iDarwin AS 0021 (2021 AD)

Volume 1

Introduction of published bookiDarwin volume 1, page 37-53
Published on February 12, AS 0021 (2021 AD)“My Thoughts on Biological Evolution” by KIMURA (2020)– translation of KIMURA (1988) –SAITOU Naruya
Population Genetics Laboratory, National Institute of Genetics (Main appointment)
School of Medicine, University of the Ryukyus
Department of Biological Sciences, Graduate School of Science, University to Tokyo
Department of Genetics, School of Life Science, Graduate University for Advanced Studies
1111 Yata, Mishima, 411-8540, Japan
Email: saitounr@nig.ac.jp
KIMURA Motoo (1924-1994), who proposed the neutral theory of molecular evolution (KIMURA 1968, 1983) published one book in April of 1988 inJapanese (KIMURA, 1988; see Figure 1) just after he officially retired from professor of National Institute of Genetics. One Japanese evolutionary
biologist, who was working in USA, initially translated this book into English just after its publication. Unfortunately, Dr. Kimura did not like thistranslation, and that English translation was never published. After Dr. Kimura passed away, some other Japanese, a science historian, translated thisbook into English. However, the publisher turned down this translation, and this second translation was again not published. In 2014, I organized one
symposium to commemorate the 90th anniversary of Dr. Kimura on November 13th (his birthday) and 14th in National Institute of Genetics. On that
symposium, Dr. Tateno Yoshio, Professor emeritus of National Institute of Genetics, declared in his talk that he translated KIMURA (1988) into
English. Later, Dr. Tateno asked me to find some appropriate publisher. I became series editor of Springer “Evolutionary Studies” Series at that time,
and was wondering of new book other than one I myself was editor (SAITOU ed., 2017). I eventually persuaded the Japanese publisher, Iwanami
Shoten, who published KIMURA (1988), to make one translation-related contract with Springer, as well as obtaining publication permission from Mr.
Kimura Akio, only child of late Kimura Motoo, for he inherited the copyrights of publications of his father. Meanwhile, I also asked Dr. Aoki Kenichi,
Professor emeritus of University of Tokyo, to check English translation made by Dr. Tateno. Dr. Aoki studied many years in Canada and USA from his
boyhood, including Ph.D. from University of Wisconsin under supervision of Dr. James F. Crow, and his English is close to that of native speakers. It
should be noted that Dr. Aoki was assistant professor at Division of Population Genetics in National Institute of Genetics from 1980 to 1988 under Dr.
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iDarwin AS 0021 (2021 AD)

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Kimura. Dr. Tateno also worked in National Institute of Genetics from 1984 to 2010, and both Drs. Tateno and Aoki personally knew and respect Dr.
Kimura pretty well.
According to my record, Drs. Tateno and Aoki visited National Institute of Genetics 24 times during 2016 and 16 times during 2017 forproceeding English translation of KIMURA (1988). After English translation was finished, I asked Dr. Ohta Tomoko, Professor emeritus of National
Institute of Genetics, to contribute preface to English translation of KIMURA (1988). She agreed and wrote preface titled “In memory”. Eventually,
KIMURA (2020; see Figure 2), English translation of KIMURA (1988), was published in summer of 2020. As successor of the head of at Division ofPopulation Genetics (its name was changed to Population Genetics Laboratory on January 1, 2020), I was very happy.
KIMURA (2020) consists of nine chapters as follows:
Chapter 1: Diversity of organisms and views on evolution
Chapter 2: History of the development of the theory of evolutionary mechanism on the basis of genetics
Chapter 3: Tracing the course of evolution
Chapter 4: Mutation as an evolutionary factor
Chapter 5: On natural selection and adaptation
Chapter 6: Introduction of population genetics
Chapter 7: Introduction to molecular evolution
Chapter 8: The neutral theory and molecular evolution
Chapter 9: An evolutionary genetic world view
Before starting to give brief explanation of each chapter, I would like to note about preface of KIMURA (1988). Dr. Kimura mentioned
KOMAI (1963) that was published when Dr. Komai was 77 years old. Dr. Komai was mentor for Dr. Kimura, and Dr. Kimura was happy to publish
KIMURA (1988) when he was still at the age of 63. I myself vividly remember to read KOMAI (1963) when I was an undergraduate in late 1970s.
While Dr. Komai passed away nine years later after his 1963 book publication, at the age of 86, Dr. Kimura passed away at the age of 70, only sevenyears after publication of KIMURA (1988).
KIMURA (2020) first mentioned number of species on earth followed by adaptation and variation, achievement of molecular biology, andbiological evolution as a fact in Chapter 1. He then discuss history of the development of evolutionary theory starting from Lamarck, followed by
Weismann, and later Darwin and Mendel. Figure 1.2 of KIMURA (2020) shows Dr. Jacques Ruffie and Ohta Tomoko standing beneath the statue of
Lamarck in the Paris Botanical Garden. Chapter 2 follows this historical aspect up to the establishment of the neutral theory. The emergence of
population genetics theory was briefly yet vividly written, with precious photos. Figure 2.3 shows R. A. Fisher discussing with young Kimura in
National Institute of Genetics, when Fisher visited Japan, and Figures 2.5 and 2.6 show Wright, Crow, and Kimura, as well as young Dr. Chung-I Wu
38

iDarwin AS 0021 (2021 AD)

Volume 1

Figure 1. Cover of KIMURA (1988).

Figure 2. Cover of KIMURA (2020).

