Molecular clocks
Download
1 / 81

Molecular clocks - PowerPoint PPT Presentation


  • 173 Views
  • Uploaded on

Molecular clocks. Molecular clock?. The molecular clock hypothesis was put forward by Zuckerkandl and Pauling in 1962. They noted that rates of amino acid replacements in animal hemoglobins were proportional to time of divergence—as judged from the fossil record. Molecular clocks?.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Molecular clocks' - gari


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript

Molecular clock
Molecular clock?

  • The molecular clock hypothesis was put forward by Zuckerkandl and Pauling in 1962.

  • They noted that rates of amino acid replacements in animal hemoglobins were proportional to time of divergence—as judged from the fossil record.


Molecular clocks1
Molecular clocks?

  • Zuckerkandl and Pauling, therefore, proposed that for any given protein, the rate of molecular evolution is approximately constant over time in all lineages.


Molecular clocks

The molecular clock hypothesis

If proteins evolve at constant rates, then the number of substitutions between two sequences may be used to estimate divergence times.

This is analogous to the dating of geological times by radioactive decay.


Molecular clocks

Example:

The rate of nonsynonymous substitution for a-globin is 0.56  10–9 nonsynonymous substitutions per nonsynonymous site per year.

Rat and human a-globins differ by 0.093 nonsynonymous substitutions per nonsynonymous site.

If the universal molecular-clock hypothesis is correct, then human and rat diverged from a common ancestor 0.093/2  0.56  10 –9 = 83 million years ago.


Molecular clocks

Pro

Con

Allan C. Wilson

Morris Goodman


Molecular clocks

The “sacrament” of the straight line


Molecular clocks

Q: How to draw a straight line?

A1: Have no more than two observation points.


Molecular clocks

Q: How to draw a straight line?

A2: With more than two observation points, use a very thick line.


Molecular clocks

Q: How to draw a straight line?

A3: With more than two observation points, deny the accuracy of the measurements on one or both axes.




Molecular clocks

KAB = KOA + KOB

KAC = KOA + KOC

KBC = KOB + KOC


Molecular clocks

KOA = (KAC + KAB –KBC)/2

KOB = (KAB + KBC –KAC)/2

KOC = (KAC + KBC –KAB)/2




Molecular clocks

No such difference is seen at nonsynonymous sites, indicating that mutational differences, rather than selectional differences, are involved.




Molecular clocks

If A true tree.1 evolves at the same rate as A2, and B1 evolves at the same rate as B2, then



Molecular clocks
Relative rate tests have shown that there is true tree.no universal molecular clock.However, sufficiently accurate local clocks may exist.


Molecular clocks

slow true tree.

fast


Molecular clocks

Mutation rate per site per year versus genome size true tree.

(Gago S, Elena SF, Flores R, Sanjuán R. Extremely high mutation rate of a hammerhead viroid. 2009. Science 323:1308.)



Molecular clocks

… and was used by Linnaeus in his true tree.Systema Naturae.

Primates (humans and monkeys)

Secundates (mammals)

Tertiates (all others)


Molecular clocks

In the literature one often encounters the adjective “ true tree.primitive” attached to the name of an organism. For example, sponges are defined as “primitive.”



Molecular clocks

Advanced true tree.

Primitive


Molecular clocks

Causes of variation in substitution rates among evolutionary lineages

The factors most commonly invoked to explain the differences in the rate of substitution among lineages are:

(1) replication-dependent factors, i.e., mutation.

(2) replication-independent factors, i.e., selection.


Molecular clocks

Generation Time lineages



Molecular clocks

Metabolic rate = amounts of O lineages2 consumed per weight unit per time unit.


Molecular clocks

metabolic-rate effect lineages

mice

whales

sharks

newts



Molecular clocks

Generation times tend to correlate with metabolic rates. lineages

The big ones are the slow ones.


