Biodiversity conservation using Phylogenetics on a global scale

Klaas HartmannTAFI, University of Tasmania

Extinction

• >100,000 extincts per year• 100-1000 times background rate• 39% of IUCN Red List species are endangered

Charismatic Megafauna

Biodiversity measures

• Species richness– Species definition unclear– Species distinctiveness not considered

• Phylogenetic diversity (PD)– Dan Faith and Ross Crozier

The Noah’s Ark Problem

• Species have a survival probability which can be increased at a cost

• Objective: maximise future expected PD

• Some algorithms to produce optimal solutions have been developed

• K. H. and M. Steel. (2006). Maximimizing phylogenetic diversity in biodiversity conservation: greedy solutions to the Noah's Ark problem. Systematic Biology 55(4), 644-651.

• K. H. and M. Steel. Phylogenetic diversity: From combinatorics to ecology. Book chapter for: Reconstructing evolution: New mathematical and computational approaches (eds. O. Gascuel and M. Steel) Oxford University Press

• T. Gernhard, K. H. and M. Steel. Stochastic properties of generalised Yule models, with biodiversity applications. Journal of Mathematical Biology

NAP with uncertain parameters

Issues

• Too complex• Difficult to integrate with existing approaches

Species Specific Indices

• An SSI attributes a single value to each species• Some are easy to understand

• Examples– Pendant edge– Fair proportion– Equal splits– Shapley value

SSI vs PD

• D.W. Redding, K. H., A. Mimoto, D. Bokal, M. Devos and A.O. Mooers. Evolutionarily distinct species capture more phylogenetic diversity than expected. Journal of Theoretical Biology 251, 606-615.

Bird EDGE

• 9,787 species

The Data:• Half of the species have sequence information• All have taxonomic information• Hundreds of (conflicting) expert trees

• How do we combine this information???

Bird EDGE approach

• Species are divided into patches • All expert trees for a patch are combined• Taxonomic information is used to enforce

monophyletic genera where possible

• The constrained patch trees are run with a modified version of mrBayes 3.1.2

Blue Fern

• Two rack IBM Blue Gene/L• 4096 cores• 1 Terabyte RAM• 11.2 Teraflops• 53kW power consumption• One run takes about 5 cpu years

Bird EDGE approach

• A BEAST skeleton tree is used to provide probability distributions of the root age for each patch

• EDGE Indices are produced

Acknowledgements

Financial contributors:• University of Canterbury (NZ)• Allan Wilson Centre for Molecular Ecology and Evolution (NZ)• Google Inc. (USA)• Simon Fraser University (Vancouver)

I am gratefully indebted to:• Arne Mooers• Mike Steel• Walter Jetz• David Redding• Gavin Thomas• Tanja Gernhard• Too many others to list!