tracking the genetic legacy of past human populations through the grid
DESCRIPTION
Tracking the genetic legacy of past human populations through the grid. Nicolas Ray University of Geneva & UNEP/GRID-Europe. Swiss Grid Day, Bern, November 26 th 2009. Adapted from Cavalli-Sforza & Feldman, 2003. Human migrations. [12,000]. [55,000]. Homo sapiens sapiens. - PowerPoint PPT PresentationTRANSCRIPT
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Swiss Grid Day, Bern, November 26th 2009
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Human migrationsHuman migrations
Adapted from Cavalli-Sforza & Feldman, 2003
[12,000]
[55,000]
Homo sapiens sapiens
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1. Better understand human evolution
• Origin of modern human (when, where, how many?)
• Relationship with other members of the Homo genus
2. Distinguish between the effect of demography and those
of selection (biomedical applications)
Why aiming at a good demographic Why aiming at a good demographic modelmodel
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Gene-specific factorsmutationsrecombinationselection
A complex past demographyfluctuation in effective pop. sizesubstructuremigrations
Observed patterns of genetic diversity in contemporary populations
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A complex demographyA complex demography
Adapted from Cavalli-Sforza & Feldman, 2003
[10,000]
[55,000]
demographic and spatial expansions
population bottlenecks
fast migration events
population isolation
secondary contacts
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SPLATCHESPLATCHESPatiaL And Temporal Coalescences in Heterogeneous Environment
(http://cmpg.unibe.ch/software/splatche)
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From environment to demographyFrom environment to demography
Spatial resolution: 100 km
low
high
Carrying capacity
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low
high
Friction
From environment to demographyFrom environment to demography
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Demographic simulationsDemographic simulations
stepping-stone model (cellular automata)
Cell or deme
Pop
. si
ze
time
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Demography and spatial expansionDemography and spatial expansion
Population density
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Genetic simulationsGenetic simulations
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Simulated genealogySimulated genealogy
MutationModèle de mutation
AC
CTA
GTA
CA
ATC
GG
TA
ATG
CC
ATTG
GT
TCCTTGTA…ATTGGT
ACCGAGTA…GTTGGT
Summary statistics– Within population:
• S, – Between populations
• Pairwise FST
• Global FST
– Globally• S,
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1-10 mio.
Computer clusters
UBELIX (>500 nodes)
Zooblythii (~40 nodes)
APPROXIMATE BAYESIAN APPROXIMATE BAYESIAN COMPUTATIONS (ABC) COMPUTATIONAL COMPUTATIONS (ABC) COMPUTATIONAL ISSUESISSUES
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Computational issuesComputational issues
A fully spatially-explicit model using 500 loci in 800 individuals:
10 CPU-years
Adding long-distance dispersal:
20 CPU-years
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SPLATCHE on the gridSPLATCHE on the grid
early 2005: joined the Biomed VO of the EGEE project
mid 2005: tested on GILDA test bed, and deployed on the Grid
since mid 2006: production mode and optimization
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Use of SPLATCHE on the gridUse of SPLATCHE on the grid
N simulations
Independent simulations: - the more CPUs, the better- job failures are not that bad
GRID
Posterior distribution of demographic/genetic parameters of interest
Statistical tools
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OptimizationsOptimizations
5 mio. simulations
GRID
Reduction of the number of simulations (Daniel Wegmann)By MCMC. Promising results (~50 times less sims)
Submission timemulti-threaded application using up to 30 RBs (used for the WISDOM project)
Fetching time of job outputsin-house multi-threaded solution for checking status and getting outputs
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Geographic origin of human dispersalGeographic origin of human dispersal
Ray et al. (2005) Genome Research
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Interactions among populationsInteractions among populations
Interaction between modern humans and Neanderthals in Europe
Currat & Excoffier (2004), PLoS Biol.
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Plausible introduction site 1LAGOON CREEK (first sight: 1979)
Initial introduction site in AustraliaGORDONVALE (1935)
KDM
NW
B
T
RE
120 0 120 240 360Kilometers
19991982
19881992
1995
1996
1997
1998
Plausible introduction site 2NORMANTON (first sight: 1964)
Cane toad invasion in AustraliaCane toad invasion in Australia
Estoup, A., Baird, S. J. E., Ray, N., Currat, M., Cornuet, J.-M., Santos, F., Beaumont, M. A. and L. Excoffier. Combining genetic, historical and geographic data to reconstruct the dynamics of the bioinvasion of cane toad Bufo marinus. Submitted
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Take-home messageTake-home message
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