Theme 2

Question 1

What is the purpose of phylogenetic trees? What are the 3 main types which are used, and what do they each show?

Answer 1

Evolutionary/phylogenetic trees are used to depict relationships between species. They allow us to model phylogeny such that we can better understand where species diverge, which have common ancestors, and in what time scale.

1) Cladograms show common ancestry and relationships of species to one another.
2) Dendrograms are the same, but also include a timescale.
3) Phylograms tell us the common ancestry and time scale as well, but also tell us the amount of evolutionary change which has occurred (represented by how long the branches are).

Question 2

Define the terms autapomorphy, plesiomorphy, and synapomorphy.

Answer 2

1) Autapomorphies are unique features of a taxon which may suggest that it is distinct.
2) Plesiomorphies are primitive, ancestral characteristics which are shared between two or more taxa. However, two organisms may appear to show a plesiomorphy when they have actally just undergone convergent evolution of one or more traits. For example, placental mammals and marsupials in different ecosystems sometimes exhibit almost identical morphologies and niches despite the fact they are very distantly related.
3) Synapomorphies are new (non-ancestral), derived characteristics which are shared by two or more taxa. These are considered to be the only evidence which can be used to infer relationships and common ancestry between organisms. However, similarly to plesiomorphies, convergent evolution of traits may appear to be a synapomorphy.

Question 3

Describe how phylogenetic trees can be constructed using traditional phylogeny.

Answer 3

Phylogenetic trees can be constructed using an outgroup - a taxon which you know is related to both/all taxa you are constructing the tree for. All characteristics of the outgroup organism are considered the primitive traits. Organisms which are being compared are polarised against the outgroup for several characteristics (said to either share the ancestral characteristic, or have a new, derived one). These results are then summed, and a tree can be constructed based on which shared characteristics are primitive/derived.

Question 4

Define a grade and a clade in taxonomy.

Answer 4

A grade is a taxon united by a particular level of morphological or physiological complexity - taxa within a grade do not necessarily have common ancestry.

A clade is a monophyletic group (comprised of a common ancestor and all its lineal descendants). For example, apes are a grade within the clade of primates.

Question 5

Explain the molecular clock hypothesis and its importance in genomic epidemiology, with reference to cytochrome C.

Answer 5

The molecular clock hypothesis suggests that the amount of evolutionary change in a given gene across different lineages is approximately constant over time. This means that we can use the amount of genetic difference between two species to estimate when they last had a common ancestor.
Cytochrome C is a gene which is massively conserved among all life (humans, fish, yeast, bacteria, etc). Bacterial cytochrome C is roughly 65% similar to ours, and cytochrome C in yeast and fish is almost identical to ours.

Question 6

Explain how phylogenetic trees can be constructed using molecular data, and describe some of the key limitations of this.

Answer 6

Similarly to how they are based on morphological characteristics, phylogenetic trees can be constructed by comparing genomic sequence data of the taxa in question to an outgroup. SNPs are considered to be derived or ancestral, and groups are polarised in the same way, and results are summed.

However, molecular data is much more constrained than morphological or physiological characteristics, as it only ever has 4 variations (A, C, T, and G). If the rate of mutation is very high, or evolution has taken place over a long period of time, many of the changes to the sequence may have been overwritten - this is known as saturation. This means that it can be very difficult to estimate the changes which have happened (usually vastly underestimated). Some genes are faster mutating than others, and faster mutating genes will give less reliable molecular data.

Question 7

What are transition and transversion SNPs? Which is more likely to yield an alternative phenotype, and why is this the case? What is the significance of this with regards to molecular phylogeny?

Answer 7

Transitions are common substitutions for an SNP - A/G and C/T. These tend to yield insignificant or no difference in amino acid sequences, and are therefore not usually associated with a significantly different phenotype.
Transversions are rarer mutations - A/C, A/T, G/C, and G/T. These do tend to yield significant changes, and these changes are more likely to be associated with an alternative phenotype, and therefore selection can act on them (usually selected against, as most significant mutations are deleterious).

When conducting genomic epidemiology, we can use this. Transversions are both rarer (saturate slower) and are more significant, meaning that they give more potential for accurate estimations of the degree of evolutionary change

Question 8

Explain the concept of long-branch attraction.

Answer 8

Long-branched attraction results from convergent evolution over time, particularly where the genes are highly saturated - because there has been a lot of evolution, there have been a lot of individual changes which have eventually led to the same outcome at present, giving the appearance that two taxa may be more related to each other than they really are.

Question 9

Explain the principle of parsimony and Dollo’s law.

Answer 9

Dollo’s law and the principle of parsimony are rules which can be used to more effectively construct accurate phylogenetic trees, based on these assumptions.

Dollo’s law states that very complex characteristics are unlikely to be regained after they have been lost - for example, it is unlikely that wings would evolve, then be lost, and then be regained (since their evolution in the first place required a significant period of time under very specific and strong selection pressures, as well as all the necessary by-chance mutations).

The principle of parsimony says that the most likely explanation for an evolutionary tree is the simplest one.

Question 10

Explain how the accuracy of phylogenetic reconstructions can be tested.

Answer 10

Ancestral reconstructions can be tested in the lab using experimental phylogenetics, where high speed mutations are induced (using mutagenic chemicals) in microorganisms or viruses to quickly produce several lineages. By comparing the known phylogenetic tree with the one which would be produced using the rules of parsimony and Dollo’s law, you can estimate the accuracy of these assumptions (it has been found that they are roughly 94% accurate).

Another method to test the accuracy of reconstructions is to test the viability of ancestral proteins (can be done by reconstructing ancestral proteins based on their phylogenetic trees and existing protein sequences, and testing whether they are functional).

Question 11

Define functional diversity with reference to functional traits and functional groups.

Answer 11

A functional trait is a set of characteristics of an organism (defined by its niche) which may determine its fitness and influence its chances of survival. A functional trait of an organism, such as a specific biochemical/physiology process, or ecosystem-modifying behaviour, may be key in sustaining specific ecosystem process(es).

A functional group is a group of organisms which all posses similar functional traits, and thus sustain similar processes. Functional diversity is the total number of functional groups within a certain area.

A high degree of functional diversity therefore means that there are many distinct functional groups which may sustain a range of ecosystem processes. Ecosystem processes come together to sustain healthy ecosystem functioning.

Question 12

Explain the concept of functional redundancy and how it contributes to security of ecosystem functioning.

Answer 12

Functional redundancy occurs where many species perform the same, or similar, functions. This means that the particular ecosystem process which is provided by the functional trait has high security, as if one of the species which sustains it disappears, there will be others which are still able to do so.

Question 13

Explain the 3 main theories as to why species richness enhances productivity and ecosystem functioning.

Answer 13

1) The complementarity hypothesis suggests that the more species rich an assemblage is, the more chances you have of distinct functional groups due to greater functional trait diversity. This allows for maximum biomass to be attained due to different species exploiting difference niches (productivity is not inhibited by competition due to resource partitioning).
2) The facilitation hypothesis suggests that one species can have a positive effect on the ecosystem role played by another species, such that the mixture of resources are more efficiently utilised leading to increased yield. For example, trees facilitate ferns by providing shade, and ferns facilitate trees by increasing ground moisture - the two organisms support one another, and maximise their respective productivity and ability to carry out their functional processes.
3) The selection effect suggests that the higher species richness there is within an ecosystem, the higher the chances are that one or more of these species is highly productive or efficient in using resources, leading to higher ecosystem processes, and thus greater ecosystem functioning.

Though the truth is likely a combination of all three factors at play, the complimentarity hypothesis is the most widely accepted.

Question 14

Explain the concept of DNA barcoding.

Answer 14

DNA barcodes are similar to regular barcodes, but where the DNA sequence is used to create a colour-coded, condensed region of code. Each nucleotide is allocated a colour, and the same equivalent section of DNA is used for each species to generate a barcode for them - this allows you to identify a species without a physical specimen, only requiring a small amount of genetic material for a sample.
Using this technique, phylogenetic trees can be constructed, animal forensics can be conducted, and biodiversity screening can be done (by analysing DNA found within blood-sucking parasites).

Question 15

Explain the different types of molecular data used to assess diversity, how they are obtained, and how they are analysed to quantify it.

Answer 15

1) Allozymes are structural variations of enzymes which were the first widely used genetic markers (allele frequency-based) - proteins are smashed up and run through charged gel, and each allele will stop at a specific point in the gel. These are called enzyme banding patterns, and each band is assumed to reflect a different allele. Allele frequencies can be calculated by counting the total number of each allele and dividing by the total of all alleles (each lane indicates one individual, with 2 alleles if diploid). This technique can be used to assess the degree of gene flow between two populations (high degrees of gene flow will homogenise populations). The benefit to this technique is that many alleles and genotypes can be quantified across multiple loci. However, it only analyses gene products, and not genes themselves, which may violate the assumption of neutrality.
2) PCR uses primers to select pieces of DNA which are then amplified and analysed by running them through charged gel. STRs, or SNPs can be used to determine distinct alleles. Because repeats are added or lost relatively frequently, and neutrally, this does not assume lack of selection biases. You can also compare many loci within individuals, and many individuals/populations at once. However, the degree of change in number of repeats is not informative (as polymerase can just as easily add four repeats as it can two). If an individual is homozygous at several loci, this can infer inbreeding.
3) DNA sequencing involves tagging each nucleotide with a fluorescent dye, and then a computer sequences it and aligns many individuals to detect polymorphisms. Where sequences are different lengths, gaps are added to make sure they stay aligned. The advantage of DNA sequencing is that as well as allele frequencies, we can observe and compare nucleotide diversity, allowing us to quantify precisely how different things are. This also allows us to compare neutral genomic regions as well as ones under selection, and most importantly analyse functional diversity at the molecular level.

