Introduction to Evolutionary Genomics

518 Pages·2018·15.03 MB·English

by  Naruya Saitou

Computational Biology
Naruya Saitou
Introduction to
Evolutionary
Genomics
Second Edition
Computational Biology
Volume 17
Editors-in-Chief
Andreas Dress
CAS-MPG PartnerInstitute for Computational Biology,Shanghai, China
Michal Linial
HebrewUniversity of Jerusalem,Jerusalem, Israel
OlgaTroyanskaya
Princeton University, Princeton, NJ, USA
Martin Vingron
MaxPlanckInstitute for Molecular Genetics, Berlin,Germany
Editorial Board
RobertGiegerich, University of Bielefeld,Bielefeld, Germany
Janet Kelso, MaxPlanckInstitute for Evolutionary Anthropology, Leipzig, Germany
Gene Myers, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden,
Germany
PavelPevzner, University of California,San Diego, CA,USA
Advisory Board
Gordon Crippen, University of Michigan,Ann Arbor,MI,USA
JosephFelsenstein, University of Washington,Seattle, WA,USA
Dan Gusfield,University of California, Davis, CA,USA
Sorin Istrail, Brown University, Providence,RI, USA
ThomasLengauer, MaxPlanckInstitute forComputer Science, Saarbrücken, Germany
Marcella McClure, MontanaState University, Bozeman,MO, USA
Martin Nowak, HarvardUniversity, Cambridge, MA, USA
DavidSankoff, University of Ottawa,Ottawa, ON,Canada
RonShamir, TelAvivUniversity, TelAviv, Israel
Mike Steel,University ofCanterbury, Christchurch, NewZealand
Gary Stormo,Washington University in St.Louis, St.Louis, MO, USA
Simon Tavaré,University ofCambridge, Cambridge, USA
Tandy Warnow,The University of Illinois at Urbana-Champaign, Urbana,IL, USA
LonnieWelch, OhioUniversity, Athens, OH, USA
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Naruya Saitou
Introduction
to Evolutionary Genomics
Second Edition
123
Naruya Saitou
Division of Population Genetics
National Institute ofGenetics (NIG)
Mishima, Shizuoka, Japan
ISSN 1568-2684
Computational Biology
ISBN978-3-319-92641-4 ISBN978-3-319-92642-1 (eBook)
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I would like to dedicate this book to
Dr. Masatoshi Nei, the academic supervisor
of my Houston days 1982–1986.
Preface
All Biology Aspire to Evolution
Organisms on the earth are rich in diversity. Each organism also contains its own
genomewithmanygenes.Thesecomplexgeneticsystemshavebeengeneratedand
constantlymodifiedthrougheonsofevolutionsincetheoriginoflife.Evolutionary
study is thus indispensable for gaining the unified view of life. Because even a
single-cell bacterium is so complex, we have to study its genetic entity, that is, its
genome,toacquireacomprehensiveviewoftheorganism.Iwilldiscussevolution
oforganismsfromtheviewpointoftemporalchangesofgenomesandmethodsfor
their study in this book, titled Introduction to Evolutionary Genomics. This is the
secondedition,5yearsafterthefirstedition[1]waspublishedin2013basedonthe
textbook written in Japanese in 2007 [2].
Evolutionisthetemporalprocessoflife.Originally,theword“evolution”meant
thedevelopmentofembryofromegg.CharlesLyellwasprobablythefirstpersonto
use this word in the modern meaning in his “Principles of Geology” published in
1830[3].ThankstothepioneeringworksofLamarck[4],Darwin[5],andWallace
[6], evolution as a biological phenomenon was gradually accepted during the last
200 years (see also Saitou [7]). Evolution, however, does not contain a predeter-
mined pathway, unlike developmental processes. As the time arrow moves from
past to present, life forms gradually change. Therefore, any temporal change of
organismsisevolution.Nowadays,theconceptofevolutionissometimesextended
to nonlife, such as evolution of the universe or evolution of the human society.
Evolutionary changes already started even before the origin of life, known as
chemicalevolution.Therefore,weneedtodigdowntothemolecularlevel,starting
from nucleotides and amino acids. In this sense, it is logically straightforward to
study evolution of life at the molecular level, that is, molecular evolution.
