EVOLUTION – Biology 4250
Dr. Adams
Review Sheet Number 1 (Test 1):
Evolution – change in frequency of alleles in a population of a species through time
(originally [Darwin]: descent with modification; adding our understanding of genetics
has resulted in the definition presented here)
Chapter 1: A Case for Evolutionary Thinking
Chapter 1 presents an overview of the HIV virus and mutational changes that have taken
place in the virus since it made its first "appearance" in the human population in the 1970’s. The
incidence of different strains of the virus has changed through time in response to the various
drugs that humans have developed and the use of the drugs in treating humans. As such, the
treatments represent selective pressures placed on the virus, which, as expected from an
evolutionary standpoint, has resulted in "allelic" changes in the virus over time – a very obvious
case of evolutionary change. This particular change, as well as changes seen in flu viruses from
year to year, etc., represents evolution taking place that is incredibly important to everyone on
the face of the planet. We will refer to this example from time to time as we go through the
course. Please be sure to read this chapter, and ask questions if you have them.
Chapter 2: The Pattern of Evolution
Definitions you should already or need to know:
evolution; natural selection; homology;
shared (common) ancestors; descent; genes; alleles
micro- and macroevolution; speciation
2.1:
Types of Evidence for Microevolution:
I. Selective
breeding -- "artificial" selection. Various breeds of domesticated
animals/plants.
"high-runner" mice
II. Evidence from Living species:
A. Direct observation of change
through time -- contrary to popular belief, change
through
time has been directly observed in hundreds of species of organisms. Note the
the Field Mustard
example in the textbook. I will cover the
Soapberry Bug
example, and, of course, microbes, too.
B. Vestigial organs: organs
which appear to be evolutionary "leftovers". We see these in
adults of numerous species. Additionally, some organs may form during
development and then
disappear,
and even at the genetic level there are inactive genes called "pseudogenes", which are
genetic "left
overs". Examples are discussed in the book.
2.2: Evidence for Speciation -- observable from
living organisms
I. Laboratory examples
II. From natural
populations -- three-spined sticklebacks (we'll talk about these again)
Ring species
2.3: New forms from old -- macroevolution
Extinction and Succession: Fossils
are traces (any type) indicating existence
of some
organism in the past. Fossils
can exist, of course, of species still living today (eg., coelacanth),
but much more interesting are
the fossils of species that are now extinct. Extinction, at both the
species and population level,
is incredibly important in the overall course of evolution. This will
become abundantly clear as
we go through this semester.
Fossils are used to support the "law of succession".
Transitional forms – one argument that has been presented against evolution is the lack
of transitional forms ("missing links"). Again, contrary to popular thought, the fossil record is
littered with abundant transitional forms; what you would expect with evolution
occurring and
support for the law of succession.
2.4: Evidence of Descent with modification -- apparent relatedness
of all life forms.
Genes are passed through descent from ancestors; organisms share genes because of
shared (common) ancestors. The end result is that shared
structures are a result of shared
genes. Structures shared because of share genes are called homologies. In biology, homology
literally means "similarity between species that
results from inheritance of traits from a common
ancestor." These can
be used to construct an
evolutionary, or phylogenetic, tree (see below*).
[In class "exercise":
your family and who’s most closely related to whom.]
It is sometimes difficult to distinguish homologous traits from homoplasies, which are
similar traits in different organisms not due to descent but from convergent evolution (the wing
of a bird and the wing of a butterfly, for example). Bones in the adult limbs of different
vertebrate species are an excellent example of homologous traits. Changes in structures during
development can also indicate closer relationships than by simply observing adults of different
species. With DNA and protein analysis techniques we now have, we can actually examine
specific gene codons (three base sequences within the DNA that code for the amino acids in
proteins) and look for similarities or differences in specific gene codes from one species to the
next, to get an indication of just how similar two species are, i.e., how closely related they are.
Species being related refers to their genetic similarity, which indicates how recently they may
have shared a common ancestor. So, comparative anatomy, embryology, and molecular
biology can all provide information on potential homologies.
2.5: Age of the Earth – the concept of evolution clearly needs time
The geologic time scale (yes, I will expect you to memorize
most of
the time line in Fig.
