annotated bibliography

annotated bibliography 

Annotated bibliography rubric

Instructions / Guidelines

An annotated bibliography is a reference list where each citation is followed by a descriptive and evaluative paragraph (the annotation). The purpose is to inform yourself (or others) of the relevance, accuracy and quality of the sources cited, and is often used as a tool to write effective scientific grants and papers. The annotation differs from an abstract in the that the latter is purely a descriptive summary. Annotations include the descriptive summary as well as a critical assessment of relevance, accuracy and quality. The purpose is a) to get better at making annotated bibliographies and b) to provide a preliminary literature survey for your final written projects. Your annotated bibliography should include the following sections:

1) topic, viewpoint and purpose (what do you aim to do with your written assignment)

2) research strategy (what tools you will use to find, access and evaluate appropriate literature)

3) Citations and annotations.

4) Conclusions

Also, please use the APA reference style for your citations

https://apastyle.apa.org/style-grammar-guidelines/references/examples

Rubric

________/12

Comments

Evolutionary Rate at the Molecular Level

b y
M O T 0 0 KIMURA
National Institute of Genetics,

Japan

Calculating the rate of evolution in terms of nucleotide substitutions
seems t o give a value so high that many of the mutations involved
must be neutral ones.

COMPARATIVE studies of haemoglobin molecules among change in for a chain consisting of some amino-
different groups of animals suggest that, during the acids. For example, by comparing the and chains of
evolutionary history of mammals, amino-acid substitution man with those of horse, pig, cattle and rabbit, the
has taken place roughly at the rate of one amino-acid figure of one amino-acid change in x was obtained’.

http://hrst.mit.edu/hrs/evolution/public/profiles/kimura.html

http://hrst.mit.edu/hrs/evolution/public/papers/zuckerkandlpauling1965/zuckerkandlpauling1965

This is roughly equivalent to the rate of one amino-acid
substitution in for a chain consisting of
amino-acids.

A comparable value has been derived from the study
of the haemoglobin of primates. The rate of amino-acid
substitution calculated by comparing mammalian and
avian cytochrome c (consisting of about 100 amino-acids)
turned out to be one replacement in 48 x 106 yr (ref. 3).
Also by comparing the amino-acid composition of human
triosephosphate dehydrogenase with that of rabbit and

figure of a t least one amino-acid substitution
for every X yr can be obtained for the chain con-
sisting of about amino-acids. This figure is roughly
equivalent to the rate of one amino-acid substitution in

x yr for a chain consisting of amino-acids.
Averaging those figures for haemoglobin, cytochrome c
and triosephosphate’ dehydrogenase gives an evolutionary
rate of approximately one substitution in 28 x 108 yr for
a polypeptide chain consisting of 100 amino-acids.

I intend to show that this evolutionary rate, although
appearing to be very low for each polypeptide chain of a
size of cytochrome c, actually amounts t o a very high
rate for the entire genome.

First, the DNA content in each nucleus is roughly the
same among different species of mammals such as man,
cattle and rat (see, for example, ref. 5 ) . Furthermore, we
note that the G-C content of DNA is fairly uniform among
mammals, lying roughly within the range of 40-44 per

These two facts suggest that nucleotide substitution
played a principal part in mammalian evolution.

I n t h e following calculation, I shall assume that the
haploid chromosome complement comprises about 4 x loo
nucleotide pairs, which is the number estimated by
Muller from the DNA content of human sperm. Each
amino-acid is coded by a nucleotide triplet (codon), and
so a polypeptide chain of 100 amino-acids corresponds to
300 nucleotide pairs in a genome. Also, amino-acid
replacement is the result of nucleotide replacement within
a codon. Because roughly 20 per cent of nucleotide
replacement caused by mutation is estimated to be
synonymous, Chat is, it codes for the same amino-acid,
one amino-acid replacement may correspond to about
1.2 bme pair replacements in the genome. The average
time taken for one bme pair replacement within a genome
is therefore

4 x 10
28 x IO6 yr + (-2) + yr

This means that in t h e evolutionary history of mammals,
nucleotide substitution has been so fast that, on average,
one nucleotide pair has been substituted in the population
roughly every

This figure is in sharp contrast to Haldane’s well known
estimate that, in horotelic evolution (standard rate
evolution), a, new allele may be substituted in a population
roughly every 300 generations. He arrived at this figure
by assuming that the cost of natural selection per genera-
tion (the substitutional load in my terminology is
roughly 0.1, while the total cost for one allelic substitu-
tion is about 30. Actually, the calculation of the cost
based on Haldane’s formula shows that if new alleles
produced by nuoleotide replacement are substituted in R
population at the rate of one substitution every 2 yr,
then the substitutional load becomes so large that no
mammalian species could tolerate it.

