A. Definition/Comparison Questions
Instructions: In your own words, define the pairs of terms given below. Write in complete
sentences, stating the differences and relationships between the two terms, and give specific
examples where appropriate. A complete answer usually requires four to eight sentences.
Each question is worth four marks, for a total of 40 marks.
natural selection / neutral variation
Natural selection is the process where individuals with certain heritable traits gains a relatively
higher fitness than others in the population when that trait increases individual’s relative fitness
and can be classified as an adaptive trait. This allows the individual to reproduce more
descendants carrying the heritable trait to be passed down their lineage until that adaptive trait
becomes the dominant characteristic in the population. Natural selection is the guiding
mechanism for the evolution of organisms. However, despite natural selection, some large
populations still exhibit significant genetic and phenotypic variation. Neutral variation
hypothesizes that some loci of alleles that code for certain enzymes or protein product that
have no effect on the fitness of the organism are not subject to natural selection (but to other
evolutionary forces). Biologists that support the neutral variation hypothesis do not question
that adaptive traits which increase the relative fitness of individuals are products of natural
selection but that not every genetic variation is caused by natural selection.
hybridization / biological species concept
Biological Species Concept defines species as group of individuals that can produce fertile and
fit offsprings and is built on assumptions of population genetic theory and non-evolving
population. The cohesiveness of species is maintained by gene flow between populations and
speciation can occur due to a discontinuity in the gene flow.
Hybridization occurs when two species produce a fit, fertile offspring which contrasts biological
species concept that species are reproductively isolated from one another. Using this definition,
technically the two separate species can be classified as one species. Hybridization blurs the
boundary between two closely-related species.
Inviability / Hybrid Breakdown
Hybrid Inviability: A postzygotic reproductive isolation. Gametes from two separate species
forms a zygote which contains two conflicting embryonic development instructions that causes
the embryonic development to fail.
Hybrid Breakdown: A postzygotic reproductive isolation. The hybrid offspring has low relative
fitness suffering from high rate of lethal and harmful mutations. Reinforcement, a natural
selection process, compounds to the elimination of hybrid offspring and increases reproductive
isolation and consequent speciation of those two species.
Hybrid Inviability: A postzygotic reproductive isolation that is caused by embryonic
development failure. Although the two species can successfully mate and have the gametes
from both species form a zygote, the zygote contains two conflicting instructions for embryonic
development and the hybrid offspring fails to develop and dies before reaching term. For
example, hybrid goat/sheep embryo dies before developing into a fetus so goat and sheep are
classified as two separate species.
Hybrid Breakdown: A postzygotic reproductive isolation where the hybrid offspring has low
relative fitness suffering from high rate of lethal and harmful mutations. Thus the hybrid
offspring has a early high mortality rate and usually dies before producing an offspring.
Reinforcement, a natural selection process, compounds to the elimination of the hybrid
offspring and increases reproductive isolation and consequent speciation of those two species.
Both occurrences reproductively isolate two species since a fertile and healthy offspring cannot
be produced and is classified as postzygotic because the reproductive error occurs after the
zygote formation.
allopatric speciation / parapatric speciation
Allopatric speciation: speciation that occurs between a geographically separated population of
one species. Physical barrier prevents gene flow between the now separate population of the
single ancestral species as well as different mutation, genetic drift, and natural selection cause
reproductive isolation between the two species. This leads to evolutionary branching
(speciation) like in the case of various Snapping shrimp species that have undergone allopatric
speciation separated on both sides by the Panama Isthmus.
Parapatric Speciation: Speciation between adjacent population with different geographical
distribution and environment. In one population of the grass Anthoxanthum that grows on
heavy metal contaminated soil, natural selection favored individuals with genetic variations
that could better tolerate the metal contaminants and spores from population that grew on
normal soil cannot migrate to the other population and have the same relative fitness as the
native population that already developed the necessary adaptive traits. Gene flow between two
adjacent grass populations slowed down until both subspecies become reproductively isolated
(temporal reproductive isolation from having different reproductive cycle time) and gene flow
could no longer occur.
