evolution

Question 1

What is the average clutch size laid by great tits and what assumption can we make about that clutch size?

Answer 1

Great tits lay between 8 and 9 eggs, and we can assume that this number reflects optimisation for offspring fitness.

Question 2

What did Fisher hypothesise about the great tit clutch size?

Answer 2

That optimisation for fitness incorporates the ‘value of offspring’ - maximising for the number of surviving young per brood.

Question 3

What is the ‘lack clutch size’?

Answer 3

The predicted clutch size of a bird species based on the hypothesis that clutch sizes with the greatest proportion of surviving young have been selected for, reflecting the fitness consequences of the size v quality trade-off.

Question 4

What is the best indicator of egg quality?

Answer 4

Weight. Heavier young are more likely to survive past three months.

Question 5

What is the lack clutch size for great tits?

Answer 5

8-12

Question 6

What is the second trade-off imposed upon laying birds, reducing yields down from the lack clutch size?

Answer 6

The second trade-off is lifetime fitness v breeding season fitness. During egg-laying season, mother birds function at seven times their basal metabolic rate; a metabolic demand which is unsustainable if improperly balanced. As clutch sizes increase, the likelihood of maternal survival decreases - reducing the optimal clutch size down from the lack clutch size.

Question 7

What evidence is there for the secondary trade-off imposed upon bird mothers?

Answer 7

Experimental evidence showed that bird mothers who were induced to lay two further eggs - paying ‘full costs’ - suffered increased fitness consequences compared with mothers who received the same number of ‘free eggs’.

Question 8

Why are trade-offs imposed?

Answer 8

Limited resources inherently result in trade-offs - as there is an opportunity cost associated with investing a limited resource in one function at the expense of another.

Question 9

What are Darwinian Demons?

Answer 9

Hypothetical organisms emancipated from resource limitation and other biological constraints on evolution, capable of maximising all aspects of fitness simultaneously - i.e. reproducing young and producing large broods of immortal offspring - and perfectly adapted to the domination of every ecosystem. A Darwinian Demon would outcompete every extant organism, forming an organismal monoculture.

Question 10

What is the ‘copulatory somersault’ performed by redback spiders?

Answer 10

The copulatory somersault is a mating behaviour exhibited by male redback spiders, whereby the male flips his abdomen into the female’s fangs during mating, typically leading to his consumption. Approximately 65% of redback spider mating events result in the male being eaten by the female.

Question 11

How does the copulatory somersault function as an adaptive strategy?

Answer 11

The copulatory somersault is believed to maximise the number of offspring a male redback spider fathers in his lifetime. This is because the female is more likely to reject a second suitor if she is ‘full’ - i.e. her relative level of hunger influences the likelihood that she engages in further mating events. Cannibalised males copulate for longer, transferring more sperm to the female and increasing the relative proportion of their offspring in the female’s clutch. The proportion of a second male’s offspring in the clutch is thus reduced by cannibalisation of the first male.

Question 12

How can the copulatory somersault optimise fitness benefit when the male effectively suicides?

Answer 12

If a male is not cannibalised, he has less than a twenty percent chance of reaching another female’s web by the end of the field season. This is because webs are often more than three metres apart and the spider is likely to be predated by ants and other spider species on his journey. The relative mating success of a non-cannibalised male is therefore estimated to approximate to 133 eggs, whereas the cannibalised male fathers, on average, 235 eggs.

Question 13

What is the process of sex change in bluehead wrasse?

Answer 13

Environmental cues trigger the release of neurochemical signals in the female bluehead wrasse, which are communicated from the brain to the gonads. These neurochemical signals stimulate complete remodelling of the gonad from an ovary producing eggs to a testis producing sperm, whilst genetic activity shifts from the production of female sex hormones to male sex hormones. This process can be observed through wrasse colour change as the transition to a new sex is completed.

Question 14

How does sex change in bluehead wrasse function as an adaptive strategy?

