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The Process of Evolution

In this module, we will examine how animals and plants to came to be

in their present forms and functions. Evolutionary adaptations are
crucial for the survival of species, with natural selection spurring on
the evolutionary process.

The Darwinian Concept of Evolution

Classification of Species and Scala Naturae

Several Greek philosophers, long before Darwin was born, suggested

that life might have changed gradually over time. What compelled
Charles Darwin to revise his view on evolution? The answer is that
much of his propositions were based on the work of many individuals.
However, one philosopher, who was greatly influential in Western
philosophy, held the view that species were fixed. Aristotle postulated
that there were certain “affinities” between species. He concluded that
life forms could be arranged in a scale, or a ladder, of increasing
complexity, which he termed scala naturae. Each form, perfect and
permanent, had its place in the ladder.

These ideas were also found in the Old Testament account of creation,
which holds that specific species were individually designed by God,
and therefore, perfect (creationism). In the 1700s, this was interpreted
by scientists as marks of God’s work, that species were so perfectly
adapted to their environments.

One such scientist was Carolus Linnaeus, who developed the binomial
system of naming species. For instance, humans are designated as
homo sapiens. In contrast to the linear hierarchy of scala naturae,
Linnaeus developed a nested classification system, which was used to
group organisms into specific categories. However, he did not ascribe

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these classifications to evolutionary adaptations. Rather, he ascribed

them to God’s creative powers.

Ideas About Change

Many scientists drew their work from the remains of living things,
which are fossils. Most fossils have been found in sedimentary rocks
formed from mud and sand that settle into the bottom of seas, lakes,
and swamps. New layers of sediments form over older ones and
compress them into superimposed layers of rocks called strata. At the
time the layers were formed, the fossils were deposited in the rocks.
Thus, the fossils provide clues about the organisms that lived during
the time that the strata were formed.

Georges Cuvier largely developed paleontology, which is the study of

fossils. Cuvier observed that there were species that were present in
one layer of rock, but then disappeared in later layers. He then inferred
that extinctions must have been a common occurrence in the history of
life. However, Cuvier opposed the idea of evolution. As explanations
for his observations, he advocated catastrophism. Catastrophism is the
principle that events in the past occurred suddenly and operated under
different mechanisms from those found in the present. He also
speculated that each boundary in the strata represented a single
catastrophe.

In 1975, James Hutton proposed that the geologic features of the Earth
could be explained by gradual mechanisms that were still operating.
The leading geologist during Darwin’s time, Charles Lyell, included
Hutton’s thinking into his principle of uniformitarianism. This
principle stated that the mechanisms of change are constant over time.
Lyell proposed that they very same geologic processes are operating
today, and at the same rate. The ideas of Hutton and Lyell influenced

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the thinking of Darwin in that if geologic processes were slow, then

the actions that are continuous rather than sudden evens, then the Earth
must be older than what was previously thought.

Lamarck’s Hypothesis of Evolution

Several naturalists, during the 18th century, suggested that life evolved
as environments change. However, only one of Darwin’s predecessors
proposed how life changes over time. French biologist, Jean-Baptiste
Lamarck proposed a mechanism for evolution, which was later found
to be incorrect. Lamarck published his hypothesis in 1809, the year
that Darwin was born. By the comparison of living things and fossils,
he found what appeared to be several lines of descent. Each
chronological order of species led to the subsequent species that was
alive at the time. He explained this occurrence using two principles.
The first was use and disuse, the idea that parts of the body that are
commonly used become larger and stronger and parts of the body that
are no longer being used shrink and become weaker. The second
principle was the inheritance of acquired characteristics, which stated
that an organism could pass the modifications to its offspring. He also
thought that organisms had an inner drive to evolve. Darwin rejected
this idea. However, he thought that variations were introduced into
species through the inheritance of modified characteristics. Today,
however, Lamarck’s hypothesis has been rejected, as there is no
genetic mechanism that would allow inheritance in the way that
Lamarck proposed.

Darwin’s Research

Darwin left England on the Beagle on December 1831. He spent most

of his time on shore, collecting and observing thousands of plants and
animals. He noted their characteristics that made them well-suited to
the environment. In addition to this, he also spent much of the time
thinking about geology. He read Lyell’s Principles of Geology. When
the Beagle stopped at Galapagos, his interest in geology was further
enhanced. He was fascinated by the unique organisms that he found
there.

