ADMIN: Introduction to Evolution FAQ

Introduction to Evolutionary Biology
Version 2
Copyright 1996-1997 by Chris Colby
[Last Update: January 7, 1996]

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

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

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

What is Evolution?

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

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

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

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

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

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

Common Misconceptions about Evolution

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

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

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

Genetic Variation

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

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

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

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

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

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

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

Evolution within a Lineage

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

Mechanisms that Decrease Genetic Variation

Natural Selection

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Common Misconceptions about Selection

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

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

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

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

Natural selection can be broken down into many components, of which

selection when they talk about this subset of natural selection.

contribute to an organism's mating success. Traits that are 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,

species males compete against other males for mates. The competition can be either direct or
mediated by female choice. In species where females choose, males compete by displaying striking
phenotypic characteristics and/or performing elaborate courtship behaviors. The females then mate
with the males that most interest them, usually the ones with the most outlandish displays. There
are many competing theories as to why females are attracted to these displays.

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

Selection for good genes can be seen in sticklebacks. In these fish, males have red coloration
on their sides. Milinski and Bakker showed that intensity of color was correlated to both
parasite load and

indicated that he was carrying fewer parasites.

Evolution can get stuck in a positive feedback loop. Another model to

selection model. R. A. Fisher proposed that females may have an innate preference for some male
trait before it appears in a population. Females would then mate with male carriers when the trait
appears. The offspring of these matings have the genes for both the trait and the preference for the
trait. As a result, the process snowballs until natural selection brings it into check. Suppose that
female birds prefer males with longer than average tail feathers. Mutant males with longer than
average feathers will produce more offspring than the short feathered males. In the next generation,
average tail length will increase. As the generations progress, feather length will increase because
females do not prefer a specific length tail, but a longer than average tail. Eventually tail length
will increase to the point were the liability to survival is matched

established. Note that in many exotic birds male plumage is often very showy and many species do in
fact have males with greatly elongated feathers. In some cases these feathers are shed after the
breeding season.

None of the above models are mutually exclusive. There are millions of

selection probably vary amongst them.

Genetic Drift

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

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

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

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

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

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

Mechanisms that Increase Genetic Variation

Mutation

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

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

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

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

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

The Fate of Mutant Alleles

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

Neutral alleles

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

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

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

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

Deleterious alleles

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

Beneficial alleles

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

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

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

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

Recombination

Each chromosome in our sperm or egg cells is a mixture of genes from our mother and our father.
Recombination can be thought of as gene shuffling. Most organisms have linear chromosomes and their
genes lie at specific location (loci) along them. Bacteria have circular

each chromosome type in every cell. For instance in humans, every chromosome is paired, one
inherited from the mother, the other inherited from the father. When an organism produces gametes,
the gametes end up with only one of each chromosome per cell. Haploid gametes are produced from
diploid cells by a process called meiosis.

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

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

Gene Flow

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

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

Overview of Evolution within a Lineage

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

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

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

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

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

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

The Development of Evolutionary Theory

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

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

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

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

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

Incorporating Genetics into Evolutionary Theory

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

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

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

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

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

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

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

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

Evolution Among Lineages

The Pattern of Macroevolution

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

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

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

Evidence for Common Descent and Macroevolution

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Closely related organisms share similar developmental pathways. The differences in development are
most evident at the

> The first photosystem to evolve, PSI, uses light to
> convert carbon dioxide (CO2) and hydrogen sulfide (H2S) to
> glucose. This process releases sulfur as a waste product.

In that case, it's obvious that all the oxygen in the
resultant glucose came from the CO2, since there isn't any
oxygen in H2S in the first place. See an analagous
question later...

But sulfur is needed in some amino acids etc. So does
that sulfur get incorporated, as I presume, by a
completely different pathway that existed long before
photosynthesis evolved? Did it, at that time, come from
H2S, or from what else?

> About a billion years later, a second photosystem (PS)
> evolved, probably from a duplication of the first
> photosystem. Organisms with PSII use both photosystems in
> conjunction to convert carbon dioxide
> (CO2) and water (H2O) into glucose.

It would seem reasonable that this variation on the original
invention would likewise get all the oxygen (for the glucose
product) from the CO2, not from the H2O. Recent isotope-
labeled experiments have confirmed this, or so I've heard in
the InterNet rumor mill. But I haven't been able to find any
FAQ or authoritive WebPage that says this clearly. Does
anybody know of such? This question arose in relation to a
completely different topic, on sci.space.science http://www-
.google.com/groups?selm=HByrLz.2vJ%40spsystems.net where
nobody seemed to know the answer for sure, so I thought I'd
ask the question here and get some good answer(s) then copy
the answer(s) back there.

RobertMaas@YahooGroups.Com wrote in message news:<c4pfbm$2imq$1@darwin.ediacara.org>...
> > The first photosystem to evolve, PSI, uses light to
> > convert carbon dioxide (CO2) and hydrogen sulfide (H2S)
> > to glucose. This process releases sulfur as a waste
> > product.
>
> In that case, it's obvious that all the oxygen in the
> resultant glucose came from the CO2, since there isn't any
> oxygen in H2S in the first place. See an analagous
> question later...

It might be true, but it is far from obvious. The complete
process of photosynthesis is MUCH more complicated than is
indicated by the stoichiometry. The part of the process that
turns CO2 into glucose is called the "dark reactions" since
the coupling to the light-absorbing aspect of photosynthesis
is very indirect. The various steps of the dark reactions
involve oxygen from CO2, from water, and even from
phosphate.

The water molecules that provide the O2 at the opposite end
of the chain of reactions are, conceptually at least,
completely different from the ones involved in the dark
reactions. The hydrogen atoms are also different.

>
> But sulfur is needed in some amino acids etc. So does
> that sulfur get incorporated, as I presume, by a
> completely different pathway that existed long before
> photosynthesis evolved? Did it, at that time, come from
> H2S, or from what else?

Probably from H2S. The sulfur in biochemicals is at that
oxidation level. The presumed primitive photosynthesis
produces sulfur at the level of pyrite or elemental sulfur -
not useful in life's "building blocks". So, presumably from
H2S thereafter as well, until heterotrophs arose that
reversed photosynthesis by reducing pyrite or sulfur (or
sulfite, or whatever). (I should probably point out that
there are probably those who believe that sulfur-reducing
heterotrophy came before photosynthesis, thus reversing my
arguments. The whole chronology is very unsettled.)
>
> > About a billion years later, a second photosystem (PS)
> > evolved, probably from a duplication of the first
> > photosystem. Organisms with PSII use both photosystems
> > in conjunction to convert carbon dioxide
> > (CO2) and water (H2O) into glucose.
>
> It would seem reasonable that this variation on the
> original invention would likewise get all the oxygen (for
> the glucose product) from the CO2, not from the H2O.
> Recent isotope-labeled experiments have confirmed this, or
> so I've heard in the InterNet rumor mill. But I haven't
> been able to find any FAQ or authoritive WebPage that says
> this clearly. Does anybody know of such?

Sorry, not me.

<RobertMaas@YahooGroups.Com> wrote in message
news:c4pfbm$2imq$1@darwin.ediacara.org...
> > The first photosystem to evolve, PSI, uses light to
> > convert carbon dioxide (CO2) and hydrogen sulfide (H2S)
> > to glucose. This process releases sulfur as a waste
> > product.
>
> In that case, it's obvious that all the oxygen in the
> resultant glucose came from the CO2, since there isn't any
> oxygen in H2S in the first place. See an analagous
> question later...

I don't want to monopolize the thread in multiple posts, so
briefly this FAQ appears to be 10+ years outdated on some
crucial pieces of information. This ascending ladder of PS I
-> PS II -> oxygen-producing photosynthesis is not accepted,
and the post is incorrect on which organisms use which type
of photosystem (PS I: green sulfur, Gram +; PS II: purple
bacteria, green nonsulfur; cyanobacteria, algae, and plants
have both types). A good recent reference on this is R.E.
Blankenship, Molecular Mechanisms in Photosynthesis (2002 or
3, I think).

> But sulfur is needed in some amino acids etc. So does
> that sulfur get incorporated, as I presume, by a
> completely different pathway that existed long before
> photosynthesis evolved? Did it, at that time, come from
> H2S, or from what else?

In general, sulfur assimilation can proceed from a variety
of different sulfur redox states (sulfate, sulfite, sulfur,
sulfide, polysulfide) to sulfide, which is the direct donor
onto cysteine. Cysteine can be converted, through a variety
of different enzymatic pathways, into other necessary
biosynthetic pathways (methionine synthesis, iron-sulfur
cluster assembly, etc.). Different organisms have vastly
different mechanisms of getting sulfur across the membrane
-- and not all organisms can use all species, i.e. the
toxicity of H2S to many organisms -- but this central
cysteine hub is essentially universal.

>
> > About a billion years later, a second photosystem (PS)
> > evolved, probably from a duplication of the first
> > photosystem. Organisms with PSII use both photosystems
> > in conjunction to convert carbon dioxide
> > (CO2) and water (H2O) into glucose.
>
> It would seem reasonable that this variation on the
> original invention would likewise get all the oxygen (for
> the glucose product) from the CO2, not from the H2O.
> Recent isotope-labeled experiments have confirmed this,
> or so I've heard in the InterNet rumor mill. But I
> haven't been able to find any FAQ or authoritive WebPage
> that says this clearly. Does anybody know of such? This
> question arose in relation to a completely different
> topic, on sci.space.science http://www.google.com/groups-
> ?selm=HByrLz.2vJ%40spsystems.net where nobody seemed to
> know the answer for sure, so I thought I'd ask the
> question here and get some good answer(s) then copy the
> answer(s) back there.

Again this misunderstanding arises from colloquialisms in
the FAQ. CO2 and H2O are not assimilated directly into
glucose (this is a bit like saying my pushing the gas petal
in my car is what makes it go; operationally useful, but a
gross technical understatement). Cyanobacteria, algae, and
plants all use rubisco for CO2 assimilation into
phosphoglyceraldehyde, which can be used in gluconeogenesis
among a variety of different things. In this process,
oxygens are picked up from both CO2 and from H2O.
Importantly though, photosynthesis in several of the other
groups of primitive organisms mentioned (green sulfur and
nonsulfur, Gram +) doesn't drive the fixation carbon by way
of rubisco. These organisms all do autotrophy via other,
arguably earlier evolving pathways such as reductive TCA and
the 3-hydroxypropionate pathway. Once again, oxygen atoms
can be picked up both from CO2 but also through H2O.

On Tue, 6 Apr 2004 16:09:20 +0000 (UTC), irr <iotarhorho@hotmail.com> wrote:
>
> <RobertMaas@YahooGroups.Com> wrote in message
> news:c4pfbm$2imq$1@darwin.ediacara.org...
>> > The first photosystem to evolve, PSI, uses light to
>> > convert carbon dioxide (CO2) and hydrogen sulfide (H2S)
>> > to glucose. This process releases sulfur as a waste
>> > product.
>>
>> In that case, it's obvious that all the oxygen in the
>> resultant glucose came from the CO2, since there isn't
>> any oxygen in H2S in the first place. See an analagous
>> question later...
>
> I don't want to monopolize the thread in multiple posts,
> so briefly this FAQ appears to be 10+ years outdated on
> some crucial pieces of information. This ascending ladder
> of PS I -> PS II -> oxygen-producing photosynthesis is not
> accepted, and the post is incorrect on which organisms use
> which type of photosystem (PS I: green sulfur, Gram +; PS
> II: purple bacteria, green nonsulfur; cyanobacteria,
> algae, and plants have both types). A good recent
> reference on this is R.E. Blankenship, Molecular
> Mechanisms in Photosynthesis (2002 or 3, I think).

I agree with you that Chris Colby's "Introduction to
Evolutionary Biology" essay is out of date. I think it's
important to emphasize that the primary goal of
photosynthesis is to produce ATP and reducing equivalents.
(Some species use light to make only ATP.) CO2 fixation and
carbohydrate synthesis are secondary pathways that use ATP
and reducing equivalents but they're not really part of
photosynthesis.

The accepted evolutionary path is to photosystems with type
I reaction centers (e.g. PSI) and type II reaction centers
(e.g. PSII) from a common ancestral photosystem. Later on
some bacteria acquired both types of photosystem, probably
by horizontal gene transfer. These bacteria then evolved a
linear coupled system where electrons were passed
sequentially from PSII to PSI. The evolution of an oxygen-
evolving complex probaly came later when bacteria could make
use of water as a source of electrons.

Larry Moran

"irr" <iotarhorho@hotmail.com> wrote in message news:<c4ukng$152c$1@darwin.ediacara.org>...
> <RobertMaas@YahooGroups.Com> wrote in message
> news:c4pfbm$2imq$1@darwin.ediacara.org... I don't want to
> monopolize the thread in multiple posts, so briefly this
> FAQ appears to be 10+ years outdated on some crucial
> pieces of information.
It is glaringly wrong in some other places. For example, it
uses "prokariote" as a synonym for eubacteria, and talks
about differences between archaea and "prokariotes".