Answer 14

Sex change allows an individual bluehead wrasse to capitalise on different reproductive opportunities depending on their social environment. When a dominant male is removed from the group, a large female can transition into a terminal phase male. This allows the wrasse to rapidly assume the territory of the lost male and increase their reproductive yield by up to 3000%. Larger female wrasse are more fecund than smaller females, but males are significantly more fecund than either - as they are capable of engaging in up to a hundred mating events per day. Sex change is thus an adaptive strategy reflecting the trade-off of the relative benefits of being male or female within a particular social environment.

Question 15

What are proximate v ultimate mechanisms/explanations?

Answer 15

Proximate explanations concern the immediate mechanisms resulting in a behaviour (i.e. the hormonal changes, genetic factors or environmental cues) whereas ultimate explanations explore why a behaviour has evolved and what the adaptive function of a behaviour might be (i.e. how a behaviour influences the survival and reproductive success of a particular species).

Example

“The hormone testosterone stimulates male wrasse to defend their territories more aggressively.”

v

“Male wrasse who defend their territories more aggressively are likely to father more offspring.”

Question 16

What is adaptive radiation?

Answer 16

Adaptive radiation is a process of rapid evolutionary diversification, whereby a single ancestral species gives rise to a multitude of descendant species through divergent adaptation, with each new species adapted to a different ecological niche.

Question 17

What is a classic example of adaptive radiation?

Answer 17

Darwin’s finches. A multitude of divergent finch species evolved across the Galapagos Islands from a single ancestral species present on the South American mainland. Across the islands, the finches adapted to novel ecological niches in the absence of competition from one another. The modern finch species display a variety of behavioural and physiological adaptations - e.g. the broad, blunt beak of the large ground finch is adapted to cracking nuts open, whereas the nectarivorous cactus finch has a longer, more slender beak.

Question 18

What did Gregor Mendel contribute to Darwin’s theory of evolution by natural selection?

Answer 18

A demonstration of particulate inheritance, with the gene as the particulate unit of heredity, serving as the ‘conceptual backbone’ of Darwinism

Question 19

What is the Hardy-Weinberg theorem?

Answer 19

A neutral model describing expected genetic variation under assumptions of infinite population size, random mating (with respect to the gene locus), and no differences in viability. The Hardy-Weinberg model yields expected patterns of allele frequency, without accounting for selective sweeps.

p² + 2pq + q² = 1

Question 20

Do we think of mating as random?

Answer 20

Not in general, as there are definitive selective processes involved in courtship. However, mating is random with respect to gene locus; preference is based on phenotype, but not specific genotype.

Question 21

What is genetic drift?

Answer 21

Stochastic variation in relative allele frequencies within non-infinite populations, owing to the chance loss of particular alleles acting independently of selection coefficients. Genetic drift reflects a loss of genetic diversity within a population - and the strength of the effect of drift negatively correlates with population size.

Question 22

What is a selection coefficient?

Answer 22

The selection coefficient (s) is a value which can be incorporated into modified versions of the Hardy-Weinberg equation, reflecting the change in fitness associated with an allele when an individual is homozygous for that allele (if the coefficient is greater than zero, the effect on fitness is beneficial).

Question 23

Does selection act on phenotypes or genotypes?

Answer 23

Selection acts on phenotypes, resulting in changes in allele frequencies within a population.

Question 24

What is fitness?

Answer 24

The relative reproductive rate of an individual with a given phenotype.

Question 25

What is a 'selective sweep' and how do selective sweeps impact the diversity of nearby gene loci?

Answer 25

The rapid spread of a beneficial mutation throughout a population due to positive selection for individuals with the resultant phenotype. Selective sweeps reduce genetic diversity near to the selective site due to 'genetic hitchhiking', whereby nearby, linked 'neutral alleles' are carried to high frequency alongside the beneficial allele.

Question 26

Why are rare mutations often heterozygous?

Answer 26

Mutations affecting fitness are most likely to be recessive - as 'loss-of-function' mutations are most common. As mutations originate in the heterozygous state, the loss of function is thus masked by the presence of a wild-type allele - enabling the perpetuation of the allele through offspring without fitness consequences. It is highly unlikely for two carriers of a rare recessive mutation to mate, meaning that rare deleterious mutations can persist at low frequencies in a population as no phenotypic changes are induced upon which selection could act.

Question 27

Are mutations driving evolution in a population more likely to be dominant or recessive?

Answer 27

All mutations typically originate in a heterozygous state. For a mutation to 'drive evolution' - i.e. confer a selective advantage, yielding an increase in allele frequency within a population - the associated phenotype must be expressed, meaning that the beneficial mutation must be dominant. Recessive mutations are effectively 'hidden' from selection by heterozygosity.

Question 28

What is the adaptive significance of the loss of body armour associated with the transition of marine sticklebacks to freshwater environments?

Answer 28

In Canada, the colonisation of lakes by marine sticklebacks has been associated with the evolution of reduced body armour (encoded by a recessive allele). In freshwater environs, the low body armour phenotype is beneficial as body armour is an adaptation to the resistance of predation (which is a lesser issue in freshwater) and requires significant energy investment (freshwater is more nutrient-poor and resource limitation has thus imposed a trade-off). The low body armour phenotype in Canadian lakes represents a selective sweep driven by a recessive mutation.

Question 29

Does an increased migration rate increase or decrease genetic divergence?

Answer 29

Migration between islands prevents divergence between populations as gene flow between populations results in convergence upon a net equilibrium allele frequency.

Question 30

Does migration increase or decrease genetic diversity?

Answer 30

Migration increases the genetic diversity of a population through the introduction of new alleles. Genetic diversity stems from an interplay of selection (the deterministic loss of low fitness alleles), drift (the stochastic loss of genetic variation in a population) and migration (which increases diversity through new allele introduction).

Question 31

What is population genetics?

Answer 31

Population genetics is a subfield of genetics examining diversity within and among populations over evolutionary time, contributing to scientific understanding of selection on standing variation. Selection on standing variation is now thought to be key to adaptation on evolutionary timescales (e.g. selection for the low body armour phenotype of marine sticklebacks).

Question 32

Are most mutations beneficial or deleterious?

Answer 32

The vast majority of mutations are lethal, deleterious or neutral in effect - and spontaneous mutation continuously yields deleterious alleles. Natural selection acts against these deleterious alleles, reducing their frequency within a population.

Question 33

What is the average mutation frequency for higher order eukaryotes?

Answer 33

One mutation per genome per generation.

Question 34

How is the persistence of cystic fibrosis in populations an example of balancing selection?

Answer 34

Balancing selection is a type of natural selection whereby multiple alleles are actively maintained within populations, preserving diversity at a given gene locus. The F508del mutation of the CFTR gene results in defective chloride ion channels and the production of thick mucus throughout the lungs and digestive system of homozygous mutants, with the average life expectancy of an individual with cystic fibrosis considerably lessened compared to that of a healthy individual. However, heterozygous carriers of the F508del mutation do not contract the disease and there is evidence suggesting that the mutation provides a selective advantage against infection by tuberculosis, cholera and typhoid. Altered chloride transport might make carrier cells less susceptible to infection by Mycobacterium tuberculosis - and altered salt and water balance may be associated with decreased dehydration in the event of diarrheal disease infection. The heterozygous carrier thus has an optimal phenotype compared to either homozygous form (healthy/diseased), leading to a balanced polymorphism whereby natural selection acts to maintain both alleles within a population.

Question 35

Is it possible to directly observe selection on mutations in real-time and are there any examples of this direct observation?

Answer 35

If we use rapidly evolving systems, such as bacterial cultures (generation times may be as low as ten minutes), we can observe selection in real-time. These cultures yield population sizes such that even if mutation rates per genome are low, mutations are both inevitable and observable. Scientists have created an evolutionary fossil record through the transfer of twelve populations of E. coli to new test tubes and glucose food sources every 24h, cryogenically freezing the previous sample. This experiment has been ongoing for thirty seven years, with rapid increases in fitness initially observed followed by deceleration. Over time, the various populations evolved novel capabilities - e.g. citrate metabolism - which were rapidly fixed.