Question 16

Explain the importance of biodiversity in conservation.

Answer 16

An ecosystem cannot be preserved based on the management of a single species - they are all interrelated. The connectivity and impacts of anthropogenic activities on biodiversity of ecosystems can be analysed for a better understanding and allow us to more effectively inform and design management interventions. Conservation priorities are the cornerstone of efforts, as they allocate limited resources to where they will have the greatest impact. By quantifying how distinct species are from one another, and better understanding populations and assemblages, we can set priorities for consercation.

Question 17

Use a case study to explain how understanding functional diversity is important in informing conservation decisions.

Answer 17

In the 1960s, a vaccine was invented for Rinderpest - a disease of cattle which was catastrophic for many poor African farmers. However, the limited functional diversity of the herbivorous megafauna of the Serengeti and Masai Mara national reserves, and the fact that Rinderpest was a high source of mortality for Wildebeest, meant that the vaccination programme of cattle had an unanticipated, cascading effect on the natural neighbouring ecosystem. A massive increase in Wildebeest population in the Serengeti resulting in grass overconsumption, which resulted in more fires, which resulted in fewer trees, which resulted in limited food for elephants and other megafauna.

Question 18

Use a case study to explain how a species should be defined to inform conservation decisions.

Answer 18

Defining species can be an important factor in influencing conservation interventions, as distinct species under threat of extinction may take priority over those which are regarded as sub-species, or populations which are not genetically distinct from others. An example of this is practice was with Giraffes - in 2016, Fennessy et al. conducted a multi-lovus analysis of population structure of Giraffes across Africa based on DNA sequences in order to ascertain how many species of Giraffe there really were. The goal was to focus conservation efforts on the smallest, most genetically distinct species to preserve the greatest genetic diversity. It was found that all the Giraffes from the southern regions of Africa belonged to the same clade (genetically similar and shared common ancestry). This was also found with the Masai, Reticulated, and Northern Giraffes, but that the two (northern and southern) were distinct form each other. As these results were not consistent with other findings, it sparked a debate as to whether “sub-species” was actually a thing. One result of this was the coining of a new term “evolutionarily significant units”, being the number of genetically distinct populations that might deserve separate protection).

Question 19

Use a case study to explain how genetic data can be used to inform conservation decisions.

Answer 19

Conservation genetics is concerned with understanding factors which affect genetic variation (e.g. barriers to gene flow as a consequence of habitat fragmentation, genetic drift, and inbreeding). Using molecular data to assess the levels of inbreeding depression within a population (or other deleterious result of anthropogenic activity), conservation interventions can be designed to rectify the issues.
For example, an investigation was conducted on African Wild Dogs when populations which were previously thought to have gone extinct reappeared. Neutral markers were used to make inferences on population dynamics and demographics, and found that there was a lot of genetic variation preserved in the wild dogs but that the northern and southern populations were highly distinct from one another. The reappearing populations were found to very similar to those which were thought to have gone extinct, and that some individuals from the northern population were interbreeding with those from the southern. It was therefore decided that opening up corridors for these two distinct populations to freely move and interbreed would vastly increase the genetic variation of the species as a whole, making them more robust and more likely to survive.

Question 20

Explain the concept of life history strategy.

Answer 20

A life history strategy of an organism encompasses all the most important stages of its life and development, including stage of development at birth, rate of growth and age of sexual maturation, reproductive strategy and parental investment per offspring, etc. It is the specific combination of trade-offs that an organisms makes in order to maximise its likelihood of survival and potential to procreate.

Question 21

Describe some reproductive strategies commonly adopted by organisms.

Answer 21

1) Harem holding is a commonly used reproductive strategy of many organisms (particularly large mammals). This usually involves a male who out-competes other males in order to gain mating rights to a group of females. This often involves physical altercations with other males, and/or having the most desirable territory possible.
2) Dowdy/gaudy sexes are exhibited by many organisms, particular birds. This relies on extreme sexual dimorphism, where the gaudy sex (usually males) is showy (brightly coloured and/or ornamented), and the dowdy sex (usually females) is less showy (lack of colour and ornamentation). It is possible for gaudy adaptations to appear maladaptive (for instance, peacock feathers) - however, these behaviours must be adaptive due to the nature of evolution.
3) Courtship is a combination of physical and behavioural displays used to attract mating decisions from individuals of the opposite sex, and can be used alongside dowdy/gaudy sexual dimorphism. Lek sites are commonly used patches of ground where gaudy sexes display themselves during the breeding season.

Polygamy (many sexual partners), polygyny (males mating with many females - often harem), polyandry (females with many males), and monogamy (one sexual partner) are all potential mating strategies, which each have their own respective trade-offs.

Question 22

Explain the factors on which breeding success depends.

Answer 22

Breeding success depends on all 3 types of selection: Survival, life history strategy, and sexual -

Survival selection contributes to viability (ability to survive to breeding age/maturity).
Life history strategy selection contributes to fecundity (investment in each bout of reproductive activity), and lifespan (longer life leads to more reproductive years).
Sexual selection contributes to mating success.

Question 23

Use the example of side-blotched lizards to explain how sexual selection can drive population dynamics within a species.

Answer 23

Side-blotched lizards exhibit a polygynous mating system, where males hold harems of females. There are 3 types of males which have paired phenotype-behaviour mating strategies - orange-throats, blue-throats, and yellow-throats.

Orange-throats are the most dominant, and usually have large harems which they guard aggressively; blue-throats have smaller harems but are more effective at guarding them for that reason; and yellow-throats are morphologically similar to females - they sneak into harems to secretly mate with females. These are nuances of breeding strategy within the same breeding system.

The frequencies of these phenotypes cycles over years - when there are lots of orange-throats, this is advantageous for yellow-throats, as they can sneak into their harems more easily than those of blue-throats. The yellow-throats therefore begin to thrive. However, as they thrive, the orange throats don’t, and this becomes an advantage to the blue-throats, because they are better at guarding their harems from yellow-throats. The yellow-throats therefore reduce, and the frequency of orange-throats then increases, because they are more aggressive and dominant than the blue throats.

Question 24

Explain game theory in the context of evolution of life history strategies, with reference to evolutionarily stable strategies and reciprocal altruism.

Answer 24

Game theory, from an ecological perspective, is the idea that two organisms can choose to either cooperate with one another (big positive payoff for both), defect from each other (big negative payoff for both), or one can defect and one can cooperate (big negative payoff for the cooperator, and positive for the defector). Whatever the most successful strategy is for an organism at a given time can be considered an evolutionarily stable strategy. For vampire bats, reciprocal altruism is an evolutionarily stable strategy - even though they are not genetically related to one another, they will share blood meals if they trust that the behaviour will be reciprocated at another time. On one repetition, defecting (not sharing a blood meal) is beneficial, as more energy is conserved for your own survival and reproduction. However, upon many repetitions, cooperation will always win out, because those who defect will not be shared with in the future.

Question 25

Describe the 3 main theorised mechanisms which may lead to the evolution of choosy females and showy males.

Answer 25

Quality of mate usually matters more for females than it does for males (resulting in male-male competition via harem holding, gaudy males, courtship, etc), as females typically have a much greater energy investment per reproductive attempt than males - average fitness of offspring may be reduced if she mates with suboptimal males.

1) Direct selection on the female’s preference: She, or the offspring, get a direct benefit from the trait (e.g. provisioning of a resource by the male).
2) Sensory bias: She likes how it looks/feels and wants to mate.
3) “Sexy sons” hypothesis: The preference for a particular male trait increases because that trait is being selected for by other females (her sons may acquire the trait and be more successful themselves). This can result in “runaway” selection, resulting in extreme traits (e.g. birds of paradise).

Question 26

Explain the processes and drivers which allowed for the diversification of Africa’s megafauna, and the mechanisms which help maintain its diversity today.

Answer 26

Rapid radiation of bovids in Africa’s savanna ecosystems is believed to have occurred in the late Miocene (10MYA). One theory as to why this happened is that when they were diversifying, the African climate was becoming much drier, converting the Sahara from savanna to desert. Since then, African ecosystems have repeatedly oscillated between wet forests, dry savannas, and arid deserts, resulting in much higher chances of pronounced geological barriers restricting gene flow, which may have been a major contributor to the radiation.

Another probable driver may have been co-evolution of browsers (grazers of trees and shrubs) with spiny plants - whose abundance was rapidly increasing. It has also been argued that we observe high diversity of mammalian megafauna in Africa due to our own bias when comparing to other continents (there was lots of megafauna across the globe until rapid extinctions occurred between 13-8MYA). The reasons why Africa’s megafauna didn’t see these extinctions could be due to high densities of small mammals providing enough food for humans (hunting large mammals was less necessary); lower densities of humans than elsewhere (potentially due to pathogen abundance); and more area which could provide safe refuge from humans for large mammals.

Niche partitioning (particularly diet and spatial partitioning) is believed to be the main way in which Africa’s savannas are able to maintain this high diversity in the present day. Studies have found that Wildebeest, Zebra, and Thomson’s Gazelles, which all follow the same annual migratory route, have distinct specialised diets to each other, and migrate in sequence such that they facilitate each other rather than competing.