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; (common) ancestors; descent; genes; alleles
Types of Evidence:
    I.  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 Soapberry Bug
example from the textbook (and I will present others).
        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.
    II.  Fossils: 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, again what you would expect with evolution occurring.
    III.  Evidence of Descent with modification -- apparent relatedness of life forms.
        Ring species
        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 common
ancestors – or homology. 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.
    IV. Age of the Earth – the concept of evolution clearly needs time
Related concepts you will need to understand:
        The geologic time scale (yes, I will expect you to memorize a good percentage of Figure
2.25 on page 62
), 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.
    V. Correspondence of data sets – age of the earth, plate tectonics, biogeography,
center/point of origin. I will discuss with you the concept of the center/point of origin, and why
in turn the distribution of organisms (biogeography) on the face of the planet is what you would
expect if new species actually do arise by evolution.
________________________________

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.
    Natural Selection -- requires significant time
        Four postulates (actually five if you include the time aspect), all testable:
                1. Individuals within species are genetically variable.
                2. This genetic variation is heritable; can be passed on to the offspring.
                3. More offspring are produced than can survive, in every generation (there are not
                        enough resources to support all the offspring).
                4. There is differential survival and reproductive capabilities in the offspring. 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. These individuals are selected
                        for and are the most fit.

     "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: 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 individuals, 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. Nature can only act directly on the phenotype. The phenotype is NOT entirely
genetic, though a significant percentage of the phenotype is directly determined by the
genotype
; so selecting for/against certain phenotypes in turn can alter which alleles are being
passed along in the population.
        3. Natural selection is not a purposeful progression. 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.
        4. 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.
        5. 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.

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.

Chapter 4: Estimating Evolutionary Trees*
    We will return to this concept a bit later in this course, but you need a basic understanding
of the concept of phylogeny and what this indicates about the history of life on the planet.
     Here's some useful terminology:
Phylogeny – "family" trees showing evolutionary relationships
        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 homoplasy, or convergent trait, is a similar trait that has evolved independently in
                more than one lineage.
           
A clade is a 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 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 represents either an extant or extinct taxon
        Age is represented on the tree by older being near the base and younger being higher up in
                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: Mechanisms of Evolutionary Change – 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 and even occasionally new genes is through mutation.

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. 
    REVIEWALL 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)com-
                bined and expressed in final transcript
        Translation:  Protein from RNA (at ribosomes)
            Codons, tRNA's with anticodons, start/stop codons
        The Codon Table (see page 146) – note start and stop codons

Mutation types:
        1. point mutations – single base alterations in DNA sequences; variable effects
        2. frame-shift – insertions/deletions (indels) of bases in a gene sequence; virtually
            ALWAYS deleterious
    DNA replication and point mutations:
        The enzymes: helicase/DNA polymerase; replication always in (5’→3’) direction.
        Point mutations: single base substitutions during replication– can be silent
(synonymous) or replacement (nonsynonymous). Can be transitions or transversions.
        Effects? Silent – neutral from a selective standpoint because protein unchanged;
            typically results from mutations in the third base of a codon (moreso with transitions)
        Replacement – radically different effects depending on the change.
    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.  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.
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 once every 100,000,000 bases.
        Individual variation in mutation rates – two reasons: differences in efficiency of DNA
            polymerases and efficiency of enzymes repairing damage (mismatch) to DNA; suggests
            mutation in the genes for these proteins are potentially extremely important.
        Species variation in mutation rates – differences between animals/plants important, as
            well as generation time.
        Gene variation – one generalization seems clear: DNA polymerase efficiency and repair
            efficiency both much higher for genes that are active (in other words, where mutations
            would potentially be most damaging)

Fitness effects of Mutations:  already mentioned. 
        many deleterious:  if mutations accumulate, populations ultimately decimated
        neutral effects:  silent mutations; but remember that what is "silent" now may not be "silent"
            later

The source of New Genes
        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 (examples?)
                Rates of duplication:  see information on pg. 153.

        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).  These may be paralogous or orthologous.

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 inherited
            with the selected alleles. We will discuss this phenomenon more later (chap. 7).
        Polyploidy
            Common in plants, but quite rare in animals. Apparently this difference is due to much
            greater developmental plasticity in plants, partly because of 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).

Genetic Variation in Natural Populations
        Measuring the variation
            Gel Electrophoresis
            Calculating allele frequencies (can be inferred in some cases from phenotypes)
                    The HIV CCR5-Δ32 allele
        How much variation is there?
            How much genetic diversity actually exists in populations? For individual genes, this
can vary tremendously, depending in large part on the function of the proteins made from that
gene. There are some genes that have one allele only, and so for those genes, ALL individuals
in the population will be homozygous for that gene (NO variation). However, as we’ve studied
more and more genes and organisms, the amount of genetic variability (polymorphism) that is
present in most populations is significant. The genes within individuals in a "typical" natural
population are between 5 and 15% polymorphic [heterozygous], and the "typical" population
as a whole has between 33 and 50% polymorphic loci.
        Why are populations so genetically diverse?
            Two views: 1. Balancing selection – of rare individuals (with different alleles),
heterozygous individuals, or different alleles at different times and places, and 2. Neutral
selection – different alleles do not infer either a greater or lesser selective advantage, so
different alleles are likely to be maintained in the population. It should be understood
that these two views are not mutually exclusive – either or both could be working on different
traits in specific populations.