GEN2EGE Population Genetics Assignment Sample

• Subject Code : GEN2EGE
• University : La Trobe University My Assignment Services is not sponsored or endorsed by this college or university.
• Subject Name : Biology

Section A: Z. Hristova

Ecological Genetics - Question 1

Devise an experiment which will help you determine whether the variation seen in a species of plants living in different habitats is the result of phenotypic plasticity or natural selection. In your answer include a definition of phenotypic plasticity and how it differs from evolution by natural selection. 

Answer 1. The experimental design can involve a qualitative approach. However, the major challenges in the experimental approach would include the following points:

• The population is not usually sufficient for handling the stochaticity of the process of evolution.
• The environmental conditions are uncontrollable
• Measurement of the selection and inheritance of the traits that affect the health is a tedious task among natural populations.

To overcome all the drawbacks, prediction from various evolutionary theories and study of literature on experimental evolution of plasticity can be done. In the laboratory different specimens of plants from different habitats can be collected and similarities and dissimilarities can be observed. The similarities and dissimilarities can be addressed by the help of developing a questioner and hence, successful scaling can be done. The questioner framework can also be used to test the robustness of the predictions from various theories.

Abrupt environmental variations can enhance the risk of extinction of any species and also promotes sudden changes in the phenotype. The changes occur to counter the climatic change, introduction of new species or any anthropogenic changes in the environment.

The experimental approach will include:

• Pedigree Analysis of different plants
• Monitoring of wild type of species and using them as control
• Collection of specimens of different parts of plants from various habitat.
• Observing the similarities and dissimilarities.

The observation can be done at three level:

• Morphological level

At morphological level, some of the factors on which the change can be observed include

• Size of leaf
• Size of plant
• Type of venation
• Type of root
• Colour of fruit
• Size of fruit

• Anatomical level

At anatomical level the transverse and lateral section from different parts of plant can be done and the changes can be observed in the arrangement of cells, type of cells and so on

• Chromosomal level

At chromosomal level the similarity and dissimilarity can be observed at the percentage of match of genetic material and identification of similar and dissimilar DNA.

To identify the DNA, the protein expression can be observed using flow cytometry

Ecological Genetics - Question 2

Using the figure below as a reference, explain how extinction can change the way we view evolutionary history (Hint: (g) is what exists now. Think about how the view of (g) would differ if it was drawn as time t1 vs t2)

Answer 2 The extinction of any species clearly determines the process of natural selection. As per the principles described by Darwin, a species is required to adapt themselves with the changes in environment and if that species that describes the struggle for existence. The species that reflects strong traits as per the demand of the environment is naturally selected and the species which fails to do so is rejected by nature and hence faces extinction. The process is called as natural selection. The species are required to constantly evolved with the environment and hence, evolution can be described as a never-ending process. The Neo-Darwinism principles also describes the necessity of variation. Variations are essential for survival and each and every individual except for clones in a controlled environment show variation at different level including phenotype, behavioural, genetic level or at the level of expression. The variations can either be produced by mutations that are the events of sudden genetic changes that can result in change in the genetic makeup of an organism or the other process of inducing variations is via crossing over.

The given diagram described the evolution of three species ‘e’, ‘f’ and ‘g’ with respect to time. According to the mentioned figure, all three species co-existed at time scale t₀and all three species were naturally selected. However, as the environment stared to change, the conditions for all three species started to get unfavourable and as a result the species started to evolve. The changes were either due to crossing over with is the result of sexual reproduction or due to mutations resulted into the development of new species. The descendants of ‘e’, ‘f’ and ‘g’ species were entirely different form the first generation. The variations that occurred in all three species were suitable for that particular environment and hence were selected by nature. However, in the case of species ‘f’ not all the individuals were evolved, few members of species ‘f’ resisted the change and co-existed with their descendent species at a particular time scale.

However, by the time t₁the environment became so unfavourable that it could not sustain the original members of species f and it resulted in their extinction. On the other hand, some of the descendant members of species ‘e’ and ‘f’ undergone changes that were unacceptable by the nature and were not favourable with the environmental condition and hence, those species faced the rejection by nature and hence got entirely extinct. The result was the rejection of all the members of species ‘f’ and some members of species ‘e’. However, species ‘g’ undergone changes that were acceptable by nature and hence, they passed natural selection. The conclusion that can be drawn from the given diagram are:

• Evolution is a continuous process
• Species are required to undergo constant changes
• The changes must be accepted by the nature
• The unacceptable changes would be rejected by nature and can result in the extinction of a species

Ecological Genetics - Question 3

The two phylogenetic trees (a) and (b) are of Lake Victoria cichlids and British Columbian Rockfish respectively. Both fish lineages show a great diversity of colour, form and feeding strategy, but their phylogenetic trees are very different. What information can you derive about the way evolution has proceeded in these two groups from their phylogenetic trees?

Ecological Genetics - Question 4

How do co-evolution and an evolutionary arms race help explain why there are so many species of beetles?

