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Evolution of Eukaryotes
10 9 8 7 6 5 4 3 2 1
Keywords
domains, bacteria, archaea, prokaryotes, missing links, evolutionary tree,
bioinformatics, ring of life, chromatin, histones, nucleosomes, epigen-
etic, central dogma, falsification, fabrication, plagiarism, mitochondria,
chloroplasts, orthologs, division of labor
Contents
Preface...................................................................................................ix
Acknowledgments....................................................................................xi
Introduction.........................................................................................xiii
Chapter 1 The Origins of Eukaryotes from Prokaryotes......................1
Chapter 2 Fitting a Genome into aTinyNucleus...............................9
Ethical, Legal, Social Implications: Ethical Guidelines
for Scientific Research...................................................14
Chapter 3 The Origins of Mitochondria and Chloroplasts................19
Chapter 4 The Evolution of Multicellular Organisms.......................25
Conclusion............................................................................................33
Glossary................................................................................................35
Index....................................................................................................37
Preface
This book the evolutionary origins of eukaryotic cells is part of a thirty
book series that collectively surveys all of the major themes in biology.
Rather than just present information as a collection of facts, the reader
is treated more like a scientist, which means the data behind the major
themes are presented. Reading any of the thirty books by Campbell and
Paradise provides readers with biological context and comprehensive per-
spective so that readers can learn important information from a single
book with the potential to see how the major themes span all size scales:
molecular, cellular, organismal, population and ecologic systems. The
major themes of biology encapsulate the entire discipline: information,
evolution, cells, homeostasis and emergent properties.
In the twentieth century, biology was taught with a heavy emphasis
on long lists of terms and many specific details. All of these details were
presented in a way that obscured a more comprehensive understanding.
In this book, readers will learn how eukaryotes evolved, how they stuff
all their DNA into the tiny nucleus, the origins of chloroplasts and mi-
tochondria as well as one way that multicellular organisms evolved, as
well as some of the supporting evidence behind our understanding. The
historic and more recent experiments and data will be explored. Instead of
believing or simply accepting information, readers of this book will learn
about the science behind the origins of eukaryotes the same way profes-
sional scientists dowith experimentation and data analysis. In short,
data are put back into the teaching of biological sciences.
Readers of this book who wish to see the textbook version of this
content can go to www.bio.davidson.edu/icb where they will find
pedagogically-designed and interactive Integrating Concepts in Biology for
introductory biology college courses or a high school AP Biology course.
Acknowledgments
Publishing this book would not have been possible without the generous
gift of Dr. David Botstein who shared some of his Breakthrough Prize
with AMC. Davids gift allowed us to hire talented artists (Tom Webster
and his staff at Lineworks, Inc.) and copyeditor Laura Loveall. Thanks go
to Kristen Mandava for project management and guidance on the pub-
lishing process. In particular, we are indebted to Katie Noble and Melissa
Hayban for their many hours of help and attention to detail.
Kristen Eshleman, Paul Brantley, Bill Hatfield and Olivia Booker
helped us with technology at Davidson College. We are grateful to ad-
ministrators Tom Ross, Clark Ross, Carol Quillen, Wendy Raymond,
Verna Case, and Barbara Lom who had confidence in us and encouraged
us to persist despite setbacks along the way.
These books were the product of the shared labor of my two vision-
ary coauthors Laurie Heyer and Chris Paradise. We shared the dream
and the hardships and developed this book from scratch. My family has
been very supportive and I thank Susan, Celeste and Paulina for their
support and patience. I also want to thank Jan Serie, my pedagogical
mentor, who taught me so much about the art and science of helping
students learn. I benefited from the support of the Howard Hughes Med-
ical Institute grant 52006292, the James G. Martin Genomics Program,
and Davidson College. This book would not have survived its first draft
without my students who endured the typos and the early versions of this
book. These undergraduates participated in a bold experiment to see if
beginners could construct their own knowledge, retain what they learned,
and transform the way they see themselves and the discipline of biology.
While many people said that beginning students were not up to the task,
my students proved them wrong.
Introduction
Eukaryotes occupy a unique place in the evolution of life. No other do-
main of life has cells with multiple internal organelles that are membrane
bound. Cells from no other domain of life contain organelles that carry
their own genomes. Eukaryotes are the only organisms that form multi-
cellular species produced after the fusion of two unrelated haploid cells.
