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
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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
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
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