39

iDarwin AS 0021 (2021 AD)

Volume 1(only appearing in Figure 2.6) when he was a post-doctoral fellow. It should be noted that Dr. Wu was mentioned only in KIMURA (2020).
Chapter 3 covers the outline of the history of life, evolution of vertebrates, evolution of mammals, and eventually emergence of hominids.
Center of Chapter 4 is mutation, however, the first section, titled “A genetic view of life” discuss various key issues of genetics. Natural selection andadaptation is discussed in Chapter 5. Starting from discussion of DARWIN (1859), various types of natural selection was discussed in this chapter.
Figure 5.1 shows five orchid flowers, and the center flower is named “Tree Village”, or English character-to-character translation of KI-MURA (木村).
This flower was registered in 1976 by Dr. Kimura according to the legend of this figure. Developments of population genetics theory related to natural
selection is discussed in section 5.2. I would like to note that “positive selection” and “negative selection” explained in this section were coined by Dr.
Kimura himself in his book (KIMURA, 1983), as SAITOU (2013, 2018) mentioned.
Population genetics is fully discussed in Chapter 6, starting from its historical perspective in section 6.1, and Mendelian population to computer
simulation are covered here. The Hardy-Weinberg ratio is discussed in section 6.2 to some details. However, Dr. Kimura criticized DOBZHANSKY(1951) for exaggerating this ratio to be called a “principle”. I examined some recent text books of population genetics, and unfortunately stillassumptions of no natural selection, no mutation, no migration, no genetic drift are written for obtaining the Hardy-Weinberg “equilibrium” in somebooks. As Dr. Kimura stated, the Hardy-Weinberg ratio is just useful but simple. The realistic situations for equilibrium are discussed in section 6.3.
The genetic load concept is explained in this section, partly because this concept is closely related to the emergence of the neutral theory in 1968.
Random genetic drift is discussed in section 6.4, followed by behavior of a mutant gene in section 6.5. A sketch of the early days of molecular
evolutionary studies is given in Chapter 7. Genetic code table and its general nature is discussed after a brief historical perspective. How to estimate therate of molecular evolution and characteristics of molecular evolution are discussed. Finally, accumulation process of mutations are discussed. These
are all preludes for the proposal of the neutral theory by KIMURA (1968).
Chapter 8 is thus logically and naturally about the neutral theory and molecular evolution. This is the longest chapter of this book. The
approximate constancy of the evolutionary rate in various organisms is first discussed in section 8.1. While the generation time is 40 times higher inmouse than human, the rate of amino acid substitution per year is only 50% higher in mouse than human. In recent years, whole genome sequences
became available for many species, and it is now possible to compare genomic evolutionary rates between various organism lineages. For example,
BABARINDE and SAITOU (2020) compared genome data of 39 mammalian species, and they found that the amino acid evolutionary rates of rodents
is about two times higher than that of primates. This difference is more closer to the physical year difference (no difference) than the generation timedifference (40-fold). In KIMURA (2020), discussions on mutation rates continues, including those between mammalian X and Y chromosomes. The
mutation rate constancy per generation or per year was again discussed. This enigma is still not fully solved now. Conservative nature of molecular
evolution is discussed at the end of this section, and KIMURA was pleased to know that the evolutionary rate of a pseudogene, that is expected to
evolve with no conservation, was in fact abnormally high as he predicted. Intraspecific variation at the molecular level is discussed in section 8.2, and40

iDarwin AS 0021 (2021 AD)

Volume 1again that DNA polymorphism data supported the neutral theory. NEI’s (1972) genetic distance is mentioned in this section, and Figure 8.1. shows therelationship of three major human populations based on NEI and ROYCHOUDHURY (1974). When that paper was published in 1970s, “race” wasstill used in anthropology and human genetics, and the paper title included three racial names. These are kept in KIMURA (2020), however, Figure 8.1
of KIMURA (2020) uses new terms: “African”, “East Eurasian”, and “West Eurasian” based on my suggestion. I would like to note that these newterms were first proposed by SAITOU (1995a).
Molecular evolutionary clock and molecular phylogenies are discussed in Section 8.3. Four topics were introduced in this section; 5S RNA
data used for phylogeny of many organisms, DNA-DNA hybridization technique used for the bird phylogeny construction, influenza virus gene
phylogeny, and oncogene/HIV phylogenies. I am pleased that Dr. Kimura mentioned our work (SAITOU and NEI 1986) on influenza A virus gene data
analysis here. When this paper was accepted to Molecular Biology and Evolution, I sent one copy of accepted manuscript to Dr. Kimura. He sent me aletter, and criticized us for not citing his neutral theory. I was at that time a devoted neutralist already, and I (and probably Dr. Nei too) thought that itwas not surprising to find a higher evolutionary rates for the third position of codons than those for the first and second positions of codons. Thispattern is consistent with the neutral theory. In any case, we added KIMURA (1983) in our paper proof. I included this episode in SAITOU (1995b).
Other topics related to neutral evolution is discussed in Section 8.4. Two topics, one study conducted by Dr. Ikemura Toshimichi, and the otherconducted by Dr. Osawa Shozo’s group, are on codon evolution, and the origin of life is also discussed in this section. I was associate professor of
Division of Evolutionary Genetics, National Institute of Genetics from January 1991 to February 2001, before becoming professor of the Division ofPopulation Genetics, National Institute of Genetics. Dr. Ikemura was professor of Division of Evolutionary Genetics, and I heard from Dr. Ikemura
how Dr. Kimura came to like Dr. Ikemura’s codon evolution study many times during the lunch time. This episode was written by Dr. Ikemura in his
short memoire on Dr. Kimura (IKEMURA, 1995).
How to bridge between evolution at the molecular level and phenotypic level is discussed at the last section of Chapter 8. After introducing
micro- and macro-evolution for phenotypic level changes, Dr. Kimura wrote “In this case, Darwinian natural selection undoubtedly plays the major
role.” He then discussed evolutionary changes of “regulatory genes” that can include DNA signals that regulate transcription, citing one review article
by FUJITA et al. (1986). Dr. Fujita was assistant professor of Division of Molecular Genetics at the National Institute of Genetics at that time, and Dr.
Nagata and Ishihama, coauthors of this review article, were assistant professor and professor of this division, respectively, at that time. Dr. Kimura
seems to be right on the characteristics of the “bridge” between molecular and phenotypic evolutions. We recently discovered that ancestral sequencesof highly conserved noncoding sequences among family Hominidae (SABER et al. 2016) and super-family Hominoidea (SABER and SAITOU 2017)
experienced often many substitutions whose evolutionary rates were much larger than those expected under the neutral evolution. This suggests thatDarwinian natural selection (positive selection) operates to create regulatory functions to some DNA sequences, after gaining certain function related to41

