Evolution of Eukaryotes

Evolution of Eukaryotes

A. Malcolm Campbell, PhD

Christopher J. Paradise, PhD
Evolution of Eukaryotes
Copyright A. Malcolm Campbell and Christopher J. Paradise. 2016.

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 Abstract
Many people have a vague sense that the hypothesized origin of life, in the
form of bacteria, sounds plausible. However, few people can fathom how the
first eukaryotic cell, complete with nucleus, mitochondria and maybe chlo-
roplast, came into being. This book presents the evidence that reveals the
origins of all three DNA-containing organelles. In addition, this book will
illustrate how DNA, a molecule that is 2 meters (6 feet) long, can fit into all
cells nuclei that are only about 2 microns (0.000002 meters) in diameter.
Once eukaryotes evolved, the next obvious question is how multicellular
organism could have evolved from simpler unicellular species. This book
looks at multicellular algae as a case study on the origins of multicellularity.

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

The Origins of Eukaryotes

from Prokaryotes

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

Figure 1 Tree of life from Darwins On the Origin of Species. Species

B, C, and D went extinct, but species A continued to evolve over time
(vertical axis) to give rise to the three species listed at the top.
Source: Reproduced from Darwin, 1859.

regular. He explained, I do not suppose that the process ever goes on so

regularly as is represented in the diagram.
Darwin knew it would be difficult to formulate rules in a field where
the object of study changes over time. Biology is an unusual science in that
it is very difficult to make broad statements without citing exceptions. For
example, plants do not move, except algae that can swim; birds fly, except
kiwi, ostrich, and penguins; lizards have four legs, except for the legless
ones, and so on. Similarly, it is difficult to construct a set of rules that
can distinguish all eukaryotes with nuclei from the other two domains
of life: bacteria and archaea. For example, a very common misconcep-
tion is that only eukaryotes have internal membrane-bound organelles,
and prokaryotes lack internal membranes. This misconception is incor-
rect and some prokaryotes do have internal membranes. Cyanobacteria
 The Origins of Eukaryotes from Prokaryotes 3

are a very common prokaryote that have stacks of photosynthetic mem-

branes similar to the structures found inside chloroplasts. A quick search
of the Internet for images using the terms Cyanobacteria EM will reveal
many internal membranes. Another Internet search for a large bacterium
called Gemmata obscuriglobus will result in electron micrographs showing
internal membranes. This species has an internal double-membrane that
is attached to the inner cell membrane and surrounds a fibrous-looking
genome and a granular matrix. G. obscuriglobus looks like a prokaryote
with an primitive nucleus. Prokaryotes with membrane-bound organelles
reinforce the truism in biology: Rules without exceptions are rare.
In G. obscuriglobus, one can observed a structure that looks transi-
tional, as if the bacterium is trapped between its evolutionary past and a
future species yet to come. Transitional species are sometimes referred to
as missing links, as if all of evolution were a chain and each species a
link. If someone were to hold two halves of a chain with an anchor on one
side and a boat on the other, it would be logical to suspect a chain link
was missing that used to connect the two halves. Similarly, lungfish have
lungs and gills and are a link in the evolution of fish from water to land
dwellers and the beginning of amphibians. However, one cannot realisti-
cally expect every transitional species to survive unchanged for millions
of years while other species continue to change and compete for limited
resources. In the absence of live missing links, scientists need alternative
data to search for clues about the first eukaryotes and how they came into
being from prokaryotes. This chapter will present DNA evidence about
the origin of the eukaryote nucleus, because gene sequences contain clues
about how our eukaryotic relatives evolved the first nucleus.
When DNA sequencing became readily available, biologists searched
for the best gene to sequence in order to uncover the evolutionary rela-
tionships of all species to complete Darwins tree of life. They reasoned
that if each species evolved from a previous species, then it should be
possible to discern the relationship between ancestral and modern species
by comparing their DNA. Lets look at a simplistic example of five hypo-
thetical species and their contrived DNA (Table 1).
Table 1 shows how the DNAs are similar to each other, indicating they
are closely related, but the middle four bases (bold font) have changed
over time. It should be possible to use these sequences to determine which
4 EVOLUTION OF EUKARYOTES

Table 1 Simplistic examples of DNA sequences that reveal

evolutionary relatedness.
hypothetical species names contrived DNA sequences
S. singularis GCATGCATGCAT
S. doubletus GCATGCTTGCAT
S. tripletus GCATGTTTGCAT
S. reversus GCATTACGGCAT
S. reversusdoublecus GCATTACCGCAT

GTTT TACC

GCTT TACG

GCAT

Figure 2 Evolutionary tree showing the changes in simulated DNA

(from Table 1) over time, the vertical axis. The original species at the
base is represented by the variable sequence GCAT. Only the four
central bases are shown in the tree for clarity.
Source: Original Art.

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

Eubacteria Archaea Eukarya

Figure 3 Evolutionary tree based only on ribosomal genes from many

species. Each domain is labeled, with archaea and eukarya sharing a
common ancestor.
Source: From Woese et al., 1990. Modified from their Figure 1.

(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

Table 2 Subset of results from BLASTing human protein

sequences against microbial protein sequences.
human protein protein protein best match
number function location domain
NP_001009 translation cytoplasm/rER archaea
NP_003185.1 transcription factor nucleus archaea
NP_001001937 ATP synthase mitochondria bacteria
NP_005521 energy harvesting mitochondria bacteria
NP_000393 energy harvesting cytoplasm bacteria
NP_004138 cell signaling cytoplasm archaea
NP_061816 cytoskeleton cytoplasm bacteria
Source: Original table.

based on gene sequence alignments are best at evaluating the conservation

of sequences for particular genes not entire species.
Rather than comparing just one gene across many species, a group of
genomicists evaluated every human gene by using the BLAST sequence
alignment tool against many prokaryotic genomes sequences (Table 2).
Their goal was to see if they could detect a pattern of evolutionary linkage
between eukaryotes (humans) and prokaryotes. Rather than comparing
nucleotides, they used the genetic code to convert all the gene sequences
to amino acid sequences prior to using the BLAST tool.
From the BLAST results similar to those in Table 2, the scientists
noticed that some human proteins are more closely related to eubacte-
ria, whereas others are more closely related to archaea. Human proteins
involved in energy production are more similar to bacteria proteins, but
human transcription and translation proteins are more similar to archaea
proteins. Signaling and cytoskeleton are both cytoplasmic communica-
tion systems, and they were split between the two microbial domains.
Using information similar to those from the protein BLAST results, sci-
entists found it difficult to draw a single tree that accurately represented
the evolutionary origins of all human proteins. Which gene would be the
best one to help understand the evolutionary origin of eukaryotes? When
investigators finally let go of their bias toward a Darwinesque tree, they
realized what had happened (Figure 4). This tree looked very different
from a typical Darwinian tree. Humans and all eukaryotes contain genes
from both eubacteria and archaea that diverged from a common ancestor
long ago, species . Furthermore, nuclei and prokaryotes are surrounded
 The Origins of Eukaryotes from Prokaryotes 7

eukaryotes
bacteria archaea

species 

Figure 4 Non-tree based evolutionary relationships. This diagram

illustrates how a primitive species a could diverge into two branches,
which later merged genomes to produce a third branch that became
eukaryotes. Note the atypical branching structure with a hole in the
middle.
Source: Data from Campbell and Heyer textbook Discovering Genomics, Proteomics, and
Bioinformatics. Figure 3.11.

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
stem cells from, 15
-proteobacteria, 23
Bell, Graham, 2728
Bioinformatics tools, 5
BLAST sequence
alignment tool, 6
human gene evaluation by, 67
Bootstrap values, 20
Brenner, Sydney, 3
Cell biology, 13
Chlamydomonas, 27
Chloroplasts, origins of, 1923
Chromatin, 9
from chicken cells, 11
higher levels of, 11
histone complex in, 10
protein as temporary glue, 12
Chromosomes, 12
Colonial cells, 2526
Colonial green algae, 27
Covalent modulation, of histones, 13
Cyanobacteria, 23, 23
Cytoplasmic communication
systems,6
Darwin, Charles, 1
Darwinesque tree, 67
Division of labor
among individual cells, 27
selective advantage of, 2728
DNA
accessible for replication and
transcription, 9
based evolutionary tree, 20
BLAST sequence alignment tool, 6
of chromosomes, 910
compaction in eukaryotes, 14
genes encoding complex, 78
genetic information, source of, 2
nuclei of eukaryotic cells, 56
overview of, 12
packing of, 10
proteins importance of, 23
sequencing of, 34
stretched-out length of, 9
template for RNA production, 18
visualize packing of, 10
Energy harvesting genes, 7
Epigenetic regulation, 13, 14
Eukaryotes from prokaryotes,
originsof, 18
Evolutionary trees, 20
branching pattern of, 2021
interpretation of, 45
of Volvox, 26
Falsification, fabrication, and
plagiarism (FFP), 1415
Gel electrophoresis, 2, 3
Gemmata obscuriglobus, 3
Genes encoding complex
processes, 7
Genome
ethical, legal, social implications,
1416
into nucleus, 914
Gonium, 30
Histones, 910
amino acid conservation among,
1314
complex in chromatin, 10
covalent modulation of, 13
Human embryonic stem cells from
adult human cells, cases of
misconduct in, 15
Human eye cells, 2
Human gene, by BLAST sequence, 6
Human nucleus, diameter of, 9
38 INDEX

Intact colonies, total volume of Ribosomal RNA (rRNA), 4

somatic cells, 29 Ribosomes, 34
Isolated reproductive cells, growth Rickettsia prowazekii, 23
rates of, 2930 Ring of life, 7
RNA polymerase, 2
Jacob, Franois, 3
Second law of thermodynamics,
Kennedy, Donald, 15 1213
Simian virus 40 (SV40), 1011
Meselson, Matthew, 3 SV40 DNA, 10
Missing links. See Transitional species genomic database at, 1011
Mitochondria, origins Synechocystis, 23
of, 1923
Multicellular organisms, evolution Transcription, 2
of,2531 Transitional species, 3
Multicellularity species, selective
advantage of, 29 Unicellular species
relative frequency distributions of
Nozaki, Hisayoshi, 26 cell sizes in, 2829
Nucleosomes, 11 US Office of Science and Technology
Nucleus, localization to periphery Policy, 15
of, 12
Volvox
Orthologs, 22 division of labor among individual
cells, 27
Partially disrupted colonies, 29 evolutionary tree of, 26
Phospholipid bilayers, 5 family of green algae, 2526
Plagiarism, 1415 growth rates of, 3031
Prokarotes, 2122 in hollow sphere, 29
Proteins spherical structure of, 27
-coding RNA, 45 Volvox carteri
cytoplasm of eukaryotic, 3 growth rates of, 29, 31
importance of, 2 three types of, 29
 OTHER TITLES IN OUR BIOLOGY
COLLECTION

Cellular Structure and Functionby A. Malcolm Campbell and Christopher J. Paradise

Cellular Consequences of Evolutionby A. Malcolm Campbell and Christopher J. Paradise
Cellular Respirationby A. Malcolm Campbell and Christopher J. Paradise
Using DNA Information to Make Proteinsby A. Malcolm Campbell and Christopher
J.Paradise
The Source of Genetic Informationby A. Malcolm Campbell and Christopher J. Paradise
Neurons and Musclesby A. Malcolm Campbell and Christopher J. Paradise
Evolution and Origin of Cellsby A. Malcolm Campbell and Christopher J. Paradise
Reproduction and Cell Divisionby A. Malcolm Campbell and Christopher J. Paradise
Molecular Structure and Functionby A. Malcolm Campbell and Christopher J. Paradise
Animal Physiologyby A. Malcolm Campbell and Christopher J. Paradise
Cell Networksby A. Malcolm Campbell and Christopher J. Paradise
Molecular Switchesby A. Malcolm Campbell and Christopher J. Paradise
Photosynthesisby A. Malcolm Campbell and Christopher J. Paradise
Plant Physiologyby A. Malcolm Campbell and Christopher J. Paradise

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