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                    Introduction to Evolutionary Biology
                                 Version 2
                    Copyright © 1996-1997 by Chris Colby



    volution is the cornerstone of modern biology. It unites all the fields
    of biology under one theoretical umbrella. It is not a difficult
concept, but very few people -- the majority of biologists included -- have
a satisfactory grasp of it. One common mistake is believing that species can
be arranged on an evolutionary ladder from bacteria through "lower" animals,
to "higher" animals and, finally, up to man. Mistakes permeate popular
science expositions of evolutionary biology. Mistakes even filter into
biology journals and texts. For example, Lodish, et. al., in their cell
biology text, proclaim, "It was Charles Darwin's great insight that
organisms are all related in a great chain of being..." In fact, the idea of
a great chain of being, which traces to Linnaeus, was overturned by Darwin's
idea of common descent.

Misunderstandings about evolution are damaging to the study of evolution and
biology as a whole. People who have a general interest in science are likely
to dismiss evolution as a soft science after absorbing the pop science
nonsense that abounds. The impression of it being a soft science is
reinforced when biologists in unrelated fields speculate publicly about
evolution.

This is a brief introduction to evolutionary biology. I attempt to explain
basics of the theory of evolution and correct many of the misconceptions.

What is Evolution?

Evolution is a change in the gene pool of a population over time. A gene is
a hereditary unit that can be passed on unaltered for many generations. The
gene pool is the set of all genes in a species or population.

The English moth, Biston betularia, is a frequently cited example of
observed evolution. [evolution: a change in the gene pool] In this moth
there are two color morphs, light and dark. H. B. D. Kettlewell found that
dark moths constituted less than 2% of the population prior to 1848. The
frequency of the dark morph increased in the years following. By 1898, the
95% of the moths in Manchester and other highly industrialized areas were of
the dark type. Their frequency was less in rural areas. The moth population
changed from mostly light colored moths to mostly dark colored moths. The
moths' color was primarily determined by a single gene. [gene: a hereditary
unit] So, the change in frequency of dark colored moths represented a change
in the gene pool. [gene pool: the set all of genes in a population] This
change was, by definition, evolution.

The increase in relative abundance of the dark type was due to natural
selection. The late eighteen hundreds was the time of England's industrial
revolution. Soot from factories darkened the birch trees the moths landed
on. Against a sooty background, birds could see the lighter colored moths
better and ate more of them. As a result, more dark moths survived until
reproductive age and left offspring. The greater number of offspring left by
dark moths is what caused their increase in frequency. This is an example of
natural selection.

Populations evolve. [evolution: a change in the gene pool] In order to
understand evolution, it is necessary to view populations as a collection of
individuals, each harboring a different set of traits. A single organism is
never typical of an entire population unless there is no variation within
that population. Individual organisms do not evolve, they retain the same
genes throughout their life. When a population is evolving, the ratio of
different genetic types is changing -- each individual organism within a
population does not change. For example, in the previous example, the
frequency of black moths increased; the moths did not turn from light to
gray to dark in concert. The process of evolution can be summarized in three
sentences: Genes mutate. [gene: a hereditary unit] Individuals are selected.
Populations evolve.

Evolution can be divided into microevolution and macroevolution. The kind of
evolution documented above is microevolution. Larger changes, such as when a
new species is formed, are called macroevolution. Some biologists feel the
mechanisms of macroevolution are different from those of microevolutionary
change. Others think the distinction between the two is arbitrary --
macroevolution is cumulative microevolution.

The word evolution has a variety of meanings. The fact that all organisms
are linked via descent to a common ancestor is often called evolution. The
theory of how the first living organisms appeared is often called evolution.
This should be called abiogenesis. And frequently, people use the word
evolution when they really mean natural selection -- one of the many
mechanisms of evolution.

Common Misconceptions about Evolution

Evolution can occur without morphological change; and morphological change
can occur without evolution. Humans are larger now than in the recent past,
a result of better diet and medicine. Phenotypic changes, like this, induced
solely by changes in environment do not count as evolution because they are
not heritable; in other words the change is not passed on to the organism's
offspring. Phenotype is the morphological, physiological, biochemical,
behavioral and other properties exhibited by a living organism. An
organism's phenotype is determined by its genes and its environment. Most
changes due to environment are fairly subtle, for example size differences.
Large scale phenotypic changes are obviously due to genetic changes, and
therefore are evolution.

Evolution is not progress. Populations simply adapt to their current
surroundings. They do not necessarily become better in any absolute sense
over time. A trait or strategy that is successful at one time may be
unsuccessful at another. Paquin and Adams demonstrated this experimentally.
They founded a yeast culture and maintained it for many generations.
Occasionally, a mutation would arise that allowed its bearer to reproduce
better than its contemporaries. These mutant strains would crowd out the
formerly dominant strains. Samples of the most successful strains from the
culture were taken at a variety of times. In later competition experiments,
each strain would outcompete the immediately previously dominant type in a
culture. However, some earlier isolates could outcompete strains that arose
late in the experiment. Competitive ability of a strain was always better
than its previous type, but competitiveness in a general sense was not
increasing. Any organism's success depends on the behavior of its
contemporaries. For most traits or behaviors there is likely no optimal
design or strategy, only contingent ones. Evolution can be like a game of
paper/scissors/rock.

Organisms are not passive targets of their environment. Each species
modifies its own environment. At the least, organisms remove nutrients from
and add waste to their surroundings. Often, waste products benefit other
species. Animal dung is fertilizer for plants. Conversely, the oxygen we
breathe is a waste product of plants. Species do not simply change to fit
their environment; they modify their environment to suit them as well.
Beavers build a dam to create a pond suitable to sustain them and raise
young. Alternately, when the environment changes, species can migrate to
suitable climes or seek out microenvironments to which they are adapted.

Genetic Variation

Evolution requires genetic variation. If there were no dark moths, the
population could not have evolved from mostly light to mostly dark. In order
for continuing evolution there must be mechanisms to increase or create
genetic variation and mechanisms to decrease it. Mutation is a change in a
gene. These changes are the source of new genetic variation. Natural
selection operates on this variation.

Genetic variation has two components: allelic diversity and non- random
associations of alleles. Alleles are different versions of the same gene.
For example, humans can have A, B or O alleles that determine one aspect of
their blood type. Most animals, including humans, are diploid -- they
contain two alleles for every gene at every locus, one inherited from their
mother and one inherited from their father. Locus is the location of a gene
on a chromosome. Humans can be AA, AB, AO, BB, BO or OO at the blood group
locus. If the two alleles at a locus are the same type (for instance two A
alleles) the individual would be called homozygous. An individual with two
different alleles at a locus (for example, an AB individual) is called
heterozygous. At any locus there can be many different alleles in a
population, more alleles than any single organism can possess. For example,
no single human can have an A, B and an O allele.

Considerable variation is present in natural populations. At 45 percent of
loci in plants there is more than one allele in the gene pool. [allele:
alternate version of a gene (created by mutation)] Any given plant is likely
to be heterozygous at about 15 percent of its loci. Levels of genetic
variation in animals range from roughly 15% of loci having more than one
allele (polymorphic) in birds, to over 50% of loci being polymorphic in
insects. Mammals and reptiles are polymorphic at about 20% of their loci - -
amphibians and fish are polymorphic at around 30% of their loci. In most
populations, there are enough loci and enough different alleles that every
individual, identical twins excepted, has a unique combination of alleles.

Linkage disequilibrium is a measure of association between alleles of two
different genes. [allele: alternate version of a gene] If two alleles were
found together in organisms more often than would be expected, the alleles
are in linkage disequilibrium. If there two loci in an organism (A and B)
and two alleles at each of these loci (A1, A2, B1 and B2) linkage
disequilibrium (D) is calculated as D = f(A1B1) * f(A2B2) - f(A1B2) *
f(A2B1) (where f(X) is the frequency of X in the population). [Loci (plural
of locus): location of a gene on a chromosome] D varies between -1/4 and
1/4; the greater the deviation from zero, the greater the linkage. The sign
is simply a consequence of how the alleles are numbered. Linkage
disequilibrium can be the result of physical proximity of the genes. Or, it
can be maintained by natural selection if some combinations of alleles work
better as a team.

Natural selection maintains the linkage disequilibrium between color and
pattern alleles in Papilio memnon. [linkage disequilibrium: association
between alleles at different loci] In this moth species, there is a gene
that determines wing morphology. One allele at this locus leads to a moth
that has a tail; the other allele codes for a untailed moth. There is
another gene that determines if the wing is brightly or darkly colored.
There are thus four possible types of moths: brightly colored moths with and
without tails, and dark moths with and without tails. All four can be
produced when moths are brought into the lab and bred. However, only two of
these types of moths are found in the wild: brightly colored moths with
tails and darkly colored moths without tails. The non-random association is
maintained by natural selection. Bright, tailed moths mimic the pattern of
an unpalatable species. The dark morph is cryptic. The other two
combinations are neither mimetic nor cryptic and are quickly eaten by birds.

Assortative mating causes a non-random distribution of alleles at a single
locus. [locus: location of a gene on a chromosome] If there are two alleles
(A and a) at a locus with frequencies p and q, the frequency of the three
possible genotypes (AA, Aa and aa) will be p2, 2pq and q2, respectively. For
example, if the frequency of A is 0.9 and the frequency of a is 0.1, the
frequencies of AA, Aa and aa individuals are: 0.81, 0.18 and 0.01. This
distribution is called the Hardy-Weinberg equilibrium.

Non-random mating results in a deviation from the Hardy-Weinberg
distribution. Humans mate assortatively according to race; we are more
likely to mate with someone of own race than another. In populations that
mate this way, fewer heterozygotes are found than would be predicted under
random mating. [heterozygote: an organism that has two different alleles at
a locus] A decrease in heterozygotes can be the result of mate choice, or
simply the result of population subdivision. Most organisms have a limited
dispersal capability, so their mate will be chosen from the local
population.

Evolution within a Lineage

In order for continuing evolution there must be mechanisms to increase or
create genetic variation and mechanisms to decrease it. The mechanisms of
evolution are mutation, natural selection, genetic drift, recombination and
gene flow. I have grouped them into two classes -- those that decrease
genetic variation and those that increase it.

Mechanisms that Decrease Genetic Variation

Natural Selection

Some types of organisms within a population leave more offspring than
others. Over time, the frequency of the more prolific type will increase.
The difference in reproductive capability is called natural selection.
Natural selection is the only mechanism of adaptive evolution; it is defined
as differential reproductive success of pre- existing classes of genetic
variants in the gene pool.

The most common action of natural selection is to remove unfit variants as
they arise via mutation. [natural selection: differential reproductive
success of genotypes] In other words, natural selection usually prevents new
alleles from increasing in frequency. This led a famous evolutionist, George
Williams, to say "Evolution proceeds in spite of natural selection."

