bioinfo1 5 2016 HEMOGLOBIN α-CHAIN Human Horse Cow Kangaroo Newt Carp Human 17 17 26 61 68 Horse...

BIOINFORMATICS 1or why biologists need computers

http://www.bioinformatics.uni-muenster.de/teaching/courses-2016/bioinf1/index.hbi

Prof. Dr. Wojciech Makałowski Institute of Bioinformatics

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MOLECULAR EVOLUTION

INTRODUCTION TO

2

DUALITY OF “MOLECULAR EVOLUTION”

Early stages of evolution - from primordial conditions to the first cell

Evolution of the living organisms at the molecular level

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EVOLUTION BY DESCENT WITH MODIFICATION

…I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed.

On the Origin of Species, p. 484 Charles Darwin (1809 - 1882)

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MATERIAL BASIS OF GENETIC CONTINUITY

Germ plasm theory

Germline is separated from soma

Immortal germline passes genetic information from one generation to the next

The germ cells are influenced neither by environmental influences nor by learning or morphological changes that happen during the lifetime of an organism, which information is lost after each generation. August Weismann (1834 - 1914)

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DNA AS A GENETIC MATERIAL

Alfred Hershey (1908-1997)

Nobel Prize in Physiology or Medicine in 1969

Hershey–Chase experiment (1952)

6bioinfo1_5_2016 - November 28, 2016

-Johnny Appleseed

“Type a quote here.”

Hershey–Chase experiment

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DISCOVERY OF DAN STRUCTURE

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CENTRAL DOGMA OF MOLECULAR BIOLOGY

Protein

RNA

DNA

transcription

translation

CCTGAGCCAACTATTGATG

PEPTID

CCUGAGCCAACUAUUGAUG

Francis Crick (1970) Nature, 227: 561-562.

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FIRST BOOK ON MOLECULAR EVOLUTION

Christian Anfinsen (1916 – 1995)

The Molecular Basis of Evolution (1959)

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GENETIC MATERIAL CHANGES OVER TIME

THISISCOMPLETELYNEWSEQUENCE

THISISANANCESTRALSEQUENCETime

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MUTATIONAL CHANGES OF DNA SEQUENCES

Small scale Large scale

Substitutions Chromosomal rearrangements

Insertions Gene duplications

Deletions Transposable elements

Inversions Horizontal gene transfer


SMALL SCALE MUTATIONS AND THEIR CONSEQUENCES

Substitutions (synonymous)

Thr Tyr Leu Leu ACC TAT TTG CTG ACC TAC TTG CTG

Thr Tyr Leu Leu

Thr Tyr Leu Leu ACC TAT TTG CTG ACC TCT TTG CTG

Thr Tyr Leu Leu

Substitutions (nonsynonymous)

Thr Tyr Leu Leu ACC TAT TTG CTG ACC TAA TTG CTG Thr Stop

Substitutions (nonsense)

13

SMALL SCALE MUTATIONS AND THEIR CONSEQUENCES

Deletion

Thr Tyr Leu Leu ACC TAT TTG CTG ACC TAC TGC TG Thr Tyr Cys

Thr Tyr Leu Leu ACC TAT TTG CTG ACC TAC TTT GCT G Thr Tyr Phe Ale

Insertion

Thr Tyr Leu Leu ACC TAT TTG CTG ACC TTT ATG CTG Thr Phe Met Leu

InversionFrameshift Frameshift

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LARGE SCALE MUTATIONS CHROMOSOMAL REARRANGEMENTS

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Chromosomal translocation

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Unbalanced translocation

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Inversions


LARGE SCALE MUTATIONS TRANSPOSABLE ELEMENTS

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LARGE SCALE MUTATIONS HORIZONTAL GENE TRANSFER

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EVOLUTIONARY CHANGES OF AMINO ACID SEQUENCES

Human V-LSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHF-DL SHGSAQVKGHHorse ....A..... .....S...G .......... .....G.... .......... ........A.Cow ....A...G. .........G ..A....... .......... .......... ..........Kangaroo ....A...GH ...I.....G .....A..G. ..T.H..... .......... ......IQA.Newt MK..AE..H. ..TT.DHIKG .EEAL..... F...T.L.A. R....AK... .E..SFLHS.Carp S...DK..AA ..I..A.ISP K.DDI..... G..LTVY.Q. ....A.WA.. .P..GP..-.