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During the voyage on the Beagle, Darwin was able to observe that
there were many examples of adaptations. These are characteristics
that enable organisms to thrive in the environment that they are in.
Later, he perceived adaptations to the environment and the origin of
new species as closely related processes. By the 1840s, the hypotheses
of Darwin were published in a paper. He anticipated that there would
be uproar about the implications of his proposal, but he continued on
his pursuit.

The Origin of Species

Darwin’s book, The Origin of Species, had two main ideas: that
descent with modifications explains life’s unity and diversity and that
natural selection brings about the match between organisms and their
environment.

Descent with modification summarized Darwin’s view of life. He

perceived unity in life, which he attributed to the descent of all
organisms from a common ancestor in the past. He also believed that
these ancestors also acquired diverse modifications, or adaptations,
that fit them to specific ways of life. Darwin viewed the history of life
as like that of a tree, with multiple branches coming from a common
trunk.

Natural selection was proposed by Darwin as a mechanism to explain

the observable patterns of evolution. He observed that humans have
modified species over time through selective breeding to produce
desired traits. He called this artificial selection. As a result of artificial
selection, animals and crops bear little resemblance to their wild
ancestors.

Darwin also perceived that there was an important connection between

the capacity of organisms to overreproduce and natural selection. He

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realized that all species held the capacity to overreproduce. He was

influenced by the works of Thomas Malthus, who contended that all
suffering, such as disease, war, and famine, were caused by the
explosion of populations and the limited resources found on Earth.

Aside from this, Darwin also observed that an organism’s traits can
influence not only its own performance, but also how well its
offsprings cope with environmental changes. Organisms with offspring
that are able to obtain food or withstand physical conditions are able to
survive and reproduce, thus producing more offspring. Thus, natural
selection is imposed by factors such as predators and environmental
conditions, which can increase the favorable traits in a population.

A Summary of Natural Selection

Natural selection is the process by which organisms that have certain

heritable characteristics survive and reproduce at a higher rate than
other individuals.

Over time, natural selection can increase the match between organisms
and their environment.

If an environment changes, or if organisms move to a new

environment, natural selection may result in adaptations to these new
conditions, sometimes giving rise to new species in the process.

An important point to note is that individuals do not evolve, rather,

populations evolve. A second important point is that natural selection
can only diminish or amplify heritable traits. Thus, although an
organism may acquire modifications over its lifetime, these may not be
heritable traits. Third, a trait that is favorable in one environment may
be unfavorable in another. Natural selection is always operating, but
which traits are favorable depend on the context of the environment.

Evidence for Evolution

The evidence for evolution is overwhelming. The first such evidence is

the direct observations of evolutionary change. Predators are potent

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forces shaping the adaptations of their prey. The predator is more

likely to feed on prey organisms that are less able to avoid detection,
escape, or defend themselves. As a result, prey individuals are less
likely to reproduce and pass their traits onto their offspring that are
individuals who whose traits allow them to evade predators.

Consider the example of the evolution of drug-resistant HIV. HIV is

the virus that causes AIDS. Researchers have developed numerous
drugs to combat this pathogen, but using these medications selects
viruses which are resistant to them. Those that survive the early doses
may reproduce, passing on the alleles that enable them to resist the
drug. In this way, the frequency of resistant viruses increases rapidly
in the population. A drug does not create resistant pathogens; rather it
selects for resistant individuals that are already present in the
population. Thus, natural selection is a process of editing rather than a
creating mechanism. Second, natural selection depends on time and
place. It favors those characteristics in a genetically viable population
that provide advantages in the local, current environment.

The fossil record is the second evidence for evolution. Fossil records
show that present-day organisms differ significantly from organisms
that existed before. Many species have also become extinct. Fossils
show the evolutionary changes that have occurred over time in various
groups of organisms.

Over longer time scales, fossils are able to document the origins of
major new groups of organisms. An example of this is the fossil record
of early cetaceans, which is the mammalian order to includes whales,
dolphins, and porpoises. The early cetaceans lived about 60 million
years ago. Fossil records indicate that, prior to that time period, most
mammals were terrestrial. However, fossils were recovered in
Pakistan, Egypt, and North America that document the transition from

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life on land to life in the sea. Collectively, these and other early fossils
document the formation of new species and the origin of a major group
of mammals, the cetaceans. In addition to providing evidence for the
pattern of evolution, fossil records can also be used to test the
evolutionary hypotheses. For instance, based on anatomical data,
scientists believe that early land vertebrates evolved from a group of
fishes. They also believe that early amphibians also evolved from
descendants of land vertebrates. If these relationships were correct, we
would predict that the earliest fossils of fishes would be older than the
earliest fossils of amphibians. These predictions can be tested using
radioactive dating techniques.