Natural selection can maintain or deplete genetic variation depending on how
it acts. When selection acts to weed out deleterious alleles, or causes an
allele to sweep to fixation, it depletes genetic variation. When
heterozygotes are more fit than either of the homozygotes, however,
selection causes genetic variation to be maintained. [heterozygote: an
organism that has two different alleles at a locus. | homozygote: an
organism that has two identical alleles at a locus] This is called balancing
selection. An example of this is the maintenance of sickle-cell alleles in
human populations subject to malaria. Variation at a single locus determines
whether red blood cells are shaped normally or sickled. If a human has two
alleles for sickle-cell, he/she develops anemia -- the shape of sickle-cells
precludes them carrying normal levels of oxygen. However, heterozygotes who
have one copy of the sickle-cell allele, coupled with one normal allele
enjoy some resistance to malaria -- the shape of sickled cells make it
harder for the plasmodia (malaria causing agents) to enter the cell. Thus,
individuals homozygous for the normal allele suffer more malaria than
heterozygotes. Individuals homozygous for the sickle- cell are anemic.
Heterozygotes have the highest fitness of these three types. Heterozygotes
pass on both sickle-cell and normal alleles to the next generation. Thus,
neither allele can be eliminated from the gene pool. The sickle-cell allele
is at its highest frequency in regions of Africa where malaria is most
pervasive.

Balancing selection is rare in natural populations. [balancing selection:
selection favoring heterozygotes] Only a handful of other cases beside the
sickle-cell example have been found. At one time population geneticists
thought balancing selection could be a general explanation for the levels of
genetic variation found in natural populations. That is no longer the case.
Balancing selection is only rarely found in natural populations. And, there
are theoretical reasons why natural selection cannot maintain polymorphisms
at several loci via balancing selection.

Individuals are selected. The example I gave earlier was an example of
evolution via natural selection. [natural selection: differential
reproductive success of genotypes] Dark colored moths had a higher
reproductive success because light colored moths suffered a higher predation
rate. The decline of light colored alleles was caused by light colored
individuals being removed from the gene pool (selected against). Individual
organisms either reproduce or fail to reproduce and are hence the unit of
selection. One way alleles can change in frequency is to be housed in
organisms with different reproductive rates. Genes are not the unit of
selection (because their success depends on the organism's other genes as
well); neither are groups of organisms a unit of selection. There are some
exceptions to this "rule," but it is a good generalization.

Organisms do not perform any behaviors that are for the good of their
species. An individual organism competes primarily with others of it own
species for its reproductive success. Natural selection favors selfish
behavior because any truly altruistic act increases the recipient's
reproductive success while lowering the donors. Altruists would disappear
from a population as the non- altruists would reap the benefits, but not pay
the costs, of altruistic acts. Many behaviors appear altruistic. Biologists,
however, can demonstrate that these behaviors are only apparently
altruistic. Cooperating with or helping other organisms is often the most
selfish strategy for an animal. This is called reciprocal altruism. A good
example of this is blood sharing in vampire bats. In these bats, those lucky
enough to find a meal will often share part of it with an unsuccessful bat
by regurgitating some blood into the other's mouth. Biologists have found
that these bats form bonds with partners and help each other out when the
other is needy. If a bat is found to be a "cheater," (he accepts blood when
starving, but does not donate when his partner is) his partner will abandon
him. The bats are thus not helping each other altruistically; they form
pacts that are mutually beneficial.

Helping closely related organisms can appear altruistic; but this is also a
selfish behavior. Reproductive success (fitness) has two components; direct
fitness and indirect fitness. Direct fitness is a measure of how many
alleles, on average, a genotype contributes to the subsequent generation's
gene pool by reproducing. Indirect fitness is a measure of how many alleles
identical to its own it helps to enter the gene pool. Direct fitness plus
indirect fitness is inclusive fitness. J. B. S. Haldane once remarked he
would gladly drown, if by doing so he saved two siblings or eight cousins.
Each of his siblings would share one half his alleles; his cousins, one
eighth. They could potentially add as many of his alleles to the gene pool
as he could.

Natural selection favors traits or behaviors that increase a genotype's
inclusive fitness. Closely related organisms share many of the same alleles.
In diploid species, siblings share on average at least 50% of their alleles.
The percentage is higher if the parents are related. So, helping close
relatives to reproduce gets an organism's own alleles better represented in
the gene pool. The benefit of helping relatives increases dramatically in
highly inbred species. In some cases, organisms will completely forgo
reproducing and only help their relatives reproduce. Ants, and other
eusocial insects, have sterile castes that only serve the queen and assist
her reproductive efforts. The sterile workers are reproducing by proxy.

The words selfish and altruistic have connotations in everyday use that
biologists do not intend. Selfish simply means behaving in such a way that
one's own inclusive fitness is maximized; altruistic means behaving in such
a way that another's fitness is increased at the expense of ones' own. Use
of the words selfish and altruistic is not meant to imply that organisms
consciously understand their motives.

The opportunity for natural selection to operate does not induce genetic
variation to appear -- selection only distinguishes between existing
variants. Variation is not possible along every imaginable axis, so all
possible adaptive solutions are not open to populations. To pick a somewhat
ridiculous example, a steel shelled turtle might be an improvement over
regular turtles. Turtles are killed quite a bit by cars these days because
when confronted with danger, they retreat into their shells -- this is not a
great strategy against a two ton automobile. However, there is no variation
in metal content of shells, so it would not be possible to select for a
steel shelled turtle.

Here is a second example of natural selection. Geospiza fortis lives on the
Galapagos islands along with fourteen other finch species. It feeds on the
seeds of the plant Tribulus cistoides, specializing on the smaller seeds.
Another species, G. Magnirostris, has a larger beak and specializes on the
larger seeds. The health of these bird populations depends on seed
production. Seed production, in turn, depends on the arrival of wet season.
In 1977, there was a drought. Rainfall was well below normal and fewer seeds
were produced. As the season progressed, the G. fortis population depleted
the supply of small seeds. Eventually, only larger seeds remained. Most of
the finches starved; the population plummeted from about twelve hundred
birds to less than two hundred. Peter Grant, who had been studying these
finches, noted that larger beaked birds fared better than smaller beaked
ones. These larger birds had offspring with correspondingly large beaks.
Thus, there was an increase in the proportion of large beaked birds in the
population the next generation. To prove that the change in bill size in
Geospiza fortis was an evolutionary change, Grant had to show that
differences in bill size were at least partially genetically based. He did
so by crossing finches of various beak sizes and showing that a finch's beak
size was influenced by its parent's genes. Large beaked birds had large
beaked offspring; beak size was not due to environmental differences (in
parental care, for example).

Natural selection may not lead a population to have the optimal set of
traits. In any population, there would be a certain combination of possible
alleles that would produce the optimal set of traits (the global optimum);
but there are other sets of alleles that would yield a population almost as
adapted (local optima). Transition from a local optimum to the global
optimum may be hindered or forbidden because the population would have to
pass through less adaptive states to make the transition. Natural selection
only works to bring populations to the nearest optimal point. This idea is
Sewall Wright's adaptive landscape. This is one of the most influential
models that shape how evolutionary biologists view evolution.

Natural selection does not have any foresight. It only allows organisms to
adapt to their current environment. Structures or behaviors do not evolve
for future utility. An organism adapts to its environment at each stage of
its evolution. As the environment changes, new traits may be selected for.
Large changes in populations are the result of cumulative natural selection.
Changes are introduced into the population by mutation; the small minority
of these changes that result in a greater reproductive output of their
bearers are amplified in frequency by selection.

Complex traits must evolve through viable intermediates. For many traits, it
initially seems unlikely that intermediates would be viable. What good is
half a wing? Half a wing may be no good for flying, but it may be useful in
other ways. Feathers are thought to have evolved as insulation (ever worn a
down jacket?) and/or as a way to trap insects. Later, proto-birds may have
learned to glide when leaping from tree to tree. Eventually, the feathers
that originally served as insulation now became co-opted for use in flight.
A trait's current utility is not always indicative of its past utility. It
can evolve for one purpose, and be used later for another. A trait evolved
for its current utility is an adaptation; one that evolved for another
utility is an exaptation. An example of an exaptation is a penguin's wing.
Penguins evolved from flying ancestors; now they are flightless and use
their wings for swimming.

Common Misconceptions about Selection

Selection is not a force in the sense that gravity or the strong nuclear
force is. However, for the sake of brevity, biologists sometimes refer to it
that way. This often leads to some confusion when biologists speak of
selection "pressures." This implies that the environment "pushes" a
population to more adapted state. This is not the case. Selection merely
favors beneficial genetic changes when they occur by chance -- it does not
contribute to their appearance. The potential for selection to act may long
precede the appearance of selectable genetic variation. When selection is
spoken of as a force, it often seems that it is has a mind of its own; or as
if it was nature personified. This most often occurs when biologists are
waxing poetic about selection. This has no place in scientific discussions
of evolution. Selection is not a guided or cognizant entity; it is simply an
effect.

A related pitfall in discussing selection is anthropomorphizing on behalf of
living things. Often conscious motives are seemingly imputed to organisms,
or even genes, when discussing evolution. This happens most frequently when
discussing animal behavior. Animals are often said to perform some behavior
because selection will favor it. This could more accurately worded as
"animals that, due to their genetic composition, perform this behavior tend
to be favored by natural selection relative to those who, due to their
genetic composition, don't." Such wording is cumbersome. To avoid this,
biologists often anthropomorphize. This is unfortunate because it often
makes evolutionary arguments sound silly. Keep in mind this is only for
convenience of expression.

The phrase "survival of the fittest" is often used synonymously with natural
selection. The phrase is both incomplete and misleading. For one thing,
survival is only one component of selection -- and perhaps one of the less
important ones in many populations. For example, in polygynous species, a
number of males survive to reproductive age, but only a few ever mate. Males
may differ little in their ability to survive, but greatly in their ability
to attract mates -- the difference in reproductive success stems mainly from
the latter consideration. Also, the word fit is often confused with
physically fit. Fitness, in an evolutionary sense, is the average
reproductive output of a class of genetic variants in a gene pool. Fit does
not necessarily mean biggest, fastest or strongest.

Sexual Selection

In many species, males develop prominent secondary sexual characteristics. A
few oft cited examples are the peacock's tail, coloring and patterns in male
birds in general, voice calls in frogs and flashes in fireflies. Many of
these traits are a liability from the standpoint of survival. Any
ostentatious trait or noisy, attention getting behavior will alert predators
as well as potential mates. How then could natural selection favor these
traits?

Natural selection can be broken down into many components, of which survival
is only one. Sexual attractiveness is a very important component of
selection, so much so that biologists use the term sexual selection when
they talk about this subset of natural selection.

Sexual selection is natural selection operating on factors that contribute
to an organism's mating success. Traits that are a liability to survival can
evolve when the sexual attractiveness of a trait outweighs the liability
incurred for survival. A male who lives a short time, but produces many
offspring is much more successful than a long lived one that produces few.
The former's genes will eventually dominate the gene pool of his species. In
many species, especially polygynous species where only a few males
monopolize all the females, sexual selection has caused pronounced sexual
dimorphism. In these species males compete against other males for mates.
The competition can be either direct or mediated by female choice. In
species where females choose, males compete by displaying striking
phenotypic characteristics and/or performing elaborate courtship behaviors.
The females then mate with the males that most interest them, usually the
ones with the most outlandish displays. There are many competing theories as
to why females are attracted to these displays.

