Trees, taxonomy & location:mapping phylogeography using Biodiverse

Dan Rosauer & Shawn Laffan

University of New South Wales&

Centre for Plant Biodiversity Research

Taxonomic Databases Working Group22 October 2008

New tools and measures for practical phylogenetic diversity analysis Tools: Biodiverse – a tool for spatial

analysis of biodiversity

Measures: Phylogenetic Endemism - an index of localised evolutionary history

Summary area cladogram resulting from the analysis of Australian Rhamnaceae, tribe Pomaderreae. From Ladiges et al. 2005

Why map phylogenies? (1)

To study the spatial component of evolution…

Dung beetle evolution in Australia’s wet tropics – from Bell et al 2007

To inform biodiversity conservation…

Why map phylogenies? (2)

Red and yellow areas represent centres of current speciation.

They are identified as important areas to protect for maintenance of evolutionary processes

Mammalian evolutionary hotspots in California

Davis et al, 2008Molecular Ecology

Because diversity is not distributed equally between taxa…

Why map phylogenies? (3)

All species are equal, but some are more equal than others…

after Rest et al (2003)Snakes & Lizards (several thousand species)

Tuatara (2 species)

Part of an ITS tree for tribe Pomaderreae (Rhamnaceae)Kellerman et al (2005)

Pomaderris elliptica

Phylogenetic diversity

A practical slant on phylogenetic mapping Theory and methods – robust but developing

Data (+ ability to access it) – exploding! Specimen and survey data Molecular data Published phylogenies

How can we make phylogenetic mapping more accessible and useful for study and management of biodiversity?

Biodiverse –a tool for spatial analysis of biodiversity indices of richness, endemism, compositional

dissimilarity, sampling redundancy clustering Monte Carlo randomisations

…and now phylogenetic measures

Biodiverse has been used to investigate:Endemism in the Australian Flora - Crisp et al (2001), Laffan & Crisp (2003)Taxonomic and genetic patterns in Pultenaea (Fabaceae) - Bickford et al (2004)Scale dependence of relationships between climate and fern species richness

- Bickford & Laffan (2006)

Mean genetic similarity in Pultenaea Bickford et al (2004)

Load species location records

~25,000 herbarium and survey records for Daviesia (Fabaceae) loaded against chosen cell size (1 degree)

View distributions of

individual taxa

View distributions of

individual taxa

View distributions of

individual taxa

Load phylogeny froma nexus or tree file

Display phylogeny

D. abnormis

D. ovata

D. euryloba

Explore phylogeography

View species list for

selected clade

View distribution of a clade

Explore phylogeography

View distribution of a clade

Explore phylogeography

View distribution of a clade

Explore phylogeography

View distribution of a clade

Explore phylogeography

View distribution of a clade

Explore phylogeography

Select a cell to highlight its taxa on the tree

Choose from a range of analyses

Select radius for neighbourhood analysis

Linking spatial data to the tree via namesName on tree Names in spatial data

- Stenanthemum leucophractum

- Cryptandra leucophracta

- Stenanthemum leucophractum (Schldl.) Reissek

- Cryptandra leucophracta Schltdl.

- Stenanthemum leucophractum (Schltdl.) Reissek

- Cryptanda leuc.

