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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Questions?

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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