The good genes model states that the display indicates some component of
male fitness. A good genes advocate would say that bright coloring in male
birds indicates a lack of parasites. The females are cueing on some signal
that is correlated with some other component of viability.

Selection for good genes can be seen in sticklebacks. In these fish, males
have red coloration on their sides. Milinski and Bakker showed that
intensity of color was correlated to both parasite load and sexual
attractiveness. Females preferred redder males. The redness indicated that
he was carrying fewer parasites.

Evolution can get stuck in a positive feedback loop. Another model to
explain secondary sexual characteristics is called the runaway sexual
selection model. R. A. Fisher proposed that females may have an innate
preference for some male trait before it appears in a population. Females
would then mate with male carriers when the trait appears. The offspring of
these matings have the genes for both the trait and the preference for the
trait. As a result, the process snowballs until natural selection brings it
into check. Suppose that female birds prefer males with longer than average
tail feathers. Mutant males with longer than average feathers will produce
more offspring than the short feathered males. In the next generation,
average tail length will increase. As the generations progress, feather
length will increase because females do not prefer a specific length tail,
but a longer than average tail. Eventually tail length will increase to the
point were the liability to survival is matched by the sexual attractiveness
of the trait and an equilibrium will be established. Note that in many
exotic birds male plumage is often very showy and many species do in fact
have males with greatly elongated feathers. In some cases these feathers are
shed after the breeding season.

None of the above models are mutually exclusive. There are millions of
sexually dimorphic species on this planet and the forms of sexual selection
probably vary amongst them.

Genetic Drift

Allele frequencies can change due to chance alone. This is called genetic
drift. Drift is a binomial sampling error of the gene pool. What this means
is, the alleles that form the next generation's gene pool are a sample of
the alleles from the current generation. When sampled from a population, the
frequency of alleles differs slightly due to chance alone.

Alleles can increase or decrease in frequency due to drift. The average
expected change in allele frequency is zero, since increasing or decreasing
in frequency is equally probable. A small percentage of alleles may
continually change frequency in a single direction for several generations
just as flipping a fair coin may, on occasion, result in a string of heads
or tails. A very few new mutant alleles can drift to fixation in this
manner.

In small populations, the variance in the rate of change of allele
frequencies is greater than in large populations. However, the overall rate
of genetic drift (measured in substitutions per generation) is independent
of population size. [genetic drift: a random change in allele frequencies]
If the mutation rate is constant, large and small populations lose alleles
to drift at the same rate. This is because large populations will have more
alleles in the gene pool, but they will lose them more slowly. Smaller
populations will have fewer alleles, but these will quickly cycle through.
This assumes that mutation is constantly adding new alleles to the gene pool
and selection is not operating on any of these alleles.

Sharp drops in population size can change allele frequencies substantially.
When a population crashes, the alleles in the surviving sample may not be
representative of the precrash gene pool. This change in the gene pool is
called the founder effect, because small populations of organisms that
invade a new territory (founders) are subject to this. Many biologists feel
the genetic changes brought about by founder effects may contribute to
isolated populations developing reproductive isolation from their parent
populations. In sufficiently small populations, genetic drift can counteract
selection. [genetic drift: a random change in allele frequencies] Mildly
deleterious alleles may drift to fixation.

Wright and Fisher disagreed on the importance of drift. Fisher thought
populations were sufficiently large that drift could be neglected. Wright
argued that populations were often divided into smaller subpopulations.
Drift could cause allele frequency differences between subpopulations if
gene flow was small enough. If a subpopulation was small enough, the
population could even drift through fitness valleys in the adaptive
landscape. Then, the subpopulation could climb a larger fitness hill. Gene
flow out of this subpopulation could contribute to the population as a whole
adapting. This is Wright's Shifting Balance theory of evolution.

Both natural selection and genetic drift decrease genetic variation. If they
were the only mechanisms of evolution, populations would eventually become
homogeneous and further evolution would be impossible. There are, however,
mechanisms that replace variation depleted by selection and drift. These are
discussed below.

Mechanisms that Increase Genetic Variation

Mutation

The cellular machinery that copies DNA sometimes makes mistakes. These
mistakes alter the sequence of a gene. This is called a mutation. There are
many kinds of mutations. A point mutation is a mutation in which one
"letter" of the genetic code is changed to another. Lengths of DNA can also
be deleted or inserted in a gene; these are also mutations. Finally, genes
or parts of genes can become inverted or duplicated. Typical rates of
mutation are between 10-10 and 10-12 mutations per base pair of DNA per
generation.

Most mutations are thought to be neutral with regards to fitness. (Kimura
defines neutral as |s| < 1/2Ne, where s is the selective coefficient and Ne
is the effective population size.) Only a small portion of the genome of
eukaryotes contains coding segments. And, although some non-coding DNA is
involved in gene regulation or other cellular functions, it is probable that
most base changes would have no fitness consequence.

Most mutations that have any phenotypic effect are deleterious. Mutations
that result in amino acid substitutions can change the shape of a protein,
potentially changing or eliminating its function. This can lead to
inadequacies in biochemical pathways or interfere with the process of
development. Organisms are sufficiently integrated that most random changes
will not produce a fitness benefit. Only a very small percentage of
mutations are beneficial. The ratio of neutral to deleterious to beneficial
mutations is unknown and probably varies with respect to details of the
locus in question and environment.

Mutation limits the rate of evolution. The rate of evolution can be
expressed in terms of nucleotide substitutions in a lineage per generation.
Substitution is the replacement of an allele by another in a population.
This is a two step process: First a mutation occurs in an individual,
creating a new allele. This allele subsequently increases in frequency to
fixation in the population. The rate of evolution is k = 2Nvu (in diploids)
where k is nucleotide substitutions, N is the effective population size, v
is the rate of mutation and u is the proportion of mutants that eventually
fix in the population.

Mutation need not be limiting over short time spans. The rate of evolution
expressed above is given as a steady state equation; it assumes the system
is at equilibrium. Given the time frames for a single mutant to fix, it is
unclear if populations are ever at equilibrium. A change in environment can
cause previously neutral alleles to have selective values; in the short term
evolution can run on "stored" variation and thus is independent of mutation
rate. Other mechanisms can also contribute selectable variation.
Recombination creates new combinations of alleles (or new alleles) by
joining sequences with separate microevolutionary histories within a
population. Gene flow can also supply the gene pool with variants. Of
course, the ultimate source of these variants is mutation.

The Fate of Mutant Alleles

Mutation creates new alleles. Each new allele enters the gene pool as a
single copy amongst many. Most are lost from the gene pool, the organism
carrying them fails to reproduce, or reproduces but does not pass on that
particular allele. A mutant's fate is shared with the genetic background it
appears in. A new allele will initially be linked to other loci in its
genetic background, even loci on other chromosomes. If the allele increases
in frequency in the population, initially it will be paired with other
alleles at that locus -- the new allele will primarily be carried in
individuals heterozygous for that locus. The chance of it being paired with
itself is low until it reaches intermediate frequency. If the allele is
recessive, its effect won't be seen in any individual until a homozygote is
formed. The eventual fate of the allele depends on whether it is neutral,
deleterious or beneficial.

Neutral alleles

Most neutral alleles are lost soon after they appear. The average time (in
generations) until loss of a neutral allele is 2(Ne/N) ln(2N) where N is the
effective population size (the number of individuals contributing to the
next generation's gene pool) and N is the total population size. Only a
small percentage of alleles fix. Fixation is the process of an allele
increasing to a frequency at or near one. The probability of a neutral
allele fixing in a population is equal to its frequency. For a new mutant in
a diploid population, this frequency is 1/2N.

If mutations are neutral with respect to fitness, the rate of substitution
(k) is equal to the rate of mutation(v). This does not mean every new mutant
eventually reaches fixation. Alleles are added to the gene pool by mutation
at the same rate they are lost to drift. For neutral alleles that do fix, it
takes an average of 4N generations to do so. However, at equilibrium there
are multiple alleles segregating in the population. In small populations,
few mutations appear each generation. The ones that fix do so quickly
relative to large populations. In large populations, more mutants appear
over the generations. But, the ones that fix take much longer to do so.
Thus, the rate of neutral evolution (in substitutions per generation) is
independent of population size.

The rate of mutation determines the level of heterozygosity at a locus
according to the neutral theory. Heterozygosity is simply the proportion of
the population that is heterozygous. Equilibrium heterozygosity is given as
H = 4Nv/[4Nv+1] (for diploid populations). H can vary from a very small
number to almost one. In small populations, H is small (because the equation
is approximately a very small number divided by one). In (biologically
unrealistically) large populations, heterozygosity approaches one (because
the equation is approximately a large number divided by itself). Directly
testing this model is difficult because N and v can only be estimated for
most natural populations. But, heterozygosities are believed to be too low
to be described by a strictly neutral model. Solutions offered by
neutralists for this discrepancy include hypothesizing that natural
populations may not be at equilibrium.

At equilibrium there should be a few alleles at intermediate frequency and
many at very low frequencies. This is the Ewens- Watterson distribution. New
alleles enter a population every generation, most remain at low frequency
until they are lost. A few drift to intermediate frequencies, a very few
drift all the way to fixation. In Drosophila pseudoobscura, the protein
Xanthine dehydrogenase (Xdh) has many variants. In a single population,
Keith, et. al., found that 59 of 96 proteins were of one type, two others
were represented ten and nine times and nine other types were present singly
or in low numbers.

Deleterious alleles

Deleterious mutants are selected against but remain at low frequency in the
gene pool. In diploids, a deleterious recessive mutant may increase in
frequency due to drift. Selection cannot see it when it is masked by a
dominant allele. Many disease causing alleles remain at low frequency for
this reason. People who are carriers do not suffer the negative effect of
the allele. Unless they mate with another carrier, the allele may simply
continue to be passed on. Deleterious alleles also remain in populations at
a low frequency due to a balance between recurrent mutation and selection.
This is called the mutation load.

Beneficial alleles

Most new mutants are lost, even beneficial ones. Wright calculated that the
probability of fixation of a beneficial allele is 2s. (This assumes a large
population size, a small fitness benefit, and that heterozygotes have an
intermediate fitness. A benefit of 2s yields an overall rate of evolution:
k=4Nvs where v is the mutation rate to beneficial alleles) An allele that
conferred a one percent increase in fitness only has a two percent chance of
fixing. The probability of fixation of beneficial type of mutant is boosted
by recurrent mutation. The beneficial mutant may be lost several times, but
eventually it will arise and stick in a population. (Recall that even
deleterious mutants recur in a population.)