Human GKKVA-DALT NAVAHVDDMP NALSALSDLH AHKLRVDPVN FKLLSHCLLV TLAAHLPAEFHorse .......G.. L..G.L..L. G...D..N.. .......... .........S ...V...ND.Cow .A....A... K..E.L..L. G...E..... .......... ......S... ...S...SD.Kangaroo ...I.....G Q..E.I..L. GT..K..... .......... .......... .F....GDA.Newt ....M.G..S .....I..ID A..CK...K. .QD.M...A. .PK.A.NI.. VMGI..K.HLCarp ....IMG.VG D..SKI..LV GG.AS..E.. .S......A. ..I.ANHIV. GIMFY..GD.

Human TPAVHASLDK FLASVSTVLT SKYRHorse .......... ..S....... ....Cow .......... ...N...... ....Kangaroo ..E....... ...A...... ....Newt .YP..C.V.. ..DV.GH... ....Carp P.E..M.V.. .FQNLALA.S E...

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EVOLUTIONARY CHANGES OF AMINO ACID SEQUENCES

Human V-LSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHF-DL SHGSAQVKGH 60Horse ....A..... .....S...G .......... .....G.... .......... ........A.Cow ....A...G. .........G ..A....... .......... .......... ..........Kangaroo ....A...GH ...I.....G .....A..G. ..T.H..... .......... ......IQA.Newt MK..AE..H. ..TT.DHIKG .EEAL..... F...T.L.A. R....AK... .E..SFLHS.Carp S...DK..AA ..I..A.ISP K.DDI..... G..LTVY.Q. ....A.WA.. .P..GP..-.

Human GKKVA-DALT NAVAHVDDMP NALSALSDLH AHKLRVDPVN FKLLSHCLLV TLAAHLPAEF 120Horse .......G.. L..G.L..L. G...D..N.. .......... .........S ...V...ND.Cow .A....A... K..E.L..L. G...E..... .......... ......S... ...S...SD.Kangaroo ...I.....G Q..E.I..L. GT..K..... .......... .......... .F....GDA.Newt ....M.G..S .....I..ID A..CK...K. .QD.M...A. .PK.A.NI.. VMGI..K.HLCarp ....IMG.VG D..SKI..LV GG.AS..E.. .S......A. ..I.ANHIV. GIMFY..GD.

Human TPAVHASLDK FLASVSTVLT SKYR 144Horse .......... ..S....... ....Cow .......... ...N...... ....Kangaroo ..E....... ...A...... ....Newt .YP..C.V.. ..DV.GH... ....Carp P.E..M.V.. .FQNLALA.S E...

p = nd/nNote: indels are excluded from calculation

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AMINO ACID DIFFERENCES BETWEEN HEMOGLOBIN α-CHAIN

Human Horse Cow Kangaroo Newt Carp

Human 17 17 26 61 68

Horse 0.121 17 29 66 67

Cow 0.121 0.121 25 63 65

Kangaroo 0.186 0.207 0.179 66 71

Newt 0.436 0.471 0.450 0.471 74

Carp 0.486 0.479 0.464 0.507 0.529

Number of amino acid differences are presented above the diagonal and proportions of different amino acids (p distances) are presented below the diagonal.

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GRADUAL UNDERESTIMATION OF THE REAL DISTANCE

Num

ber o

f sub

stitu

tions

per

site

0.0

0.4

0.8

1.1

1.5

Time in million years

p distance

25 50 75


POISSON CORRECTION TO THE RESCUE

P(k;t) = e-rt(rt)k/k!

P(0;t) = e-rt(rt)0/0! = e-rt *1/1 = e-rt

Probability that no amino acid change has occurred at a given site:

If r is the rate of aa substitution per year, the mean number of aa substitutions per site after t years is then rt, and the probability of occurrence of k aa substations at a given site (k = 0, 1, 2, …) is given by the following Poisson distribution.

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POISSON CORRECTION TO THE RESCUE

q = (e-rt)2 = e-2rt

This probability can be estimated by q = 1 - p. If we use the equation above, the total number of amino acid substitution per site for the two sequences (d = 2rt) is given by

d = -ln(1-p)

Since we don’t know the ancestral sequence, we compare two homologous sequences that diverged t years ago, the probability (q) that neither of the homologous sites has changed is:

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Human 0.129 0.129 0.205 0.572 0.665

Horse 0.121 0.129 0.232 0.638 0.651

Cow 0.121 0.121 0.197 0.598 0.624

Kangaroo 0.186 0.207 0.179 0.638 0.708

Newt 0.436 0.471 0.450 0.471 0.752

Carp 0.486 0.479 0.464 0.507 0.529

Poisson-correction (PC) distances are presented above the diagonal and proportions of different amino acids (p distances) are presented below the diagonal.

