Charles Darwin and Natural Selection Slide 2 Now that we have explored many of

the processes involved in producing and sustaining living organisms, it’s time to think
about the big picture again. When we begin to look at populations, growth rates, genetic
variability within populations, and so on, we are going to be struck by some of the same
things that struck Charles Darwin before, during, and after his famous voyage aboard the
Beagle. During that voyage Darwin had the opportunity to observe how organisms might
be related to recent fossils of their predecessors. He also saw how organisms had changed
as they had moved into different environments. His ideas took shape during a time when
scientists were beginning to understand that the earth was old and that geologic processes
took time to produce the landforms that we see today. He began to think about changes in
species through time and made some important observations:
• Organisms do not reproduce exponentially even though they theoretically could.
• Individuals within a species are similar but not exactly identical.
• Those individuals with subtle differences that help them adapt to their environment
have the best chance of surviving and reproducing. Slide 3 Based on his observations,
Darwin came up with a theory that does a very good job of explaining how organisms are
related to each other, their environments, and the fossil record. He proposed natural
selection as the major agent of evolution. Natural selection acts to ensure that traits that
give an organism an advantage in a particular environment are conserved while traits that
put an organism at a disadvantage are removed from a population. Descent with
modification, or the passing of advantageous traits to successive generations, follows
logically from natural selection, allowing species to change over time, depending on
environmental conditions and the genetic variability inherent in a species. In our
discussion of evolutionary processes, remember that biological evolution is defined as the
change in the genetic composition of a population over time. While natural selection is
not the only process that can change the genetic composition of a population, it is an
important one to consider. Slide 4 When he proposed the theory of natural selection,
Darwin had no actual examples of the process to put forward. However, examples of
natural selection in action abound, particularly in the areas of pesticide and antibiotic
resistance. Antibiotics are used to kill bacteria and are very useful in stopping bacterial
infections in humans and animals. When an antibiotic is given to a person with a bacterial
infection, it usually kills all the bacteria, and the person gets better. If a few bacteria in
the infecting population carry a gene that makes them resistant to the antibiotic that is
being used, however, some of the bacteria survive the antibiotic treatment and are free to
begin multiplying in the host again. Because bacteria reproduce by simple binary fission,
the genes for antibiotic resistance are passed on to all of the offspring, and a resistant
population is produced. Further treatment with the same antibiotic is ineffective because
virtually all of the bacteria in the population are resistant. In these cases the gene for
antibiotic resistance is selected for by the environmental conditions (the presence of the
antibiotic) in which the bacteria find themselves. Slide 5 The theory of natural selection
states that certain individuals in a population will have traits that increase the likelihood
that they will survive and reproduce in the current environment. Natural selection helps
ensure that the alleles for those advantageous traits are passed on to the next generation.
Environments, as we are becoming painfully aware, have a way of changing, and
environmental changes can put selective pressure on populations. The result is that traits
that once gave an individual an advantage become deleterious or neutral. We will look at
three types of natural selection:
• Stabilizing selection
• Directional selection
• Disruptive selection
Slide 6 Many phenotypic characteristics, such as human height or hair color, span a range
and will show some sort of normal distribution. Stabilizing selection reinforces the
“average” phenotype, selecting against the less common phenotypes at the extremes of
the graph shown here. Let’s look at frog leg length as an example. Since frogs are
amphibians, they have to be able to move efficiently both on land and in water. There are
all sorts of frogs adapted to all sorts of habitats, but let’s consider bullfrogs living in and
around a pond. They need legs that work well for swimming and for jumping. What they
have are long, muscular legs with webbed feet – a good compromise for the environment
they live in. You could imagine that some bullfrogs would have more flipper-like legs
that would be great for swimming but not so great for jumping. Other bullfrogs might
have big burly jumping legs without webbed feet – good for jumping but not very
effective for swimming. Individuals with these traits out on either edge of the distribution
would be less likely to survive and reproduce, so the range of phenotypes becomes
narrower. As long as bullfrogs, such as the one shown here, continue to live around
ponds, it is likely that the optimum leg length will not change much. Slide 7 Let’s keep
thinking about the frogs. When it’s time to eat, the frog sits quietly, waits for a tasty bug
to come by, sends out its long, sticky tongue, and snags the bug. The longer the frog’s
tongue is, the more bugs it can snag. Because frogs with longer tongues will have a better
chance of surviving and reproducing (because they can capture more resources), longer
tongue length will be selected for. In time the average tongue length will be shifted
towards longer tongue length. This type of selection is known as directional selection.
Directional selection usually cannot continue indefinitely because some physical factors
may limit how far a particular trait can go. In the case of frog tongue length the size of
the frog’s mouth will ultimately limit how long its tongue can get. If the tongue gets too
long, it won’t fit in the frog’s mouth anymore, or it may interfere with actually
swallowing the bug it has helped to catch. Slide 8 Disruptive selection, where phenotypes
at the extremes of the normal distribution are favored, appears to be somewhat rare. Beak
shape in birds is the example most often cited for disruptive selection. Because of the
major types of food sources available in an environment, having a specialized beak shape
may be more advantageous than having an “average” beak shape. In the case of the
black-bellied seed cracker, large beaks are good for cracking hard seeds from one food
source, small beaks are useful for feeding on the small, soft seeds of the other major food
source, and intermediate beaks aren’t very good for eating either type of seed. Birds with
the intermediate beak size never quite get enough to eat and don’t survive or reproduce
well. Slide 9 Natural selection is a dynamic process that occurs in a dynamic world.
Although humans don’t like to admit it, the earth is constantly changing. The climate of
the earth has fluctuated widely over time from extensive ice ages to periods of wide-
spread subtropical conditions and everything in between. The positions of the land
masses have changed, bringing formerly separated species into competition with each
other or separating different populations of the same species. Pollution, like the filling of
the atmosphere with oxygen as photosynthetic organisms began to flourish, and
catastrophic events, such as asteroid impacts and wide-spread volcanism, have all
presented organisms with environmental changes to which they must adapt … or else.
Natural selection constantly acts as an agent of evolution, selecting for the most
successful individuals and allowing those species that have sufficient genetic variation to
adapt to changing environments.

The Evolution of Populations I

Slide 2 When we discuss evolution, we often equate evolution and natural selection.
However, natural selection is only an agent of evolution, it is not evolution itself. We
define evolution as a change in the genetic constitution of a population. Most simply,
then, evolution may occur in two ways: 1) by changing the frequency of the existing
alleles of a gene or genes in a population, or 2) by changing the alleles themselves, for
example by mutation or by introducing new alleles into a population. There are many
ways by which populations may evolve, or by which the genetic makeup of populations
may change. These mechanisms of evolutionary change, including natural selection, will
be discussed in the following lesson. In this lesson, however, we will consider the
characteristics of a hypothetical population that is not evolving. Such populations are said
to be in Hardy-Weinberg equilibrium.
Slide 3 Consider a large, isolated population of a diploid species. A particular gene,
called gene A, is present in all members of this population. Further, gene A has two
alleles – big A and little a – so that there are homozygous individuals (AA and aa) and
heterozygous individuals (Aa or aA) within the population. Now, imagine if all of the
individuals in the population mated randomly with other individuals in the population to
produce many offspring. Essentially, this would be akin to putting all of the alleles of
gene A from all of the individuals in the population into a hat, and pulling out two at a
time to represent new, diploid offspring. If enough offspring were produced, eventually
the same frequency of alleles present in the parental population would be present in the
offspring population.
Slide 4 We can show this to be true by calculating the allele frequencies from generation
to generation. For example, the frequency of each allele, big A or little a, may be
calculated as the total number of that type of allele, divided by the total number of both
alleles. Say our population has 40 AA individuals, 40 Aa individuals, and 20 aa
individuals. In total, we have 100 individuals, but 200 alleles, since each individual has
two alleles. The frequency of the big A allele would simply be 40 x 2 (since 40
homozygous individuals have two copies of big A) plus 40 (since the 40 heterozygous
individuals carry only one copy of big A), divided by 200 total alleles. This gives an
allele frequency of 0.6, or 60%, for big A. The same calculation can be performed for
little a, in this case to give a frequency of 0.4, or 40%. At this point, you may notice that
the frequencies of the two alleles, A and a, add to equal one. When the frequencies of the
different alleles of a gene in a population are added, they will always add to equal one.
Take a moment and think about why this is true…
When our hypothetical population reproduces at random, i.e., when the gametes carrying
one or the other allele are ‘drawn out of the hat,’ there is a 60% chance for big A to be
drawn, and a 40% chance for little a to be drawn. As more and more offspring are
produced, then, the new allele frequencies will tend toward the frequencies of the original
population.
Slide 5 While it is not difficult to see how the allele frequencies remain the same, it is
also true that the genotype frequencies will remain the same from generation to
generation. This occurs because the genotype frequencies in large, randomly mating
populations are determined by the frequencies of alleles. If the allele frequencies do not
change, genotype frequencies also will not change. For example, the odds in our
population of producing a homozygous dominant offspring are equal to the odds of
receiving two big A alleles. There is a 60% chance that any offspring will receive one big
A allele, and a 60% chance that they will receive a second big A allele. The odds of
receiving both big A alleles are then 60% times 60%, or 36%. Alternatively, the odds of
producing a homozygous recessive offspring are obtained by multiplying the frequencies
of little a and little a, in this case to give 0.16, or 16%. Genotype frequencies for entire
populations are calculated using a special equation, called the Hardy-Weinberg equation.
This equation is written as p2 + 2pq + q2 = 1, where p2 and q2 are the frequency of
homozygous genotypes, and 2pq is the frequency of heterozygotes. As you might guess,
p and q represent the allele frequencies of any gene with two alleles, like gene A that we
have been considering. For example, if p equals the frequency of the big A allele, the
frequency of the AA genotype is p times p, or p2. The same holds true when q equals the
frequency of the little a allele. To determine the frequency of heterozygotes, we multiply
the allele frequencies of the big A allele by the frequencies of the little a allele, and then
multiply that by two, since heterozygous individuals could be either Aa or aA.
As we have seen previously, the allele frequencies in our hypothetical population are not
changing from generation to generation. It follows, then, by the Hardy-Weinberg
equation, that the genotype frequencies also will not change, because the same allele
frequencies will be plugged into the equation, generation after generation. Since allele
and genotype frequencies are not changing from generation to generation, our population
is not evolving. Populations in these cases are said to be in Hardy-Weinberg equilibrium.
Slide 6 So, how do we use the Hardy-Weinberg equation for real populations? Scientists
use Hardy-Weinberg equilibrium as a baseline, or a null hypothesis, against which to
measure the genetic change of real populations. As a null hypothesis, Hardy-Weinberg
equilibrium is usually considered to rest on five assumptions:
1) population size is large
2) mating is random
3) there is no migration into or out of the population
4) there is no mutation
5) there are no selective forces on the alleles under consideration

If the frequencies of the alleles of a gene are changing, it is clear that one or more of the
above assumptions is incorrect.
Slide 7 As you might guess, many characters in populations are evolving. In fact, Hardy-
Weinberg equilibrium is more often the exception, rather than the rule, when
investigating the genetic structure of populations. What factors cause populations to
evolve, or drive populations away from Hardy-Weinberg equilibrium? Any factor that
causes the assumptions of Hardy-Weinberg equilibrium to be violated can be considered
an agent of evolutionary change. As we mentioned before, natural selection is one factor
that can cause populations to evolve. There are others, too, such as mutation, sexual
selection, gene flow and genetic drift that also play important roles in the evolution of
populations. We will discuss these mechanisms of evolutionary change in the following
lesson.

Evolution of Populations II
Slide 2 As discussed in the previous lesson, evolution is defined as a change in the
genetic structure of a population. Populations that are not evolving for a particular
character or characters are said to be in Hardy-Weinberg equilibrium. This equilibrium
rests on five basic assumptions, as listed on this slide. If any of these assumptions are
violated in a population, allele and genotype frequencies will change. When this happens,
the population is no longer in Hardy-Weinberg equilibrium, and is said to be evolving. In
this lesson, we will take a closer look at the agents of evolutionary change that cause
populations to evolve.
Slide 3 To start, remember that our hypothetical population was isolated. This means that
no individuals are leaving the population, and none are entering the population from the
outside. You could surmise that if one or several new individuals entered the population
and contributed their alleles to the genetic makeup of the population by breeding, the
allele frequencies might change, depending on the genetic makeup of the new
individuals. The magnitude of change would depend on the number of individuals
entering, their genotypes, and the size of the population. When individuals migrate
between populations to contribute their alleles to new populations, we call this gene flow.
Gene flow is one agent of evolutionary change.
Slide 4 We also stated that our population was large, and that all members mated to
produce offspring. Because of this, many individuals contributed their alleles to the
offspring generation, and the allele frequencies were maintained. What might happen if
the population was small, though, say a population with 10 members, or 5, or 3? In a
small population, the consequences of not mating, i.e., not contributing your alleles to the
next generation, may very well be that your alleles are lost permanently. Essentially,
there is a smaller chance that other members will carry and contribute the same alleles in
the same frequencies, simply because there are fewer individuals. The change in allele
frequencies due to chance events, such as missed mating opportunities, is called genetic
drift.
Genetic drift is a significant problem in the conservation of many endangered species. A
goal of most conservation plans is the maintenance of relatively high levels of genetic
diversity in threatened or endangered populations. The small size of endangered
populations, however, often makes this very challenging.
Slide 5 Similarly, consider how allele frequencies might change if our large population
was suddenly reduced in size by half, or by 90%. There is a good chance that the allele
frequencies in the resulting smaller population will differ to some degree from the
original, larger population. As a result, when the population re-establishes its original
size, allelic and genotypic frequencies will be changed. This type of occurrence is not
uncommon. For example, many populations go through such bottlenecks, when a
significant portion of the population is lost or separated due to a die-off or a substantial
environmental change. Similarly, a few individuals from a population may colonize a
new habitat, such as an island. Again, the genetic makeup of the resulting population in
the new habitat will likely differ from the original population. This phenomenon is a
specific type of genetic drift called the founder effect. It is believed that the
diversification of the picture-winged fruit fly on the Hawaiian islands is largely a result of
the founder effect. In this case, there were likely at least 45 founder events where some
members of a population on one island founded a new population on another island.
Slide 6 In our hypothetical population, mating between individuals was also random with
regard to gene A. Because of this, the chance of inheriting either of the alleles was based
solely on the frequencies of each allele. In most natural populations, however, mating is
non-random, in that potential mates are selected to some degree by their partners, and
vice versa. Take a second to look around the computer lab, for example. Would you mate
with just anyone of the opposite sex, or would you be more inclined to specifically
choose a mate based on various characters? Similar mate selection processes occur in
many types of organisms. Non-random mating, also known as sexual selection, can
greatly affect allele frequencies in populations over time.
Slide 7 We also assumed that in our population there was no benefit for individuals to
have a particular genotype. If, for example, there was an advantage to carrying and
expressing one of the alleles of gene A, we could expect that allele to increase in
frequency over time, because individuals carrying that allele would be more likely to
survive and reproduce. This is natural selection, an agent of evolution that we have
considered in more detail in a previous lesson.
Slide 8 Finally, we did not consider what would happen if new, unique alleles were
introduced into the population, such as a third allele of gene A. This theoretically could
happen by immigration of new individuals carrying the new allele into the population, or
by mutation of the alleles that already exist in the population. Both of these processes can
play significant roles in affecting the genetic structure of populations. Mutations, in fact,
are the ultimate source of genetic variation, and help provide novel genetic material on
which natural selection may act. Although mutation rates are generally extremely low,
over many generations they play a significant role in the evolution of populations.
Slide 9 Although we have now covered a number of mechanisms of evolution
individually, it is important to realize that in natural populations these mechanisms do not
generally act alone. Rather, evolution, or the genetic change of populations, is often the
sum of several or even all of these processes working together. In some cases, certain
processes may play more important roles than others, but generally over time more than
one of these processes contribute to the evolution of populations.
Take for instance the finches of the Galapagos Islands. It is probable that the various
species of finch on the island arose from a single ancestor species that colonized the
islands from the South American mainland. The founding population likely differed to
some degree genetically from the mainland population, resulting in a founder effect. Over
time, the finches were exposed to different selective pressures resulting from the different
habitats on the islands, and so natural selection must have played a role in the
diversification and speciation process. You could probably also imagine that as the
finches diversified, different phenotypes could have resulted in different mating
behaviors. As a result, sexual selection likely played a role in the diversification process.
In addition, there is always the possibility that favorable mutations could have occurred
in the DNA of certain individuals on the island, resulting in their increased fitness and
contribution to the gene pool of their populations.
 Events Leading to Speciation
Slide 2 As we have seen, populations of organisms tend to change genetically over time
due to various agents of evolution, such as natural selection, genetic drift, or non-random
mating. In the previous lesson, we focused mainly on the genetic change within
individual populations. What would happen, however, if two populations of a particular
species of organism were isolated from one another in some way. Over time, the genetic
makeup of each population would change independently of the other population, due to
the various agents of evolutionary change. If enough change occurred in the members of
each population, it is possible that the two populations would not be able to interbreed if
brought back together. The process just described, that of genetic isolation and the
resulting genetic incompatibility of populations, is called speciation.
There are numerous ways by which speciation can occur. A common theme to all of them
is the cessation of gene flow, or reproductive isolation, between populations, and the
resulting independent genetic change of each population over time. In addition, you
should note in this lesson that reproductive isolation, and the resulting speciation events,
are often a result of some significant change in the environment.
Slide 3 Changes in the environment leading to speciation may be very marked, or may be
quite subtle. For example, consider a population of plants that occupies facing mountain
ranges and the intervening valley. At some point in time, this continuous population
could be divided into two separate, isolated populations by some physical barrier, such as
a change in water levels that results in the flooding of the valley. Since the two new
populations are now separated from each other, changes may occur independently within
each population, due to differing selective pressures, genetic drift, or other agents of
evolution. If water levels remained high for long enough, perhaps several hundreds or
thousands of years, enough differences might accumulate between the two isolated
populations that they might not be able to interbreed if and when water levels recede and
each population re-colonizes the valley. If this were the case, the two populations might
then be considered different species.
The rising and falling water levels in our hypothetical valley are only one example of a
geographic barrier. It should not be difficult to imagine other possible geographic barriers
that could effectively block gene flow between populations. Examples could be the rising
of a mountain range, or the formation of a canyon, or even, on a smaller level, the
construction of a highway. Speciation resulting from such geographic barriers is called
allopatric speciation.
In our previous lessons on the evolution of populations, we discussed the evolution of
both fruit flies on the Hawaiian Islands and finches on the Galapagos Islands. Both of
these groups of organisms represent good examples of allopatric speciation. In both
cases, the geographical barrier separating populations of these organisms is water. This is
true whether one is considering populations on different islands or comparing island
populations to mainland populations. The isolation of the island populations, coupled
with time, genetic drift, and selective pressures, has ultimately resulted in the complete
reproductive isolation of different populations, and the development of new species.
Slide 4 In many cases, the environmental changes that separate two populations may be
less obvious than in the previous example. For instance, consider environments where a
sharp temperature gradient exists, such as the thermocline of an underwater spring in a
warm lake. Alternatively, imagine a soil substrate that varies from shallow and rocky to
deep and loamy due to the underlying bedrock. In such cases, the environments of
organisms may vary over short distances, to the point that very different environmental
conditions exist directly adjacent to one another. If individuals in a population of one
species were spread out over such an area, they would be subject to very different
environmental conditions, depending on the habitat in which they are found. The
differing conditions may lead to different selective pressures, which in turn could result
in genetic divergence between the individuals in each habitat. If enough divergence
occurs, speciation may be the result. Speciation that occurs due to differences in directly
adjacent environments is termed parapatric speciation.
A possible instance of parapatric speciation is currently occurring in a European grass,
Anthoxanthum odoratum. Some populations of this species live in soil contaminated with
the heavy metals from nearby mining activity. Directly adjacent to this contaminated soil,
however, can be uncontaminated soil that also supports populations of A. odoratum.
Populations of A. odoratum living in contaminated soil have been selected for a genotype
that allows them to be tolerant of heavy metals. In addition, the flowering period of
populations in contaminated soil has changed since mining activity began so that these
plants now flower at a different time than populations of A. odoratum living in non-
contaminated soils. Researchers have discovered that the different populations of this
grass are still able to cross-fertilize to produce viable offspring, but only by manually
cross-pollinating since they flower at different times of the year. It is likely that the
change in flowering period, and different selective pressures in the adjacent soil types,
are both leading to divergence of what was once one continuous population into two
distinct populations and, perhaps, two distinct species.
Slide 5 While speciation often occurs as a result of differences or changes in the
environment, there are instances where speciation is essentially independent of
environmental conditions. In such cases, speciation may occur within the same
environment, and so is called sympatric speciation. Often, sympatric speciation involves
a change in the ploidy level of certain members of a population, so that some members
carry extra chromosomes or entire extra sets of chromosomes. Individuals with extra sets
of chromosomes are known as polyploids. Polyploid individuals in many cases are not
able to mate with individuals carrying the original genotype.