Directional selection depletes genetic variation at the selected locus as
the fitter allele sweeps to fixation. Sequences linked to the selected
allele also increase in frequency due to hitchhiking. The lower the rate of
recombination, the larger the window of sequence that hitchhikes. Begun and
Aquadro compared the level of nucleotide polymorphism within and between
species with the rate of recombination at a locus. Low levels of nucleotide
polymorphism within species coincided with low rates of recombination. This
could be explained by molecular mechanisms if recombination itself was
mutagenic. In this case, recombination with also be correlated with
nucleotide divergence between species. But, the level of sequence divergence
did not correlate with the rate of recombination. Thus, they inferred that
selection was the cause. The correlation between recombination and
nucleotide polymorphism leaves the conclusion that selective sweeps occur
often enough to leave an imprint on the level of genetic variation in
natural populations.

One example of a beneficial mutation comes from the mosquito Culex pipiens.
In this organism, a gene that was involved with breaking down
organophosphates - common insecticide ingredients -became duplicated.
Progeny of the organism with this mutation quickly swept across the
worldwide mosquito population. There are numerous examples of insects
developing resistance to chemicals, especially DDT which was once heavily
used in this country. And, most importantly, even though "good" mutations
happen much less frequently than "bad" ones, organisms with "good" mutations
thrive while organisms with "bad" ones die out.

If beneficial mutants arise infrequently, the only fitness differences in a
population will be due to new deleterious mutants and the deleterious
recessives. Selection will simply be weeding out unfit variants. Only
occasionally will a beneficial allele be sweeping through a population. The
general lack of large fitness differences segregating in natural populations
argues that beneficial mutants do indeed arise infrequently. However, the
impact of a beneficial mutant on the level of variation at a locus can be
large and lasting. It takes many generations for a locus to regain
appreciable levels of heterozygosity following a selective sweep.

Recombination

Each chromosome in our sperm or egg cells is a mixture of genes from our
mother and our father. Recombination can be thought of as gene shuffling.
Most organisms have linear chromosomes and their genes lie at specific
location (loci) along them. Bacteria have circular chromosomes. In most
sexually reproducing organisms, there are two of each chromosome type in
every cell. For instance in humans, every chromosome is paired, one
inherited from the mother, the other inherited from the father. When an
organism produces gametes, the gametes end up with only one of each
chromosome per cell. Haploid gametes are produced from diploid cells by a
process called meiosis.

In meiosis, homologous chromosomes line up. The DNA of the chromosome is
broken on both chromosomes in several places and rejoined with the other
strand. Later, the two homologous chromosomes are split into two separate
cells that divide and become gametes. But, because of recombination, both of
the chromosomes are a mix of alleles from the mother and father.

Recombination creates new combinations of alleles. Alleles that arose at
different times and different places can be brought together. Recombination
can occur not only between genes, but within genes as well. Recombination
within a gene can form a new allele. Recombination is a mechanism of
evolution because it adds new alleles and combinations of alleles to the
gene pool.

Gene Flow

New organisms may enter a population by migration from another population.
If they mate within the population, they can bring new alleles to the local
gene pool. This is called gene flow. In some closely related species,
fertile hybrids can result from interspecific matings. These hybrids can
vector genes from species to species.

Gene flow between more distantly related species occurs infrequently. This
is called horizontal transfer. One interesting case of this involves genetic
elements called P elements. Margaret Kidwell found that P elements were
transferred from some species in the Drosophila willistoni group to
Drosophila melanogaster. These two species of fruit flies are distantly
related and hybrids do not form. Their ranges do, however, overlap. The P
elements were vectored into D. melanogaster via a parasitic mite that
targets both these species. This mite punctures the exoskeleton of the flies
and feeds on the "juices". Material, including DNA, from one fly can be
transferred to another when the mite feeds. Since P elements actively move
in the genome (they are themselves parasites of DNA), one incorporated
itself into the genome of a melanogaster fly and subsequently spread through
the species. Laboratory stocks of melanogaster caught prior to the 1940's
lack of P elements. All natural populations today harbor them.

Overview of Evolution within a Lineage

Evolution is a change in the gene pool of a population over time; it can
occur due to several factors. Three mechanisms add new alleles to the gene
pool: mutation, recombination and gene flow. Two mechanisms remove alleles,
genetic drift and natural selection. Drift removes alleles randomly from the
gene pool. Selection removes deleterious alleles from the gene pool. The
amount of genetic variation found in a population is the balance between the
actions of these mechanisms.

Natural selection can also increase the frequency of an allele. Selection
that weeds out harmful alleles is called negative selection. Selection that
increases the frequency of helpful alleles is called positive, or sometimes
positive Darwinian, selection. A new allele can also drift to high
frequency. But, since the change in frequency of an allele each generation
is random, nobody speaks of positive or negative drift.

Except in rare cases of high gene flow, new alleles enter the gene pool as a
single copy. Most new alleles added to the gene pool are lost almost
immediately due to drift or selection; only a small percent ever reach a
high frequency in the population. Even most moderately beneficial alleles
are lost due to drift when they appear. But, a mutation can reappear
numerous times.

The fate of any new allele depends a great deal on the organism it appears
in. This allele will be linked to the other alleles near it for many
generations. A mutant allele can increase in frequency simply because it is
linked to a beneficial allele at a nearby locus. This can occur even if the
mutant allele is deleterious, although it must not be so deleterious as to
offset the benefit of the other allele. Likewise a potentially beneficial
new allele can be eliminated from the gene pool because it was linked to
deleterious alleles when it first arose. An allele "riding on the coat
tails" of a beneficial allele is called a hitchhiker. Eventually,
recombination will bring the two loci to linkage equilibrium. But, the more
closely linked two alleles are, the longer the hitchhiking will last.

The effects of selection and drift are coupled. Drift is intensified as
selection pressures increase. This is because increased selection (i.e. a
greater difference in reproductive success among organisms in a population)
reduces the effective population size, the number of individuals
contributing alleles to the next generation.

Adaptation is brought about by cumulative natural selection, the repeated
sifting of mutations by natural selection. Small changes, favored by
selection, can be the stepping-stone to further changes. The summation of
large numbers of these changes is macroevolution.

The Development of Evolutionary Theory

Biology came of age as a science when Charles Darwin published "On the
Origin of Species." But, the idea of evolution wasn't new to Darwin. Lamarck
published a theory of evolution in 1809. Lamarck thought that species arose
continually from nonliving sources. These species were initially very
primitive, but increased in complexity over time due to some inherent
tendency. This type of evolution is called orthogenesis. Lamarck proposed
that an organism's acclimation to the environment could be passed on to its
offspring. For example, he thought proto-giraffes stretched their necks to
reach higher twigs. This caused their offspring to be born with longer
necks. This proposed mechanism of evolution is called the inheritance of
acquired characteristics. Lamarck also believed species never went extinct,
although they may change into newer forms. All three of these ideas are now
known to be wrong.

Darwin's contributions include hypothesizing the pattern of common descent
and proposing a mechanism for evolution -- natural selection. In Darwin's
theory of natural selection, new variants arise continually within
populations. A small percentage of these variants cause their bearers to
produce more offspring than others. These variants thrive and supplant their
less productive competitors. The effect of numerous instances of selection
would lead to a species being modified over time.

Darwin's theory did not accord with older theories of genetics. In Darwin's
time, biologists held to the theory of blending inheritance -- an offspring
was an average of its parents. If an individual had one short parent and one
tall parent, it would be of medium height. And, the offspring would pass on
genes for medium sized offspring. If this was the case, new genetic
variations would quickly be diluted out of a population. They could not
accumulate as the theory of evolution required. We now know that the idea of
blending inheritance is wrong.

Darwin didn't know that the true mode of inheritance was discovered in his
lifetime. Gregor Mendel, in his experiments on hybrid peas, showed that
genes from a mother and father do not blend. An offspring from a short and a
tall parent may be medium sized; but it carries genes for shortness and
tallness. The genes remain distinct and can be passed on to subsequent
generations. Mendel mailed his paper to Darwin, but Darwin never opened it.

It was a long time until Mendel's ideas were accepted. One group of
biologists, called biometricians, thought Mendel's laws only held for a few
traits. Most traits, they claimed, were governed by blending inheritance.
Mendel studied discrete traits. Two of the traits in his famous experiments
were smooth versus wrinkled coat on peas. This trait did not vary
continuously. In other words, peas are either wrinkled or smooth --
intermediates are not found. Biometricians considered these traits
aberrations. They studied continuously varying traits like size and believed
most traits showed blending inheritance.

Incorporating Genetics into Evolutionary Theory

The discrete genes Mendel discovered would exist at some frequency in
natural populations. Biologists wondered how and if these frequencies would
change. Many thought that the more common versions of genes would increase
in frequency simply because they were already at high frequency.

Hardy and Weinberg independently showed that the frequency of an allele
would not change over time simply due to its being rare or common. Their
model had several assumptions -- that all alleles reproduced at the same
rate, that the population size was very large and that alleles did not
change in form. Later, R. A. Fisher showed that Mendel's laws could explain
continuous traits if the expression of these traits were due to the action
of many genes. After this, geneticists accepted Mendel's Laws as the basic
rules of genetics. From this basis, Fisher, Sewall Wright and J. B. S..
Haldane founded the field of population genetics. Population genetics is a
field of biology that attempts to measure and explain the levels of genetic
variation in populations.

R. A. Fisher studied the effect of natural selection on large populations.
He demonstrated that even very small selective differences amongst alleles
could cause appreciable changes in allele frequencies over time. He also
showed that the rate of adaptive change in a population is proportional to
the amount of genetic variation present. This is called Fisher's Fundamental
Theorem of Natural Selection. Although it is called the fundamental theorem,
it does not hold in all cases. The rate at which natural selection brings
about adaptation depends on the details of how selection is working. In some
rare cases, natural selection can actually cause a decline in the mean
relative fitness of a population.

Sewall Wright was more concerned with drift. He stressed that large
populations are often subdivided into many subpopulations. In his theory,
genetic drift played a more important role compared to selection.
Differentiation between subpopulations, followed by migration among them,
could contribute to adaptations amongst populations. Wright also came up
with the idea of the adaptive landscape -- an idea that remains influential
to this day. Its influence remains even though P. A. P. Moran has shown
that, mathematically, adaptive landscapes don't exist as Wright envisioned
them. Wright extended his results of one-locus models to a two-locus case in
proposing the adaptive landscape. But, unbeknownst to him, the general
conclusions of the one-locus model don't extend to the two-locus case.

J. B. S. Haldane developed many of the mathematical models of natural and
artificial selection. He showed that selection and mutation could oppose
each other, that deleterious mutations could remain in a population due to
recurrent mutation. He also demonstrated that there was a cost to natural
selection, placing a limit on the amount of adaptive substitutions a
population could undergo in a given time frame.

For a long time, population genetics developed as a theoretical field. But,
gathering the data needed to test the theories was nearly impossible. Prior
to the advent of molecular biology, estimates of genetic variability could
only be inferred from levels of morphological differences in populations.
Lewontin and Hubby were the first to get a good estimate of genetic
variation in a population. Using the then new technique of protein
electrophoresis, they showed that 30% of the loci in a population of
Drosophila pseudoobscura were polymorphic. They also showed that it was
likely that they could not detect all the variation that was present. Upon
finding this level of variation, the question became -- was this maintained
by natural selection, or simply the result of genetic drift? This level of
variation was too high to be explained by balancing selection.