Larry Moran <lamoran@bioinfo.med.utoronto.ca> wrote:

> On Tue, 6 Apr 2004 16:09:20 +0000 (UTC), irr
> <iotarhorho@hotmail.com> wrote:
> >
> > <RobertMaas@YahooGroups.Com> wrote in message
> > news:c4pfbm$2imq$1@darwin.ediacara.org...
> >> > The first photosystem to evolve, PSI, uses light to
> >> > convert carbon dioxide (CO2) and hydrogen sulfide
> >> > (H2S) to glucose. This process releases sulfur as a
> >> > waste product.
> >>
> >> In that case, it's obvious that all the oxygen in the
> >> resultant glucose came from the CO2, since there isn't
> >> any oxygen in H2S in the first place. See an analagous
> >> question later...
> >
> > I don't want to monopolize the thread in multiple posts,
> > so briefly this FAQ appears to be 10+ years outdated on
> > some crucial pieces of information. This ascending
> > ladder of PS I -> PS II -> oxygen-producing
> > photosynthesis is not accepted, and the post is
> > incorrect on which organisms use which type of
> > photosystem (PS I: green sulfur, Gram +; PS II: purple
> > bacteria, green nonsulfur; cyanobacteria, algae, and
> > plants have both types). A good recent reference on this
> > is R.E. Blankenship, Molecular Mechanisms in
> > Photosynthesis (2002 or 3, I think).
>
> I agree with you that Chris Colby's "Introduction to
> Evolutionary Biology" essay is out of date. I think it's
> important to emphasize that the primary goal of
> photosynthesis is to produce ATP and reducing equivalents.
> (Some species use light to make only ATP.) CO2 fixation
> and carbohydrate synthesis are secondary pathways that use
> ATP and reducing equivalents but they're not really part
> of photosynthesis.
>
> The accepted evolutionary path is to photosystems with
> type I reaction centers (e.g. PSI) and type II reaction
> centers (e.g. PSII) from a common ancestral photosystem.
> Later on some bacteria acquired both types of photosystem,
> probably by horizontal gene transfer. These bacteria then
> evolved a linear coupled system where electrons were
> passed sequentially from PSII to PSI. The evolution of an
> oxygen-evolving complex probaly came later when bacteria
> could make use of water as a source of electrons.
>
Larry, would you be prepared to revise it? If we can't
contact Chris, at least we can keep his version on the
archive site and tag your revision uner your name.

Also, Chris uses N where he ought to use Ne, acc. to a
feedback a couple of years back.

[moderator's note: ISAGN. - JAH]

--
John Wilkins john_SPAM@wilkins.id.au
http://www.wilkins.id.au "Men mark it when they hit, but do
not mark it when they miss"
- Francis
Bacon

As of my last check a few weeks ago, EvoWiki (evowiki.org) -- which is IMO
growing quite beautifully -- also needed an update vis a vis current
thinking on the evolution of photosynthesis. Maybe an opportunity to kill
two birds here ?

> From: jimmenegay@sbcglobal.net (Jim Menegay)
> > In that case, it's obvious that all the oxygen in the
> > resultant glucose came from the CO2, since there isn't
> > any oxygen in H2S in the first place. See an analagous
> > question later...
> It might be true, but it is far from obvious. The complete
> process of photosynthesis is MUCH more complicated than is
> indicated by the stoichiometry. The part of the process
> that turns CO2 into glucose is called the "dark reactions"
> since the coupling to the light-absorbing aspect of
> photosynthesis is very indirect. The various steps of the
> dark reactions involve oxygen from CO2, from water, and
> even from phosphate. The water molecules that provide the
> O2 at the opposite end of the chain of reactions are,
> conceptually at least, completely different from the ones
> involved in the dark reactions. The hydrogen atoms are
> also different.

I think I was making the, perhaps unwarranted, assumption
that all the pathways in H2S and H2O photosynthesis are
identical except for the point(s) where hydrogens are
removed from that hydrogen donor, where the source molecule
and the resultant atomic S or O are different. If that
assumption is false, if there are other differences in the
two mechanisms, very different pathways that somehow merge
in overall effect, i.e. all the other changes in inputs and
outputs cancel, to make the stoichiometry come out identical
except for those two differences, then indeed it's two
unrelated problems to study. But if the pathways are the
same as I assumed, then mathematically we would have a
contradiction to that pathways-same premise if my conclusion
were false.

