Author: Chris Colby (colby@bu-bio.bu.edu) Title: FAQ: Introduction to Evolutionary Biology

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Author: Chris Colby (colby@bu-bio.bu.edu)
 Title: FAQ: Introduction to Evolutionary Biology
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AN INTRODUCTION TO EVOLUTIONARY BIOLOGY -- BY CHRIS COLBY
*********************************************************

INTRODUCTION
------------

Evolution is one of the most powerful theories science has ever
known. For a variety of reasons, however, it is also one of the
most misunderstood. One common misunderstanding is that the
phrase "survival of the fittest" summarizes evolutionary theory. It
does not. The phrase is both incomplete and misleading. Two other
common misinterpretations are that evolution is progress and
organisms can be arranged on an evolutionary ladder from bacteria
to man.

This post is an outline of the basics of evolutionary biology. It is
intended to be an overview of the concepts and mechanisms of
evolution and dispel pervasive misunderstandings about the theory.
Creationist arguments are not addressed here; and many
interesting topics in evolutionary biology are not covered
(symbiosis and endosymbiosis, origins of life, evolution of sex,
human evolution and much more) because I can't include everything
and keep this down to a readable length.

WHAT IS EVOLUTION?

Evolution is a change in the gene pool of a population over time.
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. In this moth, rare black variants spread
through the population as a result of their habitat becoming
darkened by soot from factories. Birds could see the lighter
colored moths more readily and ate more of them. The moth
population changed from mostly light colored moths to mostly dark
colored moths. Since their color was determined by a single gene,
the change in frequency of dark colored moths represented a
change in the gene pool. This change was, by definition, evolution.

The kind of evolution documented above is called "microevolution".
Larger changes (taking more time) are termed "macroevolution".
Some biologists feel the mechanisms of macroevolution are
different from those of microevolutionary change. Others,
including myself, feel the distinction between the two is
arbitrary. Macroevolution is cumulative microevolution.

In any case, evolution is defined as a change in the gene pool. This
means that evolution is a population level phenomena. Only groups
of organisms evolve. An individual organism does not evolve, nor
do subunits of organisms evolve (with limited exceptions). So,
when thinking of evolution, is necessary to view populations as a
collection of individuals with different traits. For example, in the
example above the frequency of black moths increased, the
"average" moth did not get progressively darker. Indeed there were
no "average" half-white/half-black moths ever in the population.

I have defined evolution, here, as a process and that is how I will
use the term in this essay. Keep in mind, however, that in everyday
use evolution refers to a variety of things. The fact that all
organisms are linked via descent to a common ancestor is often
called evolution. The theory that life arose solely via natural
processes is often called evolution (instead of abiogenesis). And
frequently, people use the word evolution when they really mean
natural selection -- one of the many mechanisms of evolution.

WHAT ISN'T EVOLUTION?

For many, evolution is equated with morphological change, i.e.
organisms changing shape or size over time. An example would be a
dinosaur species evolving into a species of bird. It is important to
note that evolution is often accompanied by morphological change,
but this need not be the case. Evolution can occur without
morphological change; and morphological change can occur without
evolution. For instance, humans are larger now than in the past,
but this is not an evolutionary change. Better diet and medicine
brought about this change, so it is not an example of evolution. The
gene pool did not change -- only its manifestation did.

An organism's phenotype is determined by its genes and its
environment. Phenotype is the morphological, physiological,
biochemical, behavioral and other properties exhibited by a living
organism. Phenotypic changes 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. Most changes due to environment are fairly
subtle (e.g. size differences). Large scale phenotypic changes (such
as dinosaur to bird) are obviously due to genetic changes, and
therefore are evolution.

WHAT EVOLUTION ISN'T

Evolution is not progress. Organisms simply adapt to their current
surroundings and do not necessarily become "better" over time. A
trait or strategy that is successful at one time may be deleterious
at another. Studies in yeast have shown that "more evolved"
strains of yeast can be competitively inferior to "less evolved"
strains. An organism's success depends a great deal on the
behavior of its contemporaries; for most traits or behaviors there
is likely no optimal design or strategy, only contingent ones.

HOW DOES EVOLUTION WORK?