2.31, pg. 63 . . . but not yet!), radiometric dating, uniformitarianism,
plate tectonics.
The surface of the earth has clearly changed, and is continuing to change through time,
with processes that take a LONG amount of time ... and, if the surface of the earth is constantly
changing, if the organisms DON’T change, then extinction would appear inevitable.
In most cases, you will be responsible for examples of the concepts that are presented in the
text book, as well as the other examples that I present in the classroom.
Chapter 3: Darwinian Natural Selection
Artificial Selection: although not "natural",
indicates that species CAN change genetic
makeup through time based on very
specific selective pressures. (see Brassica example)
Natural Selection -- requires significant time
Four postulates (actually five if you include the time aspect), all testable:
1. Individuals within species are variable.
2. This variation is genetic (heritable); can be passed on to the offspring.
3.
There is differential survival and reproductive success in the offspring. More off-
spring are produced than can survive, in every generation (there are not
enough resources to support all the offspring).
4. As follows from #3, there will be competition for resources (food, shelter, etc.)
as well as mates, and those that have the genetic variations to compete most
successfully will in turn reproduce the most,
passing these traits on to offspring.
These individuals are
selected for and are the most fit.
Nonrandom reprod.
"Survival of the "fittest": Biological fitness represents the ability of an organism to pass its
genes on to future generations.
Natural Selection, therefore, should result in populations that are better
adapted to the
current environmental conditions. An adaptation is a trait in an organism that increases its
fitness relative to other individuals without this particular version of the trait in the current
environment. Understand that what is a "good" adaptation now may not necessarily be so in
the future if the environmental conditions change.
By the way, both Charles Darwin and colleague Alfred Russell Wallace postulated the
same natural selection mechanism for evolution, and both had papers read before the Linnean
Society in London in 1858.
Testing the postulates: Snapdragon flower color; The Galápagos Finches (Darwin had personal
experience with these finches during his "Voyage on the Beagle");
The "Nature" of Natural Selection – the nonrandom selection of fitter individuals:
The following are perhaps some of the
most important basic concepts that for the
foundation of evolutionary thought.
1. Natural Selection acts on individual
phenotypes, but the evolutionary consequences
alter population genetic structure. Nature selects for or against individuals.
Some will die and
have
their biological fitness significantly reduced or eliminated, others are selected for and have
their biological fitness enhanced. The end result, therefore, is that the alleles carried by those
that are selected for increase in the population, while those alleles carried by individuals who
are selected against will decrease in, and sometimes be eliminated from, the population. It
should also be noted that the natural selective pressures occurring in one population of a
species
will not necessarily be the same in other populations.
2. Natural selection is not a purposeful progression
forward. Understand that natural
selection proceeds by selecting for or against individuals currently in the
population. That means
that
the population should become more adapted for the moment, but not necessarily beyond
that.
We’ve already made the point that the environment can continuously be changing, and
therefore what is best adapted now is not guaranteed a "free pass" into the future.
3. Natural Selection cannot instantaneously result in new traits, but new
mutations that
result in new traits through time can be selected for (if the new traits increase fitness in the trait
bearing individual). Indeed, this is the mechanism for generating NEW genes (ones that had
not even existed before). Understand that most mutations are not typically beneficial, but that
doesn’t mean that all mutations are detrimental.
4. Natural selection does NOT result in "perfection" (remember vestigial traits).
Natural selection can only provide adaptations from existing genetic characteristics. These will
typically be modified slowly with mutations providing the possible new adaptations. Natural
selection cannot generate new genes as needed. Additionally, some genes can influence more
than one trait, and selection based on one trait may alter other traits as well.
5. Selection acts on individuals, NOT for the good of the species.
The Modern Synthesis: combining Darwin’s/Wallace’s natural selection with genetics
Darwin (and Wallace) knew nothing about DNA and genes, and therefore:
1. knew nothing about mutation being the source of new variation
2. knew nothing about precisely how traits were inherited
Additionally, the age of the earth was not known, and so the amount of time estimated for
selective events to occur and evolution to proceed were completely unclear.
Now, however, we understand that mutation is the source of allelic variation, and that
occasionally mutation even results in new genes, and that the earth is VERY old. As such
natural selection has a source of variation to work with and plenty of time.
(For those that feel a need to be
able to better answer evolution deniers, section 3.7 talks
about the most
frequent arguments against evolution and how science and the evidence can
clearly explain these supposed conflicts.)
Chapter 4: Estimating Evolutionary Trees*
Here's some useful terminology:
Phylogeny – "family" tree showing likely evolutionary relationships
between organisms
Concepts: A pleisiomorphy is an ancestral (or primitive) trait
An apomorphy is a derived (descendant) trait
A synapomorphy is a shared homologous trait ("syn-" = together), that in turn can help
define relationships between species
An autapomorphy is a uniquely derived trait in a single taxon
A taxon (plural: taxa)
is any monophyletic (usually) group at any level in
classification
A monophyletic group is an ancestor and all of its
descendents (see "clade", below)
A paraphyletic group is an ancestor and some, but not all, of it's
descendents.
A homoplasy, or convergent trait, is a similar trait that has
evolved independently in
more than one lineage.
A reversal is when a mutation occurs such that an
apomorphic trait reverts to its
previous, more pleisiomorphic state.
A clade is a monophyletic group of related organisms based on synapomorphic traits;
in a phylogeny, a clade begins at a
nodal species and includes all descendents from
that point
-- a monophyletic group, in other words
A node is a point in the phylogeny representing a divergence between two species from
a single ancestor.
A branch represents a single taxon proceeding through time
A tip
(terminal
node)
represents a unique extant or extinct taxon
Sister taxa (species, genera, families, etc.) are the two taxa
that diverge from the
same node in the phylogeny; meaning they are closely related
because of a
recent common ancestor
A polytomy is a node from which three or more taxa seem to
arise; this is likely due to
not enough character sampling (I will explain this in class).
An outgroup is the taxon to which we compare the group of species for which we
are
trying to construct the phylogeny; the most useful outgroup would be the sister
taxon,
if information is available for that taxon. This allows us to
polarize character states.
Age is represented on the tree by older being near the base and younger being higher up in
the tree (although there are different ways to assemble the tree).
The difficulty is finding the synapomorphies to assemble the phylogeny; shared
pleisiomorphic or homoplasic traits do not indicate recent common ancestry and cannot define
clades. Different traits may actually indicate different relationships, so that the phylogeny that is
ultimately assembled represents the most parsimonious from different possible phylogenies.
Chapter 5: Variation among Individuals
Kinds of Variation: genetic, environmental,
and genotype-by-environment interaction
1. Genetic variation: terms to know -- genes, alleles, genotype,
phenotype, genome
This is, of course, the raw material for evolution
2. Environmental variation -- although important to the phenotype, and
potentially
therefore influencing the fitness, this variation is NOT transmitted to
offspring.
3.
Genotype-by-environment interaction -- organisms have reaction norms,
the pheno-
types they may develop upon exposure to dif. envivons. Phenotypic
plasticity
allows for organisms to change phenotypes suitable for the current living
conditions.
The fact that the plasticity has a genetic basis means that plasticity is a
selectable
trait and can significantly influence the evolution of the organism.
Mutation and Genetic Variation
As already mentioned, mutation provides the raw material of evolution. Let me
emphasize again that mutation, for the most part, is typically either neutral or detrimental from
a selective standpoint. A perfect example would be a mutation altering the function of an
enzyme in cellular respiration. If this mutation resulted in respiration stopping completely, the
organism would stop producing ATP at the rate necessary and death would occur – rather
detrimental! You should also be aware that such a mutated allele is typically "turned off" in
diploid organisms. However, not ALL mutations will be "bad", and, as mentioned above,
the only way to get truly new alleles is through mutation.
The Machinery of Life -- the structure of DNA (and RNA):
Nucleotides – the building blocks of DNA/RNA
the nucleotides themselves consist of a 5C sugar (deoxyribose), a phosphate
group, and a
nitrogenous base
The nucleotides link together, providing a sugar-phosphate backbone with the
nitrogenous bases sticking off to the side
The Nitrogenous bases:
the pyrimidines (single-ringed): cytosine and thymine
(uracil in RNA)
the purines (double-ringed): guanine and adenine
In DNA, two nucleotide strands are linked together (in a double helix) due to hydrogen
bonds
between the nitrogenous bases (two between A & T; three between G & C) sticking out
from
the single sugar-phosphate backbones. The two sides of the double helix run in opposite
(5’→3’) directions.
REVIEW: ALL processes involving
nucleic acids run in the (5’→3’) direction.
DNA replication:
Enzymes
helicase and DNA polymerase, leading/lagging strand, Okazaki fragments,
ligase. RNA primers.
Transcription: RNA from
DNA
Enzymes
helicase and RNA polymerase, promoters, termination sequences, sense/
antisense
strand, leader/trailer sequences
Post-transcriptional
modifications -- In eukaryotes, introns removed and exons
(re)combined and expressed in final transcript; allows for exon "shuffling"
Translation: Protein
from RNA (at ribosomes)
Codons,
tRNA's with anticodons, start/stop codons
The Codon Table (see page
160) – note start and stop codons
Mutations:
Premutations
-- these are initial errors made during replication, most of which are fixed by
"fixit"/repair enzymes; a typical mammalian cell suffers 100,000 replication
errors/division
Unfixed premutations
are the mutations: point mutations (single base substitutions in
DNA
sequences) have variable effects (neutral, nonsense)
-- can be silent
(synonymous) or
replacement (nonsynonymous). Can be transitions or
transversions.
Frame-shift – insertions/deletions
(indels) of bases in a gene sequence; virtually ALWAYS
deleterious
The source of New Genes: pgs. 164-166
Gene duplication – this can result from
unequal crossover, but can also result "on
purpose",
where the cell intentionally creates new copies of some genes. There are
a number of genes which are "naturally" duplicated in the genome of most species
The important result, as stated above
is that these "extra" copies of the gene may be free
to
mutate independently of the original. This may result in pseudogenes, copies of an "original"
that are in turn turned off and non-functional. OR, you may get new genes (example: the
globin
gene family). Recent estimates suggest that more of the genome
is affected by copy number
variation than point mutation variation.
Genes which are duplicated and later diverge in function
due to mutation may be paralogous
(within species) or orthologous (due to a speciation event).
Retroposition (retroduplication) -- again results in extra
copies of a gene
Chromosome alterations – involve changes in overall chromosome structure, and therefore
larger changes in the overall amount and ordering of DNA
Inversions – may "lock" linked genes in place (due to elimination of crossover in the
inverted regions); so selection may be working on a whole set of genes, OR selection
may work
on a few genes in the linked set, with the rest of the alleles being carried
with the selected alleles. We will discuss this phenomenon more later (chap. 7).
Polyploidy
Common in plants, but quite rare in animals.
This difference is probably due to much
greater developmental plasticity in plants
(less cell differentiation in plants).
The apparent most common source of polyploidy is errors in meiosis, producing diploid
(not haploid) gametes. Assuming these gametes are used in the production of new offspring,
tetraploid organisms can result. If this organism is capable of reproducing as well, then it may
function as a completely new species – new species production in ONE generation.
(einkorn/wheat example).
Mutation Rates: most obviously observable with
loss-of-function mutations, which are
often clearly visible in the phenotype. But mutation rates are higher than
observable because
of silent and subtle replacement mutations. Early work suggested that the
mutation rate per
cell division is approximately equal in most organisms, suggesting natural
selection had led to a
single, shared mutation rate for most organisms. However, recent
estimates of mutation rates
indicate that it is different for different species, and different genes within
species as well (see
Fig. 5.34, pg. 170). One
take home message from all studies suggests that whatever the rate,
mutation generates a
SIGNIFICANT amount of nuclear gene (and mitochondrial gene) variation
in each generation. EVERYONE is a mutant.
On the flip side, it is also important to note that
DNA replication on a per
site basis is still
astonishingly accurate -- for instance, for C. elegans
(a roundworm), incorrect
bases are
substituted only once every 100,000,000 bases.