iDarwin AS 0021 (2021 AD)

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some phenotype, this DNA sequence is now under strong purifying selection (negative selection). I am quite certain that phylogenetic analyses ofconserved noncoding sequences are crucial to find the bridge between molecular evolution and phenotypic evolution.
Last chapter of this book is titled “An evolutionary genetic world view”. This chapter was somewhat controversial, because Dr. Kimura
discussed about eugenics. One junior evolutionary biologist was asked to write a book review of KIMRUA (1988) to some local newspaper. However,Dr. Kimura got angry against this book review manuscript, and that book review was never published. I do not know this book review manuscript, butsomeone told me that it contained criticism on discussion of eugenics given in this chapter. Contrary to modern situation of a strong opposition against
eugenics, that concept is rather standard in human genetics in the early half of the 20th Century. For example, one journal, named “Eugenics Quarterly”
did exist at that time. This journal name was changed to Social Biology in 1969, then again changed to Biodemography and Social Biology in 2008.
After briefly discussing human evolution in section 9.1, section 9.2, titled “Thinking about the question of eugenics” starts from subsection “Taboo”.
Negative eugenics is explained in this section, as its goal limiting the accumulation of deleterious mutations below a certain level. Positive eugenics is
discussed in section 9.3. The aim of positive eugenics is to amplify characters that are thought to be desirable for mankind. Dr. Kimura discussed spermbank proposed by Muller and clone human proposed by J. B. S. Haldane.
The last section of this last chapter is titled “Human expansion into space and evolution”. Dr. Kimura mentioned Winston Churchill about one
famous word “the end of the beginning”, but I suspect that Dr. Kimura was also thinking of “Childhood’s End” written by A. C. Clarke. In any case, Dr.
Kimura then introduced the space colony project proposed by Gerald K. O’Neill, then mentioned “Rendezvous with Rama” written by A. C. Clarke. Dr.
Kimura also discussed about SETI (Search for Extraterrestrial Intelligence) project, but he is rather pessimistic for possibility of finding any
extraterrestrial intelligence. In contrast, Dr. Kimura supported the idea of “Dyson sphere” that envelops one star with a special surface composed ofmatter obtained by breaking up a planet. He further speculate creation of super human by practicing Muller’s sperm-bank using plan. Dr. Kimura ends
this book with this sentence: we can hold the entire universe inside our heads through the processes of thought. The concept of “super human” reminds
me of Kwisatz Haderach, one of the central concepts of the Dune series created by Frank Herbert. In fact, I am also a big fan of science fictions.
Index is not included in KIMURA (2020). It was my mistake as the editor of “Evolutionary Studies” series. I thus chose appropriate words fromKIMURA (2020), and index is attached at the end of this article.
References
Isaac BABARINDE and SAITOU Naruya (2020) The dynamics, causes, and impacts of mammalian evolutionary rates revealed by the analyses of
capybara draft genome sequences. Genome Biology and Evolution, vol. 12, pp. 1444-1458.
Charles DARWIN (1859) Origin of Species. John Murray, London.
Theodosius DOBZHANSKY (1951) Genetics and the Origin of Species Third Edition. Columbia University Press, New York.
42

iDarwin AS 0021 (2021 AD)

