BIOL 4160

Evolution

Phil Ganter

301 Harned Hall

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Flower of a Cornus species (the dogwoods) that grows on the ground

06 - Microevolution: Genotypes

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Remember that natural selection is a mechanism of evolution, it is not evolution

Natural Selection can enhance, reduce, or maintain variability (in the last case, natural selection resists evolution!)

  • Natural selection can, under the right conditions, favor polymorphism (two or more alleles or phenotypes in a population) and can result in a Balanced Polymorphism if selection resists change in the allele frequencies
    • more on this later
  • Natural selection can have different effects on a population, which we have divided into three "modes of selection."
    • Disruptive (Diversifying)
      • when the extremes are fittest and intermediates are less fit
      • Can split a population into two phenotypes with few intermediate forms
      • in statistical terms, the mean need not change
    • Stabilizing
      • when the fittest individuals are the average, then those with more extreme (larger and smaller) phenotypes are less fit and NS will act to reduce the number of individuals with extreme phenotypