To: All Msg #138, Jun1593 11:47AM Subject: talk.origins evolution FYI I'm going to post my
From: Chris Colby
To: All Msg #138, Jun-15-93 11:47AM
Subject: talk.origins evolution FYI
Organization: animal -- coelomate -- deuterostome
From: firstname.lastname@example.org (Chris Colby)
I'm going to post my "Introduction to evolutionary biology" file. The
point has been raised on t.o. that the term FAQ (for "frequently asked
questions") probably doesn't apply to many of the "FAQ"s posted.
So I've decided to call mine a FYI (for "for your information") --
if anyone has any other possible acronyms, email me.
This version of my FYI includes a section giving some events from
the history of life. Other minor revisions are scattered throughout.
I'll post it, as always, in two sections -- one labled "microevolution"
and the other labeled "macroevolution". I'll mail this to Mr. Vickers
as well so he can put it in the t.o. ftp site.
What is evolution?
What isn't evolution?
What evolution isn't
How is genetic variation described?
How much genetic variation is there?
Evolution within a lineage -- anagenesis
Mechanisms that decrease genetic variation
Mechanisms that increase genetic variation
Overview of anagenesis
Evolution among lineages -- cladogenesis
The pattern of macroevolution
Evidence for common descent and macroevolution
Comparative genetics and biochemistry
Natural selection and 'jury-rigged' design
The nested pattern of biological diversity
Predictions of evolutionary biology
Scientific standing of evolution and its critics
Mechanisms of macroevolution
Speciation -- increasing biological diversity
Modes of speciation
Extinction -- decreasing biological diversity
A brief history of life
The progenote and the three domains of life
Evolution of metabolism
Endosymbiosis -- chloroplasts and mitochondria
Cambrian and Ordovician radiations
Invasion of the land
Scientific Standing of Evolution and it's Critics
Chris Colby --- email: email@example.com ---
"'My boy,' he said, 'you are descended from a long line of determined,
resourceful, microscopic tadpoles--champions every one.'"
--Kurt Vonnegut from "Galapagos"
From: Chris Colby
To: All Msg #213, Jun-15-93 11:48AM
Subject: microevolution -- t.o. FYI part one
Organization: animal -- coelomate -- deuterostome
From: firstname.lastname@example.org (Chris Colby)
AN INTRODUCTION TO EVOLUTIONARY BIOLOGY -- BY CHRIS COLBY
Evolution is one of the most powerful theories in science. It is not a
difficult concept, but very few people -- the majority of biologists
included -- have a satisfactory grasp of it. One mistake, common to TV
nature shows, is that behaviors of individual organisms are aimed at
perpetuating their species. Another common mistake is that species
can be arranged on an evolutionary ladder from bacteria through
"lower" animals, to "higher" animals and, finally, up to man. These
mistakes, and many more, permeate popular science expositions of
evolutionary biology and even filter into biology journals.
All this confusion about evolution is very 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 many biologists in unrelated
fields speculate publicly about evolution without having training in it.
This essay is a brief introduction to evolutionary biology. As well as
explaining the basics of the theory of evolution, I focus on explaining
away many of the misconceptions about evolution. Creationist
arguments are not directly addressed here.
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 numerous
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. In this moth there are two color
morphs, light and dark. Black moths, which initially were rare,
increased in frequency 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 primarily 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 "microevolution". Larger
changes in a gene pool are called "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
In any case, evolution is defined as a change in the gene pool. This
means that evolution is a population level phenomenon. 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, it is necessary to view populations as a
collection of individuals with different traits. For example, in the
example above the frequency of black moths increased, the moths did
not turn from light to grey to dark in concert.
I have defined evolution as a process and that is how I will use the
term in this essay. Keep in mind, however, that in everyday use
evolution refers to a variety of things. The fact that all organisms are
linked via descent to a common ancestor is often called evolution. The
theory that life arose solely via natural processes is often called
evolution (instead of abiogenesis). And frequently, people use the word
evolution when they really mean natural selection -- one of the many
mechanisms of evolution.
WHAT ISN'T EVOLUTION?
For many, evolution is equated with morphological change, i.e.
organisms changing shape or size over time. An example would be a
dinosaur species evolving into a species of bird. It is important to note
that evolution is often accompanied by morphological change, but this
need not be the case. Evolution can occur without morphological
change; and morphological change can occur without evolution. For
instance, humans are larger now than in the recent past, but this is not
an evolutionary change. Better diet and medicine brought about this
change, so it is not an example of evolution. The gene pool did not
change -- only its manifestation did.
Phenotypic changes induced solely by changes in environment do not
count as evolution because they are not heritable; in other words the
change is not passed on to the organism's offspring. 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 (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. Populations simply adapt to their current
surroundings and do not necessarily become "better" over time. A trait
or strategy that is successful at one time may be deleterious at another.
Studies in yeast have shown that "more evolved" strains of yeast can
be competitively inferior to "less evolved" strains. 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
HOW DOES EVOLUTION WORK?
If evolution is a change in the gene pool; what causes the gene pool to
change? Several mechanisms can change a gene pool, among them:
natural selection, genetic drift, gene flow, mutation and recombination.
I will discuss these in more detail later. It is important to understand
the difference between evolution and the mechanisms that bring about
Bringing about a change in the gene pool assumes that there is genetic
variation in the population to begin with, or a way to generate it.
Genetic variation is "grist for the evolutionary mill". For example, if
there were no dark moths, the population could not have evolved
from mostly light to mostly dark. In order for continuing evolution
there must be mechanisms to increase or create genetic variation (e.g.
mutation) and mechanisms to decrease it (e.g. natural selection and
HOW IS GENETIC VARIATION DESCRIBED?
Genetic variation has two components: allelic diversity and non-
random associations of alleles. Alleles are different versions of the
same gene at a given locus (locus means location). For example, at the
blood group locus humans can have an A, B or O allele. Most animals,
including humans, are diploid. This means they contain two alleles for
every gene at every locus. If the two alleles are the same type (for
instance two A alleles) the individual would be termed "homozygous"
for that locus. An individual with two different alleles at a locus is
called "heterozygous". Allelic diversity is simply the number of alleles
at each locus scaled by their frequency in the gene pool. At any locus
there can be many different alleles, more alleles than any single
organism can possess.
Linkage disequilibrium is a measure of association between alleles at
different loci. If two alleles were found together in organisms more
often than would be expected, 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.
Assortative mating causes a non-random distribution of alleles at a
single locus. Humans, for example, mate assortatively according to
race; we are statistically 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 if the gene pool were randomly
mixed. This mating effect 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
HOW MUCH GENETIC VARIATION IS THERE?
Considerable variation has been detected in natural populations. At 45
percent of loci in plants there is more than one allele in the gene pool.
