Introduction to Bioinformatics

Introduction to Bioinformatics Substitution Patterns

Substitution Patterns • Substitutions at the level of DNA are accumulated • Analyses of number and nature of substitutions are important to • Molecular evolution study • Recognition of functionally important genes (due to natural selection)

Substitution Patterns within Genes • Mutation and mutation rate • Functional constraint • Synonymous vs. nonsynonymous substitutions • Indels and pseudogenes • Substitutions vs. mutations

Mutation and Mutation Rate • Mutations • Deleterious • Advantageous • Neutral (no effect on fitness of organism) • Well-accepted facts • Advantageous changes are in a substantial minority • Some changes in nucleotide sequences have greater consequences for an organism than do others

Mutation and Mutation Rate • Mutation rates • r = K / (2T), where r : substitution rate K : numbers of substitutions per site T : divergence time • Number of substitutions per site • Number of substitutions two sequences have undergone since they last shared a common ancestor • Can be determined by counting the differences between the two sequences

Functional Constraint • Functional constraint • Especially important portions of genes are under functional constraint • Changes are subject to natural selection • Slow in accumulating changes • Synonymous substitutions • Less subject to correction by natural selection • Relatively quick in substitutions

Functional Constraint Example • Which gene regions have a high substitution rate?

Functional Constraint Example

Synonymous vs Nonsynonymous • Discussed in sequence alignments • Not all positions in a codon are as likely to result in nonsynonymous substitutions • Categories of a nucleotide in a codon • Nondegenerate sites • Codon positions where mutations always result in amino acid substitutions (example?) • Twofolds degenerate sites • Two synonymous but other two non (example?) • Fourfold degenerate sites • All four synonymous (example?)

Synonymous vs Nonsynonymous • Which sites have the highest substitution rate?

Indels and Pseudogene • Indels • 10 times less likely to occur than substitutions • Why? • Pseudogene • Nonfunctional and transcriptionally inactive gene • Mammalian pseudogenes tend to accumulate substitutions at a fast rate • Almost 4 per site per 100 millions • Compare to regions of gene?

Substitutions vs. Mutations • Mutations are changes in nucleotide sequences occurred due to mistakes in DNA replication or repair processes • Substitutions are mutations that have passed through the filter of selection on at least some level • Synonymous substitution rates are generally considered to be fairly reflective of the actual mutation rate (why?)

Substitutions vs. Mutations

Estimating Substitution Numbers • Is counting differences enough? • Juke-Cantor model • Kimura’s two-parameter model • Models with even more parameters

Jukes-Cantor Model • PC(t) = (1 - 3)PC(t - 1) +  (1 - PC(t - 1))

Jukes-Cantor Model • PC(t) = (1 - 3)PC(t - 1) +  (1 - PC(t - 1)) • PC(t) = 1/4 + (3/4)e-4t • K = - 3/4 ln [1 - (4/3)p]

Kimura’s Two-Parameter Model • Take transition and transversion intoconsideration

Kimura’s Two-Parameter Model • Transitions occurred at least three times as frequently as and transversions • PCC(t) = (1 -  - 2)PCC(t - 1) + PGC(t - 1) + PAC(t - 1) + PTC(t - 1) • PCC(t) = 1/4 + (1/4)e-4t + (1/2)e-2( + )t • K = 1/2 ln[1/(1 - 2P - Q)] + 1/4 ln[1/(1 - 2Q)] • P : fraction of transitions • Q : fraction of transversions • There are other models with even more parameters.

Rate Variations between Genes • Evolutionary rates between genes in a genome also vary! • Examples • Table 3.3 • Histones vs. apolipoproteins • While amino acid substitutions within many genes are generally deleterious, natural selection actually favors variability within populations for some genes • Example: human leukocyte antigen • While host populations are pressured to maintain diverse immune systems, viruses are to evolve rapidly • Example: Nucleotide substitution rate within influenza NS genes is 1.9 x 10-3 per nucleotide per site per year  million times greater than that of mammalian genes.

Molecular Clock • (Hypothesis) For a given DNA sequence, mutations accumulate at a constant rate in all evolutionary lineages (suggested by E. Zuckerkandl and L. Pauling, 1965) • The molecular clock may run at different rates in different proteins • But, the number of differences between two homologous proteins appeared to be very well correlated with the amount of time since speciation caused them to diverge independently • Stimulated intense interests in molecular evolution studies • Controversial

Relative Rate Test • Estimate overall substitution rate in different lineages without specific knowledge of divergence time • To determine relative rate for species 1 and 2, • find a less related species 3 as an outgroup • d13 = dA1 + dA3 d23 = dA2 + dA3 d12 = dA1 + dA2 dA1 = (d12 + d13 - d23) / 2 dA2 = (d12 + d23 - d13) / 2 1 dA1 dA3 3 A dA2 2

Molecular Clocks ?? • Substitution rates in rats and mice  largely the same • Molecular evolution in humans  half as rapid as Old World monkeys • Accumulated substitutions in rodents  twice the rate of primates • To date the time of existence of recent common ancestor using molecular clock … • It is necessary to demonstrate the species being examined have a uniform clock • Causes of rate variations in lineages • Differences in generation time • Average repair efficiency • Metabolic rate • Adaptation to new environment

Evolution in Organelles • Mammalian mitochondrial DNA (mtDNA) • ~ 16,000 bps • From Mom, used to track human’s origin • Chloroplast DNA (cpDNA) • 120,000 – 220,000 bps • Single circular chromosome • Protein and RNA encoding genes • Substitution rate in mtDNA is almost 10-fold higher than nuclear DNA • Comparisons of mtDNA often used to study relationships between closely related populations of organisms • Less useful for species that have diverged for more than 10 million years • cpDNA has a slower substitution rate than mtDNA

Introduction to Bioinformatics