Motoo Kimura theorized that most variation found in populations was
selectively equivalent (neutral). Multiple alleles at a locus differed in
sequence, but their fitnesses were the same. Kimura's neutral theory
described rates of evolution and levels of polymorphism solely in terms of
mutation and genetic drift. The neutral theory did not deny that natural
selection acted on natural populations; but it claimed that the majority of
natural variation was transient polymorphisms of neutral alleles. Selection
did not act frequently or strongly enough to influence rates of evolution or
levels of polymorphism.

Initially, a wide variety of observations seemed to be consistent with the
neutral theory. Eventually, however, several lines of evidence toppled it.
There is less variation in natural populations than the neutral theory
predicts. Also, there is too much variance in rates of substitutions in
different lineages to be explained by mutation and drift alone. Finally,
selection itself has been shown to have an impact on levels of nucleotide
variation. Currently, there is no comprehensive mathematical theory of
evolution that accurately predicts rates of evolution and levels of
heterozygosity in natural populations.

Evolution Among Lineages

The Pattern of Macroevolution

Evolution is not progress. The popular notion that evolution can be
represented as a series of improvements from simple cells, through more
complex life forms, to humans (the pinnacle of evolution), can be traced to
the concept of the scale of nature. This view is incorrect.

All species have descended from a common ancestor. As time went on,
different lineages of organisms were modified with descent to adapt to their
environments. Thus, evolution is best viewed as a branching tree or bush,
with the tips of each branch representing currently living species. No
living organisms today are our ancestors. Every living species is as fully
modern as we are with its own unique evolutionary history. No extant species
are "lower life forms," atavistic stepping stones paving the road to
humanity.

A related, and common, fallacy about evolution is that humans evolved from
some living species of ape. This is not the case -- humans and apes share a
common ancestor. Both humans and living apes are fully modern species; the
ancestor we evolved from was an ape, but it is now extinct and was not the
same as present day apes (or humans for that matter). If it were not for the
vanity of human beings, we would be classified as an ape. Our closest
relatives are, collectively, the chimpanzee and the pygmy chimp. Our next
nearest relative is the gorilla.

Evidence for Common Descent and Macroevolution

Microevolution can be studied directly. Macroevolution cannot.
Macroevolution is studied by examining patterns in biological populations
and groups of related organisms and inferring process from pattern. Given
the observation of microevolution and the knowledge that the earth is
billions of years old -- macroevolution could be postulated. But this
extrapolation, in and of itself, does not provide a compelling explanation
of the patterns of biological diversity we see today. Evidence for
macroevolution, or common ancestry and modification with descent, comes from
several other fields of study. These include: comparative biochemical and
genetic studies, comparative developmental biology, patterns of
biogeography, comparative morphology and anatomy and the fossil record.

Closely related species (as determined by morphologists) have similar gene
sequences. Overall sequence similarity is not the whole story, however. The
pattern of differences we see in closely related genomes is worth examining.

All living organisms use DNA as their genetic material, although some
viruses use RNA. DNA is composed of strings of nucleotides. There are four
different kinds of nucleotides: adenine (A), guanine (G), cytosine (C) and
thymine (T). Genes are sequences of nucleotides that code for proteins.
Within a gene, each block of three nucleotides is called a codon. Each codon
designates an amino acid (the subunits of proteins).

The three letter code is the same for all organisms (with a few exceptions).
There are 64 codons, but only 20 amino acids to code for; so, most amino
acids are coded for by several codons. In many cases the first two
nucleotides in the codon designate the amino acid. The third position can
have any of the four nucleotides and not effect how the code is translated.

A gene, when in use, is transcribed into RNA -- a nucleic acid similar to
DNA. (RNA, like DNA, is made up of nucleotides although t he nucleotide
uracil (U) is used in place of thymine (T).) The RNA transcribed from a gene
is called messenger RNA. Messenger RNA is then translated via cellular
machinery called ribosomes into a string of amino acids -- a protein. Some
proteins function as enzymes, catalysts that speed the chemical reactions in
cells. Others are structural or involved in regulating development.

Gene sequences in closely related species are very similar. Often, the same
codon specifies a given amino acid in two related species, even though
alternate codons could serve functionally as well. But, some differences do
exist in gene sequences. Most often, differences are in third codon
positions, where changes in the DNA sequence would not disrupt the sequence
of the protein.

There are other sites in the genome where nucleotide differences do not
effect protein sequences. The genome of eukaryotes is loaded with 'dead
genes' called pseudogenes. Pseudogenes are copies of working genes that have
been inactivated by mutation. Most pseudogenes do not produce full proteins.
They may be transcribed, but not translated. Or, they may be translated, but
only a truncated protein is produced. Pseudogenes evolve much faster than
their working counterparts. Mutations in them do not get incorporated into
proteins, so they have no effect on the fitness of an organism.

Introns are sequences of DNA that interrupt a gene, but do not code for
anything. The coding portions of a gene are called exons. Introns are
spliced out of the messenger RNA prior to translation, so they do not
contribute information needed to make the protein. They are sometimes,
however, involved in regulation of the gene. Like pseudogenes, introns (in
general) evolve faster than coding portions of a gene.

Nucleotide positions that can be changed without changing the sequence of a
protein are called silent sites. Sites where changes result in an amino acid
substitution are called replacement sites. Silent sites are expected to be
more polymorphic within a population and show more differences between
populations. Although both silent and replacement sites receive the same
amount of mutations, natural selection only infrequently allows changes at
replacement sites. Silent sites, however, are not as constrained.

Kreitman was the first demonstrate that silent sites were more variable than
coding sites. Shortly after the methods of DNA sequencing were discovered,
he sequenced 11 alleles of the enzyme alcohol dehydrogenase (AdH). Of the 43
polymorphic nucleotide sites he found, only one resulted in a change in the
amino acid sequence of the protein.

Silent sites may not be entirely selectively neutral. Some DNA sequences are
involved with regulation of genes, changes in these sites may be
deleterious. Likewise, although several codons code for a single amino acid,
an organism may have a preferred codon for each amino acid. This is called
codon bias.

If two species shared a recent common ancestor one would expect genetic
information, even information such as redundant nucleotides and the position
of introns or pseudogenes, to be similar. Both species would have inherited
this information from their common ancestor.

The degree of similarity in nucleotide sequence is a function of divergence
time. If two populations had recently separated, few differences would have
built up between them. If they separated long ago, each population would
have evolved numerous differences from their common ancestor (and each
other). The degree of similarity would also be a function of silent versus
replacement sites. Li and Graur, in their molecular evolution text, give the
rates of evolution for silent vs. replacement rates. The rates were
estimated from sequence comparisons of 30 genes from humans and rodents,
which diverged about 80 million years ago. Silent sites evolved at an
average rate of 4.61 nucleotide substitution per 109 years. Replacement
sites evolved much slower at an average rate of 0.85 nucleotide
substitutions per 109 years.

Groups of related organisms are 'variations on a theme' -- the same set of
bones are used to construct all vertebrates. The bones of the human hand
grow out of the same tissue as the bones of a bat's wing or a whale's
flipper; and, they share many identifying features such as muscle insertion
points and ridges. The only difference is that they are scaled differently.
Evolutionary biologists say this indicates that all mammals are modified
descendants of a common ancestor which had the same set of bones.

Closely related organisms share similar developmental pathways. The
differences in development are most evident at the end. As organisms evolve,
their developmental pathway gets modified. An alteration near the end of a
developmental pathway is less likely to be deleterious than changes in early
development. Changes early on may have a cascading effect. Thus most
evolutionary changes in development are expected to take place at the
periphery of development, or in early aspects of development that have no
later repercussions. For a change in early development to be propagated, the
benefit of the early alteration must outweigh the consequences to later
development.

Because they have evolved this way, organisms pass through the early stages
of development that their ancestors passed through up to the point of
divergence. So, an organism's development mimics its ancestors although it
doesn't recreate it exactly. Development of the flatfish, Pleuronectes,
illustrates this point. Early on, Pleuronectes develops a tail that comes to
a point. In the next developmental stage, the top lobe of the tail is larger
than the bottom lobe (as in sharks). When development is complete, the upper
and lower lobes are equally sized. This developmental pattern mirrors the
evolutionary transitions it has undergone.

Natural selection can modify any stage of a life cycle, so some differences
are seen in early development. Thus, evolution does not always recapitulate
ancestral forms -- butterflies did not evolve from ancestral caterpillars,
for example. There are differences in the appearance of early vertebrate
embryos. Amphibians rapidly form a ball of cells in early development.
Birds, reptiles and mammals form a disk. The shape of the early embryo is a
result of different yolk concentrations in the eggs. Birds' and reptiles'
eggs are heavily yolked. Their eggs develop similarly to amphibians except
the yolk has deformed the shape of the embryo. The ball is stretched out and
lying atop the yolk. Mammals have no yolk, but still form a disk early. This
is because they have descended from reptiles. Mammals lost their yolky eggs,
but retained the early pattern of development. In all these vertebrates, the
pattern of cell movements is similar despite superficial differences in
appearance. In addition, all types quickly converge upon a primitive,
fish-like stage within a few days. From there, development diverges.

Traces of an organism's ancestry sometimes remain even when an organism's
development is complete. These are called vestigial structures. Many snakes
have rudimentary pelvic bones retained from their walking ancestors.
Vestigial does not mean useless, it means the structure is clearly a vestige
of an structure inherited from ancestral organisms. Vestigial structures may
acquire new functions. In humans, the appendix now houses some immune system
cells.

Closely related organisms are usually found in close geographic proximity;
this is especially true of organisms with limited dispersal opportunities.
The mammalian fauna of Australia is often cited as an example of this;
marsupial mammals fill most of the equivalent niches that placentals fill in
other ecosystems. If all organisms descended from a common ancestor, species
distribution across the planet would be a function of site of origination,
potential for dispersal, distribution of suitable habitat, and time since
origination. In the case of Australian mammals, their physical separation
from sources of placentals means potential niches were filled by a marsupial
radiation rather than a placental radiation or invasion.

Natural selection can only mold available genetically based variation. In
addition, natural selection provides no mechanism for advance planning. If
selection can only tinker with the available genetic variation, we should
expect to see examples of jury-rigged design in living species. This is
indeed the case. In lizards of the genus Cnemodophorus, females reproduce
parthenogenetically. Fertility in these lizards is increased when a female
mounts another female and simulates copulation. These lizards evolved from
sexual lizards whose hormones were aroused by sexual behavior. Now, although
the sexual mode of reproduction has been lost, the means of getting aroused
(and hence fertile) has been retained.

Fossils show hard structures of organisms less and less similar to modern
organisms in progressively older rocks. In addition, patterns of
biogeography apply to fossils as well as extant organisms. When combined
with plate tectonics, fossils provide evidence of distributions and
dispersals of ancient species. For example, South America had a very
distinct marsupial mammalian fauna until the land bridge formed between
North and South America. After that marsupials started disappearing and
placentals took their place. This is commonly interpreted as the placentals
wiping out the marsupials, but this may be an over simplification.