Any given plant is likely to be heterozygous at about 15 percent of its
loci. Levels of genetic variation in animals range from roughly 15% of
loci having more than one allele (polymorphic) in birds, to over 50% of
loci being polymorphic in insects. Mammals and reptiles are
polymorphic at about 20% of their loci - - amphibians and fish are
polymorphic at around 30% of their loci. Most loci assort
independently (this implies linkage equilibrium). In most populations,
there are enough loci and enough different alleles that every
individual (barring monozygotic (identical) twins) has a unique
combination of alleles.
EVOLUTION WITHIN A LINEAGE (ANAGENESIS)
The following sections deal with evolution within a population or
lineage -- this is called anagenesis. Several mechanisms can bring about
anagenetic change. I have grouped them into two classes -- those that
decrease genetic variation and those that increase it.
MECHANISMS THAT DECREASE GENETIC VARIATION
MECHANISMS OF EVOLUTION: NATURAL SELECTION
Natural selection is the only mechanism of adaptive evolution; it is
defined as differential reproductive success of pre-existing classes of
genetic variants in the gene pool. In other words, some genotypes are
(on average) better than others at contributing their alleles to the next
generation's gene pool.
Selection is not a force in the sense that gravity or magnetism is.
However, 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 something in the environment
instructs the organism as to how to evolve, or "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.
Also, when selection is spoken of as a force, it often seems that it is has
a mind of it's own; or as if it was nature personified. This most often
occurs when biologists are waxing poetic about selection. This kind of
talk should be identified for the feebleminded crap it is and 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 thus and so 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 and 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.
When supplied with genetic variation, natural selection allows
organisms to adapt to their current environment. It does not have any
foresight. Structures or behaviors do not evolve for future utility. An
organism must be adapted to its environment at each stage of its
evolution. As the environment changes, new traits (new combinations
of alleles) may be selected for. Large changes in populations are the
result of cumulative natural selection -- numerous small changes are
introduced into the population by mutation; the small minority of
these changes that result in a greater reproductive output of their
bearers are amplified in frequency by selection.
If evolution proceeds without any foresight, it is logical to wonder how
complex traits evolve? If half a wing is no good for flying, how did
wings evolve? Half a wing may be no good for flying, but it may be
useful in other ways. Feathers are thought to have evolved as
insulation (ever worn a down jacket?) and/or as a way to trap insects.
Later, proto-birds may have learned to glide when leaping from tree to
tree. Eventually, the feathers that originally served as insulation now
became co-opted for use in flight.
This illustrates the point that a trait's current utility is not always
indicative of its past utility. It can evolve for one purpose, and be used
later for another. A trait evolved for its current utility is an adaptation;
one that evolved for another utility is an exaptation. An example of an
exaptation is a penguin's wing. Penguins evolved from flying
ancestors; now they are flightless and use their wings for swimming.
Natural selection works at the level of the individual. The example I
gave earlier was an example of evolution via natural selection. Dark
colored moths had 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 reproduces or
fails to reproduce and are hence the unit of selection. 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
The individual organism reproduces or fails to reproduce. It competes
primarily with others of it own species for its reproductive success. For
this reason organisms do not perform any behaviors that are for the
good of their species. Natural selection favors selfish behavior because
any truly altruistic act increases the recipient's reproductive success
while lowering the donors. Altruists would quickly disappear from a
population as the non-altruists would reap the benefits, but not pay the
cost, of any altruistic act.
Of course, many behaviors appear to be altruistic. Biologists, however,
can demonstrate (in the cases they have studied) that these behaviors
are only apparently altruistic. Cooperating with or helping other
organisms is often the most selfish strategy for an animal. Often this is
called "reciprocal altruism" (an oxymoron if there ever was one). A
good example of this is blood sharing in vampire bats. In these bats,
those lucky enough to find a meal will often share part of it with an
unsuccessful bat by regurgitating some blood into the other's mouth.
Biologists have found that these bats form bonds with partners and
help each other out when the other is needy. If a bat is found to be a
"cheater", (i.e. he accepts blood when starving, but does not donate
when his partner is) his partner will abandon him. The bats are thus
not helping each other altruistically; they form pacts that are mutually
Helping closely related organisms can appear altruistic; but this is also a
selfish behavior. Reproductive success (or 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.
Natural selection favors 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, 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 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.
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 optimal set of traits (the global optimum); but
there are probably several 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. So, natural selection only works to bring
populations to the nearest optimal point.
SEXUAL SELECTION -- A SUBSET OF NATURAL SELECTION
Darwin, and others, noticed that in many species males developed
prominent secondary sexual characteristics. A few oft cited examples
are the peacock's tail, coloring and patterns in male birds in general,
voice calls in frogs and flashes in fireflies. Many/most of these traits are
a liability from the standpoint of survival, mainly because any
ostentatious trait or noisy, attention-getting behavior will alert
predators as well as potential mates. How then could natural selection
favor these traits?
Natural selection can be broken down into many components, of
which survival is only one. Sexual attractiveness is a very important
component of selection, so much so that biologists use the term sexual
selection when they talk about this subset of natural selection.
Sexual selection occurs when the sexual attractiveness of a trait
outweighs the liability incurred for survival. A male who lives a short
time, but produces many offspring is much more successful than a long
lived one that produces few. The former's genes will eventually
dominate the gene pool of his species. In many species, especially
polygynous species where only a few males monopolize all the
females, sexual selection has caused pronounced sexual dimorphism.
In these species males compete against other males for mates. The
competition can be either direct (i.e. the largest males guarding their
harems and fending off other males physically) or mediated by female
In species where females chose, males compete by displaying striking
phenotypic characteristics and/or performing elaborate courtship
behaviors. The females then mate with the males that most interest
them, usually the ones with the most outlandish displays. There are
many competing theories as to why females are attracted to these
displays. One model, the "good genes" model, states that the display
indicates some component of male fitness. A "good genes" advocate
would say that bright coloring in male birds indicates a lack of parasites.
The females are cueing on some signal that is correlated with some
other component of viability.
Another model, proposed by Fisher, is called the "runaway sexual
selection" model. In his model he proposes that females may have a
preference for some male trait (without regards to fitness) and then
mate with these males when the trait appears. The offspring of these
matings will therefore have the genes for both the trait _and_ the
preference for the trait. Note, these genes would be expressed in the
males and females respectively. As a result, the process snowballs out
of control until natural selection brings it into check. Here is an
example to clarify.
Suppose that, due to some quirk of brain chemistry, female birds of one
species prefer males with longer than average tail feathers. Mutant
males with longer than average feathers will produce more offspring
than the short feathered males. In the next generation, average tail
length will increase.
As the generations progress, feather length will increase because
females do not prefer a specific length tail, but a longer than average
tail. Eventually tail length will increase to the point were the liability to
survival is matched by the sexual attractiveness of the trait and an
equilibrium will be established. Note that in many exotic birds male
plumage is often very showy and many species do in fact have males
with greatly elongated feathers. In some cases these feathers are shed
after the breeding season.
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 a non-random mechanism of evolution. It is the
only mechanism that causes adaptive evolution. The phrase "survival
of the fittest" is often used synonymously with natural selection.
IMHO, the phrase is both incomplete and misleading. For one thing,
survival is only one component of selection -- and perhaps one of the
less important ones in many populations. For example, in polygynous
species, a number of males survive to reproductive age, but only a few
ever mate. Males may differ little in their ability to survive, but greatly
in their ability to attract mates -- the difference in reproductive success
stems mainly from the latter consideration. Also, the word "fit" is
often confused with physically fit. Fitness, in an evolutionary sense, is
the average reproductive output of a class of genetic variants in a gene
pool. Fit does not mean biggest, fastest or strongest -- sexiest might be
closer to the truth in many animal species.
Of all the mechanisms of evolution, natural selection has the potential
to change gene frequencies the fastest. It usually acts to keep gene
frequencies constant, however. This led a famous evolutionist, George
Williams, to say "Evolution proceeds in spite of natural selection".
MECHANISMS OF EVOLUTION: GENETIC DRIFT
Another important mechanism of evolution is genetic drift. Drift is a
binomial sampling error of the gene pool. What this means is, the
alleles that form the next generation's gene pool are a sample of the
alleles from the current generation.
Drift is a rather abstract concept to some; I will try to explain it via an
analogy. Imagine you had a swimming pool full of one million
marbles. This will represent the parental gene pool -- half are red and
half are blue. If you repeatedly picked ten marbles out, do you think
you would get five red and five blue every time (assume you replaced
your sample to the pool each time)? If you picked one hundred marbles
out, do you think you would get fifty red and fifty blue out every time?
In both cases the answer is no, some times the frequency of red marbles
in the sample would deviate from 0.50. In the case of the 100 marble
sample, the frequency of red marbles would deviate much less,
If, after picking out ten or one hundred marbles, you refilled the pool
with marbles at the frequency of that sample (for example, if you picked
6 red and four blue and refilled the pool with 600,000 red marbles and
400,000 blue) 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
In small populations, the rate of change in the frequency of alleles is
greater than in large populations. However, the overall rate of genetic
drift is independent of population size. If the mutation rate is constant,
large and small populations lose alleles to drift at the same rate. This is
because large populations will have more alleles in the gene pool, but
they will lose them more slowly. Smaller populations will have fewer
alleles, but these will quickly cycle through. This assumes that selection
is not operating on any of these alleles.
Sharp drops in population size can greatly affect the gene pool. When a
population crashes, the alleles in the surviving sample may not be
representative of the pre-crash gene pool. This change in the gene pool
is called the founder effect, because small populations of organisms
that invade a new territory (founders) are subject to this. Many
biologist feel the genetic changes brought about by founder effects may
contribute to isolated populations developing reproductive isolation
from their parent populations.
Both natural selection and genetic drift decrease genetic variation. If
they were the only mechanisms of evolution, populations would
eventually become homogeneous and further evolution would be
impossible. There are, however, mechanisms that replace variation
depleted by selection and drift. These are discussed below.
MECHANISMS THAT INCREASE GENETIC VARIATION
MECHANISMS OF EVOLUTION: MUTATION
A mutation is a change in a gene. There are many kinds of mutations.
A point mutation is a mutation in which one "letter" of the genetic
code is changed to another. Lengths of DNA can also be deleted or
inserted in a gene; these are also mutations. Finally, genes or parts of
genes can become inverted or duplicated.
Mutation is a mechanism of evolution because it changes allele
frequencies very slightly. If an allele "A" mutates to another allele "a",
the frequency of "a" has increased from zero to some small number
(1/2N in a diploid population where N is the effective population size).
The allele "A" will also decrease slightly in frequency. Evolution via
mutation alone is very slow; for the most part, mutation just supplies
the raw material for evolution -- genetic variation.
Most mutations are slightly deleterious or neutral. The genome of
most organisms (certainly all eukaryotes) contains enormous amounts
of junk sequences. In addition, even in coding regions, many sites can
undergo mutation and still maintain the original meaning. In other
words, the genetic code is redundant. So, most mutations are neutral or
nearly so; but, the overwhelming majority of mutations that produce
any detectable phenotypic effect are deleterious. "Good" mutations,
however, do occur.
One example of a beneficial mutation comes from the mosquito
_Culex_ _pipiens_. In this organism, a gene that was involved with
breaking down organophosphates - common insecticide ingredients -
became duplicated. Progeny of the organism with this mutation quickly
swept across the worldwide mosquito population. There are numerous
examples of insects developing resistance to chemicals, especially DDT -
which was once heavily used in this country. And, most importantly,
even though "good" mutations happen much less frequently than
"bad" ones, organisms with "good" mutations thrive while organisms
with "bad" ones die out.
It has long been dogma that mutations occur without regard 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. Recently, this notion
has been challenged.
A new class of mutation has recently been documented in bacteria and
yeast. It appears that some unicellular organisms can undergo adaptive
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 mutation rate at other loci is unaffected. The mechanism of
adaptive mutagenesis is unknown at this time, but it has been shown
to be under genetic control - - i.e. adaptive mutations are not errors like
normal mutations are; they are actively created (or selectively retained)
by the organism in response to the environment.
The importance of directed mutagenesis is not yet known. The
majority of evolution on this planet probably proceeded by natural
selection sifting through random, spontaneous mutants, but, adaptive
mutagenesis may have played a significant role in some microbe
lineages. Biologists have not yet studied if directed mutations can
produce novel solutions to environmental challenges. It is also
unknown if they can occur in multi-cellular organisms with separate
germ and somatic cell lines. In any case it appears that, in at least a few
instances, the potential for selection to operate induces adaptive genetic
variation to appear.
MECHANISMS OF EVOLUTION: RECOMBINATION
Recombination can be thought of as gene shuffling. Most organisms
have linear chromosomes and their genes lie at specific location (loci)
along them (bacteria have circular chromosomes). In most sexually
reproducing organisms, there are two of each chromosome type in
every cell. For instance in humans, there are two chromosomes
number one (through 22 and two sex chromosomes), one inherited
from the mother, the other inherited from the father. When an
organism produces gametes, the gametes end up with only one of each
chromosome per cell. Haploid gametes are produced from diploid cells
by a process called meiosis.
In meiosis, homologous chromosomes line up. The DNA of the
chromosome is broken on both chromosomes in several places and
rejoined with the other strand. Later, the two homologous
chromosomes are split into two separate cells that divide and become
gametes. But, because of recombination, both of the chromosomes are a
mix of alleles from the mother and father.
For example, let's say an organism has a chromosome with three
genes, (A,B and C -- in that order). Assume that at each of these three
loci there are at least two alleles. From the father, the organism
inherited a chromosome with the alleles A1, B1 and C1. From the
mother the organism inherited A2,B2 and C2 alleles. In meiosis the
two chromosomes would line up and the two A alleles would line up,
as would the B and C alleles. If recombination occurred between locus
A and locus B, the resulting chromosomes in the two gametes would
be; one chromosome carrying A1, B2 and C2 alleles and one
chromosome carrying A2, B1 and C1 alleles.
Real chromosomes carry many more than three genes and
recombination occurs at many locations along the chromosome. The
end result is that the two homologous chromosomes have "shuffled"
Recombination can occur not only between genes, but within genes as
well. Recombination within a gene can form a new allele.
Recombination is a mechanism of evolution because it adds new
alleles and combinations of alleles to the gene pool.
A beneficial aspect of recombination is that beneficial mutants can be
brought together onto the same chromosome, even if they arose in
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.
This is called horizontal transfer. One interesting case of this involves
genetic elements called P elements. In the genus _Drosophila_, P
elements were transferred 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 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 are
devoid of P elements. All natural populations today harbor them.
OVERVIEW OF EVOLUTION WITHIN A LINEAGE (ANAGENESIS)
Evolution is a change in the gene pool of a population over time; it can
occur due to several factors. Three mechanisms add new alleles to the
gene pool: mutation, recombination and gene flow. Two mechanisms
remove alleles, genetic drift and natural selection. Drift removes alleles
randomly from the gene pool. Selection removes deleterious alleles
from the gene pool. Natural selection can also increase the frequency of
an allele (or combination of alleles) in the gene pool. Selection that
weeds out harmful alleles is called negative selection. Selection that
increases the frequency of helpful alleles is called positive, or
sometimes positive Darwinian, selection.
A new allele can also drift to high frequency. But, since the change in
frequency of an allele each generation is random, nobody speaks of
positive or negative drift.
Except in rare cases of high gene flow, all new alleles enter the gene
pool as a single copy. Most new alleles added to the gene pool are lost
almost immediately due to drift or selection; only a small percent ever
reach a high frequency in the population. Even most moderately
beneficial alleles are lost due to drift when they appear.
The fate of any new allele depends a great deal on the organism it
appears in. This allele will be linked to the other alleles near it for
many generations. A mutant allele can increase in frequency simply
because it is linked to a beneficial allele at a nearby locus. This can occur
even if the mutant allele is deleterious, although it must not be so
deleterious as to offset the benefit of the other allele. Likewise a
potentially beneficial new allele can be eliminated from the gene pool
because it was linked to deleterious alleles when it first arose.
An allele "riding on the coat tails" of a beneficial allele is called a
hitchhiker. Eventually, recombination will bring the two loci to
linkage equilibrium. But, the more closely linked two alleles are, the
longer the hitchhiking will last.
The effects of selection and drift are coupled. Drift is intensified as
selection pressures increase. This is because increased selection (i.e. a
greater difference in reproductive success among organisms in a
population) reduces the effective population size, the number of
individuals contributing alleles to the next generation.
Adaptation is brought about by cumulative natural selection, the
repeated "sifting" of mutations by natural selection. Small changes,
favored by selection, can be the stepping-stone to further changes. The
summation of large numbers of these changes is macroevolution. This
is discussed below.
EVOLUTION AMONG LINEAGES (CLADOGENESIS)
The following sections deal with how single populations ramify to
become multiple populations and eventually separate species - this is
called cladogenesis. In addition, the overall pattern of macroevolution
and evidence for common descent of all living species is presented.
Also, a brief history of life on the planet is given.
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. Humanities closest relatives are, collectively, the
chimpanzee and the pygmy chimp. Our next nearest relative is the
EVIDENCE FOR COMMON DESCENT AND MACROEVOLUTION
Whereas microevolution can be studied directly, macroevolution is
studied by examining patterns in biological populations and clades
(groups of organisms) and inferring process from pattern. Given the
observation of microevolution and the knowledge that the earth is
billions of years old -- macroevolution could be postulated. But this
extrapolation, in and of itself, does not really provide a compelling
explanation of the patterns of biological diversity we see today.
Evidence for macroevolution, or common ancestry and modification
with descent, comes from several other fields of study. These include:
comparative biochemical and genetic studies, comparative
developmental biology, patterns of biogeography, comparative
morphology and anatomy and the fossil record.
Comparative genetic and biochemical data provide data supporting the
inference of common descent. DNA sequence comparisons of closely
related species (as determined by morphologists) yield similar
sequences. Overall sequence similarity is not the whole story, however.
The pattern of differences we see in closely related genomes is worth
Genes are sequences of nucleotides that code for proteins. There are
four different kinds of nucleotides commonly incorporated into DNA:
adenine (A), guanine (G), cytosine (C) and thymine (T) -- each block of
three is called a codon. Each codon designates an amino acid (the
subunits of proteins). The gene, or sequence of codons, is transcribed
into RNA -- a nucleic acid similar to DNA. (RNA, like DNA, is made
up of nucleotides although the nucleotide uracil (U) is used in place of
thymine (T).) The RNA is then translated via cellular machinery into a
string of amino acids -- a protein.
All living organisms use DNA as their genetic material, although
some viruses use RNA. The three letter code is the same for all
organisms. The universal genetic code is redundant. There are 64
codons, but only 20 amino acids to code for; so, most amino acids are
coded for by several codons. In many cases the first two nucleotides in
the codon designate the amino acid. The third position can have any of
the four nucleotides and not effect how the code is translated.
In addition to showing overall similarity, gene sequences from closely
related species show the same codon is often used for amino acids. In
cases where there are differences, however, they are usually in these
"silent" sites. In addition, the genome is loaded with 'dead genes'
called pseudo-genes. Pseudogenes occupy the same location in the
genome in closely related species. The same can be said for introns,
sequences of DNA that interrupt a gene, but do not code for anything.
Introns are spliced out of the RNA prior to translation, so they do not
contribute information needed to make the protein. They are
sometimes, however, involved in regulation of the gene.
Third codon positions (silent sites), pseudo-genes and introns show
more sequence differences between species than coding sections of a
gene. This is because mutations that change the code of a gene, and
hence the protein made, usually affect the organism adversely and are
selected against. Mutations in non-coding regions do not affect the
phenotype of the organism and get passed on.
If two species shared a recent common ancestor one would expect
genetic information, even information such as redundant nucleotides
and the position of introns or pseudogenes, to be similar. Both species
would have inherited this information from their common ancestor.
The degree of similarity would be a function of divergence time.
Studies in comparative anatomy also provide support for common
descent. Groups of related organisms are 'variations on a theme' -- the
same set of bones are used to construct all mammals. The bones of the
human hand grow out of the same tissue the bones of a bat's wing or a
whale's flipper does and they share many identifying features (muscle
insertion points, ridges). The only difference is that they are scaled
differently. Evolutionary biologists say this indicates that all mammals
are modified descendents of a common ancestor which had the same
set of bones.
Evidence for common descent also comes from studying comparative
developmental biology. Closely related organisms share similar
developmental pathways, the differences in development are most
evident at the end. This is, again, usually illustrated using mammalian
(or sometimes vertebrate) examples. As organisms evolve, their
developmental pathway gets modified. It is easier to modify the end of
a developmental pathway than the beginning since changes early on
have a cascading effect. Therefore, organisms pass through stages of
early development that their ancestors passed through. These stages,
however, are modified because selection "sees" all phases of an
organism's life cycle. So, an organism's development mimics its
ancestors although it doesn't recreate it exactly.
Traces of an organisms ancestry sometimes remain even when an
organisms ontogeny (development) is complete. These are called
vestigial structures. Many snakes have rudimentary pelvic bones
retained from their walking ancestors. This is an example of a vestigial
Biogeography also supports the inference of common descent.
Organisms clustered spatially are frequently also clustered
phylogenetically; this is especially true of organisms with limited
dispersal opportunities. The mammalian fauna of Australia is often
cited as an example of this; marsupial mammals fill most of the
equivalent niches that placentals fill in other ecosystems. If all
organisms descended from a common ancestor, species distribution
across the planet would be a function of site of origination, potential
for dispersal and time since origination. In the case of Australian
mammals, their physical separation from sources of placentals means
potential niches were filled by a marsupial radiation rather than a
placental radiation or invasion.
Natural selection can only mold available genetically based variation.
In addition, natural selection provides no mechanism for advance
planning. If selection can only tinker with what it has to work with
and, if all organisms share a common ancestor, we should expect to see
examples of suboptimal design in living species. This is indeed the
In African locusts, the nerve cells that connect to the wings originate in
the abdomen, even though the wings are in the thorax. When the
insect send the message to fly from its brain to its wings, the nerve
impulse travels down the ventral nerve cord past its target then
backtracks to the wing.
In _Cnenidophoran_ lizards, females reproduce parthenogenetically.
Fertility in these lizards is increased when a female mounts another
female and simulates copulatory behavior. This is because these lizards
evolved from sexual lizards whose hormones were aroused by sexual
behavior. Now, although the sexual mode of reproduction has been
lost, the means of getting aroused (and hence fertile) has been retained.
Fossils show hard structures of organisms less and less similar to
modern organisms as you go down the strata (layers of rocks). In
addition, patterns of biogeography apply to fossils as well as extant
organisms. When combined with plate tectonics, fossils provide
evidence of distributions and dispersals of ancient species. For example,
South America had a very distinct marsupial mammalian fauna until
the land bridge formed between North and South America. After that
marsupials started disappearing and placentals took their place. This is
commonly interpreted as the placentals wiping out the marsupials (but
this may be an over simplification).
Further strong evidence for macroevolution comes from the fact that
suites of traits in biological entities fall into a nested pattern. For
example, plants can be divided into two broad categories, non-vascular
(mosses) and vascular. Vascular plants can be divided into seedless
(ferns) and seeded. Vascular seeded plants can be divided into
gymnosperms (pines) and flowering plants or angiosperms. And
angiosperms can be divided into monocots and dicots. Each of these
types of plants have several characters that distinguish them from
other plants -- traits are not "mixed and matched" in groups of
organisms. For example, flowers are only seen in plants that carry
several other characters that distinguish them as angiosperms. This
pattern arises due to lineages splitting (speciation), retaining ancestral
traits and deriving new traits. Derived traits only appear in lineages
descended from the population that first displayed the trait. This
hierarchical pattern of diversity is what one expects to see if species
branch into new species and are modified with descent.
Thus, it is not just that similar species share similar traits (although
that is evidence in and of itself); when you look at large groups of
organisms, a pattern on a larger scale is seen. This hierarchical pattern
can be produced even if the process responsible is not hierarchical. For
example, microevolution leads to hierarchical patterns of genetic
diversity even though it works at a single level. The question of
hierarchical processes in evolution is still being debated.
The real test of any scientific theory is its ability to generate testable
predictions and, of course, have the predictions borne out. Evolution
easily meets this criterion. In several of the above examples I stated,
closely related organisms share X. If I define closely related as sharing X,
this is a contentless statement. It does however, provide a prediction. If
two organisms share (oh lets say) a similar anatomy (two birds, for ex.),
I would then predict that their gene sequences would be more similar
than a morphologically distinct organism (like a plant, for ex.). This has
been spectacularly borne out by the recent flood of gene sequences -- the
correspondence to trees drawn by morphological data is very high. The
discrepancies are never too great and usually confined to cases where
the pattern of relationship was hotly debated.
MECHANISMS OF MACROEVOLUTION
The next three sections (speciation, extinction and punctuated
equilibrium) deal with mechanisms of evolution above the species
SPECIATION -- INCREASING BIOLOGICAL DIVERSITY
Speciation is the process of a single species becoming two or more
species. Many biologists feel speciation is key to understanding
evolution and that certain evolutionary phenomena apply only at
speciation and macroevolutionary change cannot occur without
speciation. Other biologists think major evolutionary change can occur
without speciation. Changes between lineages are only an extension of
the changes within each lineage. In general, paleontologists fall into
the former category and geneticists in the latter.
MODES OF SPECIATION
Biologists recognize two types of speciation: allopatric and sympatric
speciation. The two differ in geographical distribution of the
populations in question.
Allopatric speciation is thought to be the most common form of
speciation. It occurs when a population is split into two (or more)
geographically isolated subdivisions that organisms cannot bridge.
Eventually, the two populations' gene pools change independently
until they could not interbreed even if they were brought back together.
In other words, they have speciated.
Sympatric speciation occurs when two subpopulations become
reproductively isolated without first becoming geographically isolated.
Monophytophagous insects (insects that live on a single host plant)
provide a model for sympatric speciation. If a group of insects switched
host plants they would not breed with other members of their species
still living on their former host plant. The two subpopulations could
diverge and speciate. Some biologists call sympatric speciation
microallopatric speciation to emphasize that the subpopulations are
still physically separate at an ecological level.
Biologists know little about the genetic mechanisms of speciation.
Some think series of small changes in each subdivision gradually lead
to speciation; others think there may be a few key genes that could
change and confer reproductive isolation. One famous biologist thinks
most speciation events are caused by changes in internal symbionts.
Most doubt this, however. Populations of organisms are very
complicated. It is likely that there are many ways speciation can occur.
Thus, all of the above ideas may be correct, each in different
It comes as a surprise to some to hear that speciation has been
observed. In the genus _Tragopogon_ (a plant genus consisting mostly
of diploids), two new species (_T._ _mirus_ and _T._ _miscellus_)
have evolved within the past 50-60 years. The new species are
allopolyploid descendants of two separate diploid parent species.
Here is how this speciation occurred. The new species were formed
when one diploid species fertilized a different diploid species and
produced a tetraploid offspring. This tetraploid offspring could not
fertilize or be fertilized by either of its two parent species types. It is
reproductively isolated, the definition of a species.
Two other plant species have also arisen within the past 110 years in
this manner, _Senecio_ _cambrensis_ and _Spartina_ _townsendii_.
EXTINCTION -- DECREASING BIOLOGICAL DIVERSITY
Extinction is the ultimate fate of all species. The reasons for extinctions
are numerous. A species can be competitively excluded by a closely
related species, the habitat a species lives in can disappear and/or the
organisms that the species exploits could come up with an unbeatable
Some species enjoy a long tenure on the planet while others are short-
lived. Some biologists believe species are "programmed" to go extinct
in a manner analogous to organisms being destined to die. The
majority, however, believe that if the environment stays fairly
constant, a well adapted species could continue to survive indefinitely.
Mass extinctions shape the overall pattern of macroevolution. If you
view evolution as a branching tree, it's best to picture it as one that has
been severely pruned a few times in its life. The history of life on this
earth includes many episodes of mass extinction in which many taxa
(groups of organisms) were wiped off the face of the planet. Mass
extinctions are followed by periods of radiation where new species
evolve to fill the empty niches left behind. It is probable that surviving
a mass extinction is largely a function of luck. Thus contingency plays a
large role in patterns of macroevolution.
The most famous extinction occurred at the boundary between the
Cretaceous and Tertiary Periods (the K/T Boundary- 65MYA). This
extinction eradicated the dinosaurs. Some hypothesize that the K/T
event was caused by environmental disruption brought on by a large
impact on earth. Several lines of evidence point to a large collision at
the time of the extinction, but attempts to link the two have not been
convincing to all biologists. Following this extinction the mammalian
radiation occurred. Mammals coexisted for a long time with the
dinosaurs but were confined mostly to nocturnal insectivore niches.
With the eradication of the dinosaurs, mammals radiated to fill the
The largest mass extinction came at the end of the Permian (250MYA);
and coincides with the formation of Pangaea II, when all the world's
continents were brought together by plate tectonics. A worldwide drop
in sea level also occurred at this time. Currently, human alteration of
the ecosphere is causing a global mass extinction.
Some paleontologists believe evolution is a hierarchical process. The
theory of punctuated equilibria attempts to infer the process of
macroevolution from the pattern of species documented in the fossil
record. In the fossil record, transition from one species to another is
usually abrupt in most geographic locales -- no transitional forms are
found. In short, it appears that species remain unchanged for long
stretches of time and then are quickly replaced by new species.
However, if wide ranges are searched, transitional forms that bridge the
gap between the two species are sometimes found in small, localized
For example, in Jurassic brachiopods of the genus _Kutchithyris_, _K.
acutiplicata_ appears below another species, _K. euryptycha_. Both
species were common and covered a wide geographical area. They
differ enough that some have argued they should be in a different
genera. In just one small locality an approximately 1.25m sedimentary
layer with these fossils is found. In the narrow (10 cm) layer that
separates the two species, both species are found along with transitional
forms. In other localities there is a sharp transition.
Gould and Eldredge, the authors of punctuated equilibria, interpret this
in light of theories of allopatric speciation. They concluded that isolated
populations of organisms will often speciate and then invade the range
of their ancestral species. Thus at most locations that fossils are found,
transition from one species to another will be abrupt. This abrupt
change will reflect replacement by migration however, not evolution.
In order to find the transitional fossils, the area of speciation must be
They also argue that evolution can proceed quickly in small
populations so that the tempo of evolution is not continuous. This has
lead to some confusion about the theory. Some popular accounts give
the impression that abrupt changes in the fossil record are due to
blindingly fast evolution; this is not what the theory of punctuated
Some PE proponents envision the theory as a hierarchical theory of
evolution because they see speciation as analogous to mutation and the
replacement of one species by another (which they call species
selection) as analogous to natural selection. Speciation adds new
species to the species pool just as mutation adds new alleles to the gene
pool and species selection favors one species over another just as
natural selection can favor one allele over another. This is the most
controversial part of the theory. Most biologists agree with the pattern
of macroevolution these paleontologists posit, but many disagree with
the mechanism -- species selection. Critics would argue that species
selection is not analogous to natural selection and therefore evolution
is not hierarchical.
The theory of punctuated equilibrium was designed to replace the
theory of phyletic gradualism. Phyletic gradualists held that a species
would slowly transform into another species over its entire range.
Phyletic gradualism is often associated with the assumption of a
uniform rate of evolution, but this need not be the case.
A BRIEF HISTORY OF LIFE
Biologists studying evolution do a variety of things: population
geneticists study the process as it is occurring; systemetists seek to
determine relationships between species and paleontologists seek to
uncover details of the unfolding of life in the past. Discerning these
details is often difficult, but hypotheses can be made and tested as new
evidence comes to light. This section should be viewed as the "best
guess" scientists have as to the history of the planet. The material here
ranges from some issues that are fairly certain to some topics that are
nothing more than informed speculation. For some points there are
opposing hypotheses -- I have tried to compile a "consensus" picture.
In general, the more remote the time, the more likely the story is
incomplete or in error.
Life evolved in the sea. It stayed there for the majority of the history of
The first replicating molecules were most likely RNA. RNA is a
nucleic acid similar to DNA. In laboratory studies it has been shown
that some RNA sequences have catalytic capabilities. Most importantly,
certain RNA sequences act as polymerases -- enzymes that form strands
of RNA from its monomers. This process of self-replication is the
crucial step in the formation of life.
The common ancestor of all life probably used RNA as its genetic
material and was most likely a progenote -- an organism whose genes
were not arranged into a genome. The progenote gave rise to three
major lineages of life. These are: the prokaryotes ("ordinary" bacteria),
archaebacteria (thermophilic, methanogenic and halophilic bacteria)
and eukaryotes. Eukaryotes include protists (single celled organisms
like amoebas and diatoms and a few multicelluar forms such as kelp),
fungi (including mushrooms and yeast), plants and animals.
Eukaryotes and archaebacteria are the two most closely related of the
three. The process of translation (making protein from the instructions
on a messenger RNA template) is similar in these lineages, but the
organization of the genome and transcription (making messenger
RNA from a DNA template) is very different in prokaryotes than in
eukaryotes and archaebacteria. Scientists interpret this to mean that the
progenote (common ancestor) was RNA based; it gave rise to two
lineages that independently formed a DNA genome and hence
independently evolved mechanisms to transcribe DNA into RNA.
The first cells must have been anaerobic because there was no oxygen
in the atmosphere. In addition, they were probably thermophilic
("heat-loving") and fermentative. Rocks as old as 3.5 Billion years old
have yielded prokaryotic fossils. Specifically, some rocks from Australia
called the Warrawoona series give evidence of bacterial communities
organized into structures called stromatolites. Fossils like these have
subsequently been found all over the world. These mats of bacteria still
form today in a few locales (for example, Shark Bay Australia). Bacteria
are the only life forms found in the rocks for long, long time --
eukaryotes (protists) appear about 1.5 BYA and fungi-like things appear
about 900 MYA (0.9 Billion years ago).
Somewhere along the way, photosynthesis evolved. Photosynthesis is
a process that allows organisms to harness sunlight to manufacture
sugar from simpler precursors. The first photosystem to evolve (PSI)
uses light to convert CO2 and H2S to glucose. This process releases
sulfur as a waste product. Later a second photosystem (PSII) evolved,
probably from a duplication of the first photosystem. Organisms with
PSII use both photosystems in conjunction to convert C02 and water
(H2O) into glucose. This process releases oxygen as a waste product.
Anoxygenic (or H2S) photosynthesis, using PSI, is seen in living purple
and green bacteria. Oxygenic (or H2O) photosynthesis, using PSI and
PSII, takes place in cyanobacteria. Cyanobacteria are closely related to
and hence probably evolved from purple bacterial ancestors. Green
bacteria is an outgroup. Since oxygenic bacteria are a lineage within a
cluster of anoxygenic lineages, scientists infer that PSI evolved first.
This also corroborates with geological evidence.
Green plants and algae also use PSI and PSII for photosynthesis. In
these organisms, photosynthesis occurs in organelles (membrane
bound structures within the cell) called chloroplasts. These organelles
originated as free living bacteria related to the cyanobacteria that were
engulfed by ur-eukaryotes and eventually entered into an
endosymbiotic relationship. This endosymbiotic theory of eukaryotic
organelles was championed by Lynn Margulis. Originally very
controversial, this theory is now virtually universally accepted. One
key line of evidence in support of this idea came when the DNA inside
chloroplasts was sequenced -- the gene sequences were more similar to
free-living cyanobacteria sequences than to sequences from the plants
the chloroplasts resided in.
The advent of photosystem II brought about a large change in the
atmosphere of earth -- the "oxygen holocaust". Oxygen is a very good
electron acceptor and can be very damaging to living organisms. Many
bacteria are anaerobic and die almost immediately in the presence of
oxygen. Other organisms, like animals, have special ways to avoid
cellular damage due to this element (and in fact require it to live.)
Initially, when oxygen began building up in the environment, it was
neutralized by materials already present. Iron, which existed in high
concentrations in the sea was oxidized and precipitated. Evidence of
this can be seen in banded iron formations from this time, layers of
iron deposited on the sea floor. As one geologist put it -- "the world
rusted". Eventually, it grew to high enough concentrations to be
dangerous to living things. In response, many species went extinct,
some continued (and still continue) to thrive in anaerobic
microenvironments and several lineages independently evolved
One lineage to evolve oxygen respiration was the purple bacteria.
Purple bacteria also enabled the eukaryotic lineage to become aerobic.
Eukaryotic cells have membrane bound organelles called mitochondria
that take care of respiration for the cell. These are also endosymbionts
just like chloroplasts. Mitochondria formed this symbiotic relationship
very early in eukaryotic history, all but a few groups of eukaryotic cells
have mitochondria. Later, a few lineages picked up chloroplasts. Red
algae picked up ur-chloroplasts from the cyanobacterial lineage. Green
algae, the group plants evolved from, picked up different ur-
chloroplasts from a prochlorophyte, a lineage closely related to
Prior to the Cambrian (~600 MYA), animals start appearing; the first
animals dating from just before the Cambrian were found in rocks near
Adelaide, Australia. They are called the Ediacarian fauna and have
subsequently been found in other locales as well. It is unclear if these
forms have any surviving descendents. Some look a bit like Cnidarians
(jellyfish, sea anemones and the like); others resemble annelids
All the phyla (the second highest taxonomic category) of animals
appeared around the Cambrian. The Cambrian 'explosion' may have
been a result of higher oxygen concentrations enabling larger
organisms with higher metabolisms to evolve. Or it might be due to
the spreading of shallow seas at that time providing a variety of new
niches. In any case, the radiation produced a wide variety of animals.
Some paleontologists think more animal phyla were present then than
now. The animals of the Burgess shale are an example of Cambrian
animal fossils. These fossils, from Canada, show a bizarre array of
creatures, some which appear to have unique body plans unlike those
seen in any living animals.
Although creationists are fond of pointing to the Cambrian explosion
as evidence of their views -- they ignore four things 1.) Evidence of life
(including animals) prior to the Cambrian 2.) Although quick, the
Cambrian explosion is not instantaneous in geologic time 3.) Although
all the phyla of animals came into being, these were _not_ the
modern, derived forms we see today. Our own phylum (which we
share with other mammals, reptiles, birds, amphibians and fish) was
represented by a small, sliver-like thing called _Pikaia_. 4.) Plants were
not yet present. The Cambrian explosion is not evidence of a single
creation event producing the current biota.
Following the Cambrian, the number of marine families leveled off at
a little less than 200. The Ordovician explosion (~500MYA) followed.
This 'explosion', larger than the Cambrian, introduced numerous
families of the Paleozoic fauna (including crinoids, articulate
brachiopods, cephalopods and corals). The Cambrian fauna, (trilobites,
inarticulate brachiopods, etc.) declined slowly during this time. By the
end of the Ordovician, the Cambrian fauna had mostly given way to
the Paleozoic fauna and the number of marine families was just over
400. It stayed at this level until the end of the Permian period.
Somewhere in between these two points, plants and fungi (in
symbiosis) invaded the land (~400 MYA). The first plants were moss-
like and required moist environments to survive. Later, evolutionary
developments such as a waxy cuticle and a vascular system allowed
some plants (for example ferns) to exploit more inland environments.
The first vascular land plant known is _Cooksonia_, a spiky,
branching, leafless structure. At the same time, or shortly thereafter,
arthropods (myriapods -- centipedes and millipedes) followed plants
onto the land.
By the Devonian period (~380 MYA) vertebrates had moved onto the
land, _Ichthyostega_ is the among the first known land vertebrates, an
amphibian. It was found in Greenland and was derived from lobe-
finned fishes called Rhipidistians. Amphibians gave rise to reptiles,
animals with scales to decrease water loss and a shelled egg permitting
young to be hatched on land. Among the earliest well preserved
reptiles is _Hylonomus_, from rocks is Nova Scotia.
The Permian extinction (~250MYA) was the largest extinction in
history. The last of the Cambrian Fauna went extinct. The Paleozoic
fauna took a nose dive from about 300 families to about 50. It is
estimated that 96% of all species in existence met their end. Some
estimate that as many as 50% of all families went extinct (you have to
kill of 100% of the species in a family before it goes extinct, hence the
difference between the two numbers.) Following this event, the
Modern fauna, which had been slowly expanding since the Ordovician,
took over. The Modern fauna (including fish, bivalves, gastropods and
crabs) was barely affected by the Permian extinction and increased to
over 600 marine families at present. (The Paleozoic fauna held steady at
about 100 families.) A second extinction event shortly following the
Permian kept animal diversity low for awhile.
