215hopefully useful in improving understanding of the importance of rarefaction in
ecology and in guiding future applications of the method. There are, I believe, excit-
ing prospects for PD rarefaction in the future, including as a general method for
standardising PD by removing variation with species richness, and for predicting
unseen (i.e. un-sampled) PD. The recent availability of comprehensive phylogenies
(Bininda-Emondsetal. 2007 ; Jetz et al. 2012 ) and rich data on species occurrences
(Flemons et al. 2007 ), coupled with analytical advances such as PD rarefaction,
allows us to better understand the distribution of Phylogenetic Diversity on the sur-
face of the Earth and the processes giving rise to that distribution. This is valuable
for its own sake but will also inform efforts to conserve as much of the Tree of Life
aspossibleinthefaceoffutureextinctions(RosauerandMooers 2013 ).
Acknowledgements IwouldliketothankFrederickMatsen(FredHutchinsonCancerResearch
Center),DanielFaith(AustralianMuseum),PeterWilson(MacquarieUniversity),AnneChao
(NationalTsingHuaUniversity)andRobertColwell(UniversityofConnecticut)fortheirinput
regardingtherarefactionofPDandwhatitallmightmean.DanielMiranda-Esquivel(Universidad
IndustrialdeSantander)andPedroCardoso(UniversityofHelsinki)providedhelpfulfeedbackon
an earlier version of this chapter. This research was supported by the Australian Research Council
(DP0665761andDP1095200).
References
AllenB,KonM,Bar-YamY(2009)Anewphylogeneticdiversitymeasuregeneralizingthe
Shannonindexanditsapplicationtophyllostomidbats.AmNat174:236–243
AlroyJ(2010)Theshiftingbalanceofdiversityamongmajormarineanimalgroups.Science
329:1191–1194
AndersonMJ,CristTO,ChaseJMetal(2010)Navigatingthemultiplemeaningsofβ diversity: a
roadmapforthepracticingecologist.EcolLett14:19–28
ArrheniusO(1921)Speciesandarea.JEcol9:95–99
Bininda-EmondsORP,CardilloM,JonesKEetal(2007)Thedelayedriseofpresent-daymam-
mals.Nature446:507–512
BryantJA,LamannaC,MorlonHetal(2008)Microbesonmountainsides:contrastingelevational
patternsofbacterialandplantdiversity.ProcNatlAcadSci105:11505–11511
ChaoA,JostL(2012)Coverage-basedrarefactionandextrapolation:standardizingsamplesby
completenessratherthansize.Ecology93:2533–2547
ChaoA,ChiuCH,JostL(2010)PhylogeneticdiversitymeasuresbasedonHillnumbers.Phil
TransRSocB365:3599–3609
ChiarucciA,BacaroG,RocchiniD,FattoriniL(2008)Discoveringandrediscoveringthesample-
basedrarefactionformulaintheecologicalliterature.CommunityEcol9:121–123
ColwellRK,CoddingtonJ(1994)Estimatingterrestrialbiodiversitythroughextrapolation.Phil
TransRSocB345:101–118
CristTO,VeechJA(2006)Additivepartitioningofrarefactioncurvesandspecies-arearelation-
ships: unifying alpha, beta and gamma-diversity with sample size and habitat area. Ecol Lett
9:923–932
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The Rarefaction of Phylogenetic Diversity: Formulation, Extension and Application