Polyploidy can arise in different ways. In some instances, errors in DNA replication or
cell division result in cells with twice the amount of DNA than they would normally
have. An example of this would be a diploid organism producing diploid, rather than
haploid, gametes. Alternatively, errors in DNA replication could result in a chromosome-
doubling event, where the entire genome of a cell is doubled. Imagine if a chromosome
doubling event occurred in a diploid zygote. A tetraploid zygote would result. The
subsequent mitotic cell divisions that occur would lead to a multicellular, tetraploid
individual.
Polyploidy may also occur when closely related species interbreed, resulting in hybrid
offspring that carry a set of chromosomes from each of the parent species. Because these
chromosomes are from different species, they are not homologous chromosomes, and so
cells of the hybrid offspring cannot undergo meiosis. The result? Hybrid offspring are
often infertile, at least initially, and cannot mate with each other or with either of the
parent species. Once again, there is a barrier to gene flow. Several species of
Tragopogon, a sunflower relative introduced to eastern Washington and northern Idaho,
appear to have evolved due to hybridization.
Sympatric speciation seems to be most important in organisms that are able to reproduce
asexually, such as plants, although the polyploid condition is fairly common in some
other types of organisms, most notably amphibians. Asexual reproduction in plants and
parthenogenetic animals allows the polyploid condition, such as that resulting from
hybrid offspring, to persist for many generations. This in turn increases the chance that at
some point a duplication of chromosomes will occur, allowing the polyploid cells to once
again go through meiosis and produce gametes.
Slide 6 Sympatric speciation does not always involve changes in the ploidy level of
members of a population. In some cases, relatively small changes in morphology or
behavior can also apparently lead to sympatric speciation, or speciation within the same
geographic area. In one well-studied case, a species of fruit fly of the genus Rhagoletus,
historically reproduced by depositing eggs in the fruits of hawthorn trees. However, in
the early 1800s, many domesticated apples were introduced into the native ranges of
Rhagoletus. In some areas, populations of Rhagoletus diverged to include individuals
who deposited eggs on hawthorn fruits, and individuals who deposited eggs on
domesticated apples. Over the last two centuries, these populations have diverged
sufficiently so that in a given area containing both types of flies, only about 6% of
matings involve crosses between the different types of flies. In addition, other
differences, including the metabolic rate of pupa, breeding time, and response to the
different smells of apples and hawthorns, appear to have evolved along with egg-laying
habits.
Slide 7 As you can probably guess, the genetic isolation that develops between separated
populations varies in its degree, depending on a number of factors. In turn, the degree of
divergence between isolated populations determines the likelihood of successful
interbreeding if and when the populations are brought back together. What are the factors
that influence the divergence between populations? First, because genetic differences
between populations accumulate over time, it would seem reasonable to conclude that the
longer two populations of one species are separated, the more likely it is that they will
accumulate enough differences to prevent successful interbreeding if they are brought
back together.
But what if two populations were isolated from each other over time, yet their
environments remained essentially identical? It is probable that the populations would
diverge more slowly than if they were subject to very different environments, hence very
different selective pressures. In addition to time, then, the environments that different
populations inhabit also play an important role in determining speciation rates.
You might also consider how speciation rates can be affected by other factors, such as the
size or range size of a population, or mating behavior, or generation times. For example,
species that reproduce very quickly may be able to adapt to changing environments at a
more rapid rate than species that reproduce more slowly (compare bacteria to elephants).
A population with a large range, or one that is very mobile, may be subject to very
different environmental conditions over its range, as opposed to a population that inhabits
only a very small area.
In essence, the more that isolated populations evolve independently, regardless of
whether their evolution is due to genetic drift, natural selection, or other influences, the
less likely they will be able to interbreed when brought back together.
Slide 8 In the end, it may be helpful to view divergence between populations as a ‘sliding
scale’. The amount and types of differences, such as genetic differences, that accumulate
between isolated populations determine the eventual genetic isolation between the
members of each population. If the differences are substantial enough, so that gene flow
is blocked between members of the two populations, the populations may continue to
diverge over time as two separate species. On the other hand, populations that have not
accumulated substantial differences are more likely to be able to interbreed when brought
together.
In the cases where populations are brought back together before substantial differences
have accumulated, reproductive isolation is often incomplete. Because of this, hybrid
zones, consisting of fertile hybrid individuals that may mate with members of either
population or with each other, may be present where the ranges of the two populations
overlap.
Intrinsic Mating Barriers
Slide 2 So far we have been looking at the general aspects of the genetic divergence of
populations. But what exactly do we mean when we say that enough ‘differences’
accumulate to hinder interbreeding among different populations? Or, in other words,
what types of barriers may develop within different populations to prevent successful
interbreeding? In a general sense, there are two types of such intrinsic barriers -
barriers that prevent interbreeding, called prezygotic barriers, and barriers that
diminish the fitness of offspring produced from interbreeding, called postzygotic
barriers. In either case, mating barriers act to restrict gene flow in some way between
members of different populations. As a result, the degree of divergence between
populations may increase.
Slide 3 There are several general types of prezygotic mating barriers, ranging from
those that preclude any mating events, to instances where different species may
interbreed but not produce any offspring. Any differences that arise between separated
populations that prevent formation of a zygote when individuals of each population
come into contact are defined as prezygotic mating barriers. For example, members of
separated populations may develop behavioral differences that preclude interbreeding
if and when the separated populations are brought back together. Behavioral
differences could include differences in habitat preferences, so that individuals from
different populations remain spatially separated, or differences in mating habits, such
as mating displays or the timing of mating. Alternatively, if enough physical differences
accumulate between the separated populations, interbreeding may be mechanically
impossible due to differences in the sizes or shapes of reproductive organs or other
structures. Lastly, in some instances mating may still occur, but the gametes from
individuals of different populations may not be compatible. For instance, egg cells may
not carry the appropriate receptor molecules to bind the sperm cells of members of the
opposing population.
Slide 4 As opposed to prezygotic mechanisms, postzygotic mating barriers involve the
mating of different species and the subsequent formation of a zygote. However, there is
still some level of incompatibility that ultimately results in a barrier to gene flow.
Difficulties may occur immediately or soon after zygote formation, resulting in the
hybrid zygote or embryo dying during early development. Alternatively, hybrid
offspring may survive, but with a reduced fitness compared to non-hybrid offspring. In
diploid organisms that carry sex chromosomes, hybrid individuals heterozygous for the
sex chromosomes (such as XY males) may have reduced fitness, or may not ever
develop, as deleterious recessive alleles inherited on one or the other chromosome are
not masked by a second copy of the chromosome. One oft-cited example of a postzygotic
mating barrier occurs when horses and donkeys, two different species, interbreed to
produce mules. Mules, as a hybrid offspring, are generally robust organisms. However,
the genetic incompatibility of the horse and the donkey result in sterility in the mule.
Because mules are infertile, gene flow between the horse and donkey is effectively
blocked, even though they are able to producde hybrid offspring.

Metronome of Genetic Variation

Slide 2 When we use the term ‘genetic variation’, what exactly are we talking about? Genetic
variation refers to differences in the sequences of nucleotides that make up the DNA of
different organisms. Genetic variation occurs between different species, and between
different populations and individuals of the same species.
Slide 3 Ultimately, genetic variation comes from mutations. Remember that mutations
technically are heritable changes in the DNA of organisms. As we learned earlier in the
semester, while mutations occur randomly in DNA, not all mutations are ‘equal’. Some
mutations have no effect at all on the proteins that an organism produces. This may be either
because the mutation occurs in a non-coding region of the DNA, or because a codon is
changed but still codes for the same amino acid. On the other hand, some mutations can have
significant effects on the protein produced, and even on the organism that is producing it.
Remember, as an example, the single mutation in the β-hemoglobin gene that can result in
sickle cell anemia.
Because different mutations have different effects on organisms, it should not be too
surprising that they have different evolutionary fates. In general, mutations with negative, or
deleterious effects, are removed from populations by natural selection. Beneficial mutations
are often fixed into the gene pool of populations. Neutral mutations, mutations with little or
no affect, tend to accumulate very slowly over time.
Slide 4 While different types of mutations are fixed or lost from populations at different
rates, mutation rates themselves are stable over time. That is to say that mutations occur with
great regularity, much like the ticking of a metronome. We refer to this regular occurrence of
mutations over evolutionary time as the ‘metronome of genetic variation’. Think about it,
mutations are occurring in the cells of our bodies, and in the cells of all other types of
organisms, at a relatively regular rate – tick…tick…tick…tick…At some point, a mutation
will occur that has extremely negative effects on an organism. As a result, the organism
might die before it reproduces, and the mutation is immediately removed from the
population. Tick…tick…tick…tick… Alternatively, as the metronome ticks away a mutation
might occur that confers some type of advantage. As a result, an organism might reproduce
effectively, and pass on the new allele to further generations. Mutations occur regularly, but
how they are treated in an evolutionary sense depends on the magnitude and direction of
change they represent for the fitness of the organism.
Slide 5 In an evolutionary sense, one of the most significant types of mutations is called gene
duplication. Gene duplication technically can occur at many different levels, from the
duplication of part of a gene to the duplication of an entire gene to the duplication of the
entire genome. In fact, duplication of the entire genome has been an important process in
speciation, particularly among plants and some amphibians. Some types of such ‘polyploidy’
can give rise to reproductively viable individuals, because all of the chromosomes are
duplicated. It should be noted, however, that in the majority of
cases large changes to an organisms genome have catastrophic effects, leading to severe
defects or death.
Individuals that carry duplicate copies of single or several genes, however, often do survive.
The extra copies of a gene generally continue to function like the original gene, ensuring that
there will always be plenty of that gene product. You might also imagine, though, that
accumulating extra copies of a gene also frees the copies to some degree from selective
pressures, as long as at least one copy remains functional. As a result, copies may accumulate
mutations fairly freely. In some cases, so many mutations may accumulate that the copies
become non-functional pseudogenes. Alternatively, a copy may accumulate mutations to the
point that it acquires a new function.
Slide 6 One of the strongest lines of support for the importance of gene duplication in
evolution is the presence of gene families. Gene families are thought to have come about by
gene duplication followed by mutation. This illustration shows the hypothesized evolution of
one such gene family, the globin family. The globin family contains several genes that code
for different types of myoglobin and hemoglobin molecules in vertebrates. Myoglobin, the
oldest of member of the globin family, stores oxygen in muscles. Hemoglobin, of course,
carries oxygen in the bloodstream. The different polypeptides that make up hemoglobin and
myoglobin appear to have evolved by gene duplication from a single, original myoglobin-like
gene. Presently in humans, there are several types of hemoglobin and myoglobin molecules
produced that are essential to our development and survival because they are produced
specifically in different tissues and at different stages of development. This demonstrates the
importance of gene duplication in evolution.