Transitional fossils between groups have been found. One of the most
impressive transitional series is the ancient reptile to modern mammal
transition. Mammals and reptiles differ in skeletal details, especially in
their skulls. Reptilian jaws have four bones. The foremost is called the
dentary. In mammals, the dentary bone is the only bone in the lower jaw. The
other bones are part of the middle ear. Reptiles have a weak jaw and a
mouthful of undifferentiated teeth. Their jaw is closed by three muscles:
the external, posterior and internal adductor. Each reptile tooth is single
cusped. Mammals have powerful jaws with differentiated teeth. Many of these
teeth, such as the molars, are multi-cusped. The temporalis and masseter
muscles, derived from the external adductor, close the mammalian jaw.
Mammals have a secondary palate, a bony structure separating their nostril
passages and throat, so most can swallow and breathe simultaneously.
Reptiles lack this.

The evolution of these traits can be seen in a series of fossils.
Procynosuchus shows an increase in size of the dentary bone and the
beginnings of a palate. Thrinaxodon has a reduced number of incisors, a
precursor to tooth differentiation. Cynognathus (a doglike carnivore) shows
a further increase in size of the dentary bone. The other three bones are
located inside the back portion of the jaw. Some teeth are multicusped and
the teeth fit together tightly. Diademodon (a plant eater) shows a more
advanced degree of occlusion (teeth fitting tightly). Probelesodon has
developed a double joint in the jaw. The jaw could hinge off two points with
the upper skull. The front hinge was probably the actual hinge while the
rear hinge was an alignment guide. The forward movement of a hinge point
allowed for the precursor to the modern masseter muscle to anchor further
forward in the jaw. This allowed for a more powerful bite. The first true
mammal was Morgonucudon, a rodent-like insectivore from the late Triassic.
It had all the traits common to modern mammals. These species were not from
a single, unbranched lineage. Each is an example from a group of organisms
along the main line of mammalian ancestry.

The strongest evidence for macroevolution comes from the fact that suites of
traits in biological entities fall into a nested pattern. For example,
plants can be divided into two broad categories, non- vascular (ex. mosses)
and vascular. Vascular plants can be divided into seedless (ex. ferns) and
seeded. Vascular seeded plants can be divided into gymnosperms (ex. pines)
and flowering plants (angiosperms). Angiosperms can be divided into monocots
and dicots. Each of these types of plants have several characters that
distinguish them from other plants. Traits are not mixed and matched in
groups of organisms. For example, flowers are only seen in plants that carry
several other characters that distinguish them as angiosperms. This is the
expected pattern of common descent. All the species in a group will share
traits they inherited from their common ancestor. But, each subgroup will
have evolved unique traits of its own. Similarities bind groups together.
Differences show how they are subdivided.

The real test of any scientific theory is its ability to generate testable
predictions and, of course, have the predictions borne out. Evolution easily
meets this criterion. In several of the above examples I stated, closely
related organisms share X. If I define closely related as sharing X, this is
an empty statement. It does however, provide a prediction. If two organisms
share a similar anatomy, one would then predict that their gene sequences
would be more similar than a morphologically distinct organism. This has
been spectacularly borne out by the recent flood of gene sequences -- the
correspondence to trees drawn by morphological data is very high. The
discrepancies are never too great and usually confined to cases where the
pattern of relationship was debated.

Mechanisms of Macroevolution

The following deals with mechanisms of evolution above the species level.

Speciation -- Increasing Biological Diversity

Speciation is the process of a single species becoming two or more species.
Many biologists think speciation is key to understanding evolution. Some
would argue that certain evolutionary phenomena apply only at speciation and
macroevolutionary change cannot occur without speciation. Other biologists
think major evolutionary change can occur without speciation. Changes
between lineages are only an extension of the changes within each lineage.
In general, paleontologists fall into the former category and geneticists in
the latter.

Modes of Speciation

Biologists recognize two types of speciation: allopatric and sympatric
speciation. The two differ in geographical distribution of the populations
in question. Allopatric speciation is thought to be the most common form of
speciation. It occurs when a population is split into two (or more)
geographically isolated subdivisions that organisms cannot bridge.
Eventually, the two populations' gene pools change independently until they
could not interbreed even if they were brought back together. In other
words, they have speciated.

Sympatric speciation occurs when two subpopulations become reproductively
isolated without first becoming geographically isolated. Insects that live
on a single host plant provide a model for sympatric speciation. If a group
of insects switched host plants they would not breed with other members of
their species still living on their former host plant. The two
subpopulations could diverge and speciate. Agricultural records show that a
strain of the apple maggot fly Rhagolettis pomenella began infesting apples
in the 1860's. Formerly it had only infested hawthorn fruit. Feder, Chilcote
and Bush have shown that two races of Rhagolettis pomenella have become
behaviorally isolated. Allele frequencies at six loci (aconitase 2, malic
enzyme, mannose phosphate isomerase, aspartate amino-transferase,
NADH-diaphorase-2, and beta-hydroxy acid dehydrogenase) are diverging.
Significant amounts of linkage disequilibrium have been found at these loci,
indicating that they may all be hitchhiking on some allele under selection.
Some biologists call sympatric speciation microallopatric speciation to
emphasize that the subpopulations are still physically separate at an
ecological level.

Biologists know little about the genetic mechanisms of speciation. Some
think a series of small changes in each subdivision gradually lead to
speciation. The founder effect could set the stage for relatively rapid
speciation, a genetic revolution in Ernst Mayr's terms. Alan Templeton
hypothesized that a few key genes could change and confer reproductive
isolation. He called this a genetic transilience. Lynn Margulis thinks most
speciation events are caused by changes in internal symbionts. Populations
of organisms are very complicated. It is likely that there are many ways
speciation can occur. Thus, all of the above ideas may be correct, each in
different circumstances. Darwin's book was titled "The Origin of Species"
despite the fact that he did not really address this question; over one
hundred and fifty years later, how species originate is still largely a
mystery.

Observed Speciations

Speciation has been observed. In the plant genus Tragopogon, two new species
have evolved within the past 50-60 years. They are T. mirus and T.
miscellus. The new species were formed when one diploid species fertilized a
different diploid species and produced a tetraploid offspring. This
tetraploid offspring could not fertilize or be fertilized by either of its
two parent species types. It is reproductively isolated, the definition of a
species.

Extinction -- Decreasing Biological Diversity

Ordinary Extinction

Extinction is the ultimate fate of all species. The reasons for extinction
are numerous. A species can be competitively excluded by a closely related
species, the habitat a species lives in can disappear and/or the organisms
that the species exploits could come up with an unbeatable defense.

Some species enjoy a long tenure on the planet while others are short-
lived. Some biologists believe species are programmed to go extinct in a
manner analogous to organisms being destined to die. The majority, however,
believe that if the environment stays fairly constant, a well adapted
species could continue to survive indefinitely.

Mass Extinction

Mass extinctions shape the overall pattern of macroevolution. If you view
evolution as a branching tree, it's best to picture it as one that has been
severely pruned a few times in its life. The history of life on this earth
includes many episodes of mass extinction in which many groups of organisms
were wiped off the face of the planet. Mass extinctions are followed by
periods of radiation where new species evolve to fill the empty niches left
behind. It is probable that surviving a mass extinction is largely a
function of luck. Thus, contingency plays a large role in patterns of
macroevolution.

The largest mass extinction came at the end of the Permian, about 250
million years ago. This coincides with the formation of Pangaea II, when all
the world's continents were brought together by plate tectonics. A worldwide
drop in sea level also occurred at this time.

The most well-known extinction occurred at the boundary between the
Cretaceous and Tertiary Periods. This called the K/T Boundary and is dated
at around 65 million years ago. This extinction eradicated the dinosaurs.
The K/T event was probably caused by environmental disruption brought on by
a large impact of an asteroid with the earth. Following this extinction the
mammalian radiation occurred. Mammals coexisted for a long time with the
dinosaurs but were confined mostly to nocturnal insectivore niches. With the
eradication of the dinosaurs, mammals radiated to fill the vacant niches.

Currently, human alteration of the ecosphere is causing a global mass
extinction.

Punctuated Equilibrium

The theory of punctuated equilibrium is an inference about the process of
macroevolution from the pattern of species documented in the fossil record.
In the fossil record, transition from one species to another is usually
abrupt in most geographic locales -- no transitional forms are found. In
short, it appears that species remain unchanged for long stretches of time
and then are quickly replaced by new species. However, if wide ranges are
searched, transitional forms that bridge the gap between the two species are
sometimes found in small, localized areas. For example, in Jurassic
brachiopods of the genus Kutchithyris, K. acutiplicata appears below another
species, K. euryptycha. Both species were common and covered a wide
geographical area. They differ enough that some have argued they should be
in a different genera. In just one small locality an approximately 1.25m
sedimentary layer with these fossils is found. In the narrow (10 cm) layer
that separates the two species, both species are found along with
transitional forms. In other localities there is a sharp transition.

Eldredge and Gould proposed that most major morphological change occurs
(relatively) quickly in small peripheral population at the time of
speciation. New forms will then invade the range of their ancestral species.
Thus, at most locations that fossils are found, transition from one species
to another will be abrupt. This abrupt change will reflect replacement by
migration however, not evolution. In order to find the transitional fossils,
the area of speciation must be found.

There has been considerable confusion about the theory. Some popular
accounts give the impression that abrupt changes in the fossil record are
due to blindingly fast evolution; this is not a part of the theory.

Punctuated equilibrium has been presented as a hierarchical theory of
evolution. Proponents of punctuated equilibrium see speciation as analogous
to mutation and the replacement of one species by another as analogous to
natural selection. This is called species selection. Speciation adds new
species to the species pool just as mutation adds new alleles to the gene
pool. Species selection favors one species over another just as natural
selection can favor one allele over another. Evolutionary trends within a
group would be the result of selection among species, not natural selection
acting within species. This is the most controversial part of the theory.
Many biologists agree with the pattern of macroevolution these
paleontologists posit, but believe species selection is not even
theoretically likely to occur.

Critics would argue that species selection is not analogous to natural
selection and therefore evolution is not hierarchical. Also, the number of
species produced over time is far less than the amount of different alleles
that enter gene pools over time. So, the amount of adaptive evolution
produced by species selection (if it did occur) would have to be orders of
magnitude less than adaptive evolution within populations by natural
selection.

Tests of punctuated equilibrium have been equivocal. It has been known for a
long time that rates of evolution vary over time, that is not controversial.
However, phylogenetic studies conflict as to whether there is a clear
association between speciation and morphological change. In addition, there
are major polymorphisms within some species. For example, bluegill sunfish
have two male morphs. One is a large, long-lived, mate-protecting male; the
other is a smaller, shorter-lived male who sneaks matings from females
guarded by large males. The existence of within species polymorphisms
demonstrates that speciation is not a requirement for major morphological
change.

