Evolution FAQ (Frequently Asked Questions)

EVOLUTIONARY BIOLOGY
Introduction
		What is evolution?
		What isn't evolution?
		What evolution isn't
Genetic variation
		How is genetic variation described?
		How much genetic variation is there?
Evolution within a lineage -- anagenesis
		Mechanisms that decrease genetic variation
				  Natural selection
							 Sexual selection
				  Genetic drift
		Mechanisms that increase genetic variation
				  Mutation
							 Directed mutagenesis
				  Recombination
				  Gene flow
		Overview of anagenesis
Evolution among lineages -- cladogenesis
		Speciation -- increasing biological diversity
				  Modes of speciation
				  Observed speciations
				  Macroevolution vs. microevolution
		Extinction -- decreasing biological diversity
				  "Ordinary" extinctions
				  Mass extinctions
		Punctuated equilibria
Conclusion

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.  In fact, 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 a brief overview of the concepts and mechanisms of
evolution. Creationist arguments are not addressed directly here; nor
is a "laundry list" of reasons to believe in evolution provided. 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 of 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 neccessary to view populations as a collection
of individuals.

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 often 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 people evolution is equated with morphological change, i.e.
organisms changing shape or size over time. An example would be a
dinosaur species slowly turning into a bird species.  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 few
hundred years, 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 both its genes and its
environment. Phenotype means the morphological, physiological, bio-
chemical, behavioral and other properties exhibited by a living
organism. Phenotypic changes induced solely by changes in
environment do not count as evolution because this change is 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 for an organism at one time may be
deleterious at another. Studies in yeast have shown that "more evolved"
strains of yeast can sometimes be competitively inferior to "less
evolved" strains. An organism's success or failure depends to a great
deal on the behavior of its contemporaries; for most traits or
behaviors there is likely no optimal design or strategy, only
contingent designs or strategies.

HOW DOES EVOLUTION WORK?

If evolution is a change in the gene pool; what causes the gene pool to
change? Several mechanisms can bring about a change in the 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 (change in the
gene pool) 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 both increase genetic variation, or create it,
(e.g. mutation) and decrease variation (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. For example, at the blood group locus (locus means
location) humans can have an A, B or O allele. There are subtypes of
these alleles as well.  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 given locus there can be
many different alleles in the gene pool.  It is important to realize
that there can be more alleles in the gene pool at a given locus than
any single organism can possess.

Linkage disequilibrium is a measure of association of 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 (ie. 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 it's 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.

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 at contributing their alleles to the subsequent
generations 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.

Natural selection allows organisms to adapt to their current environment
only; it does not have any foresight. Structures or behaviors do not
evolve for future utility. The 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.

Of course, this raises the question; how do 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
called 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
moths 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 is what 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 observable behaviors appear, at first glance, to be
altruistic in nature. 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 of 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 others mouth. Biologists have found
that these bats form bonds with other bats and help each other out when
the other is needy. If a bat is found to be a "cheater", (ie. he
accepts blood when starving, but does not donate when his partner is)
the partner will abandon the cheater.

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 organisms
direct fitness is a measure of how many alleles it contributes to the
subsequent generation's gene pool by reproducing. An organisms indirect
fitness is a measure of how many alleles that are identical it's 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 increase an organism's inclusive fitness.

Closely related organisms share many of the same alleles.
For example, in a 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 some 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 occur, 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 charactoristics. A few oft cited ex-
amples 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. His 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 charactoristics and/or undergoing elaborate courtship
behaviors or both. 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" advo-
cate would say that bright coloring in male birds indicates a lack of
parasites. The females are cueing on some signal, in this example color,
that is correlated with some other important trait (ex. parasite load).

Another model, proposed by Fisher, is called the "runaway sexual
selection" model. In his model he proposes that females develop a
preference for some male trait (without regards to fitness) and then
mate with these males. 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 respect-
ively. 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.
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 sexaul attract-
iveness 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 synonomously 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 out-
put 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
frequncies 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 are a sample of the alleles in
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 genetically 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, but not all, 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 its 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.

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.

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 that it is under genetic control -- i.e. directed
mutations are not errors like normal mutations are, the 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 occur.

MECHANISMS OF EVOLUTION: RECOMBINATION

Recombination can be loosely thought of as gene shuffling.  Most
organisms have linear chromosomes and their genes lie at specific
locations  (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 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 in to 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, lets 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 new alleles can
be brought together onto the same chromosome, even if the mutations
originally occurred 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 "bad" alleles in called
negative selection. Selection that increases the frequency of
"good" 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 moderately beneficial
alleles can be lost due to drift when they appear.

The fate of any given new allele depends a great deal on the organism
it first appears in. This allele will be linked to the other alleles
near it for many generations. A mutant allele can increase in frequency
in the gene pool 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 to the next generation's gene pool.

End of part one