Volume 1

FUJITA Nobuyuki, NAGATA Kyosuke, and ISHIHAMA Akira (1986) Molecular mechanisms for information expression of genes (written in
Japanese). IDEN, vol. 40, 20-xx.｛藤田信之・永田恭介・石浜明 (1986) 遺伝子の情報発現の分子機構. 遺伝, 40巻2号、20-X頁｝
IKEMURA Toshimichi (1995) Unforgettable memory for me (written in Japanese). In OHTA Tomoko and TAKAHATA Naoyuki Eds.,
Commemoration of Dr. Kimura Motoo, pp. 30-31. ｛池村淑道 (1995) 私にとって忘れられない思い出. 太田朋子・高畑尚之共編『木村資生博士追悼記念誌』, 30-31頁.｝
KIMURA Motoo (1968) Evolutionary rate at the molecular level. Nature, vol. 217, pp. 624–626.
KIMURA Motoo (1983) The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.
KIMURA Motoo (1988) My Thoughts on Biological Evolution. Iwanami-Shinsho series, Iwanami Shoten, Tokyo (written in Japanese).｛木村資生(1988)『生物進化を考える』. 岩波新書、岩波書店.｝
KIMURA Motoo (2020) My Thoughts on Biological Evolution. Translated by TATENO Yoshio and AOKI Kenichi. Springer Evolutionary Studies
Series. Springer, Tokyo.
KOMAI Taku (1963) Evolution of Organisms on the Basis of Genetics. Baifukan, Tokyo (written in Japanese).｛駒井卓 (1963) 『遺伝学に基づく生物の進化』. 培風館.}
NEI Masatoshi (1972) Genetic distance between populations. American Naturalist, vol. 106, pp. 283-292.
NEI Masatoshi and Arun K. ROYCHOUDHURY (1974) Genic variation within and between the three major races of man, Caucasoids, Negroids, andMongoloids. American Journal of Human Genetics, vol. 26, pp. 421-443.
SABER Morteza Mahmoudi, BABARINSE Isaac A., HETTIARACHCHI Nilmini, and SAITOU Naruya (2016) Emergence and evolution of
Hominidae-specific coding and noncoding genomic sequences. Genome Biology and Evolution, vol. 8, pp. 2076-2092.
SABER Morteza Mahmoudi and SAITOU Naruya (2017) Silencing effect of Hominoid highly conserved non-coding sequences on embryonic brain
development. Genome Biology and Evolution, vol. 9, pp. 2037-2048.
SAITOU Naruya (1995a) A genetic affinity analysis of human populations. Human Evolution, vol. 10, pp. 17-33.
SAITOU Naruya (1995b) Remembering Dr. Kimura Motoo - from one who was charmed with the neutral theory (written in Japanese). In OHTA
Tomoko and TAKAHATA Naoyuki Eds., Commemoration of Dr. Kimura Motoo, pp. 74-76. ｛斎藤成也 (1995) 木村資生先生をしのぶ–中立説に魅せられたひとりより. 太田朋子・高畑尚之共編『木村資生博士追悼記念誌』, 74-76頁.｝
SAITOU Naruya (2013) Introduction to Evolutionary Genomics. Springer Computational Biology Series. Springer, London.
SAITOU Naruya (2018) Introduction to Evolutionary Genomics Second Edition. Springer Computational Biology Series. Springer, London.
SAITOU Naruya ed. (2017) Evolution of the Human Genome I. Springer Evolutionary Studies Series. Springer, Tokyo.
SAITOU Naruya and NEI Masatoshi (1986) Polymorphism and evolution of influenza A virus genes. Molecular Biology and Evolution, vol. 3, pp.
57-74.
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iDarwin AS 0021 (2021 AD)
Index of KIMURA (2020)
Numerals and Symbols
5S rRNA 128
A
A mathematical theory of natural and artificial
selection 20
Abbot of Brno Monastery 13
Achondroplasia 143
achondroplasia 92
acquired immune deficiency syndrome 130
actual population number 116
adaptation 7
adaptive evolution 8, 79
adaptive radiation 37, 45, 137
adenine 49
Aegilops tauschii 53
African apes 48
Agnatha 39
AIDS 130
albinism 143
albino 120
algae 1alleles 12
alphabet 150
altruism 149
altruistic behavior 71
Alvarez, L. W. 44
ameba 81
amino acid substitutions 108
ammonites 38,43
amniocentesis 144
amnion 41
amphibians 38, 41
amphidiploids 53
Anaerobic 36

Volume 1
anagenesis 33
aneuploidy 53
Animal Species and Evolution 29
animals 1, 37
Antarctica 1
Antennapedia 52
Antibiotic 59
anticodon 133
Aoki, Kenichi iv, vi, vii, 72
archaebacteria 128
Archosauria 43
argininosuccinate synthetase 121
arginosuccinate lyase 138
Aristotle 4
artificial selection 9, 76
Artiodactyla 45
AS gene 121
assortative mating 91
asteroid 42, 44
astronomy 149
attached X 56
Australopithecus 46
Austria 10
Autobiography of Charles Darwin 8
autosome 121
Avalokiteshwara 40
average heterozygote frequency 127
B
Bach 139
Bacon, Francis 69
bacteria 1, 12, 34
bacterial weapons 142
bacteriophages 2
Baifukan xbalance hypothesis 28
balancing selection 29, 125

44

Bar 55
Bateson, William 15, 16
Beagle 8, 65
behavior of mutants 115
biased usage of synonymous codons 130
Biblical Genesis 3
Big Bang ii
biological evolution ix, 3, 8
biological resources 2
Biology of Altruistic Behavior 72
biometricians 15, 16
biometrics 142
biostatistics 15
biotechnology 145
birds 38, 43
Biston betularia 21
bithorax 52
bivalves 39
Blind Watchmaker 83
blood type 125
blue whale 2
blueprints 2
Boltzmann, Ludwig 8
botany ix
Bothriolepis 40
brain 140
Bridges, C. B. 55
Brno 10
Brno Natural Science Society 11
Brno Practical High School 11
Brünn 10C
C peptide 112
Calder, N. 45
Cambrian Period 37
carapace 39

iDarwin AS 0021 (2021 AD)
Carboniferous Period 38, 41
carnivores 45
cat’s cry syndrome 54
Caucasoids 125
Causes of Evolution 22
Cech, Thomas 134
cell theory 49
Cenozoic 44
Cenozoic Era 38
centripetal selection 79
centromere 56
centromeric fusion 56
century of Darwin 8
Cephalopoda 39
cerebrum 43
Cetacea 45
chance effects ix
cheetah 124
Chi-square method 15
Chihuahua 137
Chiroptera 45
chloroplasts 34
Christian sect 3
chromosomal aberrations 17
chromosomal abnormalities 143
chromosomal mutations 52
chromosome theory 12
chromosomes 37,49
Churchill, Winston 147
ciliates 132
civilization 38
cladogenesis 33
Clark, Arthur 148
classical hypothesis 28
clone 147
codon 104
coelacanths 41, 139

