diversity

hot topics

News – The IPBES phylogenetic diversity indicator for “maintenance of options” (Faith et al 2018; IPBES 2018; see also Phylogenetic Diversity and IPBES ) now has been proposed by the CBD as an indicator to help monitor progress in the implementation of its post-2020 global biodiversity framework. See CBD/SBSTTA/24/3Add.1.  Goal B of the Post-2020 global biodiversity framework importantly states that “Nature’s contributions to people have been valued, maintained or enhanced…”.  The IPBES phylogenetic diversity indicator serves one of the most critical of all the nature’s contributions to people, “maintenance of options”. This contribution is not just from “nature” but specifically reflects the contribution of biodiversity-as-variety in maintaining possible benefits for future generations (“biodiversity option value”).

This indicator for the “biodiversity option value” aspect of NCP18, maintenance of options is described in Faith et al 2018 and in a submitted paper, “The Post-2020 Global Biodiversity Framework must safeguard the Tree of Life“.

see also –

Faith, Daniel P. (2021) Phylogenetic diversity (PD) provides biodiversity option value: how biodiversity has value now because it offers possible benefits in the future.  In:  30th International Congress for Conservation Biology (ICCB), Kigali, Rwanda. Abstracts.

see Phylogenetic diversity at ICCB2021.

The Convention on Biological Diversity (CBD) post-2020 biodiversity framework – The IPBES phylogenetic diversity indicator for “maintenance of options” – explained

Review comments on the draft monitoring framework for the post-2020 global biodiversity framework

COVID-19: Useful phylogenetic diversity (PD) calculations for the novel coronavirus, SARS CoV 2

related topics –

Phylogenetic diversity and IPBES

Phylogenetic diversity and biodiversity option value

Phylogenetic diversity and human health

Phylogenetic diversity and functional trait diversity

Phylogenetic diversity and extinction

See also the Wikipedia entry “phylogenetic diversity”   

Read more about testing the PD link to feature diversity.

(and read about how NOT to test the PD link to feature diversity)

More news 


The IUCN Phylogenetic Diversity Task Force

Recent paper   Faith D.P. (2019) EDGE of Existence and phylogenetic diversity. Animal Conservation 22 (2019) 537–538.  DOI:10.1111/acv.12552

Recent book

book cover2

Phylogenetic Diversity

Applications and Challenges in Biodiversity Science

Editors:    Rosa Scherson and Daniel P Faith

see also this book on phylogenetic diversity –

Biodiversity Conservation and Phylogenetic Systematics : Preserving our evolutionary heritage in an extinction crisis    Publisher: Springer   Editor: Roseli Pellens & Philippe Grandcolas  ISBN: ISBN 978-3-319-22460-2

PD symposium in Malaysia, 2019

The International Congress for Conservation Biology – PD Symposium

Scientific papers on Faith’s PD

Biological Conservation is ranked by Google Scholar as the top journal in the field of “biodiversity and conservation biology” (Costello et al. 2018). Costello et al.’s Table 2 lists Biological Conservation‘s top 20 most-cited papers (among the more than 7000 papers produced over 50 years). The Faith (1992) “PD” paper (“Conservation evaluation and phylogenetic diversity”) has the journal’s largest total number of citations (a status confirmed with a quick check of Web of Science: out of about 10,000 papers listed from the journal, Faith (1992) is most cited, approaching 3000 listed citations as we approach 30 years since publication). The Faith (1992) paper had a steady citation rate of 30-50 per year from 1992 to roughly 2010 (as indicated in Web of Science). The figure below plots the number of citations for each year, from 2010 to 2018, revealing the  increase in the citation rate over the past decade.

PD citations

Citations of the Faith (1992) paper reflect sustained interest in conserving phylogenetic diversity. The recent citation burst for the paper suggests that some of the paper’s key ideas have gained momentum.  For example, the setting of conservation priorities in phylogenetic-tree-space to conserve PD now is successfully implemented in a major global conservation program, EDGE of Existence (Isaac et al., 2007). This has catalysed much related work over the past 10 years. Also, Faith (1992)’s core proposal, that PD is a measure of biodiversity, reflecting feature diversity and biodiversity option value, is now better recognised by philosophers and others (e.g. Maclaurin and Sterelny, 2008); this has become an actively debated issue (for review, see Faith, 2018). The increased take-up and debate of these ideas is not only evidenced in recent journal papers but also in the recent books focused on conservation of phylogenetic diversity (Pellens and Grandcolas, 2016; Scherson and Faith, 2018).

The citation burst over the past decade for Faith (1992) seems to also reflect new emerging issues that were not anticipated in the original paper. Sometimes, an unanticipated new context and application of PD might be exciting, but not produce any burst in citations. For example, PD is now applied to conservation of language diversity (e.g., Gavin et al., 2013), but follow-up work still is in early stages. In contrast, the now-popular use of PD in ecology (particularly community ecology) was not anticipated in Faith (1992), but it appears to contribute strongly to the paper’s increasing citations. This has been the result of largely independent take-up in microbial and “macrobial” community ecology (Faith 2018).

