mapping genetic and taxonomic species diversity at regional and continental scales
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Mapping genetic and taxonomic species diversity at regional and continental scales. Shawn Laffan. Sophie Bickford. CSIRO Centre for Plant Biodiversity Research. Species Diversity. Conservation prioritisation Evolution & dispersion These are geographic phenomena multi-scaled - PowerPoint PPT PresentationTRANSCRIPT
Mapping genetic and taxonomic species diversity at regional and
continental scales
Shawn Laffan Sophie BickfordCSIRO
Centre for Plant Biodiversity Research
Species Diversity
• Conservation prioritisation• Evolution & dispersion
• These are geographic phenomena• multi-scaled• expensive to directly sample
• Need a source of data
Museum data
• Rich source of geocoded information• 6 million plant specimens in Australian
Herbaria• Australian Virtual Herbarium – approx. 40%
digitised in 2002• every specimen description has a
geographic coordinate or reference
• No true absence data• Variable sampling effort
Data set
• Genus Pultenaea• Eastern Australian species used
• 91 species• 3 clades used• Genetic similarity data for 49
species• Aggregated to 50 km resolution
• reduce effects of variable sampling effort & roadmap effect
• Lambert’s conic conformal projection
• 5799 samples (after aggregation)
Species richness
Genetic diversity
• Use of a taxonomy assumes it is reliable• but taxonomy is constantly revised• implies equal similarity between all species
• If we know the genetic similarity of species then we can soften the effects of taxonomy• number of base pairs in common• two sections of trnL-F and ndhF chloroplast genes
base pairs: 900 trnL-F, 674 ndhF• matrix of similarities
Genetic diversity
• We know where the species occur• we can therefore map genetic variation• useful for evolutionary history
• Explicitly spatial:• mean and coefficient of variation of genetic
similarity between all species within a local neighbourhood
• Implicitly spatial• agglomerative clustering with average genetic
similarity as similarity metric
Local genetic diversity, all species
Local genetic diversity, all species
Local genetic diversity by clade
Implicitly spatial
• Agglomerative clustering of cells• Allows for disjoint distributions
• Taxonomic similarity metric between two cells:• Jaccard distance
Shared presence divided by total number of species in two cells
a / (a + b + c)a Num species occurring in both
cellsb & c Num species occurring in only
one cell
Jac = 3 / (3 + 4 + 4) = 3 / 11= 0.27
ACT Brumbies• B. greganii• B. larkhamii• B. gitaeuii• B. mortlockii• B. rathboneii• B. gerardii• B. roffii
Australian Wallabies• B. greganii• B. larkhamii• R. flatleyii• B. mortlockii• W. tuqirii• R. sailorii• W. rogersii
Agglomerative clustering – linkage heuristic• Similarity of newly aggregated classes:
• Unweighted Pair-Group Method• UPGM-A
- average similarity of merged classes- common species counted more than once- “staircase” effect
• UPGM-R- recalculate similarity matrix from first level- each species counts only once in each merger
Similarity Similarity
Recalculated Linkage
Average Linkage
(little variation within clades 2, 3a & 3b)
What next?
• Cross-validation for genetic analyses• More sophisticated measures of genetic
similarity• able to cope with more diverse groups• mean & CofV not ideal measures for non-
symmetric distributions• Software distribution / web analysis
service• http://www.biodiverse.unsw.edu.au