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“The thing that
a lot of people cannot comprehend is that Mother Nature doesn't have a
bullet with your name on it, she has millions of bullets inscribed with
'to whom it may concern”. |
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Breeders need to
understand the complexity of Mother Nature's bullets - or alleles - if we
are to make wise breeding decisions, no matter the strategy chosen for our
breeding programs. An understanding of development is similarly important.
This brief primer, adapted from the University of Cal-Berkeley's website,
is presented to help understand the basics of DNA, heredity and
development. To follow the lessons in a logical fashion, simply pass the
links and scroll through the lessons. Otherwise, hit the link of interest.
It will take you to that lesson. |
Bottlenecks and
Founder Effect
Causes of Mutations
Development
Genetic Drift
Gene Flow
Genetic Variation
Mutations
Sampling Error
and Evolution
Sex and Genetic
Shuffling
Types of
Developmental Change
Types of Mutations
Understanding Developmental Complexity
Understanding
DNA
"Talk to Your DNA"
by Marlis Jermutus
http://www.starseedgallery.net
Understanding
DNA
DNA contains a set of
instructions for building a dog. These instructions are inscribed in the structure
of the DNA molecule through a genetic code. It works like this:
 DNA is made of a long
sequence of smaller units strung together. There are four basic types of
unit: A, T, G, and C. These letters represents the type of
base each unit carries: adenine,
thymine, guanine, and cytosine.
The sequence of these bases encodes instructions. Some parts of your DNA
are control centers for turning
genes
on and off, some parts have no function, and some parts have a function that
we don’t understand yet. Other parts of your DNA are genes that carry the
instructions for making
proteins—which
are long chains of
amino acids.
These proteins help build an organism.
Protein-coding DNA can
be divided into
codons—sets of
three bases that specify an amino acid or signal the end of the protein.
Codons are identified by the bases that make them up—in the example at right, GCA, for guanine, cytosine, and adenine. The cellular machinery uses these
instructions to assemble a string of corresponding amino acids (one amino
acid for each three bases). The amino acid that corresponds to “GCA” is
called alanine; there are twenty different amino acids synthesized this way
in humans. “Stop” codons signify the end of the newly built protein.
The completed protein is then released to do its job in the cell.
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Without genetic variation, some of the basic mechanisms of evolutionary
change cannot operate.
There are three primary sources of genetic variation:
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Mutations are
changes in the DNA. A single mutation can have a large effect, but in
many cases, evolutionary change is based on the accumulation of many
mutations.
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Gene flow is
any movement of genes from one population to another and is an important
source of genetic variation.
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Sex can
introduce new gene combinations into a population. This genetic
shuffling is another important source of genetic variation.
Genetic shuffling is a source of
variation.
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Mutations
Mutation is a
change in
DNA, the
hereditary material of life. An organism’s DNA affects how it looks, how it
behaves, and its physiology—all aspects of its life. So a change in an
organism’s DNA can cause changes in all aspects of its life.
Mutations are random.
Mutations can be beneficial, neutral, or harmful for the organism, but
mutations do not “try” to supply what the organism “needs.” In this respect,
mutations are
random—whether a
particular mutation happens or not is unrelated to how useful that mutation
would be.
Not all mutations matter to evolution.
Since all cells in our
body contain DNA, there are lots of places for mutations to occur; however,
not all mutations matter for
evolution.
Somatic mutations
occur in non-reproductive cells and won’t be passed onto offspring.
For example, the golden color on half of this Red Delicious apple was
caused by a somatic mutation. The seeds of this apple do not carry the
mutation.
The only mutations that matter to large-scale evolution are those that can
be passed on to offspring. These occur in reproductive cells like eggs and
sperm and are called
germ
line mutations.
A single germ line mutation can have a range of effects:
No change occurs in
phenotype.
You’ve probably heard of “junk
DNA,” DNA that doesn’t seem to do anything. Mutations in junk
DNA get passed on to offspring, but as far as we know, have no obvious
effect on the
phenotype.
Small change occurs
in phenotype.
A single mutation caused this cat’s ears to curl backwards
slightly.
Big change occurs
in phenotype.
Some really important phenotypic changes, like DDT resistance in insects
are sometimes caused by single mutations1. A single mutation
can also have strong negative effects for the organism. Mutations that
cause the death of an organism are called
lethals—and
it doesn't get more negative than that.