Molecular evolutionary study as a discipline was established only after biochem-
istry and genetics became the center of biology in the middle of the twentieth
century. Because of this late start, there are still some molecular biologists who
considerthestudyofevolutionascarriedoutbyspecializedresearchers,whilethere
aresomeold-fashionedevolutionistswhodonotappreciatemolecular-levelstudies.
vii
viii Preface
It would be my great pleasure if such people change their minds after reading this
book. But, of course, I hope that the majority of readers of this book are young
students and researchers. Following Walter Pater’s epigram—“All art constantly
aspirestowardstheconditionofmusic.”—Iwouldliketoconcludethissectionwith
my epigram:
Allbiologyaspiretoevolution.
What is a Genome?
Theword“genome”wascoinedin1920bybotanistHansWinkler[8].Geneswere
already localized in chromosomes in the cell nucleus at that time, and Winkler
joined two words, “gene” and “chromosome,” to produce a new word “genome.”
Plants are often polyploids, and there was a need to designate a certain unit of
chromosome sets. Later, in 1930, Hitoshi Kihara [9] defined the genome as a
minimum set of genes that are necessary for that organism. This function-oriented
definitionisstillusedtoday,butshifttothestructure-orienteddefinitionisgoingon.
Iredefinedthegenomeas“amaximumunitofself-replicatingbody”in2004[10].
A“self-replicatingbody”includesnotonlyusualorganismsbutalsoorganellaand
virus that do replicate but may not be considered as authentic organisms. Kihara
and his group conducted genome analysis on various wheat species in the early
twentieth century, and he coined this famous couplet:
Thehistoryoftheearthisrecordedinthelayersofitscrust;
Thehistoryofallorganismsisinscribedinthechromosomes.
ThiscoupletwasoriginallymentionedinKihara[11]andisincreasinglybecome
evident as we now study evolution at the genome (=chromosome) sequence level.
The word “genome” also implies completeness. It is important to grasp all the
genetic information contained in a single organism, because the whole gene set
mostly determines life patterns ofits organism. However, all genes inone genome
arenotsufficientforthatorganismtoexist.Thisinsufficiencyisclearifwelookat
genomes of parasites. For example, the genome of causative bacteria of leprosy,
Mycobacterium leprae, has many pseudogenes [12]. This bacteria apparently lost
its functional genes through a long parasitic life due to dependence on hosts. We
shouldrememberthatallorganismsonearthareinteractingwitheachother.Known
host–parasite relationships are the only prominent examples. Our human genome
gives a good example of dependency on nonhuman genomes.
Vitamins, by definition, cannot be synthesized inside the organism body in
question, and we need to obtain them through various foods. For example, defi-
ciency of vitamin C, or ascorbic acid, causes scurvy. Many nonhuman organisms
do produce ascorbic acid, as they have its chemical pathway. A gene for enzyme
Preface ix
L-gulonolactoneoxidase(E.C.no.1.1.3.8)becameapseudogene(nonfunctional)in
the common ancestor of human and Old World monkeys, and we are no longer
producing ascorbic acid, as shown by Nishikimi and his collaborators [13]. In any
case, an organism cannot survive alone. We have to always consider the environ-
ment surrounding an organism.
Everything is History
Life is a product of evolution, and there are so many chance effects. For example,
spontaneousmutationsappearrandomly.Mostofthemutationsthatlastalongtime
in the history of life are selectively neutral, and they were chosen through the
random genetic drift as emphasized by Kimura [14] and Nei [15]. Furthermore,
there are so many inorganic factors that drastically change the environment of the
earth. Examples are volcanic activities, ice ages, continental drifts, and asteroid
impacts. These events occur most probably independently from the organismic
world. These historical processes are also dominated by chance effects.