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EVOLUTIONARY CHANGES OF NUCLEOTIDE SEQUENCES

More complicated than that of protein sequences

Various types of DNA regions:

protein-coding non-coding

exons

introns

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EVOLUTIONARY CHANGES OF NUCLEOTIDE SEQUENCES

Human CCAATACGCAAAATTAACCCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCRhesus ............TCC.....AA.C......A.......T.G...C.....T..TT.A...

Human ACCCCATCCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCRhesus ......C.....C.....ATG...........T........T....CA........A..T

Human CTCCAAATCACCACAGGACTATTCCTAGCCATGCACTACTCACCAGACGCCTCAACCGCCRhesus T.A.......T......C...C.......A..A...............A....CT.....

Human TTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTRhesus ..C..C........A..T.....C.....T.....G..C..T.......CT........C

Human CACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCCTARhesus ...........T.....T...C.............T..............T........T

Human TACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCT---CCTTAATGACARhesus ..................AT...A...---..AG..C.........TTA..C..GCA...

Alignment of the mitochondrial cytochrome b coding sequences

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NUCLEOTIDE DIFFERENCES BETWEEN SEQUENCES

p distance

p = nd/n

Number of different nucleotides between two sequences

Total number of nucleotides examined


GRADUAL UNDERESTIMATION OF THE REAL DISTANCE

Estim

ated

num

ber o

f sub

stitu

tions

per

site

(d)

0.0

0.4

0.8

1.1

1.5

Expected number of substitutions per site (d)

0.0 0.4 0.8 1.1 1.5

p distance

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DIFFERENT MODELS OF NUCLEOTIDE SUBSTITUTIONS

Jukes-Cantor model nucleotide substitution occurs at any nt site with equal frequency

d = -(3/4)ln[1-(4/3)p]

Kimura’s two-parameter model assumes different rate of transitions and transversions

d = -(1/2)ln(1-2P - Q) - (1/4)ln(1 - 2Q)

transitions transvertions

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DIFFERENT MODELS OF NUCLEOTIDE SUBSTITUTIONS

Expe

cted

num

ber o

f sub

stitu

tions

per

site

(d)

0.0

0.4

0.8

1.1

1.5

Expected number of substitutions per site (d)

0.0 0.4 0.8 1.1 1.5

Tamura-Nei

Tamura

Kimura-2P

p distance

Jukes-Cantor

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NT SUBSTITUTION ESTIMATES USING DIFFERENT METHODS

Codon position p distance Jukes-

Cantor Kimura Tamura-Nei

First 0.155 0.173 0.178 0.179

Second 0.085 0.091 0.092 0.093

Third 0.368 0.506 0.523 0.879

Calculation based on 373 codons of human/rhesus mitochondrial cytochrome b gene

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Human 17 17 26 61 68

Horse 0.121 17 29 66 67

Cow 0.121 0.121 25 63 65

Kangaroo 0.186 0.207 0.179 66 71

Newt 0.436 0.471 0.450 0.471 74

Carp 0.486 0.479 0.464 0.507 0.529

Number of amino acid differences are presented above the diagonal and proportions of different amino acids (p distances) are presented below the diagonal.

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MOLECULAR CLOCK

1962 - 1965 E. Zuckerkandl and L. Pauling


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GLOBAL VS. LOCAL CLOCK

Ohta, T. (1995) J. Mol. Evol. 40: 56-63.

Higher rates in rodents than in other mammals and primate slow down.

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NEUTRAL THEORY OF MOLECULAR EVOLUTION

1968 - M. Kimura

1969 - J.L. King and T. Jukes

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NEUTRAL THEORY - BASIC LAWS OF MOL. EVOLUTION

For each protein, the rate of evolution in terms of amino acid substitution is approximately constant per year per site for various lines, as long as the function and tertiary structure of the molecule remain essentially unaltered.

Cambridge University Press, 1983

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Functionally less important molecules or parts of molecule evolve faster than more important ones.

Those mutant substitutions that are less disruptive to the existing structure and function of a molecule (conservative substitutions) occur more frequently in evolution than more disruptive ones.

