Molecular clocks

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Molecular clocks
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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 divergenceas judged from the fossil record.

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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.

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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.
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Example The rate of nonsynonymous
substitution for a-globin is 0.56 ? 109
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.
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Pro
Con
Allan C. Wilson
Morris Goodman
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The sacrament of the straight line
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Q How to draw a straight line? A1 Have no more
than two observation points.
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Q How to draw a straight line? A2 With more
than two observation points, use a very thick
line.
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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.
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Relative Rate Tests
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Sarich Wilsons Test
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KAB KOA KOB KAC KOA KOC KBC KOB KOC
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KOA (KAC KAB KBC)/2 KOB (KAB KBC
KAC)/2 KOC (KAC KBC KAB)/2
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If the molecular clock hypothesis is correct,
then KAC KBC 0
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Not significantly different from 0
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No such difference is seen at nonsynonymous
sites, indicating that mutational differences,
rather than selectional differences, are involved.
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The results of the relative rate test depend on
knowledge of true tree.
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Tests involving duplicated genes
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If A1 evolves at the same rate as A2, and B1
evolves at the same rate as B2, then
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A adult E embryonic F fetal
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Relative rate tests have shown that there is no
universal molecular clock.However, sufficiently
accurate local clocks may exist.
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Mutation rate per site per year versus genome
size (Gago S, Elena SF, Flores R, Sanjuán R.
Extremely high mutation rate of a hammerhead
viroid. 2009. Science 3231308.)
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The ranking of organisms started with the
Aristotelian Scala Naturae
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and was used by Linnaeus in his Systema
Naturae.
Primates (humans and monkeys)
Secundates (mammals)
Tertiates (all others)
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In the literature one often encounters the
adjective primitive attached to the name of an
organism. For example, sponges are defined as
primitive.
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Humans, on the other hand, are always referred to
as advanced.
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Advanced
Primitive
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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.
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Generation Time
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Rates of evolution tend to correlate with
generation times.
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Metabolic rate amounts of O2 consumed per
weight unit per time unit.
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metabolic-rate effect
mice
whales
sharks
newts
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Rates of evolution tend to correlate with
metabolic rates.
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Generation times tend to correlate with metabolic
rates. The big ones are the slow ones.
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Organelles Mutation Rates
Animals
nucleus
mitochondria
HIGH
LOW
Plants
nucleus
mitochondria
chloroplast
HIGH
LOW
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Evolution of RNA viruses
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.
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Model tree for RNA viruses 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
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l2 l1 rt2 rt1 rt l2 l1 d23 d13
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Example 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.
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03 Dec. 1984
15 Jan. 1985
Reference
t 3.4 months (0.28 year) d13 0.0655 d23
0.0675 a 7.1 ? 103 substitutions/site/year
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Tempo of Evolution
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Punctuated equilibrium (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.
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... 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
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Phyletic gradualism
time
change
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Punctuated equilibria associated with speciation
events
time
change
speciation
revolution
stasis
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Punctuated equilibria disassociated from
speciation events
time
change
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A phylogenetic tree for the growth-hormone gene
in mammals
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Mindell, Sykes Graur Test
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IS THERE A RELATIONSHIP BETWEEN MOLECULAR RATES
OF EVOLUTION MORPHOLOGICAL RATES OF EVOLUTION?
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A living fossil Limulus polyphemus (Atlantic
horseshoe crab)
fossil (500 mya)
extant
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Living fossils
Blue shark (Prionace glauca)
Alligator (Alligator mississippiensis)
Molecularly fast-evolving lineages
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Living fossils
Yellow mud turtle (Kinosternon flavescens)
Molecularly slow-evolving lineages
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IS THERE A RELATIONSHIP BETWEEN MOLECULAR RATES
OF EVOLUTION MORPHOLOGICAL RATES OF
EVOLUTION? NO!
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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