Basic Biology II: Genetics and
How organisms work
Inheritance (pp. 104
120): sexual and asexual reproduction,
Mendelian genetics, crop improvement, genetic engineering
Natural Selection and Evolution (pp. 131
Classification and Diversity (pp. 124
130, 137, 140
Contrast sexual and asexual reproduction.
Understand the difference between haploid and diploid, and how the
processes of meiosis and fertilization convert between the two states.
Use the vocabulary of genetics: gamete, allele, homozygote,
heterozygote, dominant, recessive, phenotype, genotype, to describe
explain why the offspring of a self
pollinated heterozygote appear in a
ratio of 3/4 dominant phenotype to 1/4 recessive phenotype.
Define several methods of crop improvement and their general
properties: single gene traits, polygenic traits, selection, polyploidy,
hybridization, genetic engineering.
Describe the process of molecular cloning, using a plasmid, restriction
enzymes, and DNA ligase, and transformation.
Sexual and Asexual Reproduction
Long term survival requires reproduction. Even the longest
organisms are less than 10,000 years old.
Cellular machinery wears out, or gets clogged with waste products.
Environmental conditions change
Plants often reproduce
, through cuttings or runners or buds
(e.g. potatoes). The resulting plants are
: they are genetically
identical to the parent.
Used to preserve good combinations of traits.
is also found in plants, and in all animals. Sexual
reproduction means combining genes from two different parents,
resulting in new combinations of genes. Each parent contributes a
chosen half of their genes to the offspring.
This can be a good thing, because some new combinations will survive
better than the old ones.
It can also be bad: lack of uniformity in the offspring.
: having 2 copies of each chromosome, one set from each parent.
Humans have 46 chromosomes, 23 from each parent.
Almost any organisms you can see: plant, animal, fungus, is diploid.
: having only 1 copy of each chromosome.
Sperm and eggs (=
) are haploid
moss, a primitive plant, is haploid for most of its life
Plants, animals, and other eukaryotes alternate between haploid and
diploid phases. This is called
alternation of generations
Diploid organism generates haploid
gametes using the process of
gametes combine during the process of
to form a new diploid
In animals, the haploid phase is just one
cell generation, the gametes, which
immediately do fertilization to produce a
diploid zygote, the first cell of the new
In plants, the haploid phase is several cell
generations at least.
Lower plants are mostly haploid
Higher plants are haploid for only a few
The diploid plant is called the
and the haploid plant is called the
The science of genetics is devoted to understanding the patterns of how
traits are inherited during sexual reproduction. It was founded by Gregor
Mendel in the 1850's, using pea plants. Despite the obvious differences,
humans and peas have very similar inheritance patterns.
The fundamental observation of genetics: within a species, there are a
fixed number of genes, and each gene has a fixed location on one of the
This allows genes to be mapped: a gene's neighbors are always the same.
. Many genes have several variant forms, which are called
For example, a gene the produces color in the flower might have a purple
allele and a white allele. These alleles are designated P and p.
Differences in alleles are what makes each human different from all others
. If you cross close relatives with each other for
many generations, eventually all the offspring look alike.
Mendel started with several true
breeding lines, which differed from each
other in 7 distinctive characteristics
In many plants, you can
: cross the male
parts of a plant with the female parts of the same
In this case, both copies of any given gene are
identical. This is called
The plants are
homozygotes, either PP (purple) or pp (white).
The closest cross you can do in animals is brother x
. If you cross two true
breeding lines with
each other and examine some trait where the parents
had different alleles, you produce a
two copies of the gene are different.
Surprisingly, you often find that the heterozygote
looks just like one of the parents. The Pp
heterozygote is purple, just like its PP parent.
This is the F1 generation in the diagram.
. If a heterozygote is
identical to one parent, the allele from that
. The allele from the other
. That is, the heterozygote
looks like the dominant parent.
This is why we say purple is dominant to white,
and give purple the capital letter P.
. Phenotype is the
physical appearance, and genotype is the
The heterozygote in the previous paragraph has
the same phenotype as the homozygous
dominant parent (i.e. purple flowers), but a
different genotype (the heterozygote is Pp and
the parent is PP).
Now we want to move to the next
generation, by self
When a heterozygote undergoes
meiosis to produce the haploid
gametes, half are P and half are p.
These gametes combine randomly,
producing 1/4 PP, 1/2 Pp, and 1/4
Since PP and Pp have the same
phenotype, 3/4 of the offspring are
purple and 1/4 are white.