As mutations arise, some disappear while the others remain. This process is
impossible to be fully explained through the logical cause and effect style of
mechanism.Thisisnotrestrictedtolife.Anyexistenceinthisuniverseistransient,
andtherealwaysexistsahistory,asHitoshiKiharapointedoutinhiscouplet.After
all,everythingishistory.Therefore,theessenceofnaturalscienceistodescribethe
historyoftheuniverseatvariouslevelsasSaitou[16]declared.Often,itisclaimed
that the ultimate goal of natural science is to discover the laws of nature, and the
description of nature is only one process to the eventual finding of some hidden
laws.Itfailstoputfirstthingsfirst.So-callednaturallawsaremeretoolsofhumans
for an effective description of natural phenomena. A phenomenon that can be
described succinctly is relatively simple, while it is difficult to extract some laws
from a complex phenomenon. However, such difference comes from the phe-
nomenathemselves,andtheobjectiveofnaturalscienceshouldnotberestrictedto
phenomenafromwhichitiseasytofindsomerelationshipscalled“laws.”Itshould
benotedthatgivingaflatdescriptionofeverythingisnotenough.Humanabilityto
recognize the world is physically limited, and a structured description of the his-
torical process is definitely necessary, depending on the content of each phe-
nomenon. In this sense, the time axis, which is the most important for organismal
evolution, is obligatory for the description of the nature itself. With the above
argument in mind, I am quite confident that the very historical nature of genomes
with its self-replication mechanism has the key to overcome the mechanistic view
of this universe.
x Preface
Vitalism Versus Mechanism
If we consider the history of biology, one viewpoint is a controversy between
vitalismandmechanism.Vitalismmaintainsthatlifehasauniquelawthatdoesnot
exist in nonlife forms, and thus it is dualistic. Mechanism is monistic, for it states
that lifeonlyfollowsphysicochemical lawsthat govern inorganic matters.Inother
words, there is no specific difference between organism and inorganic matters
accordingto themechanistic view. The longhistoryofbiologymay beconsidered
as series of victories of mechanism against vitalism; e.g., see Saitou [17]. For
example, William Harvey in the seventeenth century discovered that the heart is a
pump for blood circulation, and Eduard Buchner in the nineteenth century dis-
covered enzyme function in a cell-free system. Biochemistry and genetics are two
main fields of biology where the mechanistic viewpoint is always emphasized.
Molecular biology inherited this aspect from these two disciplines.
Some biologists, however, were strong proponents of vitalism. Hans Driesch, a
developmental biologist in the early twentieth century, examined development of
sea urchin and discovered that two- or four-cell stage embryo can develop adult
individuals even after they were separated. Because of this utterly mysterious
process,Driesch [18]proposedtheexistence of“entelechy”onlyinorganism.Itis
true that the animal development is still not completely known. If we consider the
informationflowbetweennucleicacids(RNAorDNA)andproteinsinsideacell,it
isnotsurprisingthatabiologist,whowasactivebeforetheriseofcomputerscience
intheearlytwentiethcentury,believedinsomemagicalpoweronthisinformation
flow.
Thereisstilltheremnantofadualisticviewsimilartovitalism,toconsidermind
andbodyastotallyseparateentities.Asvitalismtriedtodemarcateorganismsfrom
inorganic matters, this dualistic view tries to demarcate the mind from the body.
However, a logical consequence of the mechanistic view of life is, of course, to
explain the mind as some special organismic processes, most probably neuronal
ones.Thatis,themindexistsonabody,andthesetwoareinseparable.Incontrast,
may religions assume the clear dichotomy between mind and body. We biologists
shouldkeepdistancefromsuchreligionssoastodevelopbiologyontherighttrack.
Explosion of Genome and Transcriptome Data
Frederick Sanger and his research group applied their own new method [19] of
nucleotide sequencing for determination of the whole bacteriophage genome with
about 3kb [20]. They then determined the complete human mitochondrial DNA
genomeofca.16,500bp[21],followedbycompletemitochondrialDNAgenomes
ofmouse[22]andcow[23].Theseeffortsinthe1980swerebeginningsofgenome
sequence-basedbiology.Thenin1995,firstbacterialgenomewasdetermined[24],
followed by the first eukaryote genome in 1996 [25]. After the determination of
euchromatic regions of the human genome in 2004 [26], cost of de novo genome
sequencing drastically dropped thanks to the rise of next-generation sequencing
technologies (see Chap. 13 of this book). Nowadays, genome sequencing is