2.0

CRIMB

ALINr

CRMUII

SPGUN

SPHAL

STGFL

TRMI

SPPA

TRxRA

POFO

STKAL

SCJO

CRLAN

CRNT

POBI

TREL

TRDA

POOBC

SPNIT

STHUM

CRALP

CRDI

STLE

POAN

SPERI

SPMUC

STCLA

POPHNZ

CRHIS

YAL

STREI

CRWATII

CRARB

POEL

CRCOII

CRERI

CRPU

TRFLjr

TRAN

POFLA

TRMO

CRNU

CRWI

STPET

TRLE

SIDA

SPGL

ADCALjh

CRAM

STCEN

CRA

SPTRI

POTRO

POBRE

STPIM

SPCOR

SPTHY

CRSC

JAB

CRMIC

SP1

SPUL

TRWAII

POGRII

PHBUXr

POPRNZ

STGR

CRBUX

POOR

PORUr

POROT

CRIN

CECOr

SPSUB

2.0

CRIMB

ALINr

CRMUII

SPGUN

SPHAL

STGFL

TRMI

SPPA

TRxRA

POFO

STKAL

SCJO

CRLAN

CRNT

POBI

TREL

TRDA

POOBC

SPNIT

STHUM

CRALP

CRDI

STLE

POAN

SPERI

SPMUC

STCLA

POPHNZ

CRHIS

YAL

STREI

CRWATII

CRARB

POEL

CRCOII

CRERI

CRPU

TRFLjr

TRAN

POFLA

TRMO

CRNU

CRWI

STPET

TRLE

SIDA

SPGL

ADCALjh

CRAM

STCEN

CRA

SPTRI

POTRO

POBRE

STPIM

SPCOR

SPTHY

CRSC

JAB

CRMIC

SP1

SPUL

TRWAII

POGRII

PHBUXr

POPRNZ

STGR

CRBUX

POOR

PORUr

POROT

CRIN

CECOr

SPSUB

STLE

Taxon nameStenanthemum leucophractum

Names matched using Australian Natural Heritage Assessment Toolover 75,000 formal & informal synonymies for Australian taxa matched with valid names from relevant authorities – eg ABRS, APNI

Two ways to estimate endemismAbsolute endemism Estimate the species or PD restricted to a defined area

e.g. Sechrest et al (2002)

Weighted endemism (for species)For each area:

weighted endemism = sum of 1/range for species present

Grid allows continuous variation – the data determines the areas of interestWilliams & Humphries (1994)Crisp et al (2001)

Sechrest et al 2002

Only in hotspots

Hotspots & elsewhere

Not in hotspots

Primates in global biodiversity hotspots

Two ways to estimate endemismAbsolute endemism (for species or PD)

Estimate the species or PD restricted to a defined area e.g. Sechrest et al (2002)

Weighted endemism (for species)

For each area:weighted endemism = sum of 1/range for species present

Grid allows continuous variation – the data determines the areas of greatest endemism

Williams & Humphries (1994), Crisp, Laffan, Linder & Monro (2001), Slatyer, Rosauer and Lemckert (2007)

Phylogenetic endemisma measure of the degree to which elements of evolutionary history are restricted in space

Desirable properties of a phylogenetic endemism measure: Spatially consistent

data define areas of endemism allow comparison between equal areas

Independent of level apply consistently to any taxonomic unit

Conceptually simple flexibly applied to different problems and methods

Phylogenetic Endemism

AB

C

Calculate range for each branch,

not each species

Phylogenetic endemism (PE) =

lengthA / range S.humile

+ lengthB / range S.humile & S.reissekii

+ lengthC / range S.humile & S.reissekii & S.petraeum & S.argenteum

+ …

}{ Cc cR

LPE

c

A

B

C

A

BC

High PE

A

B

C

Low PE

A

B

CA

mou

nt

of s

har

ed P

DL

arge

r

==

==

==

==

==

==

==

==

S

mal

ler

Phylogenetic Endemism (PE) contributed by an area with a narrowly distributed taxon A.

Rosauer et al. (in prep)

Phylogenetic Endemism (PE) result for Daviesia

Phylogenetic endemism in Australian tree frogs

This project is supported by an ARC Linkage Grant. Partners:

www.biodiverse.unsw.edu.au

dan.rosauer@csiro.au

Thanks to:

Mike Crisp Lyn Cook Marcel Cardillo Steve Donnellan

Biodiverse software:

Shawn Laffan Eugene Lubarsky (user interface) Dan Rosauer (phylogenetic functions)

Dan Rosauer is currently a visiting fellow at the Australian National University

Centre for Macroevolution & Macroecology