A Brief History of Life

Biologists studying evolution do a variety of things: population geneticists
study the process as it is occurring; systematists seek to determine
relationships between species and paleontologists seek to uncover details of
the unfolding of life in the past. Discerning these details is often
difficult, but hypotheses can be made and tested as new evidence comes to
light. This section should be viewed as the best hypothesis scientists have
as to the history of the planet. The material here ranges from some issues
that are fairly certain to some topics that are nothing more than informed
speculation. For some points there are opposing hypotheses -- I have tried
to compile a consensus picture. In general, the more remote the time, the
more likely the story is incomplete or in error.

Life evolved in the sea. It stayed there for the majority of the history of
earth.

The first replicating molecules were most likely RNA. RNA is a nucleic acid
similar to DNA. In laboratory studies it has been shown that some RNA
sequences have catalytic capabilities. Most importantly, certain RNA
sequences act as polymerases -- enzymes that form strands of RNA from its
monomers. This process of self replication is the crucial step in the
formation of life. This is called the RNA world hypothesis.

The common ancestor of all life probably used RNA as its genetic material.
This ancestor gave rise to three major lineages of life. These are: the
prokaryotes ("ordinary" bacteria), archaebacteria (thermophilic,
methanogenic and halophilic bacteria) and eukaryotes. Eukaryotes include
protists (single celled organisms like amoebas and diatoms and a few
multicellular forms such as kelp), fungi (including mushrooms and yeast),
plants and animals. Eukaryotes and archaebacteria are the two most closely
related of the three. The process of translation (making protein from the
instructions on a messenger RNA template) is similar in these lineages, but
the organization of the genome and transcription (making messenger RNA from
a DNA template) is very different in prokaryotes than in eukaryotes and
archaebacteria. Scientists interpret this to mean that the common ancestor
was RNA based; it gave rise to two lineages that independently formed a DNA
genome and hence independently evolved mechanisms to transcribe DNA into
RNA.

The first cells must have been anaerobic because there was no oxygen in the
atmosphere. In addition, they were probably thermophilic ("heat-loving") and
fermentative. Rocks as old as 3.5 billion years old have yielded prokaryotic
fossils. Specifically, some rocks from Australia called the Warrawoona
series give evidence of bacterial communities organized into structures
called stromatolites. Fossils like these have subsequently been found all
over the world. These mats of bacteria still form today in a few locales
(for example, Shark Bay Australia). Bacteria are the only life forms found
in the rocks for a long, long time --eukaryotes (protists) appear about 1.5
billion years ago and fungi-like things appear about 900 million years ago
(0.9 billion years ago).

Photosynthesis evolved around 3.4 billion years ago. Photosynthesis is a
process that allows organisms to harness sunlight to manufacture sugar from
simpler precursors. The first photosystem to evolve, PSI, uses light to
convert carbon dioxide (CO2) and hydrogen sulfide (H2S) to glucose. This
process releases sulfur as a waste product. About a billion years later, a
second photosystem (PS) evolved, probably from a duplication of the first
photosystem. Organisms with PSII use both photosystems in conjunction to
convert carbon dioxide (CO2) and water (H2O) into glucose. This process
releases oxygen as a waste product. Anoxygenic (or H2S) photosynthesis,
using PSI, is seen in living purple and green bacteria. Oxygenic (or H2O)
photosynthesis, using PSI and PSII, takes place in cyanobacteria.
Cyanobacteria are closely related to and hence probably evolved from purple
bacterial ancestors. Green bacteria are an outgroup. Since oxygenic bacteria
are a lineage within a cluster of anoxygenic lineages, scientists infer that
PSI evolved first. This also corroborates with geological evidence.

Green plants and algae also use both photosystems. In these organisms,
photosynthesis occurs in organelles (membrane bound structures within the
cell) called chloroplasts. These organelles originated as free living
bacteria related to the cyanobacteria that were engulfed by ur-eukaryotes
and eventually entered into an endosymbiotic relationship. This
endosymbiotic theory of eukaryotic organelles was championed by Lynn
Margulis. Originally controversial, this theory is now accepted. One key
line of evidence in support of this idea came when the DNA inside
chloroplasts was sequenced -- the gene sequences were more similar to
free-living cyanobacteria sequences than to sequences from the plants the
chloroplasts resided in.

After the advent of photosystem II, oxygen levels increased. Dissolved
oxygen in the oceans increased as well as atmospheric oxygen. This is
sometimes called the oxygen holocaust. Oxygen is a very good electron
acceptor and can be very damaging to living organisms. Many bacteria are
anaerobic and die almost immediately in the presence of oxygen. Other
organisms, like animals, have special ways to avoid cellular damage due to
this element (and in fact require it to live.) Initially, when oxygen began
building up in the environment, it was neutralized by materials already
present. Iron, which existed in high concentrations in the sea was oxidized
and precipitated. Evidence of this can be seen in banded iron formations
from this time, layers of iron deposited on the sea floor. As one geologist
put it, "the world rusted." Eventually, it grew to high enough
concentrations to be dangerous to living things. In response, many species
went extinct, some continued (and still continue) to thrive in anaerobic
microenvironments and several lineages independently evolved oxygen
respiration.

The purple bacteria evolved oxygen respiration by reversing the flow of
molecules through their carbon fixing pathways and modifying their electron
transport chains. Purple bacteria also enabled the eukaryotic lineage to
become aerobic. Eukaryotic cells have membrane bound organelles called
mitochondria that take care of respiration for the cell. These are
endosymbionts like chloroplasts. Mitochondria formed this symbiotic
relationship very early in eukaryotic history, all but a few groups of
eukaryotic cells have mitochondria. Later, a few lineages picked up
chloroplasts. Chloroplasts have multiple origins. Red algae picked up
ur-chloroplasts from the cyanobacterial lineage. Green algae, the group
plants evolved from, picked up different urchloroplasts from a
prochlorophyte, a lineage closely related to cyanobacteria.

Animals start appearing prior to the Cambrian, about 600 million years ago.
The first animals dating from just before the Cambrian were found in rocks
near Adelaide, Australia. They are called the Ediacarian fauna and have
subsequently been found in other locales as well. It is unclear if these
forms have any surviving descendants. Some look a bit like Cnidarians
(jellyfish, sea anemones and the like); others resemble annelids
(earthworms). All the phyla (the second highest taxonomic category) of
animals appeared around the Cambrian. The Cambrian 'explosion' may have been
a result of higher oxygen concentrations enabling larger organisms with
higher metabolisms to evolve. Or it might be due to the spreading of shallow
seas at that time providing a variety of new niches. In any case, the
radiation produced a wide variety of animals.

Some paleontologists think more animal phyla were present then than now. The
animals of the Burgess shale are an example of Cambrian animal fossils.
These fossils, from Canada, show a bizarre array of creatures, some which
appear to have unique body plans unlike those seen in any living animals.

The extent of the Cambrian explosion is often overstated. Although quick,
the Cambrian explosion is not instantaneous in geologic time. Also, there is
evidence of animal life prior to the Cambrian. In addition, although all the
phyla of animals came into being, these were not the modern forms we see
today. Our own phylum (which we share with other mammals, reptiles, birds,
amphibians and fish) was represented by a small, sliver-like thing called
Pikaia. Plants were not yet present. Photosynthetic protists and algae were
the bottom of the food chain. Following the Cambrian, the number of marine
families leveled off at a little less than 200.

The Ordovician explosion, around 500 million years ago, followed. This
'explosion', larger than the Cambrian, introduced numerous families of the
Paleozoic fauna (including crinoids, articulate brachiopods, cephalopods and
corals). The Cambrian fauna, (trilobites, inarticulate brachiopods, etc.)
declined slowly during this time. By the end of the Ordovician, the Cambrian
fauna had mostly given way to the Paleozoic fauna and the number of marine
families was just over 400. It stayed at this level until the end of the
Permian period.

Plants evolved from ancient green algae over 400 million years ago. Both
groups use chlorophyll a and b as photosynthetic pigments. In addition,
plants and green algae are the only groups to store starch in their
chloroplasts. Plants and fungi (in symbiosis) invaded the land about 400
million years ago. The first plants were moss-like and required moist
environments to survive. Later, evolutionary developments such as a waxy
cuticle allowed some plants to exploit more inland environments. Still
mosses lack true vascular tissue to transport fluids and nutrients. This
limits their size since these must diffuse through the plant. Vascular
plants evolved from mosses. The first vascular land plant known is
Cooksonia, a spiky, branching, leafless structure. At the same time, or
shortly thereafter, arthropods followed plants onto the land. The first land
animals known are myriapods -- centipedes and millipedes.

Vertebrates moved onto the land by the Devonian period, about 380 million
years ago. Ichthyostega, an amphibian, is the among the first known land
vertebrates. It was found in Greenland and was derived from lobe-finned
fishes called Rhipidistians. Amphibians gave rise to reptiles. Reptiles had
evolved scales to decrease water loss and a shelled egg permitting young to
be hatched on land. Among the earliest well preserved reptiles is Hylonomus,
from rocks in Nova Scotia.

The Permian extinction was the largest extinction in history. It happened
about 250 million years ago. The last of the Cambrian Fauna went extinct.
The Paleozoic fauna took a nose dive from about 300 families to about 50. It
is estimated that 96% of all species (50% of all Families) met their end.
Following this event, the Modern fauna, which had been slowly expanding
since the Ordovician, took over.

The Modern fauna includes fish, bivalves, gastropods and crabs. These were
barely affected by the Permian extinction. The Modern fauna subsequently
increased to over 600 marine families at present. The Paleozoic fauna held
steady at about 100 families. A second extinction event shortly following
the Permian kept animal diversity low for awhile.

During the Carboniferous (the period just prior to the Permian) and in the
Permian the landscape was dominated by ferns and their relatives. After the
Permian extinction, gymnosperms (ex. pines) became more abundant.
Gymnosperms had evolved seeds, from seedless fern ancestors, which helped
their ability to disperse. Gymnosperms also evolved pollen, encased sperm
which allowed for more outcrossing.

Dinosaurs evolved from archosaur reptiles, their closest living relatives
are crocodiles. One modification that may have been a key to their success
was the evolution of an upright stance. Amphibians and reptiles have a
splayed stance and walk with an undulating pattern because their limbs are
modified from fins. Their gait is modified from the swimming movement of
fish. Splay stanced animals cannot sustain continued locomotion because they
cannot breathe while they move; their undulating movement compresses their
chest cavity. Thus, they must stop every few steps and breath before
continuing on their way. Dinosaurs evolved an upright stance similar to the
upright stance mammals independently evolved. This allowed for continual
locomotion. In addition, dinosaurs evolved to be warm-blooded.
Warmbloodedness allows an increase in the vigor of movements in erect
organisms. Splay stanced organisms would probably not benefit from warm-
bloodedness. Birds evolved from sauriscian dinosaurs. Cladistically, birds
are dinosaurs. The transitional fossil Archaeopteryx has a mixture of
reptilian and avian features.

Angiosperms evolved from gymnosperms, their closest relatives are Gnetae.
Two key adaptations allowed them to displace gymnosperms as the dominant
fauna -- fruits and flowers. Fruits (modified plant ovaries) allow for
animal-based seed dispersal and deposition with plenty of fertilizer.
Flowers evolved to facilitate animal, especially insect, based pollen
dispersal. Petals are modified leaves. Angiosperms currently dominate the
flora of the world -- over three fourths of all living plants are
angiosperms.

