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Spring 2016
Molecular Evolutionary Analysis Using BEAST
Part 2: Time-Stamped Data and Population Dynamics
Kurt Wollenberg, PhDPhylogenetics SpecialistBioinformatics and Computational Biosciences BranchOffice of Cyber Infrastructure and Computational Biology
Course Organization
• Introduction to Bayesian phylogenetics
• Introduction to BEAST
• Building a Bayesian phylogeny
• Incorporating sample time in the phylogeny
• Estimating demographic parameters
• Estimating species trees from gene trees
• Estimating ancestral trait states (esp. geography)
Lecture Organization
• How to include sample time information.• How to guess dates from encoded
information.• How to estimate changes in population
size over time.• BEAST Analysis Demo
Time-Series Data• Tips are fixed to their sample times.• Clades coalesce backwards in time from
the tips.• Tips sampled from different times can
use Δt to calibrate substitution rate.• Estimates mean time to common
ancestor (MTCA).• MCMC analysis provides 95% HPC for
MTCA estimates.
Heterochronous coalescent
Measurably Evolving Populations
Expected number of substitutions ~ 2Nμ
Expected number of substitutions ~ 2Nμ + μΔt
Encoding Sample Times
• Single field in sequence IDs• >Sequence14_Elbonia_2004• >Sequence14@2004
• Units (year, date, number of days, etc.)• >Sequence14_Elbonia_2004• >Sequence14_Elbonia_11/1958• >Sequence14_Elbonia_528
Guessing dates in Beauti.
• Specify the location of the field.
• Specify the delimiter of the field.
• Specify the format.• Adding corrections for 1900’s 2000’s
Guessing dates in Beauti.
Running BEAST
DEMO
Population Dynamics
• Genealogical patterns reflect changes in population size over time
• Genealogical patterns inferred from changes in sequence diversity over time
• Effective population size - Ne
Population Dynamics
Tree Models
• Coalescent: Constant Size
• Coalescent: Exponential Growth
• Coalescent: Logistic Growth
• Coalescent: Gaussian Markov Random Field Bayesian Skyride
Population Dynamics
Coalescent: Constant Size
Population Dynamics
Coalescent: Exponential GrowthCoalescent: Logistic Growth
http://www2.estrellamountain.edu/faculty/farabee/BIOBK/biobookpopecol.html
Population Dynamics
• Gaussian Markov Random Field – The Skyride
Piecewise demographic model
Intercoalescent intervalsI. i. + sampling events
Population Dynamics
Skyline and Skyride plots
Ho and Shapiro, 2011. Molecular Ecology Resources
Running BEAST
DEMO
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For access to past recordings, handouts, slides visit this site from the NIH network: http://collab.niaid.nih.gov/sites/research/SIG/Bioinformatics/
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Next?
Thursday, February 25 at 1:00 pm
• Estimating species trees from multiple loci• *BEAST (starBEAST)
• Estimating ancestral trait states• Phylogeography analysis