Both speciation occurs due to a discontinuity in the gene flow between separate populations of
one species.
autopolyploidy / allopolyploidy
Autopolyploidy is when a diploid progenitor produces a polyploid offspring that has more than
2n chromosomes. In many fern species, The progenitor germ cell produces a diploid gamete
instead of a haploid gamete via a nondisjunction during mitosis/meiosis and then selffertilization of the two diploid gametes creates a polyploid (tetraploid) offspring that is
reproductively isolated from the parent fern plant and hence classified as different species.
Allopolyploidy is hybridization of two species that have different number of chromosomes to
successfully beget a polyploid hybrid. The hybrid’s germ cell’s nucleus contains nonhomologous chromosomes from the two different parent species which normally cannot
undergo meiosis. However if a spontaneous doubling of the chromosomes in the hybrid’s germ
cell occurs via non-disjunction, the cell can undergo meiosis to produce gametes which can go
through self-fertilization or fertilization with another specie’s gamete to produce a zygote, cell
differentiaton, and growth to create a polyploid organism that is reproductively isolated from
the parent species.
Autopolyploidy and allopolyploidy both do not require geographical or environmental
separation between populations to occur and while speciation via genetic divergence can take
eons, autopolyploidy and allopolyploidy can occur within a single generations and is common
among plants and certain animals.
Paraphyletic Taxon/Monophyletic Taxon
Paraphyletic taxon is a taxon (a hierarchical grouping of species) that includes the common
ancestor of a lineage and some but not all of its evolutionary descendants. For example, the
Class Reptilia has a common ancestor with birds but reptilian class doesn’t include birds and
birds fall under the Class Aves.
Monophyletic taxon includes the one common ancestor and all of its descendants such as Class
Mammalia or Class Amphibia.
Clade/Derived Characters
Derived character is a genetic/phenotypic variation of descendants not found on ancestral
species, for example, feathers and wings are derived characteristics of class Aves when
compare to its ancestor Archosaurs.
Clade is a grouping of organisms that were categorized together as being under the same group
under the principle of cladistics. Clade includes all species that share only an only common
derived characters (evolutionary branching) and not morphological divergence (ancestral
character).
exotoxins / endotoxins
Exotoxins are toxins secreted by bacteria or released during bacteria cell lysis. Exotoxins destroy
host cells or disrupt cell’s metabolism through various mechanisms. Some exotoxins cause toxic
shock or perforate cell membranes. Endotoxins are lipopolysaccharides or polygylcan found on
outer membrane of gram-negative bacteria that are released during bacterial cell lysis.
Endotoxins are simply gram-negative bacteria’s membrane glycolipids that cause an immune
response from the host’s immune system.
green bacteria / Gram-positive bacteria
Green bacteria or green sulfur bacteria are obligate anaerobic photoautotrophic prokaryotes
that convert light energy into chemical energy via oxidation of sulfide ions or ferrous ions and
create its own organic molecules by capturing CO2 gas. Green bacteria are gram-negative
bacteria, meaning that it has an inner membrane made of lipid bilayer, a peptidoglycan layer, an
outer membrane, and a capsule encompassing the layers below. Gram-positive bacteria have a
single inner membrane and a thick peptidoglycan layer over top.
nitrification / nitrogen fixation
Nitrogen fixation is capture of atmospheric N2 gas and its conversion into ammonium, NH4+.
Nitrogen fixation is the first part of the nitrogen cycle which illustrates cyclic flow of nitrogen
production, usage, and elimination through various organisms. Organisms in the domain
Prokaryote and Archaea fix nitrogen but eukaryotes do not have this ability although some
eukaryotes form symbiosis with diazotrophs. Nitrification is another step in the nitrogen cycle.
Ammonium produced is converted into nitrite (NO2-) then into nitrate (NO3-), which is more
water-soluble than ammonium and more easily absorbed by plant roots.
B. Short Answer/Short Essay Questions
Instructions: Answer each of the questions given below in your own words. Write in complete
sentences where appropriate. A complete answer usually requires one to two sentences per
mark, so a three-mark question would be answered in three to six sentences. This section is
worth a total of 40 marks.
(4 marks)
1. What are mules? Is their existence a challenge to the biological
species concept? Explain why or why not.