Insects evolved from primitive segmented arthropods. The mouth parts of
insects are modified legs. Insects are closely related to annelids. Insects
dominate the fauna of the world. Over half of all named species are insects.
One third of this number are beetles.

The end of the Cretaceous, about 65 million years ago, is marked by a minor
mass extinction. This extinction marked the demise of all the lineages of
dinosaurs save the birds. Up to this point mammals were confined to
nocturnal, insectivorous niches. Once the dinosaurs were out of the picture,
they diversified. Morgonucudon , a contemporary of dinosaurs, is an example
of one of the first mammals. Mammals evolved from therapsid reptiles. The
finback reptile Diametrodon is an example of a therapsid. One of the most
successful lineages of mammals is, of course, humans. Humans are neotenous
apes. Neoteny is a process which leads to an organism reaching reproductive
capacity in its juvenile form. The primary line of evidence for this is the
similarities between young apes and adult humans. Louis Bolk compiled a list
of 25 features shared between adult humans and juvenile apes, including
facial morphology, high relative brain weight, absence of brow ridges and
cranial crests.

The earth has been in a state of flux for 4 billion years. Across this time,
the abundance of different lineages varies wildly. New lineages evolve and
radiate out across the face of the planet, pushing older lineages to
extinction, or relictual existence in protected refugia or suitable
microhabitats. Organisms modify their environments. This can be disastrous,
as in the case of the oxygen holocaust. However, environmental modification
can be the impetus for further evolutionary change. Overall, diversity has
increased since the beginning of life. This increase is, however,
interrupted numerous times by mass extinctions. Diversity appears to have
hit an all-time high just prior to the appearance of humans. As the human
population has increased, biological diversity has decreased at an
ever-increasing pace. The correlation is probably causal.

Scientific Standing of Evolution and its Critics

The theory of evolution and common descent were once controversial in
scientific circles. This is no longer the case. Debates continue about how
various aspects of evolution work. For example, all the details of patterns
of relationships are not fully worked out. However, evolution and common
descent are considered fact by the scientific community.

Scientific creationism is 100% crap. So-called "scientific" creationists do
not base their objections on scientific reasoning or data. Their ideas are
based on religious dogma, and their approach is simply to attack evolution.
The types of arguments they use fall into several categories: distortions of
scientific principles ( the second law of thermodynamics argument), straw
man versions of evolution (the "too improbable to evolve by chance"
argument), dishonest selective use of data (the declining speed of light
argument) appeals to emotion or wishful thinking ("I don't want to be
related to an ape"), appeals to personal incredulity ("I don't see how this
could have evolved"), dishonestly quoting scientists out of context
(Darwin's comments on the evolution of the eye) and simply fabricating data
to suit their arguments (Gish's "bullfrog proteins").

Most importantly, scientific creationists do not have a testable, scientific
theory to replace evolution with. Even if evolution turned out to be wrong,
it would simply be replaced by another scientific theory. Creationists do
not conduct scientific experiments, nor do they seek publication in
peer-reviewed scientific journals. Much of their output is "preaching to the
choir."

The most persuasive creationist argument is a non-scientific one -- the
appeal to fair play. "Shouldn't we present both sides of the argument?,"
they ask. The answer is no -- the fair thing to do is exclude scientific
creationism from public school science courses. Scientists have studied and
tested evolution for 150 years. There is voluminous evidence for it. Within
the scientific community, there are no competing theories. Until scientific
creationists formulate a scientific theory, and submit it for testing, they
have no right to demand equal time in science class to present their ideas.
Evolution has earned a place in the science curriculum. Creationism has not.

Science is based on an open and honest look at the data. Much of creationism
is built on dishonest debating techniques and special pleading for a case
the data does not support. Science belongs in science classes. Evolution is
science. Creationism is not. It's that simple.

The creationist attack on public school education means that school children
are denied the possibility of learning about the most powerful and elegant
theory in biology. Politicians are willing to allow the scientifically
ignorant, but politically strong, to wreck the educational system in
exchange for votes. People interested in evolution, and science education in
general, need to closely watch school board elections. Creationist "stealth"
candidates have been elected in several regions. Thankfully, many have been
voted out once their views became apparent.

The majority of Americans are religious, but only a minority are religious
nuts. The version of religion the far right wants to impose on America is as
repulsive to most mainstream Christians as it is to members of other
religions, atheists and agnostics. Most informed religious people see no
reason for biological facts and theories to interfere with their religious
beliefs.

The Importance of Evolution in Biology

"Nothing in biology makes sense except in the light of evolution." --
Theodosius Dobzhansky

Evolution has been called the cornerstone of biology, and for good reasons.
It is possible to do research in biology with little or no knowledge of
evolution. Most biologists do. But, without evolution biology becomes a
disparate set of fields. Evolutionary explanations pervade all fields in
biology and brings them together under one theoretical umbrella.

We know from microevolutionary theory that natural selection should optimize
the existing genetic variation in a population to maximize reproductive
success. This provides a framework for interpreting a variety of biological
traits and their relative importance. For example, a signal intended to
attract a mate could be intercepted by predators. Natural selection has
caused a trade- off between attracting mates and getting preyed upon. If you
assume something other than reproductive success is optimized, many things
in biology would make little sense. Without the theory of evolution, life
history strategies would be poorly understood.

Macroevolutionary theory also helps explain many things about how living
things work. Organisms are modified over time by cumulative natural
selection. The numerous examples of jury- rigged design in nature are a
direct result of this. The distribution of genetically based traits across
groups is explained by splitting of lineages and the continued production of
new traits by mutation. The traits are restricted to the lineages they arise
in.

Details of the past also hold explanatory power in biology. Plants obtain
their carbon by joining carbon dioxide gas to an organic molecule within
their cells. This is called carbon fixation. The enzyme that fixes carbon is
RuBP carboxlyase. Plants using C3 photosynthesis lose 1/3 to 1/2 of the
carbon dioxide they originally fix. RuBP carboxlyase works well in the
absence of oxygen, but poorly in its presence. This is because
photosynthesis evolved when there was little gaseous oxygen present. Later,
when oxygen became more abundant, the efficiency of photosynthesis
decreased. Photosynthetic organisms compensated by making more of the
enzyme. RuBP carboxylase is the most abundant protein on the planet
partially because it is one of the least efficient.

Ecosystems, species, organisms and their genes all have long histories. A
complete explanation of any biological trait must have two components.
First, a proximal explanation -- how does it work? And second, an ultimate
explanation -- what was it modified from? For centuries humans have asked,
"Why are we here?" The answer to that question lies outside the realm of
science. Biologists, however, can provide an elegant answer to the question,
"How did we get here?"

Some Books about Biology and Evolution

Evolutionary Biology, by Douglas Futuyma, 1986, Sinauer, Sunderland,Mass

Evolution, by Mark Ridley, 1993, Blackwell Scientific, Boston

Principles of Population Genetics, by Hartl and Clark , 1989,
Sinauer,Sunderland, Mass

Introduction to Population Genetics Theory, by Crow and Kimura, 1970,
Burgess Publishing Company, Edina, Minnesota

Fundamentals of Molecular Evolution, by Li and Graur, 1991, Sinauer,
Sunderland, Mass

The Genetic Basis of Evolutionary Change, by Richard Lewontin, 1974,
Columbia University Press, New York

The Causes of Molecular Evolution, by John Gillespie, 1991, Oxford
University Press, New York

Non-Neutral Evolution, edited by Brian Golding, 1994, Chapman and Hall,
Boston

The Neutral Theory of Molecular Evolution, by Motoo Kimura, 1983, Cambridge
University Press, Cambridge

Natural Selection in the Wild, by John Endler, 1986, Princeton University
Press, Princeton, New Jersey

Macroevolutionary Dynamics, by Niles Eldredge, 1989, McGraw- Hill, New York

History of Life, by Richard Cowen, 1990, Blackwell Scientific, Boston

The Blind Watchmaker, by Richard Dawkins, 1987, Norton, New York

Abusing Science, by Philip Kitcher, 1982, MIT, Cambridge, Mass

The Diversity of Life, by E. O. Wilson, 1992, Harvard Belknap, Cambridge,
Mass.

The Origin of Species, by Charles Darwin, 1859

Descent of Man, by Charles Darwin, 1871

The Causes of Evolution, by J. B. S. Haldane, 1932 (reprinted 1990,
Princeton University Press, Princeton, New Jersey)

Tempo and Mode in Evolution, by G. G. Simpson, 1944, Columbia University
Press, New York

The Growth of Biological Thought, by Ernst Mayr, 1982, Harvard Belknap,
Cambidge, Mass.

The Origins of Theoretical Population Genetics, by William B. Provine, 1971,
University of Chicago Press, Chicago

Appendix

Part one: Geological time

                                                     Millions of years ago
     Preambrian Time
             Archean Era                             4600-2500
             Proterozoic Era                         2500-570
     Phanerozoic Time
             Paleozoic Era
                     Cambrian Period                 570-505
                     Ordovician Period               505-438
                     Silurian Period                 438-408
                     Devonian Period                 408-360
                     Carboniferous Period            360-286
                     Permian Period                  286-245
             Mesozoic Era
                     Triassic Period                 245-208
                     Jurassic Period                 208-144
                     Cretaceous Period               144-66.4
             Cenozoic Era
                     Tertiary Period
                             Paleocene Epoch         66.4-57.8
                             Eocene Epoch            57.8-38.6
                             Oligocene Epoch         38.6-23.7
                             Miocene Epoch           23.7-5.3
                             Pliocene Epoch          5.3-1.6
                     Quarternary Period
                             Pleistocene Epoch       1.6-0.01
                             Holocene Epoch          0.01-0

Part two: Universal phylogeny

                                               *** green bacteria
                                         *******
                                         *     *** flavobacteria
               EUBACTERIA          *******
                                   *     ********* spirochetes
                       *************
                       *           *         ***** gram positive bacteria
                       *           *  ********
                       *           *  *      * *** purple bacteria
                       *           ****      ***
                       *              *        *** eukaryotic mitochondria
                  ******              *
                  *    *              *       ***** cyanobacteria
                  *    *              *********
                  *    *                      **** eukaryotic chloroplasts
     **************    *
     *            *    *************************** deinococci
     *            *
     *            ******************************** thermotagales
     *
  ****
     *     ARCHAEBACTERIA          *************** halophiles
     *                    **********
     *                    *        *************** methanogens
     *             ********
     *             *      ************************ methanogens
     *    **********
     *    *        *
     *    *        ******************************* thermophiles
     * ****
     * *  *
     * *  **************************************** thermophiles
     * *
     ***                                      **** choanoflaggelates
       *                                  *****
       *    EUKARYOTES                    *   **** animals
       *                            *******
       *                            *     ******** fungi
       *                      *******
       *                      *     ************** plants
       *                  *****
       *                  *   ******************** ciliates
       *            *******
       *            *     ************************ cellular slime molds
       *       ******
       *       *    ****************************** flaggelates
       *********
               *********************************** microsporidia