Volume 1
coevolution 38
collectivization 141
Columba livia 66
computer 87
condor 129
Confucius v
conifers 38
consciousness 139
conservatism 113
conservativeness 122
consonants 47
constraint 122
continental drift 41
continuous small variation 17
convergent evolution 135
Copernican revolution 149
copia 63
copia-like elements 63
correlation coefficient 62
Correns, C. 13
cousin marriage 91
creation science 2, 3
creative power of natural selection 81
Cretaceous 38
Crick, F. 32,49
Cro-Magnons 47
crossopterygians 40, 139
Crow and Kimura, 1970 117
Crow, J. F. 23-25, 29, 59, 80, 93, 95, 127
Crow, James F. v
Crow’s index of total selection 142
crust 35
crystallin delta 138
cultivated plant 65
cultural heritage 139
Cuvier, Georges 5
cyanobacteria 1, 34, 36

45

cycads 38
cytochrome c 31, 110
cytosine 49
Czechoslovakia 10
D
Darwin 65,140
Darwin, Charles 2
Darwin’s finches 136
Darwin’s theory 15
Darwinian natural selection 114, 117, 121, 133, 136,
138
Darwinian selection 78
Dawkins, R. 83
De Vries, H. 17
dead gene 32,121
degeneracy 105
deletion 54,56
Demark 92
density-dependent selection 80
deoxyribonucleic acid 49
Department of Population Genetics v
Dermoptera 71
deterministic treatment 85
developmental constraint 136
developmental control 144
Devonian Era 139
Devonian Period 37
dialect 131
diffusion models 27,86
dilute 120
dinosaurs 38,43,137
diploid 12
directional selection 79
distribution of deleterious effects 94
diversity 1
DNA 2, 12, 49

iDarwin AS 0021 (2021 AD)
DNA and Genetic Information 50
DNA base sequences 3
DNA base substitutions 32
DNA polymorphism 87, 126, 132
DNA replication error 120
DNA-DNA hybridization 128
Dobzhansky, T. 27, 28, 90
dog 137
Dogs 138
domesticated animal 65
dominance 11
don’t rock the boat principles 135
double mutant 23
Down’s syndrome 54, 143
Drosophila 17
Drosophila melanogaster 93, 127
duplication 54, 56
Dyson sphere 150
Dyson, F. J. 133, 134, 150
Dyson, Freeman v
E
E. coli 131
Earth ii,1,35
ecological genetics 27, 81
Ecological Genetics 30
ecological niches 44
EcoR1 126
effective number 115,117
effective population number 20, 100
Eigen, M. 133
Eldredge, N. 33
electrophoresis 31, 86, 124element 11
elephant seal 124
Empedocles 4
Encyclopedia Britannica 13, 51

Volume 1
end of the beginning 147
Endler, J. A. 81
endocranial volume 140
entrance examination 137
environmental factors 137
enzyme polymorphisms 29
epistasis 23,26
equilibrium frequency 94
Escherichia coli 58
eta globin 128
Euclid 139
eugenics 15, 142
eukaryotes 34, 37
euphenics 144
eurypterid 39
Eusthenopteron 140
Eutherian mammals 135
eutherians 45
evening primrose 17
Evolution and Life 141
Evolution by Gene Duplication 55
Evolution in Mendelian Populations 23
Evolution of Organisms on the Basis of Genetics x
evolutionary genetics 139
evolutionary legacy 139
evolutionary rates 15, 119, 120
evolutionary studies ii, ix
evolutionary theory 3
exceptional codon usage 132
excision repair 58
Experiments in Plant Hybridization 11
explosive population growth 142
extinction 1
extrasomatic cultivation of a fertilized egg 147
extreme panselectionists 29
F

46

family planning 142
Fermi, E. 149
ferns 38
fertilization 12
fertilized eggs 2
Feynman, Richard v
fibrinopeptide 110,111
first filial generation 11
Fisher, R.A. 16, 18-20, 22, 26, 72, 75, 85
fitness 72, 77
fixation 114
fixation probability 22, 30, 101, 116, 147
flagella 34
flowering plants 38
flying squirrels 70
Ford, E. B. 26, 27, 29
formyl-methionine 107
fossils 3,37
frequency-dependent selection 80, 125
fruit fly 27, 52, 54, 60, 86, 94, 124, 136
fundamental theorem of natural selection 75,77
Fundamentals of Human Genetics 74,100
fungi 1Furusho, Toshiyuki 62
fushi tarazu 52
fusion 56
G
Galapagos Archipelago 136
Galeopithecus 71
Galton, Francis 15, 142
gamete 12
gametes 11
gametic array 89
Gehring, W. J. 52
gene 17, 50
gene families 55

iDarwin AS 0021 (2021 AD)
gene frequencies 18, 87
gene frequency change 20
gene manipulation 145
gene mutations 52, 56, 57
gene pool 139
genealogical process 127
generation 119
generation effect 120
genetic code 2,3genetic code table 105, 106
genetic drift 25, 26, 97, 99, 104, 114
genetic equilibrium 92
genetic gain 76
genetic load 96
genetic polymorphism 31
genetic variance 75
Genetical Theory of Natural Selection 20, 75
genetics 16
Genetics and the Origin of Species 28 ,90
Genetics Club Meeting 31
genic selection 73, 117
genome 31, 137
genotype 7, 87
geographic distributions 3
geographical isolation 136
geological strata 3
germ plasm selection 147
giant salivary gland 54
gills 3ginkgo 38
giraffe 4
Glass, Bentley 144
God 2,83
Gojobori, Takashi 129, 130
Gould, S. 33
Great Ice Age 47
greatest scientific achievements 2

