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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?.

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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.


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.


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.


Pro

Con

Allan C. Wilson

Morris Goodman


The “sacrament” of the straight line


Q: How to draw a straight line?

A1: Have no more than two observation points.


Q: How to draw a straight line?

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


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.




KAB = KOA + KOB

KAC = KOA + KOC

KBC = KOB + KOC


KOA = (KAC + KAB –KBC)/2

KOB = (KAB + KBC –KAC)/2

KOC = (KAC + KBC –KAB)/2




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




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



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


slow true tree.

fast


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.)



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

Primates (humans and monkeys)

Secundates (mammals)

Tertiates (all others)


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.”



Advanced true tree.

Primitive


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.


Generation Time lineages



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


metabolic-rate effect lineages

mice

whales

sharks

newts



Generation times tend to correlate with metabolic rates. lineages

The big ones are the slow ones.


Organelles: Mutation Rates lineages

Animals

nucleus

mitochondria

LOW

HIGH

Plants

mitochondria

chloroplast

nucleus

LOW

HIGH


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.


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


l lineages2 – l1 = rt2 – rt1 = rt

l2 – l1 = d23 – d13


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.


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



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.


“... 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


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


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


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


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


Possible explanations for the increased rates in ruminants and primates:

(1) an increase inmutation rate

(2) positive selection

(3) relaxation of purifying selection



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


A living fossil: and primates:

Limulus polyphemus (Atlantic horseshoe crab)

fossil (500 mya)

extant


Living fossils and primates:

Blue shark (Prionace glauca)

Alligator (Alligator mississippiensis)

Molecularly fast-evolving lineages


Living fossils and primates:

Yellow mud turtle (Kinosternon flavescens)

Molecularly slow-evolving lineages


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

NO!


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”


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