And of course, only Eukaryotes can read books about biology. This book
examines four of the unique aspects of being eukaryotes. Perhaps the
most amazing feature of eukaryotes is the nucleus. The first chapter pres-
ents a subset of the data that revealed how the first nucleus evolved from
cells lacking nuclei. Once the nucleus appeared in the first eukaryote, a
new problem had to be solvedhow to jam all that DNA into a tiny
compartment. DNA is wrapped up to facilitate mitosis while still allow-
ing transcription to proceed. Plants carry not only nuclear genomes but
also mitochondrial and chloroplast genomes. Chapter three presents data
showing the origins of both of these genome-containing organelles. The
last chapter allows the read to evaluate data explaining one example of the
selective advantage provided by multicellularity. In addition to these four
case studies, this book will present research ethics and how scientists are
entrusted to conduct their research while maintaining high ethical stan-
dards. The four chapters of this book focus on evolution at the organismal
level by looking at the origins of complex life forms.
CHAPTER 1
When Charles Darwin was formulating his ideas about evolution, he drew
a branching tree to depict how individuals within a species can change
and give rise to several related species, just like we use tree-like pedigrees
to show family relationships among humans (Figure 1). In Darwins tree,
the letters A through D represent different species in a large genus. The
dotted branched lines represent the offspring of A, each with some varia-
tion. Species B to D did not diverge and went extinct, as noted by their
lines terminating before reaching the top of the page. Though his drawing
was simple, Darwins diagram had a profound effect on the way biologists
think about evolution. Only now, about 150 years later, is this way of
thinking slowly giving way to a new image. Figure 1 was Darwins only
picture in the entire 556-page 1859 edition of On the Origin of Species. As
everyone knows, trees sprout from seeds and form a trunk with branches
diverging in many directions. If life on Earth can be drawn as a tree, then
what was the seed and where is the trunk? The tree of life predisposed
biologists to think of evolution as a series of events with gradual, linear
progression toward the existing species. Whenever people go looking for
evidence to support a particular idea, they can bias themselves to find
what they were seeking even if alternatives exist.
In Darwins explanation of evolution, he stated, Only those varia-
tions which are in some way profitable will be preserved or naturally
selected. A dotted line crossing a horizontal line represents 1,000 genera-
tions. Variation would have accumulated until descendants of A looked
different from the original parent as denoted by a1 and m1. If a branch
reaches the very top line where a10, f10, and m10 are seen, then that spe-
cies avoided extinction. Darwin recognized that his diagram looked too
2 EVOLUTION OF EUKARYOTES
a10 f 10 m10
a9 f9 m9
a8 f8 k8 l8 m8
a7 f7 k7 l7 m7
a6 f6 k6 m6
a5 d5 k5 m5
a4 d4 i4 m4
a3 i3 m3
a2 s2 m2
a1 m1
GTTT TACC
GCTT TACG
GCAT
species evolved from which ancestor. If we use Darwins tree imagery and
focus on the central four bases, it is easier to understand (Figure 2).
To interpret the evolutionary tree in Figure 2, look at its base to find
the oldest species/sequence GCAT. From this ancestral sequence, three
events happened. On the middle branch, the original species remained
unchanged, GCAT. On the right branch, the sequence was first inverted
to TACG and later mutated at a single base to TACC. The left branch
mutated A to T and later mutated C to T. Each branch in this overly
simplified diagram indicates new species evolving due to changes in their
DNA. Remember that evolution is the change in allele frequency in pop-
ulation over time. The five species evolved at different times in the past
as indicated by the different lengths of the lines and the location of the
branch points. Using an evolutionary tree makes it possible to see which
species are more closely related because they share a common ancestor
The Origins of Eukaryotes from Prokaryotes 5
(a branch point), and conversely, which species are more distantly re-
lated. It is possible to imagine that producing an accurate tree would be
much easier if the data for every species was available (Figure 3). When
DNA analysis was conducted on highly conserved ribosomal genes from
many species, a more complex tree emerged. The ribosomal DNA-based
(rDNA, encoding rRNA) tree showed eukaryotes evolved from a com-
mon ancestor shared with archaea, and both domains evolving from a
common ancestor that also gave rise to eubacteria.
The nuclei of eukaryotic cells are surrounded by a pair of phospholipid
bilayers, which are similar to the pair of membranes surrounding pro-
karyote cells. Paired membranes also surround mitochondria and chloro-
plast, each of which contains DNA. For now, remember these membrane
similarities while continuing to learn about the origins of nuclei. When
investigators generated the evolutionary tree using rDNA sequences and
bioinformatics tools, they noticed some odd things. Most notably, the
mammals were barely distinguishable, because their sequences were nearly
identical for this highly conserved gene. The first lesson for generating
evolutionary tree is that highly conserved genes are better at revealing
distant relationships, but rapidly changing genes are better at distinguish-
ing closely related species. Therefore, it is impossible to find one gene that
could be used to determine the relationships of all species in the world.