Question 36

What is a repeatable example of allele fixation?

Answer 36

Positive selection of changes to the amino acid sequence encoded by the haemagglutinin gene of the human influenza virus, as alterations to this sequence aid an infecting virus in evading host antibody detection, enhancing the fitness of that virus lineage. This is paralleled by selective sweeps associated with SARS-CoV-2 spike glycoprotein mutations. These spike proteins allow the coronaviruses to penetrate host cells through binding to the ACE2 receptor. Mutations associated with enhanced binding to the human ACE2 receptor are under positive selection - resulting in multiple spike protein variant 'sweeps'.

Question 37

What is the characteristic pattern of adaptation across evolutionary time?

Answer 37

Adaptation follows a characteristic pattern of diminishing returns, with only a few adaptations driving evolution. Furthermore, traits that are tightly correlated with fitness show repeatable evolutionary dynamics throughout replicate populations.

Question 38

What are two key properties of systems displaying evolution by natural selection?

Answer 38

Heritable variance in reproductive rate and constraint by resource limitation (as the population must adapt to optimise resource use).

Question 39

What is meant by the 'two-fold cost of sex'?

Answer 39

Sexual reproduction is half as effective at passing on an individual's genetic material than asexual reproduction (e.g. apomictic parthenogenesis, where a female's unfertilised egg develops to produce genetically identical female offspring).

Question 40

If there is a 'two-fold cost of sex', why are all organisms not asexual?

Answer 40

Transitions to asexuality are an evolutionary dead-end, with asexual species comparatively short-lived on evolutionary timescales. Without genetic recombination, beneficial mutations compete with one another for fixation, driving recurrent selective swoops in asexual populations. Evolution thus occurs more slowly in asexual populations, as different beneficial mutations must evolve within the same lineage. Gamete formation entails recombination, allowing for the production of recombinants with multiple beneficial mutations - maximising recombinant fitness. This phenomenon can be observed in S. cerevisiae populations - capable of both sexual and asexual reproduction. In sexual yeast populations, there is far greater genetic diversity.

Question 41

What is clonal interference?

Answer 41

Clonal interference refers to the competition between asexual population lineages arising from different beneficial mutations. Mutations which fail to become fixed may be lost from the population altogether, reducing the rate at which asexual populations can achieve maximal fitness and reducing whole-population genetic diversity.

Question 42

What is the spectrum of sociality?

Answer 42

There is a continuum of social behaviour across evolutionary time, with ancestral animals almost entirely solitary (unsociable) and all modern animals displaying a variable form of social behaviour.

Question 43

What are some examples of 'simple' social behaviour?

Answer 43

Shoals of fish and bird nesting communities aggregate out of necessity due to the individual benefit associated with co-operation (i.e. protection). Complex, repeated individual interactions are not required within these social structures.

Question 44

What is a 'complex' social behaviour in slime moulds?

Answer 44

In nutrient-scarce environments, slime moulds form 'sorocarps' (fruiting bodies) composed of a sorus (a cluster of reproductive sporangia) and a stalk (comprised of sterile stalk cells which make the 'ultimate sacrifice' by 'dying' to form the stalk). This reproductive division of labour represents an extreme social behaviour whereby the stalk cells receive no direct benefit and suffer a direct cost. The benefit to the stalk cell is indirect - through the propagation of spores produced by the resultant sorocarp.

Question 45

What is a 'complex' social behaviour in termite colonies?

Answer 45

Termite colonies are eusocial, with a single reproductive king and queen producing up to 40,000 eggs per week. The queen is effectively immobilised, her body inflated with a vast number of eggs. These eggs hatch to form sterile workers whose sole function is to support the continued reproduction of the royal termites. This represents a sacrifice of individual reproductive potential to benefit the colony as a whole.

Question 46

What are major evolutionary transitions?

