PHYLOGENETIC DIVERSITY Methods and applications Divya B. PK lab, CES, IISc

Quantifying species diversity Captures evolutionary history Uses molecular data – DNA sequence Workshop on Molecular Phylogenetics 2014, IISc Phylogenetic diversity - PD Faith (1992)

Phylogenetic diversity Workshop on Molecular Phylogenetics 2014, IISc Alternate measures : - morphology - behaviour - physiology A A B B A A B B Which plot is more diverse ? Species richness = 6 Quantifying evolutionary history - molecular data Unambiguous, discrete, and comparable data points These traits are reflected in their evolutionary history Ambiguous, non - discrete, non - comparable data points Williams and Humphries (1996); Faith (1992)

Phylogenetic diversity Workshop on Molecular Phylogenetics 2014, IISc Plot APlot B Plot B is more phylogenetically diverse than plot A A A B B

Phylogenetic diversity Workshop on Molecular Phylogenetics 2014, IISc Low PD Less evolutionary history More shared branches More recent lineages High PD More evolutionary history Fewer shared branches More ancient lineages

Phylogeny: – Consists of all species in pooled dataset – Ultrametric or time-calibrated tree – Maximally resolved Workshop on Molecular Phylogenetics 2014, IISc Calculating PD Data: – Plot-wise presence data – Additionally include abundance data

No. of changes Calculating PD Workshop on Molecular Phylogenetics 2014, IISc A A B B Unit time

Using R – Package “picante” – Community phylogenetics analysis Workshop on Molecular Phylogenetics 2014, IISc Calculating PD

Faith’s PD (FI) Mean phylogenetic distance (MPD) Mean nearest taxon distance (MNTD) Workshop on Molecular Phylogenetics 2014, IISc Calculating PD – direct measures

Sum of branch lengths in minimum spanning path that includes all species in that plot/area Calculated directly from phylogeny Totalling index – every additional species increases index value Workshop on Molecular Phylogenetics 2014, IISc Faith’s PD

Workshop on Molecular Phylogenetics 2014, IISc plot A : plot B : A A B B < <

Average phylogenetic distance of a species to every others species in that plot/area Calculated from tree distance matrix “basal” measure – clade representation Workshop on Molecular Phylogenetics 2014, IISc MPD

Average distance of a species to its nearest neighbour in that plot/area Calculated from tree distance matrix “terminal” measure – spread at phylogeny tips Workshop on Molecular Phylogenetics 2014, IISc MNTD

PD measures Workshop on Molecular Phylogenetics 2014, IISc

Is PD more or less than that expected by chance? Using standardized effect sizes or SES values – FI SES – Net relatedness index (NRI) – Nearest taxon index (NTI) Workshop on Molecular Phylogenetics 2014, IISc Calculating PD – relative measures

If NRI or NTI = positive = clustering/low PD If NRI or NTI = negative = overdispersion/high PD Workshop on Molecular Phylogenetics 2014, IISc Calculating PD – relative measures

Decoupling PD from species richness Conservation prioritisation Inferring biogeographic history Community assembly Workshop on Molecular Phylogenetics 2014, IISc Using phylogenetic diversity

Case study: Plants in Cape of South Africa West to east gradient of species richness 735 genera rbcL marker sequence Workshop on Molecular Phylogenetics 2014, IISc Decoupling PD from SR Forest et al.(2007)

Workshop on Molecular Phylogenetics 2014, IISc Decoupling PD from SR PD comparison between observed and empirical randomisation; (blue=lower than expected) Loess regression residuals, negative in blue, positive in red Forest et al.(2007)

Use of relative PD measures – West has high SR but lower PD: multiple recent radiations – East has low SR but higher PD: highly ecotonal, & has genera from unique ecotypes Workshop on Molecular Phylogenetics 2014, IISc Decoupling PD from SR Forest et al.(2007)

Case study: Local dry deciduous forests Low diversity area Workshop on Molecular Phylogenetics 2014, IISc Decoupling PD from SR DevNandiSav

Dev: High SR low PD – many closely related species Nandi: Low SR high PD – distantly related species Nandi included evergreen species causing increase in PD Workshop on Molecular Phylogenetics 2014, IISc Decoupling PD from SR

Case study: Plants in the Cape of South Africa Maximizing phylogenetic diversity with each additional location under protection Workshop on Molecular Phylogenetics 2014, IISc PD in conservation Black = QDS that provided highest genus complementarity Red = PD complementarity of the same Green = alternate QDS that provides highest PD complementarity Blue = independent series of maximizing PD Forest et al.(2007)

Maximizing PD required 13 QDS, while maximizing genus required 15 QDS Workshop on Molecular Phylogenetics 2014, IISc PD in conservation Black = QDS that provided highest genus complementarity Red = PD complementarity of the same Green = alternate QDS that provides highest PD complementarity Blue = independent series of maximizing PD Forest et al.(2007)

Including abundance information Case study: Bats Index used: H P Favors the maintenance of taxa in proportional abundance to its uniqueness. No taxa is favored to decrease in abundance below a threshold. Workshop on Molecular Phylogenetics 2014, IISc PD in conservation Allen et al.(2009)

Q and H d maximized with 11 genera H P maximized by inclusion of all 23 genera Workshop on Molecular Phylogenetics 2014, IISc PD in conservation Allen et al.(2009)

Case study: Global mammal distribution PD and SR can vary biogeographically Rapid speciation + low immigration = low PD Slow speciation + frequent immigration = high PD Workshop on Molecular Phylogenetics 2014, IISc PD in biogeography Davies & Buckley (2011)

Workshop on Molecular Phylogenetics 2014, IISc PD in biogeography Species richness Phylogenetic diversity Davies & Buckley (2011)

Workshop on Molecular Phylogenetics 2014, IISc PD in biogeography LOESS residuals of PD Davies & Buckley (2011)

Africa & southeast Asia – greater PD South America & western North America – less PD African origins of many clades Workshop on Molecular Phylogenetics 2014, IISc PD in biogeography LOESS regression of PD Davies & Buckley (2011)

Case study: Oak trees Co-existence of 17 species Assembly process: – Environmental filtering – Competitive exclusion Workshop on Molecular Phylogenetics 2014, IISc PD in community assembly Cavender-Bares et al.(2004)

Phylogenetic patterns: – Clustering – Overdispersion Workshop on Molecular Phylogenetics 2014, IISc PD in community assembly Cavender-Bares et al.(2004)

Distantly related species co-occur: Phylogenetic overdispersion Niche overlap within clade was low Traits of habitat specialization show convergence Workshop on Molecular Phylogenetics 2014, IISc PD in community assembly Cavender-Bares et al.(2004)

PD can be used as an alternate, more useful measure of biodiversity Historical perspective Conservation science, biogeography and community ecology Workshop on Molecular Phylogenetics 2014, IISc Phylogenetic diversity

Workshop on Molecular Phylogenetics 2014, IISc