Homology is the third evidence for evolution. Homology is the

analysis of similarities between organisms. As a remodeling process,
evolution would predict that similar species would share similar
features. For example, the forelimbs of all mammals, including
humans and cats, show the same arrangement of bones from the
shoulder to the tips of the digits, even though they have very different
functions. These striking anatomical similarities would not be there if
they had arisen anew in each species. Rather, the underlying skeletal
structures of arms, flippers, and wings of different mammal are
homologous structures that show the variations in a common theme,
and also that that these animals have a common ancestor.

The early stages of development in different animals reveals additional

anatomical homologies not visible in adult organisms. For instance, at
some point in their development, all vertebrates have a tail located
posterior (behind) the anus, as well as structures called pharyngeal
(throat) pouches. These throat pouches are homologous and ultimately
develop into structures with very different functions. Some of the most
interesting homologies refer to the leftover, or marginal, structures
which are of little importance to the organism. These structures, called
vesitigial structures, are remnants of important features that were
functional in the ancestors of the organism. For instance, the skeleton
of some snakes retain vestiges of the pelvis and legs of walking
ancestors.

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At the molecular level, biologists also observe similarities among

organisms. All forms of life use the same genetic language, which is
DNA and RNA, and the genetic code is essentially universal. Thus, it
is likely that all species descended from a common ancestor that used
this genetic code. For instance, humans and bacteria share genes that
are inherited from a shared distant ancestor. Like other structures,
these genes have different functions in different organisms.

The pattern of descent from common ancestors is often represented

using an evolutionary tree, which is a diagram that reflects the
evolutionary relationships among groups of organisms. Evolutionary
trees are hypotheses that summarize our current understanding of the
patterns of descent.

Convergent evolution also occurs. This is when distantly related

organisms resemble one another for a different reason. Convergent
evolution is the independent evolution of similar features in different
lineages. For instance, marsupials are found in Australia and are
distinct from another group of mammals, the eutherians. Some
marsupials have members that look like eutherians.

A fifth type of evidence for evolution is biogeography. Biogeography

is the geographic distribution of species. The geographic distribution
of organisms is influences by many factors. One of these is continental
drift, which is the slow movement of the earth’s continents over time.
About 250 million years ago, these movements united all the
continents on earth into a single large continent, known as Pangaea.
Roughly 200 million years ago, this large mass of land began to break
apart. Around 20 million years ago, the continents as we know them
today were in their present locations.

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The Evolution of Populations

The smallest scale of evolution is called microevolution. These are
changes in allele frequencies in specific populations over generations.
There are three main mechanisms that cause allele frequencies to
change: natural selection, genetic drift (chance events that later allele
frequencies), and gene flow (the transfer of alleles between
populations). However, only natural selection is consistent in
improving the match between the organisms and their environment.

Genetic Variation Through Mutation and Sexual Reproduction

Phenotype is the product of an inherited genotype and many

environmental influences. For instance, bodybuilders may get larger
but they do not pass on their large muscles to their offsprings. Only the
genetic part of variations can have evolutionary consequences.

Characters that vary within a population may be quantitative or

discrete. Discrete characters occur on an either-or basis. For instance,
Mendel’s peas may either be green or yellow. The majority of discrete
characters are determined by a single gene locus with different alleles
that produce distinct phenotyoes. However, the majority of heritable
variation involves quantitative characters, which vary along a
continuum in a population. Heritable quantitative variation usually
results from the influence of two or more genes on a single phenotypic
character.

Biologists can measure that genetic variation in a population at both

the molecular level of DNA (nucleotide variability) and whole-gene
level (gene variability). Gene variability can be quantified as average
hetetozygosity. This is the average percentage of loci that are
heterozygous. Average heterozygosity is often surveyed by using gel
electrophoresis to meaure the products of genes. On the other hand,
nucleotide variability is measured by comparing the DNA sequences
of two individuals in a population and then averaging the data from
these comparisons. For instance, the genome of Drosophila
melanogaster has 180 million nucloetides, and the sequence of any
two fruit flies differs by an average of 1.8 million nucleotides.

