Download reconstructing ancestral bioclimatic models on phylogenetic trees

Phyloclimatic
Modelling:
Reconstructing ancestral
bioclimatic models on
phylogenetic trees
- Chris Yesson
Drosera orbiculata
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Introduction
• Bioclimatic models have been used to examine
distributions in the present, and to predict the near
future
• A few studies have looked at the recent past
• Studies on evolutionary time-scales have been
overlooked
• … such studies could provide insight into
evolutionary responses to climate change
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Phyloclimatic modelling – the idea
• There are long established
phylogenetic techniques of ancestral
state reconstruction
• These have been applied to
DNA sequences,
morphological features
& environmental preferences
• These optimised preferences can be
combined into an ancestral
bioclimatic model
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
A
T
T
T
Parsimony optimisation
on a phylogenetic tree
T
Phyloclimatic modelling – the idea
• There are long established
phylogenetic techniques of ancestral
state reconstruction
• These have been applied to
DNA sequences,
morphological features
& environmental preferences
• These optimised preferences can be
combined into an ancestral
bioclimatic model
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Parsimony optimisation of
environmental character
Phyloclimatic modelling – the idea
• There are long established
phylogenetic techniques of ancestral
state reconstruction
• These have been applied to
DNA sequences,
morphological features
& environmental preferences
• These optimised preferences can be
combined into an ancestral
bioclimatic model
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Avg
Min
Max
Stdev
Tmp Pcp Rad
25 0.2 11
22 0.1
9
27 0.7 15
2 0.32 3.06
Avg
Min
Max
Stdev
Tmp Pcp Rad
22
1
9
20 0.5 8.1
24 1.2 11
2 0.36 1.48
Tmp Pcp Rad
Avg
30 0.3 11
Min
28 0.1 9.1
Max
35 0.7 15
Stdev 3.6 0.31 3.01
Tmp Pcp Rad
Avg
30 0.3 11
Min
28 0.1 9.1
Max
35 0.7 15
Stdev 3.6 0.31 3.01
Tmp Pcp Rad
Avg
30 0.3 11
Min
28 0.1 9.1
Max
35 0.7 15
Stdev 3.6 0.31 3.01
With sufficient climate
parameters we can build
a BIOCLIM model
Projecting into the past
• Temporal calibration of
phylogenetic trees is a
widely used technique
0
5
• This establishes a timeperiod for the projection
of the ancestral
bioclimatic model
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
10
MYA
Time calibrated phylogeny
(a chronogram)
The study group –
Sundews (Droseraceae)
Sundews:
• Carnivorous
• c. 150 spp.
• Global
distribution
Locality data for Droseraceae from GBIF
(and other sources)
• Main area of diversity is the
Mediterranean-type climate of SW
Australia (c.30% of species)
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Drosera rotundifolia
• Rivadavias’ phylogeny (c.60spp. rbcL)
• Monophyletic (SW) Australian groups from
Mediterranean-type climate
• Similar pattern with African group
Rivadavia, et. al. (2003): American Journal of Botany. 90, 123-130
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Drosera in
Mediterranean-type Climate
• Hot-dry summer, wet winter
• Include SW Australia & South African Cape
• Med. Climates arose 15-10MYA
• Are Drosera radiations linked with this climate
change?
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Dating the Drosera Phylogeny
50 million years
Tuberous Sundews
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Bioclimatic Models for Tuberous
Sundews in Australia
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Tortonian projection of bioclimatic model for
ancestral tuberous sundew
Model prediction: red-core; blue-marginal
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Next Steps
• Bigger data-set
• More study groups
• More time-slices of climate data
• Automate in BiodiversityWorld
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
How can BDWorld help?
• This analysis draws on taxonomic verification,
molecular biology, phylogenetics and
bioclimatic modelling
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Key
Input Taxon
Process
Input /
Output
SPICE
Taxon search &
verification
Phylogenetic Analysis Path
External
Data
EMBL
DNA Sequence
Gathering
Names &
Synonyms
GBIF
Unaligned Sequences
Sequence Alignment
and Editing
Aligned Sequences
Phylogenetic
Analysis
Phylogenetic
Trees
Fossil Data
Date tree
Chronogram
Bioclimatic
Data
Phyloclimatic
Modelling
Bioclimatic
Model
Chronogram
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Display results
Workflow
Bioclimatic Modelling Path
Retrieve Locality
data - See Bioclimatic
Modelling Workflow
Climate
How can BDWorld help?
• This analysis draws on taxonomic verification,
molecular biology, phylogenetics and
bioclimatic modelling
• Having all these tools in an integrated system
would make my life much easier!
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
A BDWorld Workflow
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
A BDWorld Workflow
Real Tools
Input
Real Tools
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Misc
Viewers
Input
A BDWorld Workflow
Work in progress
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Putting resources into BDWorld –
An example
MrBayes – an open-source project with a CLI to do
Bayesian phylogenetic analysis
• … use the same process for other CLI tools
• … but MrBayes v3.0 cannot except path names with the
input file
MrBayes –b –f /bdworld/temp/myInput.nex
MrBayes –b –f myInput.nex
• New version 3.1 does!
• New version creates different output files
Old output: myInput.nex.t
New output: myInput.nex.run1.t, myInput.nex.run2.t, etc.
• Problems running on a 64bit server
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Hurdles
• Integrating new tools
• New ideas often require new software
• How can we incorporate new applications?
• What new helper tools do we need?
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Hurdles
• Shifting sands
• Relying on external web-sites can be problematic
• GUIs
• Phylogenetics software is often dependent on
GUIs
• BDWorld is more suited to Command Line
applications
• Long running processes
• How do we deal with a process that takes several
days?
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005
Acknowledgements
• BBSRC
• BiodiversityWorld
• A. Culham
• P. Valdes
• P. Brewer, T.Sutton, N. Caithness
D. erythrorhiza subsp. magna
BiodiversityWorld GRID Workshop
NeSC, Edinburgh – 30 June and 1 July 2005