Answer 4. The co-evolution can be described as the process by which two or more than two species evolve by means of exerting pressure om each other. The co-evolution systems can be of various types including host and parasite relationship, predators and prey relationship, mutualism and symbiotic relationships. The species changes itself in response to the variations occurring in the co-existing species. The figure describes the existence a large variety of species of beetles that is existing. The figure describes that initially all the species were feeding on the non-angiospermic plants. However, majority of the species switched their feeding habit towards angiospermic plants during the course of evolution. The reason for this could be the evolution of the angiosperms. Initially the non-angiospermic plants were dominant on the earth.

However, with the constant evolution among non-angiospermic species, resulted in the development of angiosperms which were accepted by the nature. With the course of time the angiosperms started to dominate over earth and currently majority of the plants are angiosperms. The evolution resulted in the extinction of many species of non-amgiospermic plants and as a result very few non-angiospermic species are existing at present. The beetles countered this change by making changes in their feeding habits and they switched to angiosperms which serves as the source of food for them now. This resulted in the co-evolution of the beetles in terms of their feeding habits which by accepted by the nature and the species have sufficient favourable condition to increase their numbers.

Ecological Genetics - Question 5

Explain why that is the case. In your answer, include definitions of synonymous and non-synonymous substitutions

(Hint: think about the outcomes in terms of protein function of each type of substitution and their respective relationships with selection)

Answer 5. The substitution mutation can be described as the mutation that occurs due to exchange in one base pair for another. This result in the change in the codon that could end up coding of an entirely different amino acid and hence change in the protein.

The substitution mutation can be of three types:

• Same sense mutation: Such mutations result in the formation of exactly same protein.
• Mis Sense mutation: These types of mutation can result in the formation of less functional protein
• Non sense mutation: These type of mutation results in formation on non-functional protein, protein with different function or no protein at all.

The same sense and mis-sense substitution mutations are synonyms mutations that forms exact same protein or protein with less efficiency. The body requires specific proteins for its proper functioning and since in same sense and mis sense mutation that protein is existing, that species will survive i.e. accepted by natural selection. Proteins serve as the building block of the body. The non-synonyms mutations i.e. non-sense mutation result in different protein or no protein at all, it can result in the absence of that particular protein and hence, that species would not be accepted by natural selection.

Section B: W. Grant 

Ecological Genetics - Question 7

In a wild population of the North American deer mouse Peromyscus maniculatus you find a rare natural variant that has darker fur rather than the usual light tan on the dorsal body. When these coat colour variants were studied in the laboratory, dark fur was found to be associated with a recessive allele at a single locus, with the wild type lighter fur being dominant. The frequency (q²) of [variant] dark furred mice in the wild population is 9%. Assuming that the population is at Hardy Weinberg equilibrium, estimate the frequencies of the dark and the light [wild type] alleles in this population. What approximate proportion of the light furred mice would you expect to be heterozygous?

Ecological Genetics - Question 8

Make reference to the figure above to explain why a rare allele that usually results in homozygotes for that allele dying before puberty does not disappear due to selection.

Ecological Genetics - Question 9

There are four population genetic processes that shape genetic variation in populations. What are these four processes? In which direction(s) does each of these processes affect genetic variation (increase, decrease, no change)?

Ecological Genetics - Question 10

Selection and drift can both bring about genetic change in populations but do so in different ways. Create and describe two scenarios in which

 (a) drift will dominate selection as the agent of change and

 (b) selection is more likely to dominate drift.

(Hint: think about the direction of change, and the role of N_e in determining which process may dominate where s < 1 / 2N_e).

Ans 10. The genetic drift can be observed in a small population of a species carrying a limited number of gene in a gene pool. The loss of few members of that species can result in the loss of a number of genes and it can easily affect the population and the natural selection can be easily observed in genetic drift. An example for the same is a small population of frogs that contains few brown frogs, few green frogs and grey frogs. However, by any random event that population of brown frogs gets banished form that area. This will result in the loss of genes of brown frogs and as a result on the grey and green frogs would be able to mate with each other and pass on their genes to next generation. The result would be decrease in variation in the upcoming generation.

Ecological Genetics - Question 11

Explain briefly the relevance of heritability to both natural and artificial selection (hint: recall the breeder’s equation, R=h²S and perhaps try inserting high and low values of narrow sense heritability h² and the selection differential S to illustrate your answer).

Ecological Genetics - Question 12

Using the values given in the table below, estimate the genotype frequencies following one generation of selection.

(The equation for estimating the allele frequency in the next generation is

q* = q – sq² / 1 – sq²

where s is the selection coefficient, q is the recessive allele frequency in the current generation and q* is the recessive allele frequency in the following generation (note that you need to calculate s and q from the table above, assuming that the starting population is at HWE prior to the application of selection and recalling that s = 1 – w). Is this likely to be an example of stabilising, directional or disruptive selection?

Ecological Genetics - Question 13

Note that the blue points are the phenotype values before selection has taken place and the orange dots are the values after selection has taken place…this allows calculation of the difference in trait values before and after selection.

