Original PDF Molecular and Genome Evolution PDF
Original PDF Molecular and Genome Evolution PDF
Original PDF Molecular and Genome Evolution PDF
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GRAUR
Molecular
Genome Evolution
Molecular and
and
Genome Evolution
I S B N 978-1-60535-469-9
9 781605 354699
Introduction 1
Molecular and Genome Evolution took more than a dozen years to put together. Like
all books, it could have benefited from twelve more years of contemplation, writing,
and editing. However, as writer and critic Roger Angell astutely observed, a published
book is one that the author lets go of in the end.
I am indebted to Bill Martin for supporting this project. His willingness to volun-
teer his time, his encyclopedic knowledge of all things biological, and his uncompro-
mising love of the scientific method are greatly appreciated.
My colleagues Amy Sater and Tim Cooper wrote two chapters (Chapters 12 and 13,
respectively) for this book. I wish to express my appreciation for their hard work and
willingness to undertake such a thankless and time-consuming task.
My former student Yichen Zheng thoroughly reviewed and fact-checked the manu-
script. I especially thank him for providing me with his unique points of view. Obvi-
ously, all remaining errors in the book are mine and mine only.
I am indebted to many mentors, colleagues, students, friends, and family mem-
bers for helping me put this book together. Their comments, suggestions, corrections,
discussions, and support are gratefully acknowledged. For favors great and small, I
thank Joshua Akey, John Allen, Katarina Andreasen, Lara Appleby, Ricardo Aze-
vedo, Marc Bailly-Bechet, Suganthi Balasubramanian, Michael Baudis, Dror Berel,
David Bogomil, Luciano Brocchieri, Joseph Brown, Lilia Cañas, Reed Cartwright,
Suneetha Chandanam, Benny Chor, Zofia Chrzanowska-Lightowlers, Laura Clag-
horn, Wyatt Travis Clark, Blaine Cole, Keith Cooper, Kerri Crawford, Aaron Darling,
Brigitte Dauwalder, Nora Dethloff, Lou Doucette, Stuart Dryer, Peng Du, Margaret
Dunn, Claire Duval, Xander Duval, Chris Elsik, J. J. Emerson, Toshinori Endo, Kiyoshi
Ezawa, Cédric Feschotte, Yuriy Fofanov, George Fox, Tony Frankino, Noga Ganany,
Mark Gerestein, Takashi Gojobori, Uri Gophna, Valer Gotea, Brenton Graveley, Pre-
ethi Gunaratne, Inna Gur-El, Penny Grant, Inar Graur, Lilla Graur, Mina Graur, Or
Graur, Sara Graur, Matthew Hahn, Dov Herskowits, Varda Herskowits, Simon Ho,
Hoang Hoang, Corey Hryc, Dorothée Huchon, Toby Hunt, Rhonda James, Spencer
Johnston, Krešimir Josić, Jerzy Jurka, Aurélie Kapusta, Patrick Keeling, Erin Kelleher,
Selina Khan, Marek Kimmel, Eugene Koonin, Dušan Kordiš, Shigefumi Kuwahara,
Amanda Larracuente, Jennifer Leonard, William Lewis, Wen-Hsiung Li, Wenfu Li,
Miao-Suey Lin, Jean Lobry, Hongan Long, Mannie Magid, Edward Max, Itay May-
rose, Michael McDonald, James McInerney, David McIntyre, Rich Meisel, Katsuhiko
Mineta, Claudine Montgelard, Larry Moran, Etsuko Moriyama, Joram Mwacharo,
Michael Nachman, Luay Nakhleh, Masatoshi Nei, Hoa Nguyen, Yoshihito Niimura,
Norihiro Okada, Elizabeth Ostrowski, Sally Otto, Amanda Paul, Itala Paz, Steven
Pennings, Nicole Perna, David Pollock, Ovidiu Popa, Mark Ptashne, Yonia Pulido,
Longyi Qi, Eduardo Rocha, Matthew Rockman, Mayo Roettger, Gregg Roman, Jef-
frey Ross-Ibarra, Naruya Saitou, Betsy Salazar, Rafael Sanjuán, Amy Sater, Stanley
Sawyer, Manoj Samanta, Sahotra Sarkar, Yoko Satta, Marie Scavotto, Alan Schulman,
Dean Scudder, Andy Sinauer, Chris Small, Kevin Spring, Arlin Stoltzfus, Dave Tang,
Mallory Travis, Tamir Tuller, Yun-Huei Tzeng, Esther van der Knaap, Moshe Vardi,
Lillian Warren, Hidemi Watanabe, John Welch, Dan Wells, Paul Wheeler, Thomas
Wicker, William Widger, Diane Wiernasz, Carol Wigg, Ben Wilson, Melissa Wilson
Sayres, Yuri Wolf, David Wool, Itai Yanai, Hsin-Yi Yeh, Hye-Jeong Yeo, Soojin Yi, Fei
Yuan, Zhengdong Zhang, Lei Zhao, and Rebecca Zufall.