The flora as well as the fauna changed following the Permian. During
the Carboniferous (the period just prior to the Permian) and in the
Permian the landscape was dominated by ferns and their relatives.
After the Permian extinction, gymnosperms (ex. pines) became much
more abundant. Gymnosperms had evolved seeds (which ferns lack)
which helped their ability to disperse. Gymnosperms also evolved
pollen, encased sperm which allowed for more outcrossing. In ferns,
sperm must swim from the male organs to the female organs
During the Jurassic (~200 MYA) and Cretaceous (~150MYA) periods the
dinosaurs ruled and flowering plants (angiosperms), together with
Dinosaurs evolved from reptiles. One modification may have been a
key splayed stance and walk with an undulating pattern because their
limbs are modified from fins and their gait is modified from the
movement a fish makes when swimming. These animals cannot
sustain continued locomotion because they cannot breathe while they
move; their undulating movement compresses their chest cavity.
Thus, they must stop every few steps and breath before continuing on
their way. Dinosaurs evolved an upright stance (similar to the upright
stance mammals independently evolved) and this allowed for
continual locomotion. In addition, dinosaurs evolved to be warm-
blooded. Warm-bloodedness allows an increase in the vigor of
movements in erect organisms. Splay stanced organisms would
probably not benefit from warm-bloodedness. Recently, a very
primitive dinosaur, _Eoraptor lunensis_ was found in Argentina.
Angiosperms evolved two key adaptations that allowed them to
displace gymnosperms as the dominant fauna -- fruits and flowers.
Fruits allow for animal based seed dispersal (and deposition with
plenty of fertilizer 8-). Flowers evolved to facilitate animal, especially
insect, based pollen dispersal. Angiosperms currently dominate the
flora of the world -- over three fourths of all living plants are
Insects, who radiated a great deal along with angiosperms, dominate
the fauna of the world. Over half of _all_ named species are insects.
One third of this number are beetles.
The end of the Cretaceous (~65 MYA) is marked by a minor mass
extinction that was the demise of all the lineages of dinosaurs save the
birds. Once the dinosaurs were out of the picture, mammals --
previously confined to nocturnal, insectivorous niches -- diversified.
_Morgonucudon_ , a contemporary of dinosaurs, is an example of one
of the first mammals.
The study of the history of life on this planet reveals a planet in flux.
The abundance of various lineages varies wildly across geologic time.
New lineages can evolve and radiate out across the face of the planet,
pushing older lineages to extinction, or relictual existences in protected
refugia and/or suitable microhabitats. Organisms modify their
environments, sometimes disastrously as in the case of the "oxygen
holocaust" -- their modification of the environment can be the impetus
for further evolutionary change.
Overall, diversity has increased since the beginning of life. This
increase is, however, interrupted numerous times by mass extinctions.
Diversity appears to have hit an all-time high just prior to the
appearance of humans. As the human population has increased,
biological diversity has decreased at an ever-increasing pace. The
correlation is probably causal.
SCIENTIFIC STANDING OF EVOLUTION AND IT'S CRITICS
The topics of evolution and common descent were once highly
controversial in scientific circles; this is no longer the case. Although
debates rage about how various aspects of evolution work and details
of patterns of relationships are not fully worked out, evolution and
common descent are considered fact by the scientific community.
So-called "scientific" creationists do not base their objections on
scientific reasoning or data. Nor do they have a testable, scientific
theory to replace evolution with. "Scientific creationism" is a poorly
disguised attempt to attack evolution because it contradicts the
religious beliefs of some fundamentalists.
ARE WE STILL EVOLVING?
Yes, evolution is still occurring; all organisms continue to adapt to
their surroundings and "invent" new ways of better competing with
members of their own species. In addition, allele frequencies are being
changed by drift, mutation and gene flow constantly. Studying the
process of evolution as it continues to occur is a major field of biology
today. Although evolution has been observed and all the mechanisms
have been shown to work, there is still no consensus on the relative
contribution of each of the mechanisms to the overall pattern of
evolution within a lineage. Likewise, although new species have been
seen to arise; biologists have many questions about what influences the
pattern of macroevolution. Are some groups "good" at speciating?
Who survives mass extinctions and why?
Evolution is the unifying theory of biology. The functions of biological
entities at all levels (ecosystems, populations, organisms, genes) are the
product of a non-random factor (e.g. natural selection) operating in
conjunction with random factors (such as mutation and mass
extinction) within a framework of historical constraint. Ecosystems,
species, organisms and their component parts all have a long history. A
complete explanation of any legitimate trait in biology must therefore
have two components. First, a proximal explanation -- how does it
work? And second, an ultimate explanation -- what was it modified
For centuries humans have asked, "Why are we here?". A question
such as that probably lies outside the realm of science. However,
biologists can provide an elegant answer to the question, "How did we
SOME GOOD BOOKS ABOUT BIOLOGY AND EVOLUTION
A good introductory text in evolutionary biology is:
Evolutionary Biology, by Douglas Futuyma, 1986, Sinauer, Sunderland,
The text assumes some previous knowledge of biology, but reviews
most critical background material. It contains numerous references to
the primary literature. Most of the information in this file can be found
(along with the references to the primary literature) in this text.
A good introductory text into population genetics, the field that
mathematically describes changes in the gene pool is:
Principles of Population Genetics, by Hartl and Clark , 1989, Sinauer,
None of the math is very daunting (it's just an intro text after all)
but it's really critical (IMHO) to understanding what evolution is all
about. And again, lots of refs.
A text that deals with the interface of molecular biology and evolution
Fundamentals of Molecular Evolution, by Li and Graur, 1991, Sinauer,
A very concise introduction to this field.
A text that deals with theories of macroevolution is:
Macroevolutionary Dynamics, by Niles Eldredge, 1989, McGraw-Hill,
A text that documents the history of life on earth is:
History of Life, by Richard Cowen, 1990, Blackwell Scientific, Boston
A readable introduction to the history of our planet and especially the
changes that have occurred in the biota.
A popular introduction to the field that also debunks the most
common creationist arguments is:
The Blind Watchmaker, by Richard Dawkins, 1987, Norton, New York
Dawkins is (IMHO) a very engaging writer.
A close look at the creation/evolution debate can be found in:
Abusing Science, by Philip Kitcher, 1982, MIT, Cambridge, Mass
A meticulous critique of creationism.
A book about biodiversity is:
The Diversity of Life, by E. O. Wilson, 1992, Harvard Belknap,
This book deals with the current ecological crisis facing our planet and
puts forward the strong case for preserving biological diversity. In
addition, a brief explanation of evolutionary biology is presented.
Numerous examples of the biology and natural histories of species and
ecosystems are presented. There is a lot of information packed into this
well written book.-- _very_ highly recommended.
E-Mail Fredric L. Rice / The Skeptic Tank