Answer 46

Major evolutionary transitions (METs) are 'revolutions' interrupting the gradual process of evolution and resulting in the attainment of a higher level of organisation. These transitions often involve the aggregation of individual functional units to form a larger, cohesive functional unit - representing a loss of individuality within clonal organisms.

Question 47

What are some examples of major evolutionary transitions?

Answer 47

The evolution of eukaryotic cells from prokaryotic precursors through the endosymbiotic engulfing of an alpha-proteobacterial cell, resulting in the evolution of the mitochondrion. The shift from asexual reproduction to sexuality, representing a dependence upon another individual for genetic information transfer across generations. The shift from individual cells to multicellular life forms (e.g. Volvox algae evolved from single-celled independent algae aggregating to form interdependent groups with reproductive division of labour). The shift from simple sociality to eusociality, the highest form of social organisation - a 'superorganism' characterised by total reproductive division of labour and segregation/identification of component individuals by function. Another key evolutionary transition was the transition from independently replicating molecules to molecule populations.

Question 48

What is the two-step process leading to the evolution of a major transition?

Answer 48

Solitary individuals aggregate to form a cohesive group defined by cooperative interaction. This group evolves to become a new, higher-level individual.

Question 49

How does relatedness drive cooperation?

Answer 49

Low rates of promiscuity (monogamy) within a population result in high intragroup relatedness (i.e. offspring and siblings are equally related, ~0.5). This alignment of genetic interests makes cooperation favourable and can result in the evolution of cooperative breeding and eusociality - particularly in harsh environments (e.g. meerkats). High promiscuity results in low intragroup relatedness and thus favours independent breeding.

Question 50

How does repression of competition help to form a cohesive operating unit?

Answer 50

To form a cohesive higher-level unit, conflict and competition within the unit must be eliminated. Clonality eliminates conflict as the 'value' of every other cell is identical to a cell's 'self-value' in transmitting genetic information (inclusive fitness). This is reflected in somatic cell 'sterility'. Whilst the soma is an 'evolutionary dead-end', every somatic cell contributes to the transmission of identical genetic material through the germline via reproductive division of labour. The reproductive division of labour is not an efficient means of reducing competition in chimaeras - as the soma would be helping to transmit non-self genetic material. The alignment of genetic interests - whereby individuals can only pass on genetic material collaboratively - eliminates selection within a group. An example of this is the mitochondrion, which is reliant upon the host cell for mtDNA transmission.

Question 51

What is policing and how does it repress intra-unit competition?

Answer 51

In some social insects (e.g. honeybees), the queen is the sole reproductive unit within the hive and secretes pheromones suppressing worker ovary development. If there is a temporary window where the queen does not secrete these pheromones, workers might 'cheat' and produce male offspring. In arrhenotokous populations (where the male is formed from an unfertilised egg), workers are less related to other worker laid male eggs (~0.125) than queen-laid males. Throughout the hive, cooperative workers police reproduction through the selective removal of worker-laid eggs, reducing cheating, maintaining stable intra-group relatedness and suppressing genetic competition. This occurs in semisocial populations where there is a genetic distinction between siblings (i.e. queen-laid eggs) and nieces/nephews (i.e. worker-laid eggs).

Question 52

How does the major evolutionary transition to eusociality occur?

Answer 52

The major evolutionary transition to eusociality has exclusively occurred in lineages with a strictly monogamous ancestor, as this ensures equal relatedness to siblings and offspring.

Question 53

How does the major evolutionary transition to multicellularity occur?

Answer 53

Subsocial multicellular group formation (clonal cell aggregation) is crucial for the evolution of true multicellularity (interdependence). Semisocial multicellular group formation (incorporation of non-clonal cells) often results in facultative multicellularity. Complex, obligate multicellularity requires a subsocial aggregation stage with a single-cell bottleneck (whereby the mature multicellular organism differentiates from a single progenitor cell, e.g. a zygote) - completely eliminating intra-group competition.

Question 54

What is the optimite argument?

Answer 54

The optimite argument posits that multicellular aliens must undergo the same evolutionary transitions (i.e. subsocial group formation, single-cell bottleneck) as these transitions form part of a single, general route to higher levels of organisation.