Volume 1
Greek philosophers 4
Greenland 35
group living 141
growth hormone 114
guanine 49
H
Haga, Tsutomu 53
hagfishes 40
Haldane-Muller principle 96
Haldane, J.B.S. 16, 18, 20, 40, 72, 77, 85, 92, 117,
140, 147
halobacteria 128
Hamilton, W. D. 71
haploid 12
Hardy-Weinberg law 18
Hardy-Weinberg principle 88, 90
Hardy, G. H. 18
harmless 122
Hasegawa, Masami 128
hawk 129
Hayakawa Shobo 148
heme-pocket 113
hemoglobin 3,30,107
hemoglobin alpha chain 112
hemophilia 143
heritability 62,76
heterochromatin 56
heterozygote 12
heterozygote advantage 29
heterozygous loci 124
Hienzendorf 10
Himalayan Mountain Range 140
Hiroshima University 128
histone 55
histone H4 113
history ii

47

History of Evolutionary Theory 5
History of Life 35
HIV 130
Hokkaido 53
Holocene 47
homeobox 52
homeotic genes 136
homeotic mutation 52
hominins 140
Homo 38
Homo erectus 46
Homo habilis 46
Homo sapiens 47
Homo sapiens neanderthalensis 47
Homo sapiens sapiens 47
homologous chromosomes 12
homozygotes 12
Hood, L. 55
Hori, Hiroshi 128
human 124
human ABO blood group 12
human genetics 86
human genome 50
human height 62
human populations 87
hybridism 72
hypercycle model 133
II-shaped chromosome 56
Ichtyostega 3
identical twins 139
Ikemura, Toshimichi 131
Imanishi, Kinji 9
immunological tolerance 7
inbreeding 91
inbreeding coefficient 91, 100

iDarwin AS 0021 (2021 AD)
inbreeding effect 99
incomplete dominance 12
index of total selection 80
Indian Ocean 41
induction of mutation 27
industrial melanism 21, 135
infant mortality 142
infertility 136
infinite allele model 127
infinite site model 115
influenza virus 129
informational macromolecules 3
inheritance of acquired characters 5, 7, 9
initiation 107
insecticide 59
Insectivora 45
insects 1,38
insertion sequence 57
instinct 71
Institute of Statistical Mathematics 128
Insulin 112
intelligence 140
intergroup selection 141
intermediate forms 70
International Prize for Biology 38
interspecies competition 33
intraspecific variation 124,128
inversion 54
inversion chromosomes 28
iridium 44
Ishii, Yuriko x
Ishiwa, Sadao 127
isolation 136
isozyme polymorphism 124
Iwanami pocket book 5
Iwanami Publisher x, 55, 138

Volume 1
J
Japanese 85, 86, 89
Japanese macaque 45
Johannsen, W. L. 17
Jukes, T. H. 31, 132, 133
junk 51
Jurassic 38
K
K selection 80
K-T extinction 43
K/T boundary 43
Kaimeisha 128
Karn, M. N. 78
Kettlewell, H. B. D. 22
Kihara Laboratory 23
Kihara, Hitoshi 53
Kimura, Akio vii
Kimura, Motoo iv
kin selection 71
King, J. L. 31
Kinokuniya Publisher 109, 131
Kobayashi, Shigeki x
Komai, Taku x,135
Kuchino, Yoshiyuki 132
Kuhn, Thomas 9
Kyushu University 23, 77, 32, 120, 125, 129, 131L
Lagomorpha 45
Lagrange point 148
Lamarck, Jean Baptiste 4
Lamarck’s theory 5
Lamarckism 71
lampreys 40
language 131
Lascaux Cave 48

48

Latimeria 41
Law of Segregation 12
Lederberg, J. 59,144
lemur 45lens 138
lethal equivalents 95
lethal gene 93
lichen 21
limestone 36
Linnaean Society 72
Linnaeus 68
living fossil 41
living fossils 111, 137
locally optimal state 26
lower jaw 39
Lysenkoism 59
M
MacArthur, R. H. 85
macro-evolution 135, 136
Magellanic Clouds 148
Malécot, G. 91
Malthus 67
Malthus’ theory of population 77
Malthusian parameter 73, 76
mammal 38,43
mammal-like reptiles 42
Manchester 21
Margulis, Lynn 34, 36
Margulis’ theory 133
marsupials 45,135
mass extinctions 42
Mastiff 137
Mather, K. 62, 78
mating system 88
Mayr, Ernst 27, 29
McLoughlin, J. C. 138

iDarwin AS 0021 (2021 AD)
mean fitness 76
meiosis 12
Mendel school 17
Mendel-Morgan genetic analysis 62
Mendel, Johann Gregor 10
Mendel’s First Law 12
Mendel’s laws 11,15,16
Mendel’s tragedy 13
Mendelian genetics 6, 15
Mendelian population 85
Mendelians 16
mentor x
meso-evolution 136
Mesozoic 41
Mesozoic Era 38
messenger RNA 50
metabacteria 128
meteorites 44
methane bacteria 128
methionine 107
micro-evolution 135
microcephaly 143
microtubules 113
Middle Ages 149
milk yield in cows 62
Milky Way 148
Miller, S. L. 134
Mishima i, iv, vi, vii, 23
mitochondria 34, 36, 126
Miura, Kin-ichiro 50
Miyabe, Nobuaki x
Miyata, Takashi 32, 120, 129
Mizuguchi, Masako vii
MN blood groups 89
modern humans 47
modifying genes 136
molecular biology 2