Slide 7 Gene duplication has likely also played a significant role in the expansion of genome
size over evolutionary time. In other words, genome size differs between organisms to some
degree because of gene duplication. The graph on the left shows a comparison of the number
of coding genes in a variety of organisms. As we might expect, it takes more genes to keep a
relatively complicated organisms like a pufferfish going than it does to keep a relatively
simple organism, such as yeast, on top of its game. Although there are many exceptions to
this rule, in a broad sense we find this type of pattern to hold true - the more complex the
organism, from single-celled to multi-cellular, from prokaryote to eukaryote, the more genes
it uses to direct its development, respond to signals, reproduce, and so on.
The graph on the right shows that total genome size for many organisms is out of proportion
to the number of genes that are actually expressed. While a higher vertebrate like a mouse or
a human has about 20 times as many genes as a bacterium, its total genome size, measured in
base pairs, may be tens of thousands of times larger than a bacterium’s. Clearly there must be
an enormous amount of non-coding DNA in the genomes of some organisms. Researchers
are just beginning to understand the purpose of some of the non-coding DNA. It is likely,
however, that at least some of this non-coding DNA arose from duplication processes.
Slide 8 We have now looked at genetic variation on several levels, from differences in single
nucleotides to differences in entire genomes. All of this genetic variation ultimately came
from mutations. Mutations do not work alone, though, to generate all of the genetic variation
that we see. In fact, the variation that results from mutations is maintained and even
amplified in species in a number of ways. Sexual reproduction is one of these ways. As we
have discussed previously, the gametes found in sexually reproducing organisms are
produced by meiosis. During meiosis, crossing over between homologous chromosomes, and
the independent assortment of chromosomes, occurs. This results in genetically variable
gametes. Then, after scrambling around the genetic material of an individual by meiosis, that
genetic material is combined with material from another individual. The end result of sexual
reproduction is that offspring differ from their parents and from each other, providing genetic
and phenotypic variation for natural selection to work with.
Slide 9 Sometimes the genetic variation in a species is spread out in various distinct
populations, or subpopulations. Plants, for example, are especially likely to respond to
different environmental conditions such as soil type, microclimate, and grazing. The traits
that are selected for in one location, then, may differ from the traits selected for in another, so
that individual populations are adapted to differing environments. The different selective
pressures in each environment therefore contribute to the maintenance of the genetic
variability of the species as a whole.
Slide 10 Finally, natural selection can in some cases preserve genetic variation by
maintaining different forms, or polymorphisms, of a species. This occurs when the fitness of
a certain form of a species is linked to the fitness of other forms of the same species. For
example, it is possible to find different coloration patterns within the same geographic region
in individual species of garter snakes. Some members of the species have prevalent spotting,
while others are striped. In turn, the different forms, or polymorphisms, are linked to different
behavior patterns. Striped garter snakes avoid predation by slithering away quickly from
predators. Spotted garter snakes, on the other hand, depend on remaining still and
camouflaged to avoid predators. In this species of garter snake, both coloration patterns are
maintained because they both are effective in helping the snakes avoid predators. In this
sense, both patterns contribute to the overall survival of the species. In other words, two
patterns work better than one. This type of selection, where different polymorphisms of a
species are maintained, is called frequency-dependent selection.

Metronome of Genetic Variation

Slide 2 When we use the term ‘genetic variation’, what exactly are we talking about? Genetic
variation refers to differences in the sequences of nucleotides that make up the DNA of
different organisms. Genetic variation occurs between different species, and between
different populations and individuals of the same species.
Slide 3 Ultimately, genetic variation comes from mutations. Remember that mutations
technically are heritable changes in the DNA of organisms. As we learned earlier in the
semester, while mutations occur randomly in DNA, not all mutations are ‘equal’. Some
mutations have no effect at all on the proteins that an organism produces. This may be either
because the mutation occurs in a non-coding region of the DNA, or because a codon is
changed but still codes for the same amino acid. On the other hand, some mutations can have
significant effects on the protein produced, and even on the organism that is producing it.
Remember, as an example, the single mutation in the β-hemoglobin gene that can result in
sickle cell anemia.
Because different mutations have different effects on organisms, it should not be too
surprising that they have different evolutionary fates. In general, mutations with negative, or
deleterious effects, are removed from populations by natural selection. Beneficial mutations
are often fixed into the gene pool of populations. Neutral mutations, mutations with little or
no affect, tend to accumulate very slowly over time.
Slide 4 While different types of mutations are fixed or lost from populations at different
rates, mutation rates themselves are stable over time. That is to say that mutations occur with
great regularity, much like the ticking of a metronome. We refer to this regular occurrence of
mutations over evolutionary time as the ‘metronome of genetic variation’. Think about it,
mutations are occurring in the cells of our bodies, and in the cells of all other types of
organisms, at a relatively regular rate – tick…tick…tick…tick…At some point, a mutation
will occur that has extremely negative effects on an organism. As a result, the organism
might die before it reproduces, and the mutation is immediately removed from the
population. Tick…tick…tick…tick… Alternatively, as the metronome ticks away a mutation
might occur that confers some type of advantage. As a result, an organism might reproduce
effectively, and pass on the new allele to further generations. Mutations occur regularly, but
how they are treated in an evolutionary sense depends on the magnitude and direction of
change they represent for the fitness of the organism.
Slide 5 In an evolutionary sense, one of the most significant types of mutations is called gene
duplication. Gene duplication technically can occur at many different levels, from the
duplication of part of a gene to the duplication of an entire gene to the duplication of the
entire genome. In fact, duplication of the entire genome has been an important process in
speciation, particularly among plants and some amphibians. Some types of such ‘polyploidy’
can give rise to reproductively viable individuals, because all of the chromosomes are
duplicated. It should be noted, however, that in the majority of
cases large changes to an organisms genome have catastrophic effects, leading to severe
defects or death.
Individuals that carry duplicate copies of single or several genes, however, often do survive.
The extra copies of a gene generally continue to function like the original gene, ensuring that
there will always be plenty of that gene product. You might also imagine, though, that
accumulating extra copies of a gene also frees the copies to some degree from selective
pressures, as long as at least one copy remains functional. As a result, copies may accumulate
mutations fairly freely. In some cases, so many mutations may accumulate that the copies
become non-functional pseudogenes. Alternatively, a copy may accumulate mutations to the
point that it acquires a new function.
Slide 6 One of the strongest lines of support for the importance of gene duplication in
evolution is the presence of gene families. Gene families are thought to have come about by
gene duplication followed by mutation. This illustration shows the hypothesized evolution of
one such gene family, the globin family. The globin family contains several genes that code
for different types of myoglobin and hemoglobin molecules in vertebrates. Myoglobin, the
oldest of member of the globin family, stores oxygen in muscles. Hemoglobin, of course,
carries oxygen in the bloodstream. The different polypeptides that make up hemoglobin and
myoglobin appear to have evolved by gene duplication from a single, original myoglobin-like
gene. Presently in humans, there are several types of hemoglobin and myoglobin molecules
produced that are essential to our development and survival because they are produced
specifically in different tissues and at different stages of development. This demonstrates the
importance of gene duplication in evolution.
Slide 7 Gene duplication has likely also played a significant role in the expansion of genome
size over evolutionary time. In other words, genome size differs between organisms to some
degree because of gene duplication. The graph on the left shows a comparison of the number
of coding genes in a variety of organisms. As we might expect, it takes more genes to keep a
relatively complicated organisms like a pufferfish going than it does to keep a relatively
simple organism, such as yeast, on top of its game. Although there are many exceptions to
this rule, in a broad sense we find this type of pattern to hold true - the more complex the
organism, from single-celled to multi-cellular, from prokaryote to eukaryote, the more genes
it uses to direct its development, respond to signals, reproduce, and so on.
The graph on the right shows that total genome size for many organisms is out of proportion
to the number of genes that are actually expressed. While a higher vertebrate like a mouse or
a human has about 20 times as many genes as a bacterium, its total genome size, measured in
base pairs, may be tens of thousands of times larger than a bacterium’s. Clearly there must be
an enormous amount of non-coding DNA in the genomes of some organisms. Researchers
are just beginning to understand the purpose of some of the non-coding DNA. It is likely,
however, that at least some of this non-coding DNA arose from duplication processes.

Classification of Biological Diversity

Slide 2 Classification systems serve a number of important roles. Firstly, they allow us to
recognize and interpret similarities and differences among organisms and arrange them into
groups according to specific traits. Secondly, having similar organisms classified into a group
also allows predictions of a specific trait that is consistent with the group. For example, a
secondary metabolite isolated from a particular plant species may have pharmaceutical
properties. The same molecule may be found in higher concentrations in other plant species
in the same group. Thirdly, when organisms are classified into groups they are given a unique
name according to their genera and species. The language used in naming organisms is
universal and people throughout the world are able to recognize a specific organism from its
scientific name.
Slide 3 Carl Linnaeus, a Swedish professor, physician and naturalist devised the binomial
system for classifying organisms into the hierarchical system that we use today. Evolution
was not an accepted component of biology in 1758; hence there is no consideration of
evolutionary relationships between organisms classified by this system. It is useful however,
in that an organism classified by this system can be identified anywhere in the world and by
anyone. Much of the classification was done on morphological characteristics and many
organism relationships have been confirmed after analyzing molecular traits.
Slide 4 Classification of organisms into their highest taxonomic rank is an ongoing process.
Linnaeus (1758) divided all known forms of life between two kingdoms, the plant and animal
kingdoms. Since then, the five kingdom system was adopted in 1969 and has been the
standard for the past twenty years or so. Recent evidence has divided the kingdom Monera
(prokaryotes) into two separate kingdoms, the Bacteria and the Archaea resulting in the three-
domain system. The organisms in the Archaea domain are prokaryotes that are adapted to
live in extreme environments. The remaining four kingdoms in the five kingdom system are
included in the Eukarya domain. Currently, there is much controversy over the classification
of the Protista kingdom, which includes an assortment of organisms. Sometime in the not too
distant future the classification system will undergo another change as this kingdom is
subdivided into more closely related groups.
Slide 5 The binomial nomenclature, devised by Linnaeus, names organisms according to
genus and species. In addition, he grouped similar species into hierarchical categories.
Organisms are ranked by kingdom, phylum, class, order, family, genus and species. The
kingdom classification is the most general category in which to place an organism; the
species is more specific sometimes being further reduced into subspecies. Each of the
subsequent groups (or taxa) becomes more specific, the organisms in each grouping having
more characteristics in common. In this example, the two organisms classified are Dendroica
fusca, the blackburnian warbler and Rosa gallica the moss rose. The genus name is always
capitalized and both genus and species names should be italicized.