So do "we" (the experts in this field, the body of knowledge
so-far) know for sure these two sets of pathways well enough
to say whether they are identical except for hydrogen donor
and reaction product, or whether they are different but with
all the other terms cancelling?

On Thu, 6 May 2004 17:44:03 +0000 (UTC),
RobertMaas@YahooGroups.Com <RobertMaas@YahooGroups.Com> wrote:
>> From: jimmenegay@sbcglobal.net (Jim Menegay)

>> > In that case, it's obvious that all the oxygen in the
>> > resultant glucose came from the CO2, since there isn't
>> > any oxygen in H2S in the first place. See an analagous
>> > question later...

>> It might be true, but it is far from obvious. The
>> complete process of photosynthesis is MUCH more
>> complicated than is indicated by the stoichiometry. The
>> part of the process that turns CO2 into glucose is called
>> the "dark reactions" since the coupling to the light-
>> absorbing aspect of photosynthesis is very indirect. The
>> various steps of the dark reactions involve oxygen from
>> CO2, from water, and even from phosphate.

>> The water molecules that provide the O2 at the opposite
>> end of the chain of reactions are, conceptually at least,
>> completely different from the ones involved in the dark
>> reactions. The hydrogen atoms are also different.
>
> I think I was making the, perhaps unwarranted, assumption
> that all the pathways in H2S and H2O photosynthesis are
> identical except for the point(s) where hydrogens are
> removed from that hydrogen donor, where the source
> molecule and the resultant atomic S or O are different. If
> that assumption is false, if there are other differences
> in the two mechanisms, very different pathways that
> somehow merge in overall effect, i.e. all the other
> changes in inputs and outputs cancel, to make the
> stoichiometry come out identical except for those two
> differences, then indeed it's two unrelated problems to
> study. But if the pathways are the same as I assumed, then
> mathematically we would have a contradiction to that pathways-
> same premise if my conclusion were false.
>
> So do "we" (the experts in this field, the body of
> knowledge so-far) know for sure these two sets of pathways
> well enough to say whether they are identical except for
> hydrogen donor and reaction product, or whether they are
> different but with all the other terms cancelling?

There seems to be several confusing ideas here.

First, photosynthesis, strictly speaking, is the capture of
light energy coupled to the synthesis of ATP (or NADPH). The
synthesis of molecules such as glucose (or amino acids, or
DNA, or lipids) is really an entirely separate process that
uses the ATP (NADPH) generated by photosynthesis. This
confusion arose because in most plants the primary use of
ATP is to make glucose and starch which is then transported
to other cells. It wasn't clear back in the 1950's that the
actual photosynthesis reactions and glucose synthesis were
separate. Even today, most textbooks still refer to the
Calvin cycle (CO2 fixation) as part of photosynthesis even
though they should know better.

Second, there are several different mechanisms for coupling
ATP synthesis to the uptake of photons of light. In the most
simple systems, an excited electron is transferred from
chlorophyll to a cytochrome bc complex where it passes down
a simple electron transport chain and returns to the
chlorophyll molecule. As the excited electron loses energy
it drives the transport of hydrogen ions across a membrane.
The membrane gradient that is set up is used by ATP synthase
to make ATP. In such a cyclic system there is no requirement
for any external source of electrons. The best examples of
such a simple photosystem are in purple bacteria and green
filamentous bacteria.

In some cases, excited electrons move from chlorophyll to
NADPH.

NADP+ + 2 electrons + H+ ---> NADPH

This is a more efficient process since NADPH carries more
energy than ATP and can be used in several biosynthesis
pathways. However, this type of photosynthesis is non-cyclic
and some outside source of electrons has to be found in
order to regenerate the electron deficient chlorophyll
molecules. In cyanobacteria and plants the source of
electrons is water and the product of the reaction is
oxygen. In green sulfur bacteria and heliobacteria the
electrons are extracted from various reduced sulfur
compounds such as H2S and S2O3-- and others.

Species that have evolved to use water as an electron source
have a more complex photosystem that is intimately
associated with an enzyme called the oxygen evolving complex
(OEC). Species that use other sources of electrons (e.g.
H2S) have a very different set of enzymes that reduce
cytochrome cofactors and these reduced cofactors carry
electrons to the chlorophyll molecules.

Larry Moran