Question 55

What is 'life-history theory'?

Answer 55

Life-history theory is an evolutionary framework exploring how natural selection shapes the timing and pattern of major events in an organism's life (e.g. reproduction, growth, survival), how traits influence fitness at various stages and the mechanisms underlying this variation.

Question 56

What are some examples of life-history trade-offs?

Answer 56

The size at birth trade-off (altricial v precocial development; birth in an immature state, requiring extensive parental care, or relative maturity at birth). Altricial development is associated with increased forebrain mass but extensive parental investment. The fast v slow life history continuum - wherein certain organisms mature rapidly, producing large numbers of offspring at the expense of long-term survival, whereas other species delay maturation and reproduce far less frequently (e.g. the agave 'century' cactus flowers only after a hundred years of maturation). Species exhibiting delayed maturation may be semelparous (a single, lethal reproduction event) or iteroparous (multiple reproductive events). The pygmy goby, for example, lives only three weeks, whereas 32,000 year old Silene stenophylla seeds can still be successfully germinated.

Question 57

How can we deconstruct an organism's life-history?

Answer 57

The entire life cycle of a species must be examined and a life-table created, tracking patterns of survival, growth and reproduction. Individual life-history strategies collectively determine population dynamics. Inferences about population stability may be linked to the lifetime reproductive success of female members, given that females cannot reproduce indefinitely (the rate of reproductive female replacement). If R=1, the population is stable. If it fluctuates either direction, the population is in a state of growth/decline.

Question 58

What population dynamics would we expect in resource-rich environments?

Answer 58

Newly colonising populations may display 'Malthusian' (exponential) growth in resource-rich environments, plateauing once the carrying capacity of the environment is reached.

Question 59

What was Fisher's theory of reproductive value?

Answer 59

Fisher theorised that the direct action of natural selection on an individual was proportional to the reproductive value of that individual at each age. Reproductive value can be interpreted as the average contribution to the ancestry of future generations made by an individual for each age class. Babies, for example, have very high reproductive value by virtue of future reproductive potential. Understanding of reproductive value enables sustainable resource management, e.g. fisheries may harvest fish that are not actively reproducing to reduce impact (restrictions on length).

Question 60

Do males have more genetic value than females in sex-balanced populations?

Answer 60

No. Whilst males might sire more children proportionally, this has no effect on sex ratio in diploid sexually-reproducing populations. This is because each sex contributes half of the offspring genome in a diploid population.

Question 61

Are parents adapted to favour younger or older offspring?

Answer 61

Parents are selected to value older offspring more highly as these offspring have higher reproductive potential (as they are closer to reproductive age). This is reflected in birds, where younger, weaker offspring may be neglected at the expense of older, more robust offspring when parents are subject to environmental stressors.

Question 62

At what life stage is the effect of natural selection most prominent?

Answer 62

The effect of natural selection on an individual is most prominent during early adulthood, as deleterious mutations expressed at this age have the most significant impact on future reproductive potential (increasing incidence of cancer with age reflect lessened reproductive value and, therein, lessened action of natural selection).

Question 63

What is the 'grandmother hypothesis'?

Answer 63

Human females live past the point at which their reproductive value drops to zero (menopause). The grandmother hypothesis posits that this is a form of inclusive fitness, whereby older women contribute to the reproductive/survival success of their daughters (indirectly passing on their own genetic material).

Question 64

What is the difference between positive and purifying selection?

Answer 64

Positive selection for an allele conferring a beneficial phenotype results in increased frequency within a population. Purifying selection causes deleterious alleles to decrease in frequency. Both forms of selection reduce genetic diversity.

Question 65

What is allozyme electrophoresis?

Answer 65

Allozyme electrophoresis is a laboratory technique used to study genetic variation within and between population through analysis of protein variants (allozymes) of particular enzymes. Electrophoresis separates proteins based on charge and size due to the differing electrophoretic frequencies (gel mobility) of allozymes (amino acid variation). Similarity in protein migration rates indicates similar molecular phenotypes. This technique is limited insofar as two proteins with the same mobility in gel (i.e. same-charge amino substitutions) cannot be distinguished.