Volume 1
molecular clock 110, 129
molecular evolution ii, ix, 2, 32, 104
molecular evolutionary clock 127, 135
molecular genetics 2, 30
molecular microsurgery 145
Mollusca 39
Mongolism 54
Mongoloids 125
Monte Carlo experiments 87, 99
Moravia 10
Morgan, T. H. 17
Morishima, Keiko 53
morphogenesis 52
Morton, N. 95
mouse 120
movable genetic element 57, 62, 122mRNA 105
Mukai, Terumi 29,93,94,125
Muller 150
Muller, H. J. 17, 19, 27, 46, 51, 55, 82, 93, 95, 146
Muller, Herman J. 8
multi-cellular organisms 136
multigene family 55
mutation pressure 133
mutation rate 119
mutation rates in the human 143
mutation theory 17
mutational pressure 129
Muto, Akira 132
Mycoplasma capricolum 132
N
Nagoya University 128,132
Nakazawa, Shingo 10,13
Napp, F.C. 11, 13
National Cancer Center 132
National Institute of Genetics i, iv, vi, vii, x, 16, 19,49

23, 53, 129, 131
natural laws 141
natural selection 8, 17, 20, 39, 65, 68, 83
Nazi Germany 142
Neander River 47
Neanderthals 47
negative eugenics 144
negative selection 78, 131
Negroids 125, 126
Nei, Masatoshi 125, 126, 129
Nei’s distance 125
Nemesis 42
Neo-Darwinism 7, 18, 114
Neo-Lamarckism 6,7
neonate body weight 78
neuter insects 71
neutral evolution 129
neutral mutation rate 122
neutral mutations 104
neutral theory 31, 86, 104, 119, 133
neutral theory of molecular evolution ix
Neutral Theory of Molecular Evolution 109, 131
New World 129
Nikko 21
Nirenberg, M. 105
Nishimura, Susumu 132
Nobel Prize 27, 105, 133, 147
Non-Darwinian evolution 31
non-synonymous substitutions 129
normalizing selection 79
nuclear weapons 142
nucleus 37
number of species 1O
O’Neill, Gerald K. 148
oceans 35

iDarwin AS 0021 (2021 AD)
Ochanomizu University 127
octopuses 39
Ohno, Susumu 55
Ohta, Tomoko vi, 5, 16, 32, 55
Oka, Asajiro 141
Omoto, Keiichi 126
oncogene 129
Oparin theory 133
Oparin, A. I. 20
opportunism 135
optimal genotype 96
orangutan 48
Orchid 66
order 45
Ordovician 37
organelles 34
Origin and Evolution of the Human Viewed from
DNA 128
origin of life 20, 35, 133
Origins of Life 134
Origin of Species 2, 6, 8, 9, 10, 65, 68
ornithologists 66
Osawa, Shozo 128, 132, 133
ostracoderms 39
Our load of mutations 95
overdominance 28, 29, 125
Oxford University 16
oxygen 35
oyster 77
ozone layer 35, 41
Ppaleontology 30, 34
Paleozoic 41
Paley, William 83
Pangea 41
panselectionism ix, 18, 27, 29, 30, 104, 136

Volume 1
panselectionist 7, 125, 137
Paphiopedilum 66
paradigm shift 9
parallel evolution 135
Paramecium 132
parasitization 34
Paris Botanical Garden 5partial differential equation 20, 27
patagium 70,71
path coefficients 23
patriotism 141
Pauling 110
Pearson, Karl 15
Pelecypoda 39
Penrose, L. S. 78
peppered moth 21
Perissodactyla 45
Permian Period 41
phenotype 7
phenotypic evolution ix
phenylketonuria 143
Philosophie Zoologique 4, 8phyla 37
phylogenetic theory of evolutionary mechanism 4
Phylogeny of vertebrates 109
physical chemistry 58
pigeon 65
placental mammals 45
placoderms 40
plants 1,37
Pleistocene 47
Pliocene 40
polar bear 124
pollinators 38
polygene 62, 136
Polymorphic 67
polymorphism 27

50

polypeptide 105
polyploidy 53
Pongidae 56
population biology 85
population densities 141
population genetics ix, 18, 85
population label vii
positive eugenics 145, 150
positive selection 78
presomatotropin 114
Primates 45
primitive atmosphere 134
Princeton University 133, 148
pro-insulin 111
probability model 12
Proboscidea 45
prokaryotes 34
protean 67
protein polymorphisms 87
Provine, William B. v, 24
pseudogene 32, 121, 123
Psilotopsida 38
punctuated equilibrium theory 33
pure lines 11,17
pure-line theory 17
purifying selection 78
Pygmies 126
Q
QTL 62
quagmire x
quantitative characters 61
quantitative trait loci 62
quantitative traits 137
Quaternary 38,47
RiDarwin AS 0021 (2021 AD)
r selection 80
racial phylogeny 126
radiation 86
Ramapithecus 48
random drift 31
random genetic drift 18, 20
random mating 88
random sampling of gametes 100
rate constancy 110,119
rate of decrease of variation per generation by drift
100
rate of molecular evolution 108
rate of phenotypic evolution 140
rate of substitution 115
Raup, D. M. 42
Raven, Peter 38
reverse transcription 121
recessive 11
recessive lethal genes 27, 78, 93
recessive lethals 145
reciprocal translocation 55
regulatory genes 136
religion 141
Rendezvous with Rama 148
repairing 58
replica plating method 59
replication error 57
reproductive isolation 136
reptiles 38, 41, 42
resistant bacteria 59
restriction enzyme 126
retrovirus 129
reverse transcriptase 7
Rhodentia 45
ribosomal RNA 55
rice 53
ridiculous tendency 90

