BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005 Phyloclimatic Modelling: Reconstructing ancestral bioclimatic models on phylogenetic

BiodiversityWorld GRID WorkshopNeSC, Edinburgh – 30 June and 1 July 2005

PhyloclimaticPhyloclimaticModelling:Modelling:Reconstructing ancestralReconstructing ancestralbioclimatic models on bioclimatic models on phylogenetic treesphylogenetic trees

- Chris Yesson- Chris Yesson

Drosera orbiculataDrosera orbiculata


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


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

T

T

T

TA

Parsimony optimisation on a phylogenetic tree






Parsimony optimisation of environmental character






With sufficient climate parameters we can build a BIOCLIM model

Tmp Pcp RadAvg 25 0.2 11Min 22 0.1 9Max 27 0.7 15Stdev 2 0.32 3.06

Tmp Pcp RadAvg 22 1 9Min 20 0.5 8.1Max 24 1.2 11Stdev 2 0.36 1.48

Tmp Pcp RadAvg 30 0.3 11Min 28 0.1 9.1Max 35 0.7 15Stdev 3.6 0.31 3.01




Projecting into the past

• Temporal calibration of phylogenetic trees is a widely used technique

• This establishes a time-period for the projection of the ancestral bioclimatic model

0

10

5

MYA Time calibrated phylogeny (a chronogram)


The study group – Sundews (Droseraceae)

Locality data for Droseraceae from GBIF(and other sources)

Drosera rotundifolia

• Main area of diversity is the Mediterranean-type climate of SW Australia (c.30% of species)

Sundews:

• Carnivorous

• c. 150 spp.

• Global distribution


• 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


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?


50 m

illio

n ye

ars

Tuberous Sundews

Dating the Drosera Phylogeny


Bioclimatic Models for Tuberous Sundews in Australia


Tortonian projection of bioclimatic model for ancestral tuberous sundew

Model prediction: red-core; blue-marginal


Next Steps

• Bigger data-set

• More study groups

• More time-slices of climate data

• Automate in BiodiversityWorld


How can BDWorld help?

• This analysis draws on taxonomic verification, molecular biology, phylogenetics and bioclimatic modelling


Workflow

Alig n ed S eq u en c es

Se que nc e Alignm e ntand E dit ing

C h r o n o g r am

P hylo ge ne t icAnalys is

D is play r e s ul ts

B io c lim atic M o d elling P ath

P h y lo g e n e t icT re e s

D ate t r e eF o s s il D ata

P r o c es s

I n p u t /O u tp u t

E x ter n a lD ata

K ey

R e tr ie ve L oc a lityda ta - S e e B ioc lim a ticM ode lling W o r k f lo w

D N A Se que nc eG athe r ing

I n p u t T ax o n

Taxo n s e arc h &ve r if ic at io n

P hylo genetic A nalys is P athN a me s &

S y n o n y ms

P hylo c l im aticM o de ll ing

Bio c lima t icD a ta

Un alig n ed S eq u en c es

C h r o n o g r amBio c lima t ic

M o d e l

E M BL

S P I C E

G BI F C lim ate


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!


A BDWorld WorkflowA BDWorld Workflow



Real ToolsReal Tools

Real ToolsReal Tools

InputInput InputInputViewersViewersMiscMisc



Work in progress


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 filesOld output: myInput.nex.t

New output: myInput.nex.run1.t, myInput.nex.run2.t, etc.

• Problems running on a 64bit server


Hurdles

• Integrating new tools

• New ideas often require new software

• How can we incorporate new applications?

• What new helper tools do we need?


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?


Acknowledgements

• BBSRCBBSRC

• BiodiversityWorldBiodiversityWorld

• A. CulhamA. Culham

• P. ValdesP. Valdes

• P. Brewer, T.Sutton, N. CaithnessP. Brewer, T.Sutton, N. CaithnessD. erythrorhiza subsp. magnaD. erythrorhiza subsp. magna

Documents

BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005 Phyloclimatic Modelling: Reconstructing ancestral bioclimatic models on phylogenetic