If evolution is a change in the gene pool; what causes the gene pool
to change? Several mechanisms can change a gene pool, among
them: natural selection, genetic drift, gene flow, mutation and
recombination. I will discuss these in more detail later. It is
important to understand the difference between evolution and the
mechanisms that bring about this change.

GENETIC VARIATION
 -----------------

Bringing about a change in the gene pool assumes that there is
genetic variation in the population to begin with, or a way to
generate it. Genetic variation is "grist for the evolutionary mill".
For example, 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 (e.g. mutation) and mechanisms to
decrease it (e.g. natural selection and genetic drift).

HOW IS GENETIC VARIATION DESCRIBED?

Genetic variation has two components: allelic diversity and non-
random associations of alleles. Alleles are different versions of
the same gene at a given locus (locus means location). For
example, at the blood group locus  humans can have an A, B or O
allele. Most animals, including humans, are diploid. This means
they contain two alleles for every gene at every locus. If the two
alleles are the same type (for instance two A alleles) the
individual would be termed "homozygous" for that locus. An
individual with two different alleles at a locus is called
"heterozygous". Allelic diversity is simply the number of alleles
at each locus scaled by their frequency in the gene pool. At any
locus there can be many different alleles, more alleles than any
single organism can possess.

Linkage disequilibrium is a measure of association between
alleles at different loci. If each gene assorted entirely
independently, the gene pool would be at linkage equilibrium.
However, if some alleles were often found together in organisms
(i.e. did not assort randomly) these alleles would be in linkage
disequilibrium. Linkage disequilibrium can be the result of
physical proximity of the genes or maintained by natural selection
if some combinations of alleles work better as a team.

HOW MUCH GENETIC VARIATION IS THERE?

Considerable variation has been detected in natural populations. At
45 percent of loci in plants there is more than one allele in the
gene pool. 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.
Most loci assort independently (i.e. they are at linkage
equilibrium). In most populations, there are enough loci and enough
different alleles that every individual (barring monozygotic
(identical) twins) has a unique combination of alleles.

EVOLUTION WITHIN A LINEAGE (ANAGENESIS)
***************************************

The following sections deal with evolution within a population or
lineage -- this is called anagenesis. Several mechanisms can bring
about anagenetic change. I have grouped them into two classes --
those that decrease genetic variation and those that increase it.

MECHANISMS THAT DECREASE GENETIC VARIATION
------------------------------------------

MECHANISMS OF EVOLUTION: 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. In other words, some
genotypes are (on average) better than others at contributing their
alleles to the next generation's gene pool.

Selection is not a force in the sense that gravity or magnetism is.
However, biologists often, for the sake of brevity, refer to it that
way. Selection is not a guided or cognizant entity; it is simply an
effect.

When supplied with genetic variation, natural selection allows
organisms to adapt to their current environment. It does not,
however, have any foresight. Structures or behaviors do not evolve
for future utility. An organism must be, to some degree, adapted to
its environment at each stage of its evolution. As the environment
changes, new traits (new combinations of alleles) may be selected
for.  Large changes in populations are the result of cumulative
natural selection -- numerous small 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.

If evolution proceeds without any foresight, it is logical to wonder
how complex traits evolve? If half a wing is no good for flying,
how did wings evolve? 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.

This illustrates the point that 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.

Natural selection works at the level of the individual. The example
I gave earlier was an example of evolution via natural selection.
Dark colored moths had 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). It is the individual
organism that either reproduces or fails to reproduce. 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".

The individual organism reproduces or fails to reproduce. It
competes primarily with others of it own species for its
reproductive success. For this reason organisms do not perform
any behaviors that are for the good of their species. Natural
selection favors selfish behavior because any truly altruistic act
increases the recipient's reproductive success while lowering the
donors. Altruists would quickly disappear from a population as the
non-altruists would reap the benefits, but not pay the cost, of any
altruistic act.

Of course, many behaviors appear to be altruistic. Biologists,
however, can demonstrate (in the cases they have studied) that
these behaviors are only apparently altruistic. Cooperating with or
helping other organisms is often the most selfish strategy for an
animal. Often this is called "reciprocal altruism" (an oxymoron if
there ever was one). 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", (i.e. he accepts
blood when starving, but does not donate when his partner is) his
partner will abandon him.