For example, some evolutionary trees put birds closer to amphibians than
reptiles, even though biologists are certain that birds evolved from ancient
reptiles. It is good to remember that single gene evolutionary trees should
not be over-interpreted to indicate the relationships of all species. Trees
6 EVOLUTION OF EUKARYOTES
eukaryotes
bacteria archaea
species
by two membranes. The simplest solution to make sense of all these data
was to propose that an archaeal cell and an eubacterial cell combined
genomes with one cell engulfing the other. The original, abiotically pro-
duced cell was species alpha, which evolved and became what we would
recognize as a prokaryote. Later, a subset of prokaryotes diverged and
evolved into archaea and eubacteria. Millions of years later, one archaea
and one eubacteria fused their genomes and gave rise to eukarya.
With redundant genes in this new hybrid genome of the early eukary-
otes, portions of DNA were ejected to be more efficient by minimizing
the burden of replicating duplicate genes. Genes encoding complex pro-
cesses were retained in blocks from one genome rather than a mosaic of
individual genes from both combined genomes. For example, eukaryote
pathways related to DNA replication, transcription, and translation all
appear to be archaea in origin. Energy harvesting genes were retained
predominantly from the ancestral eubacteria genome rather than the ar-
chaea genome. Some eukaryotic processes, however, were retained as a
mosaic of genes from both archaea and eubacteria. It is time to stop using
the metaphor tree of life and time to consider the ring of life, which
represents more accurately how the three domains evolved. Humans tend
to prefer tidy rules and clear distinctions. However, evolution does not
8 EVOLUTION OF EUKARYOTES
follow a set plan, nor is it linear in the adaptations that are selected over
time. The ring of life is probably more accurate than the tree of life,
and so Darwin was off a bit on his model. However, a scientific model
does not have to be correct in order to be useful. Darwin helped society
see how species were related to each other through heredity. He com-
municated how species alive today provide a partial clue to the evolution
of species over millions of years. The genome sequences available today
are similar to a puzzle with several pieces missing, because we have not
sequenced all possible genomes. It may be impossible to determine all the
details, but each experiment makes it easier to understand the origin of
life and the evolutionary relationships between species.
Bibliography
Fuerst JA, Webb RI. Membrane-bounded nucleoid in the eubacterium
Gemmata obscuriglobus. Proc Natl Acad Sci USA 88(18):81848188,
1991.
Horiike T, Hamada K, Kanaya S, et al. Origin of eukaryotic cell nuclei by
symbiosis of Archaea in bacteria is revealed by homology-hit analysis.
Nat Cell Biol 3(2):210214, 2001.
Martin W, Embley TM. Evolutionary biology: early evolution comes full
circle. Nature 431(7005):134137, 2004.
Rivera MC, Lake JA. The ring of life provides evidence for a genome
fusion origin of eukaryotes. Nature 431(7005):152155, 2004.
Index
Adult human cells, human embryonic nuclei of eukaryotic cells, 56
stem cells from, 15 overview of, 12
-proteobacteria, 23 packing of, 10
proteins importance of, 23
Bell, Graham, 2728 sequencing of, 34
Bioinformatics tools, 5 stretched-out length of, 9
BLAST sequence template for RNA production, 18
alignment tool, 6 visualize packing of, 10
human gene evaluation by, 67
Bootstrap values, 20 Energy harvesting genes, 7
Brenner, Sydney, 3 Epigenetic regulation, 13, 14
Eukaryotes from prokaryotes,
Cell biology, 13 originsof, 18
Chlamydomonas, 27 Evolutionary trees, 20
Chloroplasts, origins of, 1923 branching pattern of, 2021
Chromatin, 9 interpretation of, 45
from chicken cells, 11 of Volvox, 26
higher levels of, 11
histone complex in, 10 Falsification, fabrication, and
protein as temporary glue, 12 plagiarism (FFP), 1415
Chromosomes, 12
Colonial cells, 2526 Gel electrophoresis, 2, 3
Colonial green algae, 27 Gemmata obscuriglobus, 3
Covalent modulation, of histones, 13 Genes encoding complex
Cyanobacteria, 23, 23 processes, 7
Cytoplasmic communication Genome
systems,6 ethical, legal, social implications,
1416
Darwin, Charles, 1 into nucleus, 914
Darwinesque tree, 67 Gonium, 30
Division of labor
among individual cells, 27 Histones, 910
selective advantage of, 2728 amino acid conservation among,
DNA 1314
accessible for replication and complex in chromatin, 10
transcription, 9 covalent modulation of, 13
based evolutionary tree, 20 Human embryonic stem cells from
BLAST sequence alignment tool, 6 adult human cells, cases of
of chromosomes, 910 misconduct in, 15
compaction in eukaryotes, 14 Human eye cells, 2
genes encoding complex, 78 Human gene, by BLAST sequence, 6
genetic information, source of, 2 Human nucleus, diameter of, 9
38 INDEX
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