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. [Mention Examples] 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. [The answer is becoming too redundant. You are saying the same point about Reproductive isolation again and again. You need to merge the points together and bring out the difference/relationship like this----- Hybrid Inviability is a postzygotic reproductive isolation where Gametes from two separate species form a zygote, which contains two conflicting embryonic development instructions that cause the embryonic development to fail. On the other hand Hybrid Breakdown is a postzygotic reproductive isolation, where the hybrid offspring has low relative fitness suffering due to high rate of lethal and harmful mutations. 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 KingdomPhylumClassOrderFamilyGenusSpecies 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.