Thus the very high rate of nucleotide substitution
which I have calculated can only be reconciled with the
limit set by the substitutional load by assuming that
most mutations produced by nucleotide replacement are
almost neutral in natural selection. It can be shown that
in a population of effective size if the selective advan-
tage of the new allele over the preexisting alleles is
then, assuming no dominance, the total load for one gene

substitution is

=

IS J

where and p is the frequency of the new allele
at the start. The derivation of the foregoing formula will
be published elsewhere. In the expression given here

is the probability of fixation given

= ( 1 e –

Now, in the special case of formulae
and ( 2 ) reduce to

Formula (1’) shows that for a nearly neutral mutation the
substitutional load can be very low and there will be no
limit to the rate of gene substitution in evolution.
Furthermore, for such mutant gene, the probability of
fixation (that is, the probability by which it will be
established in the population) is roughly equal to its
initial frequency as shown by equation (2’). This means
that new alleles may be produced at the same rate per
individual as they are substituted in the population in
evolution.

This brings the rather surprising conclusion that in
mammals neutral (or nearly neutral) mutations are
occurring at the rate of roughly per yr per gamete.
Thus, if we take the average length of one generation in
the history of mammalian evolution the mutation
rate per generation for neutral mutations amounts t o
roughly two per gamete and four per zygote x 10-10 per
nucleotide site per generation).

Such a high rate of neutral mutations is perhaps not
surprising, for M u k a i has demonstrated that in Droso-
phila the total mutation rate for “viability polygenes”
which on the average depress the fitness by about 2 per
cent reaches at least some 35 per cent per gamete. This
is a much higher rate than previously considered. The
fact that neutral or nearly neutral mutations are occurring
a t a rather high rate is compatible with the high frequency
of heterozygous loci that has been observed recently by
studying protein polymorphism in human and Drosophila
populations18-16.

Lewontin and H u b b y estimated that in natural
populations of Drosophila psseudoobscura a n average of
about 12 per cent of loci in each individual is heterozygous.
The corresponding heterozygosity with respect t o nucleo-
tide sequence should be much higher. The chemical
structure of enzymes used in this study does not seem to
be known at present, but in the typical case of esterase-5
the molecular weight was estimated to be about by
Narise and H u b b y . I n higher organisms, enzymes with
molecular weight of this magnitude seem to be common
and usually they are “multimers”17. So, if we assume
that each of those enzymes comprises on the average
some 1,000 amino-acids (corresponding t o molecular
weight of some 120,000), the mutation rate for the
corresponding genetic site (consisting of about 3,000
nucleotide pairs) is

U. = 3 X 103 X B X 1.0-10 = 1.5 X 10-6

per generation. The entire genome could produce more
than a million of such enzymes.

http://hrst.mit.edu/hrs/evolution/public/papers/lewontinhubby1966/lewontinhubby1966

I n applying this value of zd t o Drosophila i t must bc
noted that the mutation rate per nucleotide pair pe:
generation can differ in man and Drosophila. There i;
some evidence that with respect to the definitely dele
terious effects of gene mutation, the rate of mutation pe.
nucleotide pair per generation is roughly ten times a;
high in Drosophila as in manl8.10, This means that tha
corresponding mutation rate for Drosophila should bl
U = 1.6 X 1O-6 rather than zc= 1-6 x 10-6. Another con
sideration allows us to suppose that u= 1.5 x 10-6 is prob
ably appropriate for the neutral mutation rate of e
cistron in Drosophila. If we assume that the frequency
of occurrence of neutral mutations is about one pel
genome per generation (that is, they are roughly two t c
three times more frequent than the mutation of the
viability polygenes), the mutation rate per nucleotide
pair per generation is 1/(2 x loa), because the DNA con
tent per genome in Drosophila is about one-twentieth o
that of manzo. For a cistron consisting of 3,000 nucleotide
pairs, this amounts to u= 1.5 x 10-5.

Kimura and C r o w have shown that .for neutra
mutations the probability that an individual is homo.
zygous is 1/(4Neu+ I ) , where N e is the effective population
number, so that the probability that an individual is
heterozygous is H e = 4Neu/(4iVeu+ 1). I n order to attain
a t least H e = 0.12, it is necessary that at least N e = 2,300
For a higher heterozygosity such as H = 0.35, N e has t c
be about 9,000. This might be a little too large for thc
effective number in Drosophila, but with migration
between subgroups, heterozygosity of 35 per cent may bc
attained even if N e is much smaller for each subgroup.