Acknowledgments ix
In the Babylonian Talmud, wisdom is likened to a tree: “Just as a small tree may
set on fire a bigger tree, so too it is with scholars, the younger sharpen the minds of
the older.” As was the case with second century Talmudic sage Haninah, I too “have
learnt much from my teachers, and from my colleagues more than from all my teach-
ers, and from my students more than from them all.” I therefore thank my former
Ph.D. students, Tal Dagan, Eran Elhaik, Einat Hazkani-Covo, Giddy Landan, Ron
Ophir, Nicholas Price, Tal Pupko, Niv Sabath, Shaul Shaul, and Yichen Zheng, for
teaching me almost everything that I know.
At the University of Houston, I have benefited from support from a John and Re-
becca Moores Professorship. I owe special gratitude to the Alexander von Humboldt
Foundation, which has consistently supported my most significant scientific accom-
plishments since 1985.
Finally, I owe a great intellectual debt to my academic mentor and friend, David
Wool, who has encouraged me and advised me for more than 37 years.
Dan Graur
University of Houston
Table of Contents
Introduction 1
If you’re alive, it’s because your ancestors were the best survivalists
They were the finalists in the genetic Olympic Games
Every one of your ancestors survived to reproductive age
And they were all better than their competitors at getting laid
Otherwise, you wouldn’t be sitting here today.
Baba Brinkman
“Darwin’s Acid” (2009)
dogenes that have no functioning counterparts. Because of gene death, humans have
to get their vitamin C from oranges and cats are not tempted by sweets. Interestingly,
functionlessness may even be advantageous. Akin to an empty ecological niche, a
gene’s death may create opportunities for subsequent mutations.
Evolutionary biologists, like most people, have a fascination with Homo sapiens.
Humans, however, do not occupy a privileged position in that grand scheme of things
called “evolution.” The human genome is smaller than that of an onion and contains
fewer protein-coding genes than cassava. Human biology is infinitely more boring
than that of ciliates, human population numbers are dwarfed by those of tardigrades,
and human genetic variability is negligible in comparison to that of the nematode
Caenorhabditis brenneri. Ever since Copernicus, our anthropocentric worldview has
repeatedly been shown to be erroneous, yet we continue to spend billions of dollars
in search of human genomic perfection, producing along the way a great many head-
lines and precious little science.
Finally, the same rules of evolutionary biology apply to all levels of its study. The
rules at the DNA level are the same as the rules at the protein level, which in turn are
the same as the rules at the morphological level. The only difference is one of resolu-
tion. Biochemists, computer jocks, medical doctors, and others who have exempted
themselves from ever studying evolutionary biology have been known to invoke “par-
adigm shifts” in our understanding of evolution as frequently as men with prostatic
hyperplasia urinate. Such bombastic proclamations may make good headlines, but
they are almost never true.
Understanding a handful of principles is all there is to evolutionary biology. The
rest is details. Molecular and Genome Evolution is about the details.
1
chapter
T his chapter provides some basics in molecular biology that are necessary
for studying evolutionary processes at the DNA, RNA, and protein levels. In
particular, we discuss the structure of the hereditary material, the attributes of
the different kinds of genes and their products, the structure of genetic codes,
and the various types of mutation.