Question 66

What do allozyme surveys reveal about genetic diversity?

Answer 66

Allozyme surveys revealed high levels of genetic diversity within populations (e.g. the persistence of both fast and slow ADH allozymes in Drosophila populations) and a 'clock-like' divergence between species (such that the distance of relation can be measured by mutation accumulation). The 'Dayhoff distance' could be used to measure the molecular divergence of foreign proteins from human proteins, identifying the last common ancestor of those two species. This extensive, continual diversity could not solely be explain by selection as most mutations are deleterious.

Question 67

How does the neutral theory of molecular evolution resolve the issue of expansive diversity?

Answer 67

Kimura's Neutral Theory of Molecular Evolution proposed that much of variation within and divergence across species stems from mutations with a neutral effect on fitness. At the molecular level, mutation and genetic drift primarily drive evolution such that positive selection can be effectively ignored.

Question 68

What is the mathematical basis of the neutral theory of molecular evolution?

Answer 68

Within a finite population, the probability of fixation by drift for a single-copy mutation is very low (1/2N). However, neutral mutations can fix by drift at any population size with a time to fixation of 4N generations (such that drift occurs faster in smaller populations). The rate of neutral evolution is constant and equal to the mutation rate (miu) per generation. This is because the rate of neutral evolution is equal to the rate of the appearance of mutations (2N*miu) multiplied by the probability of fixation (1/2N). Neutral evolution thus occurs at a constant rate of miu mutations per generation, explaining clock-like divergence between species and extensive diversity within populations.

Question 69

Does neutral evolution occur differently across variable population sizes?

Answer 69

Yes. Neutral evolution is influenced by population size, such that fixation by drift occurs more rapidly in smaller populations. Increasing the size of a population slows the rate of fixation by drift, but over evolutionary time, divergence into two extreme phenotypes would occur. Additionally, the increased rate of fixation in small populations is counterbalanced by the fact that the rate of neutral evolution depends on population size.

Question 70

How is selection re-interpreted within the neutral theory of molecular evolution?

Answer 70

Selection at a molecular level is primarily purifying, removing deleterious alleles. Beneficial mutations occur so rarely that the effects of positive selection can be ignored, reconciling theories of selection and neutral evolution. Genetic variation data within species fits with models which do not account for positive selection, as is consistent with neutral theory.

Question 71

What was the crux of the debate between neutralists and selectionists?

Answer 71

Throughout the seventies, neutralists and selectionists debated their interpretations of evolutions. Selectionists held that fixed differences and polymorphisms across species reflected positive selection for beneficial mutations. Neutralists believed that these polymorphisms reflected the fixation of neutral mutations by drift. However, neutrality offers an important null hypothesis (genetic variation patterns without selection) upon which selection studies can be based.

Question 72

What is the significance of gene conservation in studies of evolution?

Answer 72

Genes essential for fitness (e.g. polymerases) are conserved, evolving more slowly than pseudogenes or genes with superfluous functionality. This is because selection efficiently eliminates most mutations - resulting in a very low neutral mutation rate due to strong functional constraints (as the rate of neutral evolution in genes where most mutations are deleterious is very low). Deep evolutionary divergence is thus best studied through slowly diverging genes.

Question 73

What is parallelism and how does it provide evidence for positive selection?

Answer 73

The term 'parallelism' refers to the independent evolution of the same mutation or trait in different lineages or populations. This acts in contradiction to the predictions of neutral evolution, which posit that evolution driven by random genetic drift should result in the fixation of different mutations across different species without convergent evolution. The frequency of parallelism/convergent evolution provides strong evidence for positive selection as it far exceeds that which would be expected from stochastic variation. However, appropriate statistical baselines (accounting for mutation and drift) are required for certainty. Parallelism is often exclusive to genes under very strong selective pressure.

Question 74

What are some real-world examples of parallelism?