Practical consequence: Parts of a genome evolving under constrain are likely to have a biological function in the genome.

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FUNCTIONALLY LESS IMPORTANT MOLECULES OR PARTS OF MOLECULE EVOLVE FASTER

THAN MORE IMPORTANT ONES.


GENE DUPLICATION MUST ALWAYS PRECEDE OF THE EMERGENCE OF A GENE HAVING A NEW FUNCTION

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GENE DUPLICATION MUST ALWAYS PRECEDE OF THE EMERGENCE OF A GENE HAVING A NEW FUNCTION

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Selective elimination of definitely deleterious mutants and random fixation of selectively neutral or very

slightly deleterious mutants occur far more frequently in evolution than positive Darwinian selection of

definitely advantageous mutants.

Neutral mutations:

|s| < 1/2N

s - selection coefficient; N - effective population size

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PROBLEM WITH NEUTRAL MUTATION DEFINITION

If a deleterious mutation with s =-0.001 occurs in a population of N=106, |s| is much greater than 1/(2N) = 5 x 107. Therefore, this mutation will not be called ‘‘neutral.’’ However, the fitness of mutant homozygotes will be lower than that of wild-type homozygotes only by 0.002.

In the case of brother-sister mating N = 2, so that even a semilethal mutation with s = -0.25 will be called neutral. If this mutation is fixed in the population, the mutant homozygote has a fitness of 0.5 compared with the non-mutant homozygote.

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NEARLY NEUTRAL EVOLUTION

1973 - T. Ohta

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NEARLY NEUTRAL EVOLUTION

purifying selection drift

purifying selection drift&sel drift drift&sel

positive selection

positive selection


NT SUBSTITUTION ESTIMATES USING DIFFERENT METHODS

Codon position p distance Jukes-

Cantor Kimura Tamura-Nei

First 0.155 0.173 0.178 0.179

Second 0.085 0.091 0.092 0.093

Third 0.368 0.506 0.523 0.879


The third codon positions evolve much faster than the first and the second ones.

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SYNONYMOUS AND NONSYNONYMOUS CHANGES

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SYNONYMOUS AND NONSYNONYMOUS CHANGES

Very simple idea: just calculate ratio of nonsynonymous (dN) to synonymous (dS) substitution rates:

ω = dN/dS

ω = 0 -> neutral evolution

ω > 0 -> positive (Darwinian) selection

ω < 0 -> negative (purifying) selection

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HOW TO CALCULATE SYNONYMOUS AND NONSYNONYMOUS CHANGES?

Comparison of substitution rates in the first and the second codon position with the rate at the third codon position may be a good approximation:

ω = [(d(1)+d(2))/2]/d(3)

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Codon position

p distance Jukes-Cantor

Kimura Tamura-Nei

First 0.155 0.173 0.178 0.179

Second 0.085 0.091 0.092 0.093

Third 0.368 0.506 0.523 0.879

ω 0.326 0.260 0.266 0.232


ω much lower than one indicating that cytochrome b is subjected to purifying selection

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However, this method is not very accurate: not all third codon position substitutions are synonymous and not all first codon position substitutions are nonsynonymous. For instance:

TTT (Phe) <-> TTA (Leu) <-> CTA (Leu)

Therefore, more accurate calculations are required but exact estimation of synonymous and nonsynonymous substitutions is not a trivial task.


METHODS FOR ESTIMATING dN AND dS

Evolutionary pathway

Based on Kimura’s 2-P model

Likelihood with codon substitution

models*

Nei-Gojobori Li-Wu-Luo Goldman-Yang

Modified Nei-Gojobori Pamilo-Bianchi-Li Nielsen-Yang

Comeron

Ina

* implemented in codeml part of PAML package

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ISOCHORES

1975 - G. Bernardi

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Bernardi G PNAS 2007;104:8385-8390

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Bernardi G PNAS 2007;104:8385-8390

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Bernardi G PNAS 2007;104:8385-8390

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THE NEW MUTATION THEORY OF EVOLUTION

2007 - M. Nei


BIOINFORMATICS CREED

Remember about biology

Do not trust the data

Use comparative approach

Use statistics

Know the limits

Remember about biology!!!

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bioinfo1_5_2016 - November 28, 2016

bioinfo1 5 2016 HEMOGLOBIN α-CHAIN Human Horse Cow Kangaroo Newt Carp Human 17 17 26 61 68 Horse...

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