Slide 6 Ancestral traits that show anatomical similarities between species are considered as
homologous structures. For example, the forelimbs of humans, cats, bats, whales and birds all
have similar skeletal structures even though these appendages have evolved different
functions. Sometimes the trait being examined is not always obvious in the adult form of an
organism therefore, early stages of development are often observed for homologies.
On the other hand, a derived trait is different from its ancestral form in that similarities within
a group are distinguished. Derived traits are often more difficult to classify since they change
over the course of evolution. Also, identification of derived traits is often complicated by the
occurrence of homoplastic traits i.e. traits that are similar in different individuals but they are
not descended from a common ancestor. For example, convergent evolution produces
organisms that evolve independently but have similar features. Some plants that evolved in
desert habitats have features similar to cactus, i.e. succulent and prickly, but they do not
belong to the cactus family. These organisms occupy similar habitats and are influenced by
similar selective pressures producing similar phenotypes.
Slide 7 Fossil records of extinct organisms are useful in distinguishing ancestral and derived
traits. These records also provide an evolutionary time line of events on which to base the
history of life. In extant or living organisms, structural traits such as morphology and
development are an important resource in classifying organisms. Organisms possessing
similar characteristics are arranged in the same group.
The fossil record does not provide all the answers to the history of life, hence molecular
structure has become a powerful tool in determining the relationship between organisms.
Proteins such as cytochrome c and nucleic acids are particularly useful in identifying
relationships. Mitochondrial DNA is often used to investigate the evolutionary relationships
in animals whereas chloroplast DNA is often chosen to investigate the relationships between
plants.
Many different heritable traits are analyzed in order to classify organisms in relation to one
another and in the reconstruction of phylogenetic trees.
Slide 8 Systematists analyze evolutionary changes within a group of organisms and
reconstruct phylogenetic trees showing the relationship of organisms to one another and their
common ancestor. Phylogenetic trees show the sequential order of evolutionary change; in
this example the oldest split is to the left of the tree, the youngest to the right. Each
taxonomic unit is a monophyletic group (also known as a clade) containing all the
descendants of a particular ancestor. Phylogenetic trees represent monophyletic groups
nested within monophyletic groups. In this example mosses, ferns and flowering plants are
each monophyletic groups but they all belong to the monophyletic group Plantae since they
are all descended from a common ancestor believed to be a green algae.
We will be investigating the classification of biological diversity in more detail in the next
course BIO 116, “Organisms and Environments”.
Slide 8 We have now looked at genetic variation on several levels, from differences in single
nucleotides to differences in entire genomes. All of this genetic variation ultimately came
from mutations. Mutations do not work alone, though, to generate all of the genetic variation
that we see. In fact, the variation that results from mutations is maintained and even
amplified in species in a number of ways. Sexual reproduction is one of these ways. As we
have discussed previously, the gametes found in sexually reproducing organisms are
produced by meiosis. During meiosis, crossing over between homologous chromosomes, and
the independent assortment of chromosomes, occurs. This results in genetically variable
gametes. Then, after scrambling around the genetic material of an individual by meiosis, that
genetic material is combined with material from another individual. The end result of sexual
reproduction is that offspring differ from their parents and from each other, providing genetic
and phenotypic variation for natural selection to work with.
Slide 9 Sometimes the genetic variation in a species is spread out in various distinct
populations, or subpopulations. Plants, for example, are especially likely to respond to
different environmental conditions such as soil type, microclimate, and grazing. The traits
that are selected for in one location, then, may differ from the traits selected for in another, so
that individual populations are adapted to differing environments. The different selective
pressures in each environment therefore contribute to the maintenance of the genetic
variability of the species as a whole.
Slide 10 Finally; natural selection can in some cases preserve genetic variation by
maintaining different forms, or polymorphisms, of a species. This occurs when the fitness of
a certain form of a species is linked to the fitness of other forms of the same species. For
example, it is possible to find different coloration patterns within the same geographic region
in individual species of garter snakes. Some members of the species have prevalent spotting,
while others are striped. In turn, the different forms, or polymorphisms, are linked to different
behavior patterns. Striped garter snakes avoid predation by slithering away quickly from
predators. Spotted garter snakes, on the other hand, depend on remaining still and
camouflaged to avoid predators. In this species of garter snake, both coloration patterns are
maintained because they both are effective in helping the snakes avoid predators. In this
sense, both patterns contribute to the overall survival of the species. In other words, two
patterns work better than one. This type of selection, where different polymorphisms of a
species are maintained, is called frequency-dependent selection.
Measuring Genetic Divergence Slide 2 In recent years scientists who study
evolution have turned to molecules to learn about the timing of evolutionary events.
This concept of a “molecular clock” rests on the assumption that neutral mutations
accumulate in DNA at a relatively constant rate. Of course the DNA sequences of genes
are expressed as polypeptide sequences, so it is also possible to approach the molecular
clock idea using protein sequences. These slide shows a plot of amino acid substitutions
in cytochrome c, a protein involved in the respiratory chain, vs. the time at which
various organisms diverged in evolutionary history. According to this plot, cytochrome
c has evolved at a fairly constant rate.
Slide 3 We can also use the accumulation of neutral mutations in different species to
infer a number of things about how species are related to each other. In conjunction
with fossil and morphological data, molecular sequences can help determine where
lineages split and how closely or distantly related different species are. The more
differences there are in their molecular sequences, the more distantly related two
species are. But let’s back up a little. What exactly are neutral mutations? Why can we
say that they accumulate at a constant rate? What are molecular sequences, and how do
we measure the differences in those sequences?
Slide 4 Let’s start with neutral mutations. Think back to our lesson on mutations. Many
point mutations in DNA have no effect on the amino acid sequences produced by
transcription and translation, either because they occur in parts of the DNA that don’t
encode genes or because they occur in positions that don’t change the amino acid
produced. Remember that the genetic code is redundant, that is, there are usually
several codons that code for the same amino acid. These silent, or synonymous,
mutations are also called neutral mutations because they have no effect on an
organism’s ability to survive and reproduce. Even some mutations that do cause
changes in the amino acid sequence of a protein may not have any effect on the
protein’s ability to function properly. For instance the substitution of one nonpolar
amino acid for another may not change the protein’s shape or function. These mutations
can also be considered neutral mutations because they just don’t give natural selection
anything to work with. Neutral mutations are free to accumulate in a population and
may eventually become part of the genome of a species. On the other hand we have
nonsynonymous mutations – mutations that cause changes in genes that do affect an
organism’s ability to survive and reproduce. Now natural selection can get into the act.
Most nonsynonymous mutations are disadvantageous and are quickly removed from
the population (usually by the death of the organism carrying the mutation).
Occasionally nonsynonymous mutations are advantageous, and these mutations may be
quickly fixed in the population. If we want to talk about the rate at which a mutation
will become fixed in a population, we can see that nonsynonymous mutations are
usually fixed or eliminated rapidly while neutral mutations may be fixed over a longer
period of time. The result, shown in this slide, is that we see fewer nonsynonymous
mutations than synonymous mutations fixed in a population for a given period of time.
Slide 5 During the past several decades molecular sequencing capabilities have
exploded. As a result DNA, RNA, and protein sequences are easily accessible via the
internet. We are often interested in comparing similar sequences among various
organisms to see what parts of a gene or polypeptide have changed and what parts have
been conserved through evolution. An important part of this process is alignment. For
either a nucleic acid or amino acid sequence, it is important to find some starting points
where we are confident that the sequences line up. There may be nucleotide insertions
or deletions that have accumulated over time in the sequences in different species that
make this process tricky, so there are a lot of software algorithms to help solve this
problem. Once we have some sequences properly aligned, we can begin to look at the
similarities and differences among them. To estimate the degree of divergence among
different organisms, a similarity matrix can be constructed. In this matrix the number of
different amino acids are shown above the line and the number of identical amino acids
are shown below the line. The simplest assumption is that the more differences there
are between sequences, the longer the organisms have been evolving separately. Slide
6 Here is an interesting comparison of amino acid sequences. As we mentioned before
cytochrome c is an important constituent of the electron transport chain in
mitochondria. It is found in all eukaryotic organisms. By comparing aligned sequences
of cytochrome c from different organisms, we can begin to get an understanding of how
species have diverged over the course of time. We can also see what parts of the amino
acid sequence are absolutely vital to the proper functioning of the protein. Invariant
positions in the sequence must represent amino acids that cytochrome c simply can’t do
without. To get back to the idea of how mutations accumulate in a sequence, proteins
that are absolutely essential to the functioning of an organism evolve slowly while less
essential proteins can evolve more quickly. To get down to a finer scale, parts of an
amino acid sequence that are essential for the functioning of a protein, the invariants in
the cytochrome c sequences, for example, evolve very slowly (if at all).
Slide 7 Similarity matrices can be used to study DNA sequences as well. For instance,
scientists can look at the similarity matrix for a gene that is common to many organisms
and calculate relative times of divergence. With the explosion in published DNA
sequences and computer programs to compare them, whole genome comparisons are
becoming possible. Recent research has shown that the total genomes of chimpanzees
and humans differ by only about 1.5%. Using the molecular clock theory, researchers
have estimated that humans and chimpanzees shared a common ancestor around 4.6-
6.2 million years ago.
Slide 8 Just as the choice of characters is important in constructing phylogenies based
on morphology, the choice of molecules is very important in looking at where and when
organisms may have diverged from one another. To do broad studies of many kinds of
organisms, it is obviously important to use a molecule that all of those organisms have.
We looked at cytochrome c sequences in many different kinds of eukaryotes. For even
broader studies of both prokaryotes and eukaryotes, ribosomal RNA is a popular tool. It
has the advantages of being ubiquitous in all living organisms and having some portions
that evolve extremely slowly. Most mutations in rRNA cause problems with translation
and are quickly removed by natural selection. These types of slowly evolving molecules
are useful for looking at ancient lineage splits. On the other hand mitochondrial and
chloroplast DNA have proved useful in studying recent evolutionary divergence because
they accumulate mutations relatively rapidly.

Biology lab…
Meiosis Slide 2 In a previous lesson, we discussed a type of cell division called
mitosis that involved the division of one parent cell into two genetically identical
daughter cells. This type of cell division is important in the growth and asexual
reproduction of many types of organisms. Mitosis, however, is somewhat limiting for
cells in an evolutionary sense, because it results only in the production of genetically
identical individuals, or clones. Without a mechanism to increase genetic variation,
species have difficulty adapting to changing environments. Many species counter this
difficulty by constantly generating genetic variation through sexual reproduction, which
involves combining the genetic material from two different organisms to produce new,
genetically unique offspring. At the foundation of sexual reproduction is a process of cell
division that results in the production of genetically variable cells. This process is called
meiosis.