Answer the following questions by referring to the figure (which shows a linear regression for mouse tail length in an artificial selection experiment).

1. What is shown on the x-axis?
2. What is shown on the y-axis?
3. How is the narrow sense heritability, h², calculated from this regression?
4. What is R and what is S and how are they calculated from this regression?

Ecological Genetics - Question 14

Consider the processes of genetic drift, inbreeding and inbreeding depression. How are they interlinked? What is the relevance of these processes to conservation biology and how should conservation efforts align with the population genetic theory?

Answer 14 The genetic drift can be described as the process of significant loss of genes from the gene pool of a species. The genetic drift can be observed in the small population only and loss of a set of gene would result in decrease in the variations. As the small population would inter-breed that would result in highlighting the recessive traits and hence resulting in inbreeding depression. The small population cannot conserve their genes and several genes can be lost by genetic drift. Therefore, inbreeding depression should be prevented to conserve the gene pool of a population.

Ecological Genetics - Question 15

Population genetics focuses on genetic processes that take place within and between populations. Provide a clear definition of the term “population” in the context of population genetics, pointing out the key feature(s) of your definition and how it is compatible with the concept of a hierarchy of genetic organisation in population genetics.

Answer 15 Population can describe as the members of a similar species that are living in similar or dissimilar geographical areas but are able to reproduce and produce fertile off springs. The members of a population living in a different geographical area are called sister population and the individuals who migrate from one sister population to another are called meta population. The meta population brings along additional or different traits that can be observed within next or same generation. For example a person who is carrier for sickle cell anaemia migrates to a population which lacks sickle cell anaemia gene would result in introduction of the gene in that gene pool. The result would be occurrence of this disease in the upcoming generation. The major highlight of the definition is that different individuals of one population are able to interbreed and can produce fertile offsprings.

Ecological Genetics - Question 16

Name the form of likely selection and predict the likely outcome in each of the following hypothetical examples.

1. A new species of rock-dwelling beetle arrives on an island with many outcrops of black rock suitable as habitat but also birds that prey on beetles. The T locus controls the colour of the beetles, with TT beetles being black, Tt beetles grey and tt beetles nearly white. The T and t alleles are close to equal in frequency in the founding population.
2. The beetles also colonise neighbouring island with the same beetle eating birds but where there are approximately equal areas of black rock outcrops and outcrops of a much paler rock type. The founding population of this island is composed mostly of tt individuals due to the founder effect.
3. A reef fish has two different forms of males, one small and one large. The size difference is genetically determined in a simple one locus/two allele system. Large males dominate a harem of females, but small males can occasionally sneak in and mate while the large make is defending his harem against other large male competitors. This means that small males are rare they have an advantage.
4. In a tropical plant CC and Cc plants have red flowers and cc plants have yellow flowers. Red flowers are slightly more attractive to pollinators than yellow, but Cc plants have very few flowers per plant compared with CC or cc plants and produce many fewer seeds.
5. In a species of bird, the MM genotype is highly susceptible to avian malaria whereas Mm and mm birds are equally resistant. However, mm birds usually die prior to reaching sexual maturity and so almost never reproduce. (Note: assume that malaria has high prevalence in the bird population being studied).

Answer (A). The beetle with allele TT would be completely accepted on that island as they will camouflage with the environment and the beetle with allele Tt would also be present with limited number and the tt allele beetle would be completely extinct due to the presence of their natural predator

(B). The tt allele beetle is able to disguise themselves with the environment and hence making difficult to be identified by predator while Tt would be in limited number and TT would not survive.

Ecological Genetics - Question 17

State how each of the following processes is expected to vary in speed and impact in small versus large populations:

1. Selection
2. Migration
3. Genetic drift
4. Inbreeding
5. Number of new mutations accumulated in the population

Ecological Genetics - Question 18

This question refers to data in the table immediately below:

Historical records from bird watching clubs suggest that silver eyes (Zosterops lateralis, a small bird native to Australia) were first sighted in the 1830’s near Dunedin in the south of the South Island of New Zealand. Over the next 70-80 years they were observed at several sites in New Zealand moving progressively north and were sighted for the first time on Norfolk Island in 1903. Microsatellite locus allelic diversity, A, calculated from genotyping of museum specimens, and values for F_IS and F_ST estimated from those data, are shown in the table above.

Referring to the data in the table above, answer the following questions.

1. What is allelic diversity, and what does the decrease in allelic diversity tell us about these populations as we move from south (the oldest population; top of table, Dunedin) to north (the youngest population; bottom of table, Norfolk Island)?
2. What are F_IS and F_ST, and what population genetic property does each of them measure? (Note: they measure different properties at different levels of the genetic hierarchy…. illustrating your answer with the relevant equations would help but is not essential).
3. Both F_IS and F_ST rise as we move from south to north. How is this interpreted? (Note: interpretations of F_IS and F_ST are different).
4. Describe the population genetic process(es) that may have given rise to this pattern.
5. How could the relatively high value for F_IS and the low genetic diversity of the Norfolk Island population be remedied?

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