There are some sorts of changes that a single mutation, or even a lot of
mutations, could not cause. Neither mutations nor wishful thinking will make
pigs have wings; only pop culture could have created Teenage Mutant Ninja
Turtles—mutations could not have done it.
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The Causes of Mutations
Mutations happen for several reasons.
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DNA fails to copy
accurately.
Most of the
mutations
that we think matter to
evolution
are “naturally-occurring.” For example, when a cell divides, it makes a
copy of its DNA—and sometimes the copy is not quite perfect. That small
difference from the original DNA sequence is a mutation.
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External influences
can create mutations.
Mutations can
also be caused by exposure to specific chemicals or radiation. These
agents cause the DNA to break down. This is not necessarily
unnatural—even in the most isolated and pristine environments, DNA
breaks down. Nevertheless, when the cell repairs the DNA, it might not
do a perfect job of the repair. So the cell would end up with DNA
slightly different than the original DNA and hence, a mutation.
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Types of Mutations
Knowing a few basic types of mutations can help you understand why some
mutations have major effects and some may have no effect at all.
Substitution
A
substitution is a
mutation that exchanges one
base for another (i.e., a change in
a single “chemical letter” such as switching an A to a G). Such a
substitution could:
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change a codon to one
that encodes a different amino acid and cause a small change in the
protein produced. For example, sickle cell anemia
is caused by a substitution in the beta-hemoglobin gene, which alters a single
amino acid in the protein
produced.
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change a codon to one
that encodes the same amino acid and causes no change in the protein
produced. These are called
silent mutations.
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change an
amino-acid-coding codon to a single “stop” codon and cause an incomplete
protein. This can have serious effects since the incomplete
protein probably won’t
function.
Insertion
Insertions are mutations in
which extra base pairs are inserted into a new place in the
DNA.
Deletion
Deletions are mutations in
which a section of DNA is lost, or deleted.
Frameshift
Since protein-coding DNA is divided into codons three bases long, insertions
and deletions can alter a gene so that its message is no longer correctly
parsed. These changes are called
frameshifts.
For example, consider the sentence, “The fat cat sat.” Each word represents a codon. If we delete the first letter and parse the sentence in the same way,
it doesn’t make sense.
In frameshifts, a similar error occurs at the DNA level, causing the codons
to be parsed incorrectly. This usually generates proteins that are as useless
as “hef atc ats at” is uninformative.
There are other types of mutations as well, but this short list should
give you an idea of the possibilities.
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Gene Flow
Gene flow—also
called migration—is any movement of genes from one
population to another. Gene flow
includes lots of different kinds of events, such as pollen being blown to a
new destination or people moving to new cities or countries. If
genes are carried to a population where
those genes previously did not exist, gene flow can be a very important
source of
genetic variation.
In the graphic below, the gene for brown coloration moves from one population
to another.
Gene flow has several important effects on evolution:
Within a population:
It can introduce or reintroduce genes to a
population, increasing the genetic variation of that population.
Across populations:
By moving genes around, it can make distant populations genetically similar
to one another, hence reducing the chance of speciation. The less gene flow
between two populations, the more likely that two populations will evolve
into two
species.
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Sex and Genetic
Shuffling
Recombination introduces new gene combinations into populations.
Here is a quick and dirty review of the genetics of sexual canine
reproduction.
Genes are located on long chains of DNA called chromosomes.
Canines have 39 pairs
of chromosomes: one member of each pair was inherited from the dam and the
other from the sire. Correspondingly, dogs have two versions of every gene,
one from the mother and one from the father.
If dogs reproduced by taking 39 pairs of chromosomes from the dam and 39
pairs of chromosomes from the sire, the puppy would have too many chromosomes
(78 pairs). So eggs and sperm carry only half the usual number of
chromosomes—just 39 unpaired chromosomes, carrying one version of each gene.
When the egg and sperm get together, the puppy receives the normal 39 matched
pairs.
When eggs and sperm are produced, the parent cell first copies each
chromosome, leaving the duplicate pairs attached to one another.
Producing eggs and sperm is the first opportunity for mixing and matching
genes. When the dam makes an egg, her chromosomes first find their matched
partners and exchange some DNA with each other. That's called
recombination. Because of this
shuffling, genes from the dam’s dam and genes from the dam’s sire can wind up
next to one another on the same stretch of DNA. (The same thing happens in
the sire’s sperm.)
Only after chromosomes recombine do they
segregate
into different egg cells, so that each egg cell ends up with one version of
each chromosome.
Meiosis, step one (click the image
for animation):
Meiosis, step two (click the image for animation):
When egg and sperm meet, the puppy inherits a combination of genes that is
totally unique: it carries
versions of genes from all 4 grandparents plus any
mutations that occurred when the dam and
sire were making the egg and sperm.
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Genetic Drift
Genetic drift—along with
natural selection, mutation, and migration—is one of the basic mechanisms of
evolution.
In
each generation, some individuals may, just by chance, leave behind a few
more descendents (and
genes, of
course!) than other individuals. The genes of the next generation will be the
genes of the “lucky” individuals, not necessarily the healthier or “better”
individuals. That, in a nutshell, is
genetic
drift. It happens to ALL
populations—there’s
no avoiding the vagaries of chance.
Look at this cartoon.
Genetic drift affects the genetic makeup of the population but, unlike
natural selection,
through an entirely random process. So although genetic drift is a mechanism
of
evolution, it
doesn’t work to produce
adaptations.
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Genetic drift—one of the
basic mechanisms of evolution—is simply the evolutionary equivalent of a
sampling error.
Imagine a game in which
you have a bag holding 100 marbles, 50 of which are brown and 50 green. You
are allowed to draw 10 marbles out of the bag. Now imagine that the bag is
restocked with 100 marbles, with the same proportion of brown and green
marbles as you have just drawn out. The game might play out like this:
It’s clear that the ratio
of brown to green marbles “drifts” around (5:5, 6:4, 7:3, 4:6 . . .)
This drifting happens in
populations of organisms. Due to many random factors, the genes in one
generation do not wind up in identical ratios in the next generation, and
this is evolution. It is possible for the frequency of genes for brown coloration
to increase in a population of beetles without the help of natural selection.
While this is evolution, it is evolution due to chance, not selection.
Genetic drift has several
important effects on evolution:
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Drift reduces genetic
variation in populations, potentially reducing a population’s ability to
evolve in response to new selective pressures.
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Genetic drift acts faster and
has more drastic results in smaller populations. This effect is
particularly important in rare and endangered species.
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Genetic drift can contribute
to speciation. For example, a small isolated population may diverge from
the larger population through genetic drift.
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Genetic drift can cause
big losses of genetic variation for small populations.
Population bottlenecks
occur when a population’s size is reduced for at least one generation.
Because
genetic drift
acts more quickly to reduce
genetic
variation in small populations, undergoing a
bottleneck can
reduce a population’s genetic variation by a lot, even if the bottleneck
doesn’t last for very many generations. This is illustrated by the bags of
marbles shown below, where, in generation 2, an unusually small draw creates
a bottleneck.
Reduced genetic variation
means that the population
may not be able to adapt to new selection pressures, such as climatic change
or a shift in available resources, because the genetic variation that
selection would act on may have already drifted out of the population.
An example of a
bottleneck:
Northern elephant seals have reduced genetic variation probably because of a
population bottleneck humans inflicted on them in the 1890s. Hunting reduced
their population size to as few as 20 individuals at the end of the 19th
century. Their population has since rebounded to over 30,000—but their genes still carry the marks of this
bottleneck: they have much less genetic variation than a population of
southern elephant seals that was not so intensely hunted.
Founder effects
A
founder effect
occurs when a new colony is started by a few members of the original
population. This small population size means that the colony may have:
- reduced genetic variation
from the original population.
- a non-random sample of the
genes in the original population.
For example, the
Afrikaner population of Dutch settlers in South Africa is descended mainly
from a few colonists. Today, the Afrikaner population has an unusually high
frequency of the gene that causes Huntington’s disease, because those
original Dutch colonists just happened to carry that gene with unusually high
frequency. This effect is easy to recognize in genetic diseases, but of
course, the frequencies of all sorts of genes are affected by founder events.
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Development
Development is the
process through which an embryo becomes an adult organism and eventually dies.
Through development, an organism’s
genotype is expressed as a
phenotype, exposing genes to
the action of natural selection.
Studies of development
are important to evolutionary biology for several reasons:
Explaining major
evolutionary change
Changes in the genes controlling development can have major effects on the
morphology of the adult
organism. Because these effects are so significant, scientists suspect that
changes in developmental genes have helped bring about large-scale
evolutionary transformations. Developmental changes may help explain, for
example, how some hoofed mammals evolved into ocean-dwellers, how water plants
invaded the land, and how small, armored invertebrates evolved wings.