Helping closely related organisms can appear altruistic; but this is
also a selfish behavior. An organisms reproductive success (or
fitness) has two components; direct fitness and indirect fitness.
An organism's direct fitness is a measure of how many alleles it
contributes to the subsequent generation's gene pool by
reproducing. An organism's indirect fitness is a measure of how
many alleles identical to its own it helps enter the gene pool. An
organism's direct fitness plus its indirect fitness is called its
inclusive fitness. Natural selection favors behaviors that increase
an organism's inclusive fitness. Closely related organisms share
many of the same alleles. For example, in  diploid species, siblings
share at least 50% of their alleles -- the percent is higher if the
parents are related. So, helping close relatives to reproduce gets
an organisms own alleles better represented in the gene pool. The
benefit of helping relatives increases dramatically in highly
inbred species. In som  cases, organisms will completely forgo
reproducing and only help their relatives reproduce. Ants, for
example, have sterile castes that only serve the queen and allow
her to reproduce. The sterile workers are reproducing by proxy.

Keep in mind that the words "selfish" and "altruistic" have
connotations in everyday use that biologists do not intend.
"Selfish" simply means behaving in an attempt to maximize ones'
own inclusive fitness; "altruistic" means behaving in an attempt to
increase anothers fitness without regard to ones' own. This 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. For example, a steel shelled turtle would probably be
an improvement. 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.

Natural selection does not necessarily produce individually
optimal structures or behaviors. Selection targets the organism as
a whole, not individual traits. So, specific traits are not
optimized, but rather combinations of traits. In addition, natural
selection may not necessarily even select for the the most optimal
set of traits. In any population, there would be a certain
combination of possible alleles that would produce the most
optimal set of traits (the global optima); but are probably several
other sets of alleles that would yield a population almost as
adapted (local optima). Transition from a local optima to the
global optima may be hindered or forbidden because the population
would have to pass through less adaptive states to make the
transition. So, natural selection only works to bring populations to
the nearest optimal point.

SEXUAL SELECTION -- A SUBSET OF NATURAL SELECTION

Darwin, and others, noticed that in many species males developed
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/most of these traits are a liability from the standpoint of
survival, mainly because 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 occurs 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 (i.e. the largest
males guarding their harems and fending off other males
physically) or mediated by female choice.

In species where females chose, 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. One model, 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.

Another model, proposed by Fisher, is called the "runaway sexual
selection" model. In his model he proposes that females may have a
preference for some male trait (without regards to fitness) and
then mate with these males when the trait appears. The offspring
of these matings will therefore have the genes for both the trait
_and_ the preference for the trait. Note, these genes would be
expressed in the males and females respectively. As a result, the
process snowballs out of control until natural selection brings it
into check. Here is an example to clarify.

Suppose that, due to some quirk of brain chemistry, female birds
of one species prefer males with longer than average tail feathers.
Mutant males with longer than average feather will therefore
produce more offspring than the short feathered males. In the next
generation, the average tail feather 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 feather 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.

A third model, called "the handicap hypothesis" states that males
with the most costly displays (in terms of detriment to survival)
are advertising the fact that, despite their "handicap", they still
had what it took to survive.

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 varies amongst them.

Natural selection is the only non-random mechanism of evolution.
It is the only mechanism that causes adaptive evolution. The
phrase "survival of the fittest" is often used synonymously with
natural selection. IMHO, 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 mean biggest, fastest or strongest --
sexiest might be closer to the truth in most animal species.

Of all the mechanisms of evolution, natural selection has the
potential to change gene frequencies the fastest. It usually acts to
keep gene frequencies constant, however. This led a famous
evolutionist, George Williams, to say "Evolution proceeds in spite
of natural selection".

MECHANISMS OF EVOLUTION: GENETIC DRIFT

Another important mechanism of evolution is 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.

Drift is a rather abstract concept to some; I will try to explain it
via an analogy. Imagine you had a swimming pool full of one
million marbles (this will represent the parental gene pool), half
are red and half are blue. If you repeatedly picked ten marbles out,
do you think you would get five red and five blue every time
(assume you replaced your sample to the pool each time)? If you
picked one hundred marbles out, do you think you would get fifty
red and fifty blue out every time? In both cases the answer is no,
some times the frequency of red marbles in the sample would
deviate from 0.50. In the case of the 100 marble sample, the
frequency of red marbles would deviate much less, however.