Mules are a hybrid offspring between male donkey (jack) and a female horse (mare). Mules
have 63 chromosomes which is a combination of 64 chromosomes from the mare and 62
chromosomes from the jack and their germ cells cannot undergo meiosis because the odd
number of chromosomes will leave one chromosome without a homologous pair. This means
that mules cannot produce gametes and that can undergo fertilization in order to create an
embryo. Hence, mules are sterile and are manifestations of hybrid sterility, postzygotic
reproductive isolation between donkeys and horses. According to the biological species
concept, species is defined as group of individuals that can reproduce to beget a fertile and fit
offspring and mules do not challenge this definition of species because of their sterility which
still distinguishes horses and donkeys as two separate species by virtue of reproductive
isolation.
3.Outline the Linnaean system of classification with its hierarchy.
The Linnaean system taxons fall under the following hierarchical structure:
Domain KingdomPhylumClassOrderFamilyGenusSpecies
The hierarchy is shown with the highest taxon on the left and the lowest on the right.
Linnaean system historically classified species into groups called taxons based on shared
morphological traits but modern genetics have changed the Linnaean system to reflect the
phylogeny or evolutionary history based on characters that are independent markers for genetic
similarities or differences.
(5 marks)
4. When systematists create an evolutionary tree of a group, they
exclude both homoplasies and ancestral characters. Why?
Systematists study homologous characters that are identified as independent markers of genetic
similarities or differences between species which allows them to create hypothetical phylogeny
of these species and to classify the species (taxonomy) based on genetic or morphological
similarities of these homologous characters.
Homoplasies are shared character that are not the result of the ancestry but of independent
evolution of similar character so they are not homologous. Thus, homoplasious structures do
not share the same genetic basis and cannot be used as markers to help systematists determine
genetic similarity between species and can create errors in the evolutionary tree.
There are two types of homologous characters, primitive or ancestral characters and derived
characters, and because ancestral characters (symplesiomorphy) do not show significant genetic
similarities or difference between species. For example, hair, a homologous trait in all mammals,
cannot be used to distinguish taxons of mammals because it a common shared trait. Thus,
ancestral characters are not useful in determining evolutionary history.
)
5.Briefly explain the main points of Darwin's theory of evolution
a) Descent with modification. New species evolved from existing ancestral states.
b) Natural selection guides evolution of population of organisms rather than individuals.
c) There are finite amount of resources and organisms must compete for these limited resources
to survive and reproduce. This external pressure is identified as mechanism for natural
selection.
d) Survival of the Fittest. Natural selection selects individuals with variations that increase their
chances of survival and reproduction in that particular environment.
e) The unsuccessful variations are removed by natural selection and the next generation inherits
the successful variations.
f) The successful variations are inherited by the descendants of the population of species and this
principle applies to either just a population of species (microevolution) or to group of species
(macroevolution).
7.Compare generalized transduction and specialized transduction. Which of the two types will
be more useful when applied in molecular biology?
Transduction is generally host cell’s DNA fragment transferred to another bacterial cell
via a bacteriophage vector.
Generalized transduction is caused by virulent bacteriophages that cause lytic cycle in
cell where host cells are lysed to release its own DNA fragments. Sometimes the host’s
DNA fragments are packaged into bacteriophages by mistake. The bacteriophages then
infect another bacterial cell. The new genetic material is recombined with new host’s
chromosome.
Specialized transduction occurs with phage lambda, more temperate phages that initiate
lysogenic cycle after it injects its genetic material into the host cell. Bacteriophage’s DNA
that is recombined with bacteria’s chromosome in the lysogenic cycle is known as a
prophage. In lysogenic cycle, the infected cells survive and reproduce and copies of the
prophage are found in all the descendant generation of the bacteria. An external stress
(i.e. UV light) triggers the prophage to activate several genes and excise itself from the
hosts chromosome. Sometimes adjacent host’s chromosomal DNA gets excised along
with the prophage by accident. The prophage then undergoes the same lytic cycle
events and takes over host’s cellular components to replicate many copies of the
bacteriophage and the host’s DNA fragment is packaged into the bacteriophages. The
viral DNA is recombined into a new host’s chromosomal DNA in a new cycle of
infections. The host that survives is able to pass this newly acquired genetic fragment
onto its offspring.
Generalized transduction is more randomized since it is possible that any fragment of the
host’s chromosomal DNA is incorporated into the viral DNA. However, specialized
transduction is more specific since only the adjacent part of the host’s chromosomal DNA is
taken up by the bacteriophage. This specificity is more useful to molecular biology for
isolating the gene of interest and reintroducing it into a new host’s chromosome.