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Mutations in
the genes that control fruit fly development can cause major morphology
changes, such as two pairs of wings instead of one. |
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Another
developmental gene mutation can cause fruit flies to have legs where the
antennae normally are, as shown in the fly on the right. |
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Learning about
evolutionary history
An organism’s development may contain clues about its history that
biologists can use to build evolutionary trees.
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Characters
displayed by embryos such as these may help untangle patterns of
relationship among the lineages. |
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Limiting
evolutionary change
Developmental processes may constrain evolution, preventing certain
characters from evolving in certain lineages. For example, development may
help explain why there are no truly six-fingered
tetrapods.
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Types
of Developmental Change
Developmental changes have likely been involved in important morphological
changes—like the evolution of novel and complex structures.
Here are a few of the sorts of developmental changes that may have been
important:
Module duplication and adaptation
A
module refers to a unit that
can be duplicated and further adapted. For example, arthropods have various
numbers of body segments. Segment duplication and loss is a developmental
change that probably occurred many times in the
evolution of this
clade. The graphic below shows a
hypothetical example of module duplication and adaptation.
Individualization
This is the modification of a particular module, usually when there is
selection for a specialized function.
Scorpion image courtesy of the California
Academy of Sciences.
Spider image courtesy of Michael Hedin, San Diego State University.
Heterochrony
Heterochrony is a change
in the timing of developmental events. For example, a change in timing might
slow down the
development
of the body, but not alter the maturation of the reproductive system. This
change yields an adult organism with a form similar to the ancestral juvenile
form.
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Larval salamander image courtesy
of Jeff LeClere.
Tiger salamander image courtesy of Greg Sievert.
Axolotl image courtesy of Barbara Shardy.
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Salamanders go through a larval stage in which they have feathery,
external gills (left). Most salamanders lose these gills when they
metamorphose into adults (center). Because of heterochrony, axolotls now
retain the juvenile external gills as fully reproductive adults (right).
Allometric growth
Allometric growth
is a change in the rate of growth of a dimension or feature relative to other
features. For example, we can describe some of the evolutionary changes that
produced bats in terms of allometry. Bat wings are basically paws with really
long fingers and skin stretched between them. In order for these wings to
evolve, the rate of growth of finger bones must have increased relative to
the growth of the rest of the bat’s body—or perhaps the rate of growth of the
rest of the body decreased relative to the fingers. Either way, it is
allometry.
Bat image courtesy of Ben
Waggoner.
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Going from a simple
fertilized egg cell to a fly over the course of a few weeks is an amazing
transformation. A lot of things have to happen: the body form must be laid out
(head/tail, back/belly), different tissues must be built, and organs must be
grown. The adult fly is composed of a lot of very different parts made of
different cells—yet every cell carries the same genetic instructions. So how
does it “know” what to do?
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Certain genes
control where and when other genes are expressed.
Not all
genes code for “building
material”
proteins (such as keratin
that makes up part of your skin, or rhodopsin that makes eyes sensitive to
light).
Regulatory genes control when
and where other genes get turned on. For example, these sorts of genes tell
the cells of the fly when and where to start building wings. This occurs
during the larval stage on the second and third segments of the thorax.
Regulatory genes can start a “chain reaction” of effects, turning on and off
other genes, whose products affect other genes, whose products in their turn
affect other genes, and so on. A single regulatory gene can thus control the
construction of a body part as complex as a leg or eye.
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The diagram above
illustrates how the master control gene regulates other genes, which in
turn, regulate other genes.
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Different segments of the developing fly embryo express different genes.
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Different cells have
different genes expressed.
For example, eye cells turn on the genes that make proteins necessary for
vision—but the cells lining the digestive tract don’t turn on these genes.
Instead, they turn on genes that create digestive enzymes.
- Chemical signals also influence the fate of cells.
Chemical signals from
the environment and from other cells can affect which genes are turned on in
a particular cell. For example, in the developing vertebrate eye, chemical
signals from the retina probably cause adjacent cells to become lens cells
instead of some other type of cells. Here we see a diagram of the optic cup,
of which the retina is part, developing normally. As a result, it sends
signals to nearby cells, causing them to form a lens from the
epithelium. The pictures
below illustrate what happens to lens development if the optic cup is
removed, transplanted, or replaced by other tissue.
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