If, after picking out ten or one hundred marbles, you refilled the
pool with marbles at the frequency of that sample and repeated
the process over and over; what do you think would happen? What
would happen is that the frequency of red to blue would fluctuate
over time. Eventually, there would be only one color marble left in
the pool. This is roughly analogous to how genetic drift works.

In small populations, the rate of change in the frequency of alleles
is greater than in large populations. However, the overall rate of
genetic drift is independent of population size. 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 selection is not operating on any
of these alleles.

Sharp drops in population size can greatly affect the gene pool.
When a population crashes, the alleles in the surviving sample may
not be representative of the pre-crash 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 biologist feel the genetic changes
brought about by founder effects may contribute to isolated
populations developing reproductive isolation from their parent
populations.

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
------------------------------------------

MECHANISMS OF EVOLUTION: MUTATION

A mutation is a change in a gene. 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.

Mutation is a mechanism of evolution because it changes allele
frequencies very slightly. If an allele "A" mutates to another allele
"a", the frequency of "a" has increased from zero to some small
number (1/2N in a diploid population where N is the effective
population size). The allele "A" will also decrease slightly in
frequency. Evolution via mutation alone is very slow; for the most
part, mutation just supplies the raw material for evolution --
genetic variation.

Most mutations are slightly deleterious or neutral. The genome of
most organisms (certainly all eukaryotes) contains enormous
amounts of junk sequences. In addition, even in coding regions,
many sites can undergo mutation and still maintain the original
meaning. In other words, the genetic code is redundant. So, most
mutations are neutral or nearly so; but, the overwhelming majority
of mutations that produce any detectable phenotypic effect are
deleterious. "Good" mutations, however, do occur.

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.

Mutations occur at random with respect to their adaptive
significance. Organisms cannot "decide" that they need a mutation
and have it occur. The frequency of a mutation occurring is
independent of the potential effect it would have, with one
exception.

A new class of mutation has recently been documented in bacteria
and yeast. It appears that unicellular organisms can undergo
directed mutagenesis to repair "broken genes". The reversion
mutation that restores a gene to normal functioning occurs several
orders of magnitude more frequently when the gene is needed than
when it isn't. The mechanism of directed mutagenesis is unknown
at this time, but it has been shown to be under genetic control - -
i.e. directed mutations are not errors like normal mutations are;
they are actively created (or selectively retained) by the organism
in response to the environment.

The importance of directed mutagenesis is not yet known.
Biologists have not yet studied if directed mutations can produce
novel solutions to environmental challenges. It is also unknown if
it can occur in multi-cellular organisms with separate germ and
somatic cell lines. In any case it appears that in at least a few
instances, the potential for selection to operate induces adaptive
genetic variation to appear.

MECHANISMS OF EVOLUTION: RECOMBINATION

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, there are two
chromosomes number one (through 22 and two sex chromosomes),
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 in meiosis, 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.

For example, let's say an organism has a chromosome with three
genes, (A,B and C -- in that order). Assume that at each of these
three loci there are at least two alleles. From the father, the
organism inherited a chromosome with the alleles A1, B1 and C1.
From the mother the organism inherited A2,B2 and C2 alleles. In
meiosis the two chromosomes would line up and the two A alleles
would line up, as would the B and C alleles. If recombination
occurred between locus A and locus B, the resulting chromosomes
in the two gametes would be; one chromosome carrying A1, B2 and
C2 alleles and one chromosome carrying A2, B1 and C1 alleles.

Real chromosomes carry many more than three genes and
recombination occurs at many locations along the chromosome. The
end result is that the two homologous chromosomes have
"shuffled" alleles.

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.

A beneficial aspect of recombination is that beneficial mutants
can be brought together onto the same chromosome, even if they
arose in separate organisms.

MECHANISMS OF EVOLUTION: GENE FLOW

Gene flow simply means new genes added to a population by
migration from another population. 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. One interesting case of this involves genetic
elements called P elements. In the genus _Drosophila_, P elements
were transfered from some species in the _willistoni_ group, to
_D. 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 transfered 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 are devoid of P elements. All natural
populations today harbor them.

OVERVIEW OF EVOLUTION WITHIN A LINEAGE (ANAGENESIS)
---------------------------------------------------

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. Natural
selection can also increase the frequency of an allele (or
combination of alleles) in the gene pool. 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, all 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.