 The microbial ecology PD applications provide a significant contribution to Faith (1992)’s citation burst. Because it has been less species-focused, microbial ecology has embraced phylogeny, and has applied PD and its calculus, including PD dissimilarities. Applications of PD in microbial ecology owe much to the pioneering work of Lozupone and Knight (2005) and Caporaso et al. (2010). In addition to many case studies, they have provided microbial workers with the useful analysis tools leading to wide use of PD in the discipline. As one indicator of the contribution this has made to PD citations, Web of Science (searched in October 2018) revealed 203 papers citing Faith 1992 that are categorised as “microbiology”. All but 3 of these papers were published after 2008, and more than 100 of these papers were published recently (2015-2018). These increased PD pplications are well-illustrated by the rapidly-expanding microbial PD applications to human health. Loss of microbial PD (typically referred to in these studies as “Faith’s PD”) is implicated in a growing number of human diseases. This loss of biodiversity, as measured by PD, may indicatre a loss of resilience, and so conservation of microbial PD increasingly is promoted (see Faith, 2018 for review).

Related “macrobial” work using PD typically has been linked to community ecology. Here, foundational work (see Webb et al. 2002) and increased availability of phylogenies have inspired many investigations of the phylogenetic structure of communities, including new applications of PD. As one rough indicator of this contribution to the PD citation burst, Web of Science reveals that (out of its October, 2018 total of 1605 papers citing Faith, 1992) there are 479 citing papers that have “phylogenetic diversity” plus “community ecology” (or communit*) as key terms. Most of these (439 papers) were published after 2009, with 323 of these papers published post-2012. This exploration of Faith (1992)’s PD in community ecology has helped to broaden the scale of PD applications and also broaden the appreciation of the value of PD to society – complementing the option values typically relevant at the regional/global scale to include more localised values related to insurance and resilience (for related discussion, see Faith, 2018).

The rich opportunities raised by this broadening of the PD research scope are yet to be fully appreciated. One reason is a failure to fully integrate the recent community ecology PD work into the context of the previous PD work. A false history sometimes has been promoted that implies that Faith’s PD was about community ecology from the outset. For example, Mouquet et al. (2012) wrongly attributed this definition to Faith (1992): “Phylogenetic diversity: the amount of evolutionary history represented in the species of a particular community (Faith, 1992)”. Winter et al. (2013) provided a similar miss-definition. In reality, Faith (1992) did not link PD to communities. A consequence of this confusion is that some recent discussions of conservation of phylogenetic diversity have neglected the original context and rationale for PD – including its feature diversity model, corresponding option values, and global-scale applications (see Faith, 2018 for discussion). This highlights the gains that can be made by putting recent work on PD into historical context.

Faith (1992) promoted PD-based biodiversity conservation assessment primarily within phylogenies, and among areas at regional-global scales. Now, more localised PD assessments, whether in a forest patch or in the human gut, are broadening the arena for PD-based biodiversity conservation. Hopefully, future papers that cite Faith (1992) will reflect work that is inclusive and integrates across this breadth of applications.

Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K. et al IIME allows analysis of high-throughput community sequencing data. Nat thods 7, 335–336.

Costello, M. J., Beard, K. H., Primack, R, B., Devictor, V., Bates, A. E. 2018. Are killer bees good for coffee? The contribution of a paper’s title and other factors to its future Citations. Biol. Conserv. In press.

Faith, D. P. 1992. Conservation evaluation and phylogenetic diversity. Biol. Conserv. 61, 1–10.

Faith, D.P. 2018. Phylogenetic diversity and conservation evaluation: perspectives on multiple values, indices, and scales of application. In: (Scherson, R. and Faith, D.P. eds.) Phylogenetic Diversity. Applications and Challenges in Biodiversity Science (Springer, Cham, Switzerland) pp. 1-26.

Gavin, M.C. et al. 2013. Toward a mechanistic understanding of linguistic diversity. BioScience 63, 524–535.

Isaac, N.J.B., Turvey, S.T., Collen, B., Waterman, C., Baillie, J. 2007. Mammals on the EDGE: Conservation priorities based on threat and phylogeny. PLoS One 2, e296

Lozupone, C., Knight, R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71, 8228–82.

Maclaurin, J., Sterelny, K. 2008. What is biodiversity? University of Chicago Press, Chicago.

Mouquet et al. 2012. Ecophylogenetics: advances and perspectives. Biological Reviews, 87, 769–785.

Pellens, R., Grandcolas, P. (eds) 2016. Biodiversity conservation and phylogenetic systematics preserving our evolutionary heritage in an extinction crisis. Topics in biodiversity and conservation, vol 14. Springer International Publishing, Cham.

Scherson, R., Faith, D.P. (Eds.) 2018. Phylogenetic Diversity Applications and Challenges in Biodiversity Science. Springer, New York, ISBN 978-3-319-93145-6

Webb, C.O., Ackerly, D.D., McPeek, M.A., Donoghue, M.J. 2002. Phylogenies and community ecology. Annu Rev Ecol Syst 33, 475–505.

Winter, M., Devictor, V. and Schweiger, O. 2013. Phylogenetic diversity and nature conservation: where are we? Trends in Ecology & Evolution. 28, 199-204.

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