Nucleotide Sequences
The hereditary information of all living organisms, with the exception of some
viruses, is carried by deoxyribonucleic acid (DNA) molecules. DNA usually
consists of two antiparallel complementary strands twisted around each other
to form a right-handed double helix (Figure 1.1). Each strand is a linear polynu-
cleotide consisting of four kinds of nucleotides. A nucleotide is a molecule that
consists of a pentose (five-carbon) sugar, a phosphate group, and a purine or
pyrimidine base. A nucleotide without the phosphate group is called a nucleo-
side. In DNA, the nucleotides are deoxyribonucleotides, i.e., they contain the
sugar deoxyribose. There are two purines, adenine (A) and guanine (G), and
two pyrimidines, thymine (T) and cytosine (C). All one-letter abbreviations are
listed in Table 1.1.
The backbone of the DNA molecule consists of deoxyribose-phosphate
moieties covalently linked in tandem by asymmetrical 5′—3′ phosphodiester
bonds. Consequently, the DNA molecule is polar (or directional), one end hav-
ing a phosphoryl radical (—P) on the 5′ carbon of the terminal nucleotide, the
other with a free hydroxyl (—OH) on the 3′ carbon of the terminal nucleotide.
The direction of the phosphodiester bonds determines the molecule’s charac-
ter; thus, the sequence 5′—G—C—A—A—T—3′ is different from the sequence
3′—G—C—A—A—T—5′. As a rule, the phosphodiester bonds are omitted and
the nucleotides in the DNA sequence are written from the 5′ end to the 3′ end.
Hence, the sequence 5′—G—C—A—A—T—3′ is written as GCAAT. Relative to
a given location of a nucleotide in a DNA sequence, the 5′ and the 3′ directions
are referred to as upstream and downstream, respectively.
6 Chapter 1
5′ Heavy
3′ strand Light
strand
5′ Weak bond 3′
– O
O
O NH2
A P T OH
– O N HN
N
G C O
N
A
G C O N
O O
N
A
–
O O
3.4 nm P
O
T A
O
NH2
O O N
Sugar
O
P
G C
– O
C (deoxyribose)
A T
O N HN G N
O N
N
C G
O
O NH2
– Phosphodiester
O
bond
O
C O P
Deoxyribose- O O
A T phosphate O NH2
P T
O
C G backbone – O N HN
N
O N
A T A
O O
N O
N
–
O O
NH2
O P O
O O
P
3′
O
5′
O
N N
C
–
O N
NH
2 nm G
O N O O
N
NH2
Figure 1.1 The right-handed
–
double helix (left) and a schematic O O
representation of the antiparallel OH
Strong bond
P O
structure of double-stranded DNA –
O
(right). The antiparallelism is em- 3′
5′
phasized by the blue arrows. Note
complementary base pairing by
means of hydrogen bonds (dotted The two strands of DNA are joined throughout their lengths by hydrogen bonds
lines) between thymine and adenine
between pairs of nucleotides. A purine always pairs with a pyrimidine (Figure 1.1).
(weak bond) and cytosine and gua-
nine (strong bond). Specifically, adenine pairs with thymine by means of two hydrogen bonds (the weak
bond) and guanine pairs with cytosine by means of three hydrogen bonds (the strong
bond). These complementary pairs, commonly written as G:C and A:T, are also called
the canonical or Watson-Crick base pairs. Because of complementarity, usually only
one strand needs to be specified. In the double helix, the heavy strand is the one
containing more than 50% of the heavier nucleotides, the purines A and G. The light
strand is the one that contains more than 50% of the pyrimidines C and T.
Ribonucleic acid (RNA) is found as either a single- or double-stranded molecule.
RNA differs from DNA by having ribose instead of deoxyribose as its backbone
sugar moiety, and by using the nucleotide uracil (U) in place of thymine. Adenine,
cytosine, guanine, thymine, and uracil are referred to as the standard nucleotides.
Some functional RNA molecules, most notably transfer RNAs, contain nonstandard
nucleotides, i.e., nucleotides other than A, C, T, U, and G, that have been derived by
chemical modification of standard nucleotides after the transcription of the RNA. In
Graur 1e addition to the canonical complementary base pairs, which in RNA are G:C and A:U,
Sinauer Associates
Morales Studio
the G:U pair is also stable in RNA. (In DNA, stable pairing does not occur between
Graur1e_01.01.ai 08-14-15 11-06-15 G and T.)
The length of a single-stranded nucleic acid is measured in number of nucleotides.
That of a double-stranded sequence is measured in base pairs (bp), thousands of base
pairs (kilobases, Kb), millions of base pairs (megabases, Mb), or billions of base pairs
(gigabases, Gb).
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