Hickory Dickory Dock: Understanding the Molecular Clock Felisa Wolfe ERUPT: Biocomplexity Seminar 28 Feb 2003

Structure of Talk: I.Making (shakin’) a Tree 1.Basis 2.Assumptions 3.Methods II.Applying a Clock 1.Types 2.Examples (general) 3.Pros and Cons

N  population size 2N  gene copies Making a Tree: Basis What can change allele frequency? 1.Mutation 2.Natural Selection 3.Genetic drift 4.migration Allele: alternative form of a gene

Making a Tree: Basis (con’d) Mutations: 3 types 1- silent 2- missense (change in AA) 3- nonsense (termination codon) 4- indels- change length of codon

Natural Selection: 1- Hardy-Weinberg before selection 2- selection = survivorship (diploid) 3- Infinite population size Making a Tree: Assumptions

Neutral Mutation Theory (Kimura and Ohta, 1974) 1- AA substitution rate is ~ constant 2- functionally less important  evolves faster 3- deleterious and neutral more common 4- gene duplication precedes new function 5- deleterious and neutral mutation loss more often than positive beneficial fixation Making a Tree: Assumptions (con’d)

Making a Tree: Methods Phylogenetic Trees as NETWORKS Ancestral species vs. ancestral sequence Two methods to build trees: 1- Distance 2- Character Branch Lengths: -Distance -# changes -Time

n  OTUs  external nodes n-2  internal nodes n# rooted distinct topologies # unrooted distinct topologies ,459,4252,027,025 Making a Tree: Methods (con’d)

AlignmentsAlignments- Line up sequences (AA or DNA), High similarity strongly suggests homology  Basis for determining tree topologies & branch lengths Making a Tree: Methods (con’d) Distance: Build a matrix  requires decision Construct tree according to algorithm Ex. UPGMA, Neighbor Joining Character: Consider data and tree together Predict character states of internal nodes Ex. Max. Parsimony, Max. Likelihood

Making a Tree: Methods (con’d) Maximum Likelihood: Best tree is most likely under model of the probability of mutations. Ex. 1 A C T G 2 A C T G 3 A C A G 4 A C A C

Applying a Clock “The molecular clock hypothesis postulates that for any given macromolecule (a protein or DNA sequence) the rate of evolution is approximately constant over time in all evolutionary lineages” Li 1997 Can be used similar to dating of geologic time using radioactive elements.

Applying a Clock: Types 1.No Clock – each branch has an independent rate; n sequences then (2n-3) parameters (branch lengths) 2.Global Clock – all braches have same rate; (n-1) parameters  ( (n-1) internal nodes) 3.Local Clock - default rate for all branches; except for predefined branches 4.TipDate – depends on when isolated, i.e. pathogens (virus, etc.)

Applying a Clock: Examples

3 taxa 1 fossil taxa around at time of common ancestor? Fossils tend to come with data Ex Y Applying a Clock: Examples (con’d)

Applying a Clock: Pros and Cons Causes of rate variation among lineages 1- efficiency of DNA repair 2- Generation-time effect hypothesis 3- Metabolic-rate hypothesis

Conclusions: Natural selection and genetic drift both active; dependent on N. Neutral Mutation Theory widely accepted  be cautious! Analyses on “gene” evol.; remember not organism evolution (i.e. molecule vs. whole phenotype) Trees dependent on model. Maybe misleading- ML most robust. After the above 4 points: clock can be applied in wide variety of situations to understand the relationships AND timing between organisms.

Many thanks to: Ken Miller Mimi Katz Paul Falkowski Oscar Schofield Costantino Vetriani John Reinfelder Jody Hey Ed Stiefel Lee Kerkhof Colomban de Vargas Yi Sun Daniel Grzbeyk Rob Sherrell Yibu Chen Antonietta Quigg Tuo Shi Augie Trey Nick DeVito Nashwa Choudhry

General References: Hudson, R.R., (1990) “Gene genealogies and the coalescent process.” in Oxford Surveys on Evolutionary Biology. D. Futuyma and J. Antonovics, Eds. Oxford Univ. Press, NY. Pp Kimura, M. and T. Ohta. (1974) “On some principles governing molecular evolution.” PNAS 71: Li, W-H. Molecular Evolution 1997 Yang, Z. (1997). “PAML: A program package for phylogenetic analysis by maximum likelihood.” CABIOS. 13: Zuckerkandl, E. and L. Pauling (1965) “Molecules as documents of evolutionary history.” Journal of Theoretical Biology. 8(2): …and many, MANY others.