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. This is discussed below.

EVOLUTION AMONG LINEAGES (CLADOGENESIS)
***************************************

The following sections deal with how single populations ramify to
become multiple populations and eventually separate species -
this is called cladogenesis. In edition, the overall pattern of
macroevolution and evidence for common descent of all living
species is presented.

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.

Modern biologists hold that 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 living species of apes. 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 is now extinct
and was not the same as present day apes (or humans for that
matter). Our closest relatives are the chimpanzee and the pygmy
chimp.

EVIDENCE FOR COMMON DESCENT AND MACROEVOLUTION
----------------------------------------------

Whereas microevolution can be studied directly, macroevolution is
studied by examining patterns in biological populations and clades
(groups of 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 really
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.

Comparative genetic and biochemical data provide data supporting
the inference of common descent. DNA sequence comparisons of
closely related species (as determined by morphologists) yeild
similar sequences. Overall sequence similarity is not the whole
story, however. The pattern of differences we see in closely
related genomes is worth examining.

Genes are sequences of nucleotides that code for proteins. There
are four different kinds of nucleotides commonly incorporated into
DNA: adenine (A), guanine (G), cytosine (C) and thymine (T) -- each
block of three is called a codon. Each codon designates an amino
acid (the subunits of proteins). The gene, or sequence of codons, is
transcribed into RNA -- a nucleic acid similar to DNA. (RNA, like
DNA, is made up of nucleotides although the nucleotide uracil (U)
is used in place of thymine (T).) The RNA is then translated via
cellular machinery into a string of amino acids -- a protein.

All living organisms use DNA as their genetic material, although
some viruses use RNA. The three letter code is the same for all
organisms. The universal genetic code is redundant. 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.

In addition to showing overall similarity, gene sequences from
closely related species show the same codon is often used for
amino acids. In cases where there are differences, however, they
are usually in these "silent" sites. In addition, the genome is
loaded with 'dead genes' called pseudo-genes. Pseudogenes occupy
the same location in the genome in closely related species. The
same can be said for introns, sequences of DNA that interrupt a
gene, but do not code for anything. Introns are spliced out of the
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.

Third codon positions (silent sites), pseudo-genes and introns
show more sequence differences between species than coding
sections of a gene. This is because mutations that change the code
of a gene, and hence the protein made, usually affect the organism
adversely and are selected against. Mutations in non-coding
regions do not affect the phenotype of the organism and get passed
on.

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 would be a
function of divergence time.

Studies in comparative anatomy also provide support for common
descent. Groups of related organisms are 'variations on a theme' --
the same set of bones are used to construct all mammals. The
bones of the human hand grow out of the same tissue the bones of
a bat's wing or a whale's flipper does and they share many
identifying features (muscle insertion points, ridges).  The only
difference is that they are scaled differently. Evolutionary
biologists say this indicates that all mammals are modified
descendents of a common ancestor which had the same set of
bones.

Evidence for common descent also comes from studying
comparative developmental biology-- Closely related organisms
share similar developmental pathways, the differences in
development are most evident at the end. This is, again, usually
illustrated using mammalian (or sometimes vertebrate) examples.
As organisms evolve, their developmental pathway gets modified.
It is easier to modify the end of a developmental pathway than the
beginning since changes early on have a cascading effect.
Therefore, organisms pass through stages of early development
that their ancestors passed through. These stages, however, are
modified because selection "sees" all phases of an organism's life
cycle. So, an organism's development mimics its ancestors
although it doesn't recreate it exactly.

Traces of an organism's ancestry sometimes remain even when an
organisms ontogeny (development) is complete. These are called
vestigal structures. Many snakes have rudimentary pelvic bones
retained from their walking ancestors. This is an example of a
vestigal structure.

Biogeography also supports the inference of common descent.
Organisms clustered spatially are frequently also clustered
phylogenetically; 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 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 what it has to
work with and, if all organisms share a common ancestor, we
should expect to see examples of suboptimal design in living
species. This is indeed the case.

In African locusts, the nerve cells that connect to the wings
originate in the abdomen, even though the wings are in the thorox.
When the insect send the message to fly from its brain to its
wings, the nerve impulse travels down the ventral nerve cord past
its target then backtracks to the wing.