Molecular clocks

Organelles: Mutation Rates lineages

Animals

nucleus

mitochondria

LOW

HIGH

Plants

mitochondria

chloroplast

nucleus

LOW

HIGH


Molecular clocks

Evolution of RNA viruses: lineages

RNA VIRUSES evolve at rates that are about 106 times faster than those of DNA organisms. Therefore, significant numbers of nucleotide substitutions accumulate over short time periods, and differences in nucleotide sequences between strains isolated at relatively short time intervals are detectable. This property allows for a novel approach to estimating evolutionary rates.


Molecular clocks

Model tree for RNA viruses: lineages

l1 and l2 = numbers of substitutions on the branches leading to isolates 1 and 2, respectively.

Sequence 1, which was isolated at t1,was collected t years earlier than sequence 2, which was isolated at t2. r = rate of substitution per site per year


Molecular clocks

l lineages2 – l1 = rt2 – rt1 = rt

l2 – l1 = d23 – d13


Molecular clocks

Example: lineages

Two strains of the HIV1 virus, denoted as 1 and 2 were isolated from a two-year-old child on 3 October 1984 and 15 January 1985, respectively. The child was presumed to have been infected once perinatally by her mother by a single strain of HIV1.


Molecular clocks

03 Dec. 1984 lineages

15 Jan. 1985

Reference

t = 3.4 months (0.28 year)

d13 = 0.0655

d23 = 0.0675

a = 7.1  10–3 substitutions/site/year



Molecular clocks

Punctuated equilibrium lineages (Punk eek)

Niles Eldredge & Steven J. Gould (1972). Punctuated equilibrium: An alternative to phyletic gradualism. pp. 82-115. In: T. J. M. Schopf (ed.) Models in Paleobiology, Freeman, Cooper & Co., San Francisco.


Molecular clocks

“... it is probable that the periods, during which each [species] underwent modification, though many and long as measured by years, have been short in comparison with the periods during which each remained in an unchanged condition.”

Charles Darwin, from the final 6th edition (1872) of On the Origin of Species


Molecular clocks

Phyletic gradualism [species] underwent modification, though many and long as measured by years, have been short in comparison with the periods during which each remained in an unchanged condition.”

time

change


Molecular clocks

Punctuated equilibria associated with speciation events [species] underwent modification, though many and long as measured by years, have been short in comparison with the periods during which each remained in an unchanged condition.”

time

change

speciation

revolution

stasis


Molecular clocks

Punctuated equilibria disassociated from speciation events [species] underwent modification, though many and long as measured by years, have been short in comparison with the periods during which each remained in an unchanged condition.”

time

change


Molecular clocks

During most mammalian evolution, growth-hormones evolved quite slowly (~0.3 10–9 replacements per site per year). There are, however, two rate increases: a 40-fold increase prior to primatedivergence, and a 20-fold increase prior to ruminant divergence.

A phylogenetic tree

for the growth-hormone

gene in mammals


Molecular clocks

Possible explanations for the increased rates in ruminants and primates:

(1) an increase inmutation rate

(2) positive selection

(3) relaxation of purifying selection



Molecular clocks

IS THERE A RELATIONSHIP BETWEEN and primates:MOLECULAR RATES OF EVOLUTION & MORPHOLOGICAL RATES OF EVOLUTION?


Molecular clocks

A living fossil: and primates:

Limulus polyphemus (Atlantic horseshoe crab)

fossil (500 mya)

extant


Molecular clocks

Living fossils and primates:

Blue shark (Prionace glauca)

Alligator (Alligator mississippiensis)

Molecularly fast-evolving lineages


Molecular clocks

Living fossils and primates:

Yellow mud turtle (Kinosternon flavescens)

Molecularly slow-evolving lineages


Molecular clocks

IS THERE A RELATIONSHIP BETWEEN and primates:MOLECULAR RATES OF EVOLUTION & MORPHOLOGICAL RATES OF EVOLUTION?

NO!


Molecular clocks

Some scientists have even suggested that the lack of relationship between the two levels of description is so total as to deserve to be called:

“The Big Divorce”