Methods of Crop Improvement
The idea that we can improve the inherited characteristics of crop
species is fundamental. Very few of the plants we use are unmodified
wild plants: most of them have been modified to make them easier to
grow and harvest, and to increase the quality and quantity of the
We will see many examples of crop improvement this semester. Here
are some of the basic methods used.
Single Gene Traits and Mutation
Single gene traits
. Many useful traits are controlled by
a single gene. Spontaneous mutations can lead to
important, abrupt changes
A good example: sweet corn. The recessive mutation
(sugary) produces kernels that are 5
10% sugar. But,
only when homozygous: the non
sugary allele (
Single gene mutations occur rarely, but often enough
so that observant people notice and propagate them.
Sweet corn was recognized and propagated by several
Native American tribes. The Iroquois introduced it to
Mutation rate: 1 in 10,000 to 1 in 1,000,000 plants.
induced mutation occasionally works, but
most are spontaneous.
Single gene traits are inherited in a Mendelian fashion:
each individual carries one copy of the gene from each
the relationship between phenotype (sweet vs. starchy
corn) and genotype (homozygous or heteozygous) is
determined by dominance vs. recessiveness.
Polygenic Traits and
. Many traits are
controlled by many genes, each of
which contributes a small amount to
the phenotype. Grain yield is a good
example: lots of genes contribute to
Such traits respond well to
In the simplest sense, selection
means using the best seeds to start
the next generation. If this is done
consistently, the crop slowly
improves over many generations.
Genetic research has led to an
understanding of what happens
during selection. This allows much
faster and more effective selection
than just saving the best seeds.
Normal diploids have 2 copies of every
chromosome. Sometimes it is possible to
double this number, making a
copies of every chromosome.
The drug colchicine does this by causing meiosis
to produce diploid gametes instead of the normal
haploids. Then, diploid sperm + diploid egg =
Tetraploids are often bigger, healthier, more
nourishing than their diploid parents.
Examples: cotton, durum wheat, potato, daylily
Tetraploid is a form of
, which means
having more than 2 sets of chromosomes (2 sets
There are triploid (e.g. banana and watermelon),
hexaploid (bread wheat, chrysanthemum), and
octaploid (strawberry, sugar cane) crops
Plants are not as rigid in maintaining species boundaries as
animals are. It is often possible to produce
different, but closely related species.
Members of the same genus will often hybridize
The resulting plants often have characteristics different
from both parents
Often sterile, but many plants can be propagated
The grapefruit is a naturally
occurring hybrid between a
(native to Indonesia) and a sweet orange (native to Asia).. It was
discovered in Barbados in 1750, then brought to Florida and
Hybrids have an “x” in their species name:
Sometimes, a hybrid will spontaneously double its chromosomes,
so you end up with a
. These interspecies
usually fertile, and they benefit from the general effect of
: bigger, healthier plants.
In the last 30 years it has become possible to take a gene out of one organism
and put it into the DNA of another organism. This process is called genetic
engineering. The resulting organisms are
genetically modified organisms
and the gene that has been transplanted is a
There are no real interspecies barriers here: all organisms use the same
genetic code, so genes from bacteria (for example) will produce the correct
protein in a corn plant.
However, some modifications must be made to the signals that control gene
expression, since these are more species
A few examples:
, a soil bacterium, produces a protein that kills
many insect pests, especially the corn earworm. The gene for this protein has been
transplanted into much of the US corn crop.
Roundup Ready soybeans (plus other crops). Roundup is the Monsanto brand
name for the herbicide glyphosate. A bacterial gene that confers resistance to this
herbicide has been transplanted to many crops. The farmer can then spray the
fields with glyphosate and kill virtually all the weeds without harming the crop.
About 87% of the US soybean crop is now Roundup Ready transgenic plants.
Some cultural issues here: are GMOs safe to eat?
The first step in genetic engineering is
Molecular cloning means taking a gene, a piece
of DNA, out of the genome and growing it in
bacteria. The bacteria (usually
large amounts of this particular gene.
The cloned gene can then be used for further
research, or to produce large amounts of
protein, or to be inserted into cells of another
species (to confer a useful trait).
The basic tools:
: small circle of DNA that
grows inside the bacteria. It carries the gene
: cut the DNA at
specific spots, allowing the isolation of specific
, an enzyme that attached
pieces of DNA together.
. Putting the DNA back
into living cells and having it function.
The Cloning Process
1. Cut genomic DNA with a
2. Cut plasmid vector with
the same restriction enzyme.