In _Cnenidophoran_ lizards, females reproduce
parthenogenetically. Fertility in these lizards is increased when a
female mounts another female and simulates copulatory behavior.
This is because 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 as you go down the strata (layers of 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).

Further strong 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 (mosses) and vascular. Vascular plants
can be divided into seedless (ferns) and seeded. Vascular seeded
plants can be divided into gymnosperms (pines) and flowering
plants or angiosperms. And 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 pattern arises due to
lineages splitting (speciation), retaining ancestral traits and
deriving new traits. Derived traits only appear in lineages
descended from the population that first displayed the trait. This
hierarchical pattern of diversity is what one expects to see if
species branch into new species and are modified with descent.

Thus, it is not just that similar species share similar traits
(although that is evidence in and of itself); when you look at large
groups of organisms, a pattern on a larger scale is seen. This
hierarchical pattern can be produced even if the process
responsible is not hierarchical. For example, microevolution leads
to hierarchical patterns of genetic diversity even though it works
at a single level. The question of hierarchical processes in
evolution is still being debated.

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 criteria. In several of the above
examples I stated, closely related organisms share X. If I define
closely related as sharing X, this is a contentless statement. It
does however, provide a prediction. If two organisms share (oh
lets say) a similar anatomy (two birds, for ex.), I would then
predict that their gene sequences would be more similar than a
morphologically distinct organism (like a plant, for ex.). 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 hotly
debated.

SCIENTIFIC STANDING OF EVOLUTION AND IT'S CRITICS

The topics of evolution and common descent were once highly
controversial in scientific circles; this is no longer the case.
Although debates rage about how various aspects of evolution
work and details of patterns of relationships are not fully worked
out, evolution and common descent are considered fact by the
scientific community.

So-called "scientific" creationists do not base their objections on
scientific reasoning or data. Nor do they have a testable, scientific
theory to replace evolution with. "Scientific creationism" is a
poorly disguised attempt to attack evolution because it
contradicts the religious beliefs of some fundamentalists.

SPECIATION -- INCREASING BIOLOGICAL DIVERSITY
---------------------------------------------

Speciation is the process of a single species becoming two or
more species. Many biologists feel speciation is key to
understanding evolution and 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. Monophytophagous insects (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. 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 series of small changes in each subdivision gradually
lead to speciation; others think there may be a few key genes that
could change and confer reproductive isolation. One famous
biologist thinks most speciation events are caused by changes in
internal symbionts. Most doubt this, however. 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.

OBSERVED SPECIATIONS

It comes as a surprise to some to hear that speciation has been
observed. In the genus _Tragopogon_ (a plant genus consisting
mostly of diploids), two new species (_T._ _mirus_ and _T._
_miscellus_) have evolved within the past 50-60 years. The new
species are allopolyploid descendants of two separate diploid
parent species.

Here is how this speciation occured. 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.

Two other plant species have also arisen within the past 110
years in this manner, _Senecio_ _cambrensis_ and _Spartina_
_townsendii_.

EXTINCTION -- DECREASING BIOLOGICAL DIVERSITY
---------------------------------------------

"ORDINARY" EXTINCTION

Extinction is the ultimate fate of all species. The reasons for
extinctions are numerous. A species can be outcompeted 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 taxa (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 most famous extinction occurred at the boundary between the
Cretaceous and Tertiary Periods (the K/T Boundary- 65MYA). This
extinction eradicated the dinosaurs. Some hypothesize that the
K/T event was caused by environmental disruption brought on by a
large impact on earth. Several lines of evidence point to a large
collision at the time of the extinction, but attempts to link the
two have not been convincing to all biologists. 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.

The largest mass extinction came at the end of the Permian
(250MYA); it is estimated that 96 percent of all species died out
at this time. The sea animals that make up the so-called Paleozoic
Fauna (among them crinoids, cephalopods, brachiopods and corals),
suffered the worst. This assemblage did not reradiate after the
event and remains at the level of diversity it sunk to after the
extinction. In contrast, the sea animals that make up the Modern
Fauna (gastropods, bivalves, crabs, echinoids and bony fishes)
were barely affected and continued to increase in diversity after
the event.