Slide 3 Although meiosis, like mitosis, is a process of cell division, it differs from mitosis
in several key aspects. First, meiosis involves two rounds of cell division, instead of one,
and so results in the production of four daughter cells from each parent cell. Only one
round of DNA replication occurs prior to cell division, however, so the four daughter
cells produced by meiosis contain only half of the chromosomes from the original
parent cell. For instance, if a diploid cell undergoes meiosis, it will produce four haploid
daughter cells. Finally, a process called crossing over occurs in meiosis. During crossing
over, homologous chromosomes physically exchange segments of their DNA. This
mechanism is an important way by which meiosis generates genetic variation.
Slide 4 Both rounds of cell division in meiosis contain essentially the same stages as
mitosis: prophase, metaphase, anaphase and telophase. We refer to the first round of
cell division in meiosis as meiosis I, and the second round as meiosis II. The stages are
similarly named. For example, prophase of meiosis I is called prophase I, metaphase of
meiosis II is called metaphase II. After meiosis I, the cells of some organisms move
directly into meiosis II. In other types of organisms, meiosis I and meiosis II are
separated by a short period called interkinesis. In the following slides we will discuss
some of the key aspects that occur during meiosis I and meiosis II, and how they differ
from the corresponding stages in mitosis to produce four, genetically distinct daughter
cells.
Slide 5 During prophase of meiosis I, the DNA of the cell is condensed into
chromosomes, and homologous chromosomes pair tightly together in a process called
synapsis. Recall that prior to meiosis, the cell has undergone DNA replication. Because
of this, each chromosome consists of two identical sister chromatids. The chromatids of
homologous chromosomes become physically connected at points called chiasmata
(singular chiasma). Crossing over occurs at chiasmata when segments of DNA are
exchanged between homologous chromosomes. Crossing over results in a
recombination of genetic material, meaning that the sister chromatids of the
homologous chromosomes become genetically distinct from each other. This is the first
way by which meiosis generates genetic variation. In the illustrations on this and the
following slides, note that each member of a pair of homologous chromosomes is
indicated by a different color. Each color represents the genetic material (i.e., the
chromosomes) donated by one parent. When pieces of chromosomes are exchanged,
this is indicated by the different colors, as well.
Slide 6 During metaphase I, homologous chromosomes line up at the equatorial plate in
the plane of cell division. At this point, each homologous chromosome will become
attached to kinetochore microtubules from only one end of the cell. Because of this
arrangement, during anaphase I the homologous chromosomes, each with two
chromatids, separate and move to opposite ends of the cell (recall that in mitosis it was
the sister chromatids that separated and moved to opposite ends of the cell). In this
way, each of the two new cells formed in meiosis I will have one of each type of
chromosome, but only half the total number of chromosomes as the parent cell. For
example, a diploid cell going through meiosis I will produce two daughter cells, each
with one set of chromosomes instead of two. Meiosis I therefore results in a reduction in
the ploidy level, or the number of sets of chromosomes. Further, while each end of the
cell will receive one member of each pair of homologous chromosomes, exactly which
member it receives is a random process. This random assortment of homologous
chromosomes into daughter cells during meiosis I is a second mechanism employed by
meiosis to produce genetically diverse daughter cells.
Slide 7 In some species, anaphase I is followed by telophase I and cytokinesis, during
which time nuclear envelopes reform around the condensed chromosomes at each end
of the cell, and the cell divides into two daughter cells. In some organisms, there is an
interphase between cytokinesis of meiosis I and the beginning of meiosis II, called
interkinesis. During this stage each of the daughter cells will prepare for a second round
of cell division by synthesizing enzymes, cell membrane, and other components
necessary for meiosis II. It is important to note, however, that DNA is not replicated
during interkinesis, as it is during interphase of the mitotic cell cycle.
Slide 8 Meiosis II involves cell divisions that are essentially identical to mitosis. During
meiosis II, each of the two cells produced during meiosis I will divide, resulting in a total
of four daughter cells. At prophase II, the chromosomes of each cell re-condense, and
the nuclear envelopes begin to break down. The chromosomes line up on equatorial
plates during metaphase II, and the sister chromatids of each chromosome are pulled
apart to opposite ends of the cell during anaphase II, just as they are in mitosis. The
assortment of the genetically variable sister chromatids into daughter cells is a random
process, similar to the assortment of homologous chromosomes in meiosis I. And, as in
meiosis I, the process of random assortment aids in the generation of genetic diversity
among the daughter cells produced by meiosis. This is the third way by which meiosis
generates genetic variation. After the chromatids have moved to separate poles of the
cells, they begin to decondense while nuclear envelopes reform in telophase II. A second
round of cytokinesis, resulting in the four final daughter cells, follows telophase II.
Slide 9 To review, let’s briefly look again at the specific processes in meiosis that result
in four, genetically unique daughter cells. First, DNA is exchanged between homologous
chromosomes during the crossing over events of prophase I, resulting in genetically
variable sister chromatids. Second, the homologous chromosomes of meiosis I, and the
sister chromatids of meiosis II are randomly assorted into daughter cells prior to each
cell division. This assures that while each daughter cell has a complete set of
chromosomes, it will differ genetically from the chromosomes of the other daughter
cells.
Slide 10 So how exactly does meiosis play a role in sexual reproduction? In sexual
reproduction, the genetically variable cells produced by meiosis in two different
individuals combine. The resulting cell, called a zygote, develops into a new, genetically
unique individual. As an example, consider the egg and sperm cells of animals. Both of
these cell types are produced by meiosis, and so carry unique genetic material from the
parent that produced them. When these cells fuse to form a zygote during fertilization,
the resulting cell will carry only half of the chromosomes from each of its parents, and
so will differ to some degree from both of them. However, as we know from meiosis, it is
purely chance as to exactly what genetic material from each parent ends up in each egg
or sperm cell. When a number of offspring are produced, the odds are that each
offspring will be genetically distinct from all of the other offspring. In this way, the
process of meiosis generates the genetic variability that is the cornerstone of sexual
reproduction, and which is essential for the process of evolution.
Slide 11 In addition, meiosis plays one other important role in sexual reproduction.
Remember that because of the reduction in chromosome number that occurs during
meiosis I, each gamete produced contains only half of the chromosomes from the parent
that produced it. When gametes combine, the resulting zygote will then contain the
same total number of chromosomes as each of its parents. If a reduction in chromosome
number did not occur during meiosis I, each time a zygote formed it would have twice
as many chromosomes as its parents. In a short time, of course, this could cause major
difficulties for the survival and reproduction of cells and organisms. Through the
reduction in chromosome number that occurs in meiosis I, meiosis acts to maintain the
ploidy level, or number of sets of chromosomes, of sexually reproducing species.
Mendel’s Discoveries Slide 2 Gregor Mendel was an Austrian monk who lived in
the middle of the 19th century. A fair amount about Mendel’s life is known from history,
including the fact that some of his lowest grades received in school were in biology.
Despite his academic shortcomings, however, Mendel’s work as a scientist uncovered
some of the most fundamental concepts of genetics, and provided a basis for many of
the major advancements in biology that were to come in the following century.
Slide 3 Over a period of about nine years, Mendel performed breeding experiments on
bean plants by collecting data on the hereditary patterns of a number of different
characters of the plants, such as the color of fruits and flowers, the shape of seeds and
fruits, and the size of plants. Mendel’s studies involved crossing bean plants that were
true-breeding for different forms of various characters. For example, one of Mendel’s
crosses involved breeding plants that always produced smooth seeds with plants that
were true for wrinkled seeds. The outcome of this cross is shown in the illustration.
Mendel called his true-breeding plants the parental generation, or P. Crosses between
two parents result in the first filial generation, or F 1, for short. These F1 progeny were
then allowed to self-fertilize, producing a second filial generation, or F 2. Mendel
measured the characters under study as they occurred in both the F 1 and F2 generations,
and then used a fairly simple mathematical explanation to describe the results that he
found. As we will discuss in the next few slides, Mendel’s results led to the discovery of
two fundamental laws that govern heredity not just in bean plants, but in all sexually
reproducing organisms.
Slide 4 Mendel’s first experiments described the heredity patterns of single characters,
such as flower color, or seed shape. Crosses performed to follow the inheritance of a
single character are called monohybrid crosses. Invariably in these crosses, the F 1
generation displayed only one trait, or version of the character, that was present in the
parental generation. For example, when Mendel crossed purple-flowered plants with
white-flowered plants, only purple-flowered plants were observed in the F 1 generation.
When plants with smooth seeds were crossed with plants with wrinkled seeds, only
smooth-seeded plants were observed in the F1 generation. Mendel called the traits that
appeared in the F1 generation dominant traits. The traits that did not appear in the F 1
generation were called recessive traits. When Mendel allowed the F1 generation to self-
pollinate, the recessive traits reappeared in the resulting F 2 generation. However, as
shown in the table, the dominant and recessive traits always appeared in the ratio of
three dominant phenotypes to one recessive phenotype.
Slide 5 Mendel explained these results by reasoning that each plant had two units of
inheritance for any given trait. Plants could then theoretically have three possible
combinations for a character - they could have two dominant units, two recessive units,
or a dominant and a recessive unit. Furthermore, when the adult plants formed gametes
through the process of meiosis, each of the units separated so that each gamete carried
only one unit. This means that when gametes from separate parents combined and
developed into a new plant, the offspring would have one unit of inheritance for a
character from each of its parents. Today, we call Mendel’s units of inheritance genes,
and the different versions – dominant and recessive – different alleles of the same gene.
As you follow through this lesson, note that different genes are denoted by letters. The
dominant allele of a gene is represented by a capital letter, while the recessive allele is
denoted by a lower-case letter. For example, the gene for flower color is represented by
the letter ‘w’. The dominant allele that results in purple color is a capital W; the
recessive form that corresponds to white color is a lower case w. Individuals with two
of the same alleles are termed homozygous, and are represented as WW or ww, while
individuals with different alleles are termed heterozygous, and are represented as Ww.
Mendel’s true-breeding plants, therefore, were homozygous for certain characters, such
as flower color. When these homozygous parental plants produced gametes, all of the
gametes from a given parent contained the same allele. When gametes from two
different parents combined, the resulting offspring, were heterozygous. In appearance,
however, only the dominant trait was observed, because the F1 plants carried the
dominant allele, which was expressed over the recessive allele.
Slide 6 When Mendel’s F1 generations produced gametes, equal numbers of gametes
contained dominant and recessive alleles. When these gametes combined, there would
be an equal chance of each of the following allelic combinations in the offspring
genotype: dominant-dominant, dominant-recessive, recessive-dominant, and recessive-
recessive. However, the physical appearance of the F2 plants would be observed in the
ratio three dominant to one recessive, because three of the possible allele combinations
contain dominant alleles, one contains only recessive alleles. This three to one ratio is
the ratio which Mendel observed. At this point, you should note that the physical
appearance, or phenotype, of an organism, is determined by its genetic makeup, or
genotype. In addition, different genotypes, such as the homozygous dominant and
heterozygous conditions, can lead to the same phenotype.