Answer 74

Within the E. coli Long Term Evolution Experiment (LTEE), all twelve independently evolving populations acquired parallel beneficial mutations within the first 2,000 generations (often linked to a reduction in catabolic breadth, e.g. ribose catabolism gene knockouts due to prolonged exposure to glucose-only media). Furthermore, monarch butterflies and red milkweed beetles both have the same mutation to the gene encoding the sodium/potassium ATPase pump, resulting in resistance to milkweed toxins.

Question 75

How can genetic code redundancy be exploited to test for selection?

Answer 75

As the genetic code is redundant, synonymous mutations (dS) (often in the third codon position) are primarily neutral. Non-synonymous (dN) mutations can be neutral, deleterious or beneficial. If the rate of synonymous/non-synonymous mutations at a given gene locus is identical (dN/dS = 1), that gene is not under selection (neutral evolution). If dN/dS <1, mutation to the gene is under purifying selection. If dN/dS >1, mutation to the gene is under positive selection. Calculations must be normalised per site to reflect that more NS mutations occur as there are more NS sites.

Question 76

What have studies of dN/dS mutation frequency revealed about genetic divergence across species?

Answer 76

A significant proportion of non-synonymous mutations are due to positive selection (e.g. 45% across Drosophila species). This proportion is much smaller across mammals, as these tests only identify genes under recurrent positive selection. All genes identified were involved in host-pathogen interaction (reflecting selection for coevolution).

Question 77

What is evolutionary innovation?

Answer 77

An evolutionary innovation is an emergent character which causally enables an organism to exploit their environment in new ways, such as the evolution of multicellularity or crassulacean acid metabolism.

Question 78

Can evolutionary innovations arise from enzyme promiscuity?

Answer 78

Yes. The dynamic conformational flexibility of proteins enables adaptation to bind a secondary ligand. This means that a single enzyme can catalyse multiple reactions at different rates. A promiscuous enzyme can evolve new functionality through preference change with relative ease (as can be accelerated through artificial directed protein evolution).

Question 79

What is one example of the rewiring of a gene regulatory network in response to selection?

Answer 79

The experimental deletion of the FleQ gene (the regulator for flagella structural genes) rendered bacteria immotile and generated selection to regain motility as cells rapidly diminished local resources. Within a week, bacteria regained motility through mutation to the NtrC gene (nitrogen assimilation gene transcription factor). This mutation increased the promiscuity of the transcription factor (proteins influencing RNA polymerase activity), enabling regulation of flagella structural genes.

Question 80

Does horizontal gene transfer facilitate evolutionary innovation?

Answer 80

HGT enables the 'en bloc' transfer of biological functions (e.g. the acquisition of the lac operon by E. coli) and is responsible for over ninety percent of the genes comprising most bacterial genomes. It is a major driver of bacterial evolution, as exemplified by the antibiotic resistance crisis wherein the movement of antibiotic resistance genes via the plasmids of environmental bacteria enhances the virulence of pathogenic bacteria. HGT also occurs in eukaryotes (e.g. bdelloid rotifers). Novel evidence suggests that viral parasite defence genes comprising the eukaryotic immune system were acquired from bacterial HGT during early eukaryotic evolution.

Question 81

What evolutionary innovations have been derived from hybridisation/introgression events?

Answer 81

Interbreeding between distinct lineages can transfer beneficial alleles. For example, between two and five percent of the European genome is derived from Neanderthal interbreeding. Human colonisation of the highly anoxic Tibetan plateau resulted in introgression of an EPAS1 allele of Denisovan origin. This allele confers tolerance to hypoxia and may still be found in modern Tibetan peoples.

Question 82

How do gene duplication events facilitate evolutionary innovation?

Answer 82

Gene duplication events occur at high frequency, with most inactivated due to mutation. Some undergo neofunctionalisation, where one copy retains the original function and the duplicate evolves a novel function. Neofunctionalisation often results in morphological innovation. For example, in snakes, neofunctionalisation of venom metalloproteinases has resulted in the diversification of venom types.