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In addition to the genetic variability in populations, scientists are also

able to observe geographic variation, which is the difference in the
genetic composition of separate populations. Geographic variations
also occur as a cline, which is a graded change in character along a
geographic axis. Some clines are produced by a gradation in an
environmental variable. Selection, however, can only operate as
multiple alleles exist for a given gene locus.

Mutation is the ultimate source of new alleles. Mutation is the change

in nucleotide sequence of an organism’s DNA. It is not possible to
predict with accuracy which segments of DNA will be altered or in
what way. In multicellular organisms, only mutations in cell lines that
produce gametes can be passed on to the offspring. This is not as
limiting as it sounds, especially in plants and fungi, since they have
many different cell lines that produce gametes. However, in most
animals, mutations occur in somatic cells and are lost when the
individual dies.

A point mutation is a difference in a gene in as little as one base pair in

a gene, and it can have a significant effect on the organism’s
phenotype. Organisms reflect thousands of previous selections, thus,
their phenotype is generally closely matched to their environment. As
a result of this close match, any mutation in their genes is unlikely to
provide any benefit. Sometimes, it can even be harmful. However,
much of the genes in eukaryotic organisms do no code for proteins.
Point mutations in these non-coding regions are harmless. In addition,
because the genetic code is redundant, a point mutation in a gene that
encodes a protein will have no effect on the protein’s function if the
composition of the amino acid is not changed. Moreover, if there is a
change in amino acid, this may not necessarily affect the protein’s
shape and function. However, on rare occasions, a mutant allele may

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actually make the organism better suited to its environment, which

enhances its reproductive success.

Chromosomal changes that disrupt, delete, or rearrange many loci at

once are almost sure to be harmful. However, when large-scale
mutations such as this occur, but they leave genes intact, their effect on
the organism may be neutral. In rare cases, chromosomal
rearrangements may be beneficial. An important source of variation
begins when genes are duplicated due to errors in meiosis, slippage
during DNA replication, or the activities of transposable elements. The
duplication of smaller pieces of DNA may not be harmful. Gene
duplications, in addition, do not have severe effects that persist over
generations, allowing mutations to accumulate. The result is that the
genome becomes expanded with new loci that may take on new
functions.

Mutation rates tend to be low in animals and plants, averaging about

one mutation every 100,000 genes per generation. Mutation rates are
even lower in prokaryotes. However, prokaryotes generally have short
generation spans, so mutations can quicly generate genetic variation in
populations of these organisms. Viruses are also another group of
organisms where generation spans are short.

Genetic Drift
Chance events can cause allele frequencies to fluctuate unpredictably
from one generation to the next, especially in small populations. This
is known as genetic drift. Certain circumstances can result in genetic
drift having significant effects on a population. Two examples are the
founder effect and the bottleneck effect.

The Founder Effect

When a small group from a population becomes separated from the

main population, they may establish a new population whose gene
pool differs from the main population. This is known as the founder
effect. The founder effect might occur, for instance, when members of

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population are blown by the wind to a new island. Genetic drift, in

which chance events alter the allele frequencies, occur in such a case
because the wind transported individuals to another location, leaving
the rest of the population behind. The founder effect accounts for the
relatively high frequency of certain inherited disorders among isolated
human populations.

The Bottleneck Effect

A sudden change in the environment, such as a fire or a flood, may

drastically reduce the size of the population. A drastic drop in the
population can cause the bottleneck effect, which is termed that way
because the population has gone through a restrictive event. By chance
alone, certain alleles may be overrepresented in survivors, others may
be underrepresented, and some may be absent altogether. Ongoing
genetic drift is most likely to have a substantial effect on the gene pool
unless the population becomes large enough for chance events to have
less of an effect. However, a population that has gone through a
bottleneck may have little genetic variation even if the population
increases in size for a long time. Human actions create severe
bottlenecks for some species, such as when humans cause forest fires
or flooding in a certain area.

Effects of Genetic Drift

1. Genetic drift is significant in small populations.

2. Genetic drift can cause allele frequencies to change at random.

3. Genetic drift can lead to a loss of genetic variation within

populations.

4. Genetic drift can cause harmful alleles to become fixed.

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Gene Flow
Allele frequencies can also change by gene flow, which is the transfer
of alleles into or out of a population due to the movement of fertile
individuals or their gametes. Since alleles are exchanged among
populations, gene flow tends to reduce the genetic variations between
populations. If it is extensive enough, gene flow can result in
neighboring populations combining into a single population with a
common gene pool.