Slide 7 The results from Mendel’s first experiments led to the formation of Mendel’s
first law, the law of segregation. The law of segregation states that during the formation
of gametes, the alleles of a gene separate so that each gamete only receives one allele for
each gene.
Slide 8 Mendel’s second set of experiments involved measuring the heredity patterns of
two characters at a time. This type of cross is called a dihybrid cross. For example,
Mendel crossed plants that were true-breeding for seeds that were both round and
yellow with plants true-breeding for green and wrinkled seeds. The results Mendel
obtained were similar to those of his first experiments, although they were a little more
difficult to interpret due to the inclusion of two characters rather than just one. In the
F1generation, all of the plants displayed both of the dominant traits found in the
parental generation. In our example, the F1 generation all produced smooth, yellow
seeds. In the F2 generation, Mendel always found that the traits in question appeared
together in a 9:3:3:1 ratio. In other words, out of every sixteen F 2 plants measured, nine
had both dominant traits, six had only one of the dominant traits, and one displayed
both recessive traits.
Slide 9 To explain the results of his dihybrid crosses, Mendel proposed that not only did
the alleles of each of the two genes segregate during gamete formation, as he had shown
in his first experiment, but the two genes assorted independently of each other as well.
For example, take a look at the F2 results in the illustration. If you add up only the round
seeds compared to the wrinkled seeds, you will find 12 round and 4 wrinkled seeds.
This, of course, is a three to one ratio, as is expected from Mendel’s first law. The same is
true of the yellow and green seeds. However, when the characters of seed shape and
color are considered together, the resulting 9:3:3:1 ratio can only be explained if the
two genes for these characters have behaved independently of each other during
gamete formation. When this occurs, gametes with all possible allele combinations (RY,
Ry, rY, and ry) are formed with equal probability. When these gametes then combine to
form offspring, the offspring are produced in a 9:3:3:1 phenotypic ratio.
Slide 10 The results of Mendel’s dihybrid crosses led to the formulation of Mendel’s
second law, called the law of independent assortment. This law states that during gamete
formation, the alleles of different genes assort independently of one another. Due to
this, any gamete may receive any combination of the alleles present in the organism.
Recall that Mendel’s first law, the law of segregation, dealt with the segregation of
different alleles of the same gene. The law of assortment describes the assortment of the
alleles of different genes.
Slide 11 Mendel’s work helped lay the foundation for modern genetics, and his
discoveries and conclusions have largely stood the test of time. However, as we will see
in the following lesson, there are a number of exceptions to Mendel’s second law, and a
number of examples where the phenotype of an organism is not so clearly defined by
strictly dominant and recessive alleles of genes. In fact, many researchers consider it
amazing that all seven of the characters that Mendel chose for study displayed such
clear patterns of dominant-recessive heredity. The exceptions to Mendel’s rules, of
course, have presented some of the major challenges to geneticists since Mendel’s
discoveries.
Types of Inheritance Slide 2 When Gregor Mendel performed his experiments on
pea plants in the mid 1800s, all of the characters he reported showed very clear
inheritance patterns. For each character, there was a dominant and a recessive form,
the recessive form only appearing in homozygous recessive individuals (individuals
with two recessive alleles). This type of inheritance is called, appropriately enough,
Mendelian inheritance. You may also hear Mendelian inheritance referred to as
complete dominance. Slide 3 Mendelian inheritance has been demonstrated for
different characters in a number of different types of organisms. In humans alone,
several thousand characters have been shown to follow Mendelian inheritance patterns.
Because humans do not generally produce very many offspring, researchers may look to
the current and past members of families to discover patterns of inheritance for
different human characters. They may do this by assembling a human pedigree, or
family tree. In many cases, family trees are used to track inheritance patterns of
heritable diseases, such as Huntington’s disease, a degenerative brain disorder linked to
the DNA of affected individuals. The illustration here shows a possible inheritance
pattern for Huntington’s disease. The allele that causes this disease is dominant.
Therefore, in each case where the disease is present, as shown by the purple color, at
least one dominant allele is found. Only individuals that are homozygous recessive for
the Huntington’s gene are free of the disease. Other heritable diseases may be caused by
recessive alleles. In these cases, only homozygous recessive individuals will be affected
by the disease. Heterozygous individuals, on the other hand, will not show any
symptoms of the disease but will still carry the allele for the disease and may pass it on
to their offspring. Slide 4 While many heritable characters do follow clear Mendelian
patterns, at least as many or more do not exhibit such clear and simple inheritance. In
the next two lessons, we will discuss several instances where the inheritance of
characters, or the characters themselves, are somewhat more complex than those
Mendel found in pea plants. This slide lists some of the situations where Mendelian
patterns of inheritance are not clearly expressed. For example, some genes may not
exhibit clear dominant and recessive alleles. Other genes may be responsible for more
than one phenotypic trait. Still other genes may show inheritance patterns that defy
Mendel’s law of independent assortment. In each of the cases that we discuss,
remember that we are still considering how different alleles of genes in the DNA affect
the phenotypic, or physical traits of organisms. A number of factors, however, such as
the types of alleles, the interactions between alleles, and their location in the DNA, will
affect their inheritance and expression in ways that result in inheritance patterns
different from typical Mendelian inheritance.
Non-Mendelian Inheritance Slide 2 In organisms, the majority of genes are
located on autosomes. Simply put, autosomes are chromosomes that are not sex
chromosomes, or do not determine the sex of an organism. The genes that coded for the
phenotypic characters Mendel studied in pea plants, for example, were located on
autosomes. While Mendel was fortunate to have studied genes with fairly simple
inheritance, many other genes do not follow such clear patterns, even when they are
located on autosomes. In this lesson, we will discuss examples of inheritance of
autosomal genes that differ from typical Mendelian inheritance. In the following lesson,
we will discuss inheritance patterns of genes located specifically on sex-chromosomes.
Slide 3 Many genes are present in populations in more than two versions, or alleles, and
code for slightly different protein products. Even when genes have only two alleles,
however, as in Mendel’s studies, the alleles may not be clearly dominant and recessive.
One instance of this is called incomplete dominance. Incomplete dominance is
expressed in heterozygous offspring that are intermediate in appearance between their
homozygous dominant parent and their homozygous recessive parent. In this
illustration, the gene for flower color in snapdragons has two alleles. When an
individual is homozygous for the dominant allele of this gene, it produces red flowers.
Homozygous recessive individuals produce white flowers. Heterozygous individuals,
however, produce pink flowers, rather than the red flowers that would be expected if
the dominant allele were completely dominant over the recessive allele. In this case, the
gene of interest codes for a protein that makes pigment in the flowers. Individuals with
two dominant alleles of this gene are able to make enough of this enzyme to produce
red flowers. Heterozygous individuals, on the other hand, are able to produce only half
as much enzyme, because they have only one dominant copy of the gene. Because of
this, their flowers have less pigment and appear pink. Slide 4 In some instances, both
alleles of a gene are clearly expressed in the phenotype of a heterozygous individual.
This is called codominance. An example of codominance is found in human blood types.
In humans, blood type is determined by three alleles of the same gene: IA, IB, and IO.
Individuals with type AB blood produce two types of antigens, or receptor proteins on
the surface of their red blood cells – antigens A and B. Individuals of type A or B blood,
on the other hand, produce only A or B antigens, respectively. The synthesis of these
receptors is linked to two alleles of the same gene – alleles A and B. Since these two
alleles are both expressed in the heterozygote phenotype, they are codominant. Slide 5
Mendel’s pea plants had two versions of each character that he studied, such as green
vs. yellow seeds, or white vs. purple flowers. As he demonstrated, each version was due
to a different allele of a particular gene. In other words, each gene had only two alleles.
Many genes, however, have numerous alleles, each one coding for a slightly different
phenotype. The different alleles of a gene arise from mutations occurring in the DNA. An
example is the gene responsible for the coat color of domestic rabbits. In rabbits, there
is one gene that determines coat color, but it has four different alleles. When an
offspring inherits two of the alleles from its parents, its coat color will range from dark
gray to white, depending on exactly which of the two alleles it inherited. In this case, the
multiple alleles of a single gene can result in multiple phenotypic traits. Slide 6 In many
cases, an organism’s phenotype is determined by more than one gene, rather than by
one gene with two or more alleles. Multiple genes that determine a phenotype often act
in such a way that the activity of one gene is affected by the activity of another. When
the expression of one gene affects the action of another gene or genes, we call this
epistasis. The diagram on this slide displays a well-studied example of epistasis that
occurs in mice. In mice, coat color is determined by two genes. For simplicity, we’ll call
these two genes gene A and gene B. Gene A controls the formation of pigment that is
deposited in the mouse’s coat. Gene B controls whether the pigment has a continuous
distribution on each hair, or whether it appears in alternating bands. In both gene A and
gene B, the recessive allele codes for a non-functional enzyme. As a result, mice
homozygous recessive for gene A (genotype aa) are unable to produce pigment; mice
homozygous recessive for gene B (genotype bb) are unable to produce a banding
pattern, and instead deposit pigment continuously throughout each hair.
Phenotypically, mice homozygous recessive for gene A are albino, since the recessive
version of gene A will block all pigment production. Note that in mice homozygous
recessive for gene A, the genotype for gene B is inconsequential, because there is no
pigment to distribute in the coat. In mice heterozygous or homozygous dominant for
gene A, the genotype for gene B determines whether mice will be dark grey or sandy
brown. Individuals that are homozygous recessive for gene B will develop a dark grey
coat, because the enzyme produced by gene B is non-functional, hence, pigment will be
deposited continuously in each hair. Individuals homozygous dominant or heterozygous
for gene B, on the other hand, will develop a sandy brown coat, as the dominant version
of gene B codes for a functional enzyme, hence pigment will be deposited in alternating
bands. In any of these cases, note how the activity of one gene can affect the activity of
another – this causal relationship between genes is the type of activity that defines
epistasis. Slide 7 While multiple genes may combine to affect one phenotypic
characteristic, the opposite may also be true – one gene may have multiple phenotypic
effects. This phenomenon is called pleiotropy. One of the most well-known examples
occurs in Siamese cats. In this particular breed of cat, the gene that codes for coat color
also results in the crossed eyes common to this breed. Slide 8 Some organisms, such as
the snowshoe hare, or the hydrangeas on this slide, present another common theme in
the link between genotype and phenotype. In many organisms, the physical expression
of genes, or the phenotype, is affected by the environment. In hydrangeas, flower color
depends largely on the pH of the soil. In relatively acidic soils, hydrangeas will produce
blue flowers. In more basic soils, pink flowers will be produced. On a molecular level,
this change in color is caused by the availability of free aluminum ions in the soil. In
acidic soils, free aluminum ions are typically in higher concentration than in basic soils.