We return to the problem of total mutation rate
From a consideration of the average energy of hydrogen
bonds and also from the information on mutation of
r I I A gene in phage T,, Watson22 obtained IO-*- lo-9 as
the average probability of error in the insertion of a new
nucleotide during DNA replication. Because in man the
number of cell divisions along the germ line from the
fertilized egg t o a gamete is roughly 80, the rate of muta-
tion resulting from base replacement according to these
figures may be BO x 10-8- S O X 10-0 per nucleotide pair
per generation. Thus, with 4 x IO9 nucleotide pairs, the
total number of mutations resulting from base replace-
ment may amount t o 200- 2,000. This is 100-1,000 times
larger than the estimate of 2 per generation and suggests
that the mutation rate per nucleotide pair is reduced
during evolution by natural selectionl8~19.

Finally, if my chief conclusion is correct, and if the
neutral or nearly neutral mutation is being produced in
each generation at a much higher rate than has been con-
sidered before, then we must recognize the great impor-
tance of random genetic drift due t o finite population
numberz3 in forming the genetic structure of biological
populations. The significance of random genetic drift has
been deprecated during the past decade. This attitude
1as been influenced by the opinion a t almost no muta-
ions are neutral, and also that th number of individuals
forming a species is usually so Iarg f that random sampling
)f gametes should be negligdle in iletermining the course
)f evolution, except possibly through the “founder prin-
: i ~ l e ” ~ * . To emphasize the founder principle but deny
h e importance of random genetic drift due to finite
population number is, in my opinion, rather similar t o
assuming a great flood to explain the formation of deep
valleys but rejecting a gradual but long lasting process of
erosion by water as insufficient to produce such a result.
received December 18,1967.
Zuckerkandl, E., and Pauling, L., in Evolvz g &ne8 and Proteins (edit. by

Bryson, V., and Vogel, H. J.), 97 (Acad dip IC Press, New York, 1965).
Buettner-Janusch, J., and II111, R. L. in Evolving Genes and Proteins (edit.

Margoliash, E., and Smith, E. L., in Evolving Genes and Proteins (edit. by
by Bryson, V., and Vogel, H. J.), Id7 (Academic Press, New York, 1965).

Kaplan, N . O . , in Evolving Genes and Proteins (edit. by Bryson, V., and
Bryson, V., and Vogel, H. JJ, 221 (Academic Press, New York, 1905).

S:rgcr, R., and Ryan, F. J., Cell Herdily (John Wiley and Sons, New York,
Vogel, H. J,), 243 (Academic Press, New York, 1966).

1961 ).

% Sueoka, N . , J . M o t . Biol., 8, 31 (1961).

8 Eimura, M., &net. Res. (in the press).
7 Muller, R. J., BuU. Amsr. Math. SOC., 64,137 (1958).

s Haldane, J. B. S., J . Genet., 55,511 (1957).
lo Eimura, M., J . Genet., 57,21(1960).
11 Kimura, M., Ann. Math. Stat., 28,882 (1967).
1* Mukai, T.. Genetics, 80, l(1964).
I* Harris, X., Proc. Rou. Soc., B, 164, 298 (1900).
l 4 Hubby, J. L., and Lewontin, R. C., Genetics, 54,577 (1960).
Is Lewontin, R. O., and Hubby, J. L., Genetics, 54,596 (1960).
18 Narise, 8., and Hubby, J. L., Biochim. Biophus. Acta, 122, 281 (1066).
l7 Fincham, J. R. S., Uenetic Complenurnlataon (Benjamin, New York, 1906).
L B Muller, H. J., in Herfiage from Mendel (edit. by Brink, R. A:), 419 ( V n i –

9 0 Report .of the United Nations ScientiJk Commitlee o n the Eflecle of Atomic
1o Kimura, M., Uenet. Res., 9, 23 (1967).

Rdzation (New York, 1958).
EL Kimura. M.. and Crow, J. F., Genetics, 49,725 (1004).
pp Watson, J. D., Molecular Biologu ofthe Gene (Benjamitl, New Tork, 1965).
pa Wrlght, S., Uenetics,16,97 (1931).
alMayr, E., Animal Spec!es and Evolution (Harvard University Press,

vemlty of Wisconsm Press, Madison, 1967).

Cambridge, 1905).

http://hrst.mit.edu/hrs/evolution/public/kimuracrow1964/kimuracrow1964

http://hrst.mit.edu/hrs/evolution/public/papers/zuckerkandlpauling1965/zuckerkandlpauling1965

http://hrst.mit.edu/hrs/evolution/public/papers/buettnerhill1965/buettnerhill1965

http://hrst.mit.edu/hrs/evolution/public/papers/hubbylewontin1966/hubbylewontin1966

http://hrst.mit.edu/hrs/evolution/public/papers/lewontinhubby1966/lewontinhubby1966

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http://hrst.mit.edu/hrs/evolution/public/kimura1968/kimura1968

http://hrst.mit.edu/hrs/evolution/public/papers/kimura1968/kimura1968

http://hrst.mit.edu/hrs/evolution/public/papers/simpson1964/simpson1964

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