The Permian extinction coincides with the formation of Pangea II,
when all the world's continents were brought together by plate
tectonics. A worldwide drop in sea level also occurred at this
time. Currently, human alteration of the ecosphere is causing a
global mass extinction.


PUNCTUATED EQUILIBRIA
---------------------

Some paleontologists believe evolution is a hierarchical process.
The theory of punctuated equilibria attempts to infer 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 sometime 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.

Gould and Eldredge, the authors of punctuated equilibria, interpret
this in light of theories of allopatric speciation. They concluded
that isolated populations of organisms will often speciate and
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.

They also argue that evolution can proceed quickly in small
populations so that the tempo of evolution is not continuous. This
has lead to some 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 what the
theory of punctuated equilibria says.

Some PE proponents envision the theory as a hierarchical theory of
evolution because they see speciation as analogous to mutation
and the replacement of one species by another (which they call
species selection) as analogous to natural selection. Speciation
adds new species to the species pool just as mutation adds new
alleles to the gene pool and species selection favors one species
over another just as natural selection can favor one allele over
another. This is the most controversial part of the theory. Most
biologists agree with the pattern of macroevolution these
paleontologists posit, but many disagree with the mechanism --
species selection. Critics would argue that species selection is
not analogous to natural selection and therefore evolution is not
hierarchical.

The theory of punctuated equilibrium was designed to replace the
theory of phyletic gradualism. Phyletic gradualists held that a
species would slowly transform into another species over its
entire range. Phyletic gradualism is often associated with the
assumption of a uniform rate of evolution, but this need not be the
case.

CONCLUSION
----------

ARE WE STILL EVOLVING?

Yes, evolution is still occurring; all organisms continue to adapt to
their surroundings and "invent" new ways of better competing with
members of their own species. In addition, allele frequencies are
being changed by drift, mutation and gene flow constantly.
Studying the process of evolution as it continues to occur is a
major field of biology today. Although evolution has been observed
and all the mechanisms have been shown to work, there is still no
consensus on the relative contribution of each of the mechanisms
to the overall pattern of evolution within a lineage. Likewise,
although new species have been seen to arise; biologists have
many questions about what influences the pattern of
macroevolution. Are some groups "good" at speciating? Who
survives mass extinctions and why?

Evolution is the unifying theory of biology. The functions of
biological entities at all levels (populations, organisms, genes)
are the product of a non-random factor (e.g. natural selection)
operating in conjunction with random factors (such as mutation
and mass extinction) within a framework of historical constraint.
For centuries humans have asked, "Why are we here?". A question
such as that probably lies outside the realm of science. However,
biologists can provide an elegant answer to the question, "How did
we get here?"
--------------------------------------------------------------------
-
SOME GOOD EVOLUTION TEXTS (IMHO)

A good introductory text in evolutionary biology is:
Evolutionary Biology, by Douglas Futuyma, 1986, Sinauer, Sunderland, Mass
 The text assumes some previous knowledge of biology, but reviews most
critical background material. It contains numerous references to the
primary
literature. Most of the information in this file can be found (along with the
references to the primary literature) in this text.

A good introductory text into population genetics, the field that
mathematically describes changes in the gene pool is:
 Principles of Population Genetics, by Hartl and Clark , 1989, Sinauer,
Sunderland, Mass
None of the math is very daunting (it's just an intro text after all)
but it's really critical (IMHO) to understanding what evolution is all about.
And again, lots of refs.

A text that deals with the interface of molecular biology and evolution is:
Fundamentals of Molecular Evolution, by Li and Graur, 1991, Sinauer,
Sunderland, Mass
A very concise introduction to this field.

A text that deals with theories of macroevolution is:
 Macroevolutionary Dynamics, by Niles Eldredge, 1989, McGraw-Hill, New
York

 A text that documents the history of life on earth is:
History of Life, by Richard Cowen, 1990, Blackwell Scientific, Boston
A readable introduction to the history of our planet and especially the
changes that have occurred in the biota.

A popular introduction to the field that also debunks the most common
creationist arguments is:
 The Blind Watchmaker, by Richard Dawkins, 1987, Norton, New York
Dawkins is (IMHO) a very engaging writer.

A close look at the creation/evolution debate can be found in:
Abusing Science, by Philip Kitcher, 1982, MIT, Cambridge, Mass
A meticulous critique of creationism.