Aluminum ions free in the soil are taken up by the hydrangea, and ultimately bind to a
pigment found in the vacuoles of the flower cells. This binding causes a conformational
change in the pigment, changing the wavelengths of light it reflects and making the
flowers appear a different color. In the case of the snowshoe hair, the phenotype of coat
color is affected by seasonal changes in the environment. In summer, coat color is a
mottled brown; in winter, coat color is white. As you can guess, these colors help the
snowshoe hair blend in to its environment and avoid detection by predators. The
snowshoe hair is an excellent example of both environment affecting phenotype, and of
a species adapting to their environment. Remember that species have adapted over
time to their environments, so it should be no surprise that the expression of specific
genes may be affected by changes in the surroundings of an organism. Slide 9 In many
cases, the alleles of two or more genes appear together in offspring more often than
would be expected by typical Mendelian inheritance. Such results provide an exception
to Mendel’s second law, the law of independent assortment, which states that the alleles
of different genes assort independently of one another during gamete formation. When
two or more genes do not assort independently of one another, the genes in question
are said to be linked. For example, in the illustration here, a fruit fly heterozygous for
two genes is crossed with a fly homozygous recessive for both genes and the offspring
phenotypes are observed. Note that the heterozygous parent fly has a brown body and
normal wings, while the homozygous recessive parent has a black body and reduced, or
vestigial, wings. In the offspring, one would expect a random assortment of the alleles of
the two genes that determine body color and wing size, hence equal proportions of all of
the possible combinations of the phenotypic traits. However, the observed phenotypic
ratios differed from the expected phenotypic ratios. The majority of the offspring
produced exhibited the parental phenotypes. The genes that determine these two
characters are said to be linked, because they are often inherited together. Slide 10
Gene linkage occurs when two or more genes are located on the same chromosome.
Recall that during crossing over of meiosis I, chromosomes physically exchange
portions of their chromatids. If two genes are located close together on the same
chromosome, there is a greater chance that they will be transferred together during
crossing over. The alleles of these genes will then have a greater chance of appearing in
the gametes in the same combination as is found in the parents. Hence, offspring also
have a greater chance of inheriting the same combination of alleles that their parents
had if the genes under consideration are linked. Slide 11 Geneticists often use the
concept of gene linkage to identify the approximate location of genes on chromosomes
by creating a genetic map. On a genetic map, two or more genes are mapped along the
length of a chromosome in relation to one another. The units of distance separating
different genes are called centimorgans, or cM. Each centimorgan corresponds to a one
percent chance of recombination of the alleles of two genes during meiosis. For
example, when investigating the linkage between the genes for eye color and body
color, tests resulted in recombination frequencies of thirty-one percent. In other words,
thirty-one percent of the offspring had phenotypic combinations of eye color and body
color that were not present in either parent. These genes were then able to be mapped
in relation to one another at a distance of 31 cM. Slide 12 On a final note, remember
that some of a cell’s DNA is non-nuclear. Both mitochondria and chloroplasts carry their
own DNA. In sexually reproducing organisms, these organelles are passed down to the
next generation only through the maternal gamete, or egg cell. For this reason,
inheritance of mitochondrial or plastid DNA is often referred to as maternal or
cytoplasmic inheritance. In addition, mitochondria and plastid inheritance patterns are
further complicated by the fact that the DNA of these organelles typically has a higher
mutation rate than that of nuclear DNA. This mutation rate, coupled with the high
number of these organelles in some cell types, can lead to a great amount of genetic
variation even within single cells.
Sex-Linked Inheritance Slide 2 While the concept of gender is very familiar to
us, it may be surprising to learn that the majority of sexually reproducing organisms on
earth are functionally both male and female at the same time. Most flowering plants, for
example, produce functionally bisexual flowers, which produce both male and female
gametes. Many other plants produce male and female reproductive structures in
separate flowers or cones, but still on the same individual. Some members of the animal
kingdom, such as the earthworms, are also able to produce both types of gametes within
the same individual. Many animals, however, and a number of plants, are capable of
producing only male or female gametes in each individual. These types of organisms are
sometimes referred to as dioecious, meaning ‘two houses’. In dioecious species, sex may
be determined in a number of ways. In some cases, environment and nutrition affects
the development of sexual characteristics. In other cases, such as in honeybees,
fertilization or lack thereof may determine gender. In yet other organisms, including
humans, sex is determined by special sex chromosomes, which carry genes that code for
male or female characteristics. Slide 3 In addition to gender-related characteristics, sex
chromosomes often carry genes that code for characters apparently unrelated to
gender. Such genes often show inheritance that deviates from Mendelian patterns
because they are located on sex chromosomes. In Drosophila, for example, sex is
determined largely as it is in humans – females generally carry two X chromosomes,
while males carry an X and a Y chromosome. It has also been shown that the gene for
eye color is carried on the Drosophila sex chromosomes, specifically on the X
chromosome. The allele of the gene that codes for red eyes is dominant over the allele
that codes for white eyes. Because this gene is located on the X chromosome, however,
the results of crosses between red-eyed and white-eyed individuals may vary from
Mendelian ratios depending on which parent has which character. This is due to the fact
that male parents only donate a Y chromosome, which does not carry the gene for eye
color, to male offspring. Whichever allele the male offspring receives from their female
parent will be expressed in their phenotype, regardless of the genotype of the male
parent. For instance, in crosses between homozygous red-eyed females and white-eyed
males, all of the offspring have red eyes, as would be expected. When homozygous
white-eyed females are crossed with red-eyed males, however, only the female
offspring have red eyes, while all male offspring have white eyes. Slide 4 Sex-linked
inheritance also has some important consequences for humans, as a number of
hereditary diseases or disorders, such as hemophilia A and red-green color blindness,
are linked to sex chromosomes. In most cases, sex-linked hereditary diseases are caused
by recessive alleles of genes found on the X chromosome. Heterozygous females,
therefore, may carry the allele for the gene with no effect, although they may pass it on
to their offspring. Males that carry the allele, on the other hand, will always be affected,
as there is no complementary allele on the Y chromosome to mask the effects of the
recessive allele. If males live to reproduce, any daughters that they have will
automatically carry the recessive version of the gene, as a father can only donate an X
chromosome to his daughter. Any sons that they produce will not carry the recessive
version of the gene, as sons only receive the Y chromosome from their fathers.
Horizontal Gene Transfer in Prokaryotes
Slide 2 Before we explain horizontal gene transfer, some background on
prokaryotic organisms is required. Prokaryotes represent all single-cell organisms that
are not eukaryotic and can be subdivided into two majors groups: the Bacteria and the
Archaea. Humans and other animals, plants and fungi are examples of eukaryotic
organisms.
Slide 3 Prokaryotic cells are about 1 micrometer or less in size, and the cells come
in a few different shapes. Unlike in the eukaryotes, the double-stranded chromosome of
prokaryotes is not surrounded by a membrane; prokaryotes do not have a nucleus. They
have about 1/1000 of the DNA of human cells. Prokaryotes play important ecological
roles, including cycling elements in the soil, atmosphere and water. They present disease
challenges to humans, animals and plants. Prokaryotes also play a central role as tools
for biotechnology. In this lecture we will mainly focus on the group of the Bacteria.
Slide 4 Prokaryotes usually reproduce asexually by cell division, also referred to
as ‘vertical gene transfer’. The division of single cells into two identical offspring
produces clones, or genetically identical individuals. Prokaryotes can grow rapidly:
Escherichia coli can double every 20 minutes. In addition to this asexual cell division,
prokaryotes have several mechanisms through which they may acquire new genes by
‘horizontal gene transfer’.
Slide 5 There are three well-known mechanisms of horizontal gene transfer in
Bacteria:
• Transformation is the process by which bacteria take up extracellular DNA from
their environment. These DNA fragments may recombine with the host chromosome,
permanently adding new genes. This mechanism was discovered more than 75 years
ago, and was at the basis for the discovery that DNA is the heredity factor in all living
organisms.
• A second mechanism of gene transfer is transduction. During transduction, viruses
carry genes from one bacterial cell to another. Viruses are obligate intracellular
parasites, needing the biochemical machinery of living cells to reproduce. Viruses
that infect bacteria are called bacteriophages. Many get their genetic material into the
cell by attaching with tail assemblies that then inject the DNA into the cell. During
the lytic cycle (when the host cell breaks open), some bacteriophages package some
of the host bacteria’s DNA. Cells that are subsequently infected by such viruses get a
segment of DNA from another bacterium which can recombine with the
chromosomal DNA of the host and thus alter its genetic composition.
• Several bacteria can conjugate. Conjugation is the exchange of genetic information
(DNA) by direct cell-cell contact. Physical contact is initiated by a pilus, which is a
fine ‘tube’ produced by the donor cell. Before we can discuss conjugation, we must
introduce another kind of genetic element called a plasmid.
Slide 6 Plasmids are genetic elements that replicate independently of the host
chromosome. Almost all known plasmids are double-stranded DNA, and most often
circular. They typically carry genes that are only required by the host under specific
conditions. For example, genes that confer antibiotic resistance to their host are often
found on plasmids; in the presence of antibiotics, only the resistant bacterial cells will
survive. Plasmids can also carry genes that code for a wide variety of other functions,
such as resistance to heavy metals and UV light, degradation of organic compounds,
including environmental pollutants, production of antibiotics, and production of virulence
factors.
Slide 7 Conjugation is the process whereby a plasmid is replicated and
transferred to another cell by cell-to-cell contact. It was first demonstrated in 1946 by
Joshua Lederberg and Edward Tatum. Some, but not all plasmids are conjugative. This
means that these plasmids have the required genetic information to govern their own
transfer. Some plasmids are transferable to a broad range of bacteria. They are called
broad host range plasmids.
The conjugation process is as follows:
First the plasmid initiates conjugation in the ‘Donor’ cell (bacterium with plasmid) by
making a pilus that makes contact with the ‘Recipient’ cell (bacterium without
plasmid). Next, a copy of the plasmid is transferred to the Recipient, which then
becomes a ‘Transconjugant’ (recipient cell with new plasmid)
Plasmids can have 1 to about 40 copies per cell.
Slide 8 Transposable elements, found in most organisms, move genes among
plasmids and chromosomes. They facilitate gene transport within an individual cell, and
are sometimes also called ‘jumping genes’. Long transposable elements that include one
or more genes are called transposons. Transposons have contributed to the evolution of
plasmids. They often carry genes that encode antibiotic resistance or degradation of
pollutants. Recently several other mobile genetic elements have been found in bacterial
chromosomes, such as the ‘pathogenicity islands’, which code for virulence factors.