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. 
    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)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.