Volume 1
RNA viruses 129
Robertson, A. 146
Robertsonian fusion 56
rodents 149
Romer, A. 39, 43, 45, 46
Ruffié, Jacque 5
S
Saitou, Naruya i, vii
Sand Walk 8
Sawazaki, Hiroshi 138
Schleiden, M. J. 49
Schwann, T. 49
science fiction 148
science historians 2
Sciuridae 70
sea scorpion 39
search for extraterrestrial intelligence 148
second filial generation 11
segregate 11
selection 66
selection coefficient 20, 22, 73
selection limit in breeding 146
selection theory 86
selectionists 125
selective neutrality 116
selective value 73
selectively neutral 114
self-consciousness 141
self-fertilization 17
self-fertilized 11
self-replicating molecules 35
selfing 17
semi-sterility 55
Seno, Takuji 60
SETI 148
Sewall Wright and Evolutionary Biology 24

51

sex chromosomes 49, 120
sexploid 53
sexual selection 69
Shakespearean play 82
shark 111
sharks 40
shifting balance theory 25, 26, 69
sib-selection 59
Sibley, C. G. 128
Silurian Period 39
Simpson, George Gaylord 5, 27
simulation 141
Sinai Peninsula 150
Sirenia 45
Sivapithecus 48
slightly deleterious genes 27, 78, 95
Smith, Maynard 71
snails 16
social insects 71
sociobiology 72
solar system 35
somatic cell 7
SOS repair 58
Soudan Shale 36
space colony 148
Space Rendezvous 148
spacemen 149
speciation 72,136
species selection 33
sperm bank 146
spirals 16
spirochetes 34
spontaneous mutation rate 57, 119
squids 39
stabilizing selection 16, 78, 135
Steele, E. J. 7
stochastic process 30

iDarwin AS 0021 (2021 AD)
stop codon 107
stork 129
stratosphere 44
strength of natural selection 15
stromatolites 36
strong principle of inheritance 9
struggle for existence 67
struggle for life 67
Sturtevant, A. H. 93
subpopulation 25
substitution 56, 105
superhumans 150
symbiosis theory 34
Synapsida 42
synonymous alleles 124
synonymous changes 113
synonymous codons 131
synonymous substitutions 129
synthetic lethals 28
synthetic theory 103
synthetic theory of evolution ix, 18, 27, 86
systematic biology 2
TTakahata, Naoyuki 127
Tateno, Yoshio iv, vi, vii
taxonomy 2telocentric chromosomes 56
temperate zones 1
termination 107
terrestrial plants 38, 41
Tertiary Period 38
Tetrahymena 132
textbook x
thinking 141
third positions of codons 114
Thousand-armed Kannon 40

Volume 1
thymine 49
thymine dimer 58
total length of human DNA 50
total number of genes 57
transcription 50, 105transfer RNA 131
translation 50, 105translation efficiency 131translocation 54,55
transposable element 62transposition 56
Tree Village 66
treetops 1
Triassic 38
Trillium hagae 53
trilobites 37,42
triploid 53
trisomy 53
Triticum diccocum Schuebl 53
tropics 1
tsunami 42
tubulin 113
tug-of-war 56
tupai 45
type writing monkey 82
Uultraviolet light 58
ultraviolet radiation 35, 41
Universal Code All Good 107
universe ii
University of California 127
University of Chicago 23
University of Illinois 129
University of Texas 125, 129
University of Tokyo iv, 126
University of Wisconsin 23, 24, 29

52

uracil 50
urea cycle 138
VV-shaped chromosome 56
variance in fitness 76
vertebrates 37
vestigial organ 133
viability 16
viability polygenes 95
Vienna University 11
visible morphology 30
visible phenotypes 103
vowels 47
vultures 128
W
Wallace, A. R. 65
watch 83
Watson, J. 49
Wegener, Alfred 41
Weinberg, W. 18
Weismann, August 6, 7, 18
Weldon prize 16
Weldon, W. F. R. 15, 16, 79
whales 45
wheat 53
wild type gene 124
Wilson, A. C. 127
Wilson, E. O. 71
wing of a bat 70
wingless insects 38
Woese, C. 128
wolf 137
Wright, S. 16, 18, 20, 23-25, 72, 85, 91, 100
Wu, Chung-I 25

iDarwin AS 0021 (2021 AD)
X
X-ray 27
Xeroderma pigmentosum 58

Volume 1
February 12, AS 0021: this article ispublished in iDarwinYY chromosome 121
Yamada, Yukio 77
Yamao 133
Yasugi, Ryuichi 5
Yokoyama, Shozo 129
Yoshinaga, Yoshimasa xZzebra 77
zygotic array 89================================
Publication history of this article
December 12, AS 0020: Book Introduction
manuscript was submitted from Dr. SAITOU
Naruya to iDarwin (reviewed by SATTA
Yoko)
January 19, AS 0021: review result was sent
to author
January 19, AS 0021: revision was sent from
authorJanuary 20, AS 0021: this revision was
accepted for iDarwin
January 31, AS 0021: first proof of thisarticle was sent to author
53