3. Mix the two DNAs
together and join them with
4. Put the recombinant DNA
back into E. coli by
5. Grow lots of the E. coli
containing your gene.
The real trick, however, is to find
the gene that confers your desired
Once a gene of interest has been identified and cloned, it
must be put into the plant.
Usually done with plant tissue culture. Small pieces of a
plant can be grown as an undifferentiated mass of cells on
an artificial growth medium.
Then, when treated with the proper plant hormones, these
cells develop roots and shoots. They can then be transferred
to soil and grown as regular plants.
To make transgenic plants, DNA gets put into the tissue
culture cells, by one of several methods:
One method is the
: tiny gold particles are coated
with the DNA, and then shot at high speed into the cells.
The gold particles penetrate the cell wall and membrane.
Some end up in the nucleus, where the DNA gets
incorporated into the chromosomes.
An important issue: the proteins produced by transgenes
are identical to those produced in the original species,
because the genetic code is universal.
However, the signals needed to express these genes are
specific, not universal.
Natural Selection and Evolution
Define fitness, and describe how differences in fitness and natural
selection lead to changes in gene frequencies within a species.
Describe how directional, stabilizing, and disruptive
Distinguish between the “biological species concept” and the
“morphological species concept”.
Distinguish between allopatric and sympatric speciation, and list
possible causes of sympatric speciation.
List and define several possible fates for a new species.
Evolution by Natural Selection
: the ability to survive and reproduce
healthy, fertile offspring. More fit
individuals have a better chance of producing
offspring than less fit individuals.
The basic idea of
simple: those organisms that are more fit
produce more offspring than other members
of their species, and so they will have more
descendants in future generations.
Many genes increase or decrease fitness. In
fact, most genes affect fitness in some way: it
is hard for a gene to NOT affect fitness.
Genes that increase in fitness gradually take
over the species, and genes that decease
fitness gradually get eliminated.
Selection and Evolution
is all members of a
species that interbreed with each
works the same
way as natural selection: the most fit
individuals have more descendants
than the less fit. However, in
artificial selection, humans determine
which individuals are more fit: we
decide which individuals will be
allowed to reproduce.
on the small scale
(microevolution) is just changes in the
frequency of genes in the population.
This can lead to large changes in
appearance over the long term.
Selection can be artificial: caused by humans, or natural: caused by
The simplest form of selection is
: one extreme phenotype is
less fit than the rest of the phenotypes.
Caused by outside forces like climate change or disease.
Or, by the appearance of a new gene that confers greater fitness.
Plot the distribution of the trait being selected on a graph. Usually get a bell
shaped curve (normal distribution, Gaussian distribution)
most individuals are
more or less average, with a few extremes at each end
Don’t let individuals at one extreme breed.
In later generations, the population average shifts away from the less fit extreme
Selection can act to favor the most
common type, the middle of the
distribution. This can happen
when both extreme types are
attacked. The status quo is
maintained. This is
Most selection is stabilizing: most
characteristics of a species stay
pretty constant over many
Example: human birth weight.
Too small leads to unhealthy
babies and high infant mortality.
Too large leads to mothers dying
Disruptive selection is the opposite of
stabilizing selection. In disruptive selection,
the average type is the least fit. Only the
extremes survive, creating a population with
two different alternatives. This is one of the
forces that drives the splitting of one species
Example: grasses that find themselves near
mines. Mine tailings containing heavy metals
are toxic to most plants. Some grasses are
resistant to heavy metal poisoning, so they can
grow on the mine tailings. Less resistant
members of the species grow on
uncontaminated ground. Since heavy metal
resistance is expensive, the resistant plants are
less successful on uncontaminated ground.
So, the species is being cut into 2 groups: the
resistant variety growing on the mine tailings
and the sensitive variety growing on clean
What is a Species?
What is a species? Based on ability to reproduce.
Biological species concept
”: a species is a group of organisms that
interbreed under natural conditions and that are reproductively isolated
from each other.
Reproductively isolated: don’t produce fertile hybrids.
Natural conditions: artificial breeding doesn’t count. For example, artificial
insemination, keeping 2 species locked up together.
In contrast, the older “
morphological species concept
”: members of the
same species look similar to each other. Many examples of organisms
that look similar but can’t produce fertile offspring.
Problems with biological species concept:
Doesn’t work with fossils or extinct species.
Doesn’t work with asexual species , such as most bacteria.
How to deal with what is “natural”.
: splitting of one species
into 2 different species. Very
If a species is split into two groups
that don’t interbreed, they mutate and
change independently, and soon are
unable to produce fertile, healthy
Traits that directly affect
reproduction are especially prone to
changing: what is attractive to
members of the opposite sex is prone
to changes in fashion in the non
human world as well as the human.
Selection for traits directly affecting
reproductive success is called
The simplest and most common
mechanism of speciation is
: 2 groups of
one species are isolated
geographically, and diverge into
Once isolated from each other,
random mutations alter
appearance and the ability to
create a viable offspring very
If members of the two groups
meet, they won’t be able to
More Allopatric Speciation
The most common cause of
allopatric speciation is
geographical barriers: mountains,
oceans, rivers. A few members of
a species manage to cross by a
rare chance event.
This is the mechanism by which
Darwin’s finches evolved into
separate species in the Galapagos
islands. Only very rarely can
birds cross the ocean to get to
Or, the barrier develops slowly as
conditions change: the gradual
formation of the Grand Canyon
split a population into 2 isolated
groups, that have diverged into
separate species, the Kaibab and
Geographical isolation is the easiest way
for species to form, but there are other
that occurs within the same geographical
Disruptive selection can cause sympatric
So can polyploidy
An example: cichlid fish in Lake
Barombi Mbo in Cameroon, Africa
isolated volcanic lake.
Nine species, all more closely related to
each other (by DNA evidence) than to
similar fish in other lakes.
Lake has no distinct geographical zones,
and the fish can easily swim anywhere in
They feed in different locations, but all
breed in the same location, close to the
the speciation mechanism is not clear.
Sympatric Speciation by Polyploidy
About half of all flowering plants are
polyploid: more than 2 copies of each
Polyploids are the result of failure of cell
division (mitosis or meiosis) to separate
the chromosomes into 2 cells.
Most common is a tetraploid: 4 sets of
When a tetraploid crosses with a diploid,
the result is a triploid (3 sets of
chromosomes). Triploids are sterile: there
is no way to evenly divide 3 sets of
chromosomes into 2 cells during cell
Seedless bananas, watermelons, and
apples are triploids.
Result is instantaneous speciation: the
tetraploid can’t produce offspring with
its diploid parent. Only tetraploid x
tetraploid or diploid x diploid works.
When two populations of a species are
separated by a geographical barrier, they
diverge genetically. Sometimes the
barrier is removed and the two groups
come into contact with one another. The
region of contact is a “hybrid zone”.
Several possibilities exist:
If the two groups have only diverged a
bit, fertile offspring will result, and the
two groups will merge back into a single
species. Geographical differences may
exist within the species: different
subspecies or varieties, but all can
If the two groups have diverged to the
point that no fertile or healthy offspring
result from their matings, selection
pressure occurs to deter further matings.
They are now two different species.
Patterns of Speciation
What happens after 2 species separate from
In some cases, the species exists for millions
of years, gradually changing in response to
external conditions but always maintaining as
a single distinct species.
horseshoe crabs today are almost identical to
450 million year old fossil horseshoe crabs
In other cases, many new species will form
from a single species in a very short time:
this is “
”. This often
happens on isolated islands, where a new
species is blown in by a storm, and finds
many different ecological niches to fill.
Darwin’s finches are an example of this.
They are thought to have originated with a
small group of finches that blew over about 1
million years ago, to islands with no
dangerous predators and very few other land
can happen: none left of the
Various events can cause extinction:
being outcompeted for a critical resource,
having the climate change too rapidly to
” are caused by
catastrophic events. The Earth has had
several mass extinction events, where the
vast majority of species die out over a
short period of time.
This is what is seen when one moves
between various geological ages.
Asteroids hitting the Earth are
responsible for at least some of these, but
probably not all.
Disasters that lead to the extinction of
some species often open up niches for
other species to expand into: the
extinction of the dinosaurs led to a major
adaptive radiation of mammals.
Classification and Diversity
Be able to recognize a proper binomial species name.
Distinguish between taxonomic classification and
Distinguish between and recognize monophyletic groups
and polyphyletic groups.
List the three domains of life, which domains are
prokaryotic, which domain contains plants and animals,
and which domains contain microorganisms
Communication worldwide is facilitated by having a set
Lots of plants have several different common names, and
the same common name is often given to several different
(and very unrelated) plants.
To solve this problem, each species is given a unique
scientific name, or binomial name. Same name in all
System invented by Carolus Linnaeus (Carl Linne) in
In 1867, an international botany congress in Paris met to
standardize rules for naming plant species.
Rules are constantly revised. Most recent was the 17th
Congress, which met in Vienna Austria in 2005.
Published in the
International Code of Botanical
All organisms are classified into a hierarchical
arrangement, as in the figure.
Dolphin fish (mahi
Dolphin mammal (porpoise)
Carolus Linnaeus (1707
1778) a.k.a. Carl Linne
Latin was the scientific language of the day, and the
name he published under was a latinized version of the
name he used with family and friends.
Plants were grouped into genera and given multi
Latin names. Linnaeus shortened this to the binomial:
genus followed by species.
He also grouped them into larger groups (classes)
based on sexual characteristics: the Sexual System
For example: "Nine men in the same bride's chamber,
with one woman“. This meant 9 stamens with 1 pistil in
the same flower. (All in Latin, of course)
although this system was invented for convenience, it
fit evolutionary reality fairly well, and we still
basically use it (with modifications and corrections)
also had a system for animals (and one for minerals,
Binomial Name Details
Form: a binomial name
is 2 Latin words, which are the genus and the species of the organism
First word (genus) is capitalized, second (species) is not capitalized
both words are italicized (or underlined).
Sometimes followed by the "authority", the first person to publish a description of the
species. Authority is NOT italicized. It is often abbreviated: L.
common name: Peppermint (in English)
Scop is the Canada thistle; Scop stands for Giovanni Scopoli, who first
Special rules for smaller groups like cultivars, landraces, hybrids
genus name is supposed to be unique throughout the entire world of life.
Species name is often reused: for example,
= found near water,
means smooth or hairless,
means from China
Recent Developments in Classification
: how different organisms descended
from a common ancestor
: classification based on similar
It is now the goal of taxonomists to make
taxonomy fit phylogeny. A phylogenetic
classification is better at predicting how similar
other characteristics are than one based solely on
superficial traits (like presence or absence of
Linnaeus’s taxonomy was based on a hierarchy of
groups: kingdom, phylum, class, order, family,
genus, species. Organisms were grouped
according to overall similarities.
The phylogenetic approach is called
Its primary goal is to group organisms by "shared
derived characteristics": characteristics that are
shared within the group but not found in any
closely related species.
In phylogeny, every
evolutionary event is the
splitting of one species into
two species. Groups above the
species level are for
In recent times, the higher
level groups of plants have
been greatly rearranged, with
many traditional families split
or combined. The biggest
case of this: the dicots are now
put into two very different
groups, the eudicots and the
paleodicots. This split is
based on a difference in the
number of pores in the pollen
grains, plus a great deal of
The goal is to make all named groups
. This means that every group
consists of all organisms that descended
from a single common ancestor.
In contrast: many of Linnaeus’s groups were
: mixing the descendants of two
or more ancestors together. For example:
“winged animals” is a polyphyletic group
consisting of birds, bats, and insects.
Polyphyletic groups need to be split up.
groups contain some, but not all
descendants of a common ancestor. Reptiles
are a good example: don’t contain the birds.
The use of paraphyletic groups is discouraged, but
DNA Evidence in Phylogeny
Much work with DNA sequences
instead of physical characteristics.
The changes that occur in DNA are
much simpler and easier to
understand than changes in body
Also, much of the DNA in an
organism's genome has virtually no
effect on the organism's phenotype.
For this reason, it is not subject
natural selection: it is
Selectively neutral DNA mutates
freely and randomly. Random
events are easy to model with
statistics, making it easier to
determine the true relationships
Also, DNA data is much easier to
gather and less subject to bias on the
part of the observer than physical
The Tree of Life
We are quite convinced that all living things on Earth descended
from a common ancestor.
NOT the first living organism: lots of things became extinct and have
no living descendants.
All organisms have ribosomes (which are used to translate
messenger RNA into proteins). By comparing ribosomal RNA
sequences, it is possible to get develop a tree of how all organisms
The idea comes from Carl Woese
Three main branches: eukaryotes, bacteria, and archaea.
Bacteria and archaea are both prokaryotes (DNA not in a nucleus), but
they are very different from each other in many details. Many archaea
thrive in extreme conditions of heat and salinity.
Eukaryotes divided into 4 main types: animals, plants, fungi, and
Fungi are more similar to animals than to plants
Protists are the single
celled eukaryotes, plus the algae. A very
polyphyletic group that someday will be better differentiated than it is
In this view,
and most of what is in
the modern view
(previous slide) is
relegated to the
primordial slime at the