When neighboring populations live in different environments, alleles

transferred by gene flow may prevent a population from fully adapting
to its environment. There are instances when beneficial alleles are
transferred very widerly. For instance, gene flow has allowed the
spread of insecticide-resistant alleles in the mosquito Culex pipiens. C.
pipiens is a vector for malaria and the West Nile virus. Gene flow, like
mutations, can introduce new alleles into a population. However, since
gene flow can occur at a higher rate than mutation, gene flow is more
likely.

Three Aspects in Evolutionary Thinking

The last 35 years have seen a widening inquiry into evolution.

Evolution is now recognized that there is more to studying
evolutionary change than studying the evolution of populations. Three
aspects of evolutionary thinking are, in particular, important.

The first is that phenotypic evolution comes from evolutionary change

in the process of development that transforms a single-celled fertilized
cell into an adult organism. Although under genetic control, the
process of development is so complex that it cannot be understood by
studying the DNA sequences alone. Rather, the understanding of how
phenotypes evolve, and the extent to which evolution is directed and
constrained by developmental systems, requires detailed embyrologcal
and molecular knowledge.

Second, the understanding of evolution necessitates the understanding

of history. Paleontology is the study of direct evidence from the past.

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In recent years, interest has been renewed in the field because of new
findings and discoveries. There are also new theories, such as those of
mass extinction, punctuated equilibrium and stasis, and species
selection. Initially crictial in the acceptance and development of
evolutionary theory, paleontology has once again become an integral
part of evolutionary biology. Concurrently, a more important
revolution has taken place over the last 30 years. This emphasizes the
historical perspective that is based on the information on phylogenetic
relationships. That is, the tree of life, which is the pattern of descent
and relationships among species. The tree of life is critical to
understanding the aspects of evolution from above the population
level.

Finally, life is organized as a hierarchy. That is, genes are found

individuals, and individuals are found within populations, and
populations within species, and species within clades (a clade consists
of an ancestral species and its descendants). Population genetics
concerns itself with what happens within a population, however,
evolutionary change can occur on all levels. There is a possibility that
some genes are particularly adept at mutating to multiply the number
of copies of that gene within a genome. This may occur such that
genes may multiply within a genome even if it poses no benefit to the
organism. Just as selection among individuals can lead to evolutionary
change, selection among individuals at other levels (species, genes)
can lead to evolutionary change. This will occur as long as entities
have heritable traits that are transmitted to offspring. Thus, evolution
occurs at multiple levels of the hierarchy of life.

Another concept on evolution is that differences among populations

may also reflect changes in response to the environment. This does not
reflect genetic differentiation however, if these responses are
constantly retained, they may be transmitted to the next generation.

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Thus, these nongenetic differences may lead to selective, divergent

pressures on traits that are genetically determined. This promotes
evolutionary divergence among populations. One example of this
concerns behavior, which is a response to the environment. Learned
behaviors that are transmitted from one generation to the next, which
are often called culture or traditions, can occur in animals as well as
humans. These behavioral differences would not reflect differences at
the genetic level, but they might set the stage for genetic divergence in
traits relating to these behaviors. For instance, chimpanzees that use
certain tools more than others may evolve into animals that are suited
to the use of these tools, thereby supporting the underlying behavioral
pattern.

Evolution, Humans, and Society

Evolution has important implications for us in many ways. Humans

have used the principles of evolution to alter species to serve their
purposes. Conversely, wild species are responding to environmental
changes caused by humans. They may adapt to our efforts to control
them and responde to new opportunities. Thus, the knowledge of
evolution is important for our knowledge of artificial selection and to
fight our evolutionary enemies. There are diverse areas where
evolution is relevant to society. These include criminal forensics and
medicine. They also include important pursuits such as the creation of
novel molecules in laboratories.

Beyond a focus that is purely utilitarian, an understanding of evolution

can tell us about ourselves. Through evolutionary biology, we can
understand where we came from, where we might be heading to, and it
may even shed light on what it means to be human.

Glossary
Heterozygosity: refers to two different alleles in a single gene locus

Homologous: two structures that may seem alike, or look alike

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Videos and Resources

Mechanisms of Evolution

What is the Evidence for Evolution?

Genetic Variation, Gene Flow, and New Species

Population Genetics

Population Genetics: A Concise Guide

Misconceptions About Evolution

References
Ferrell, V. (2001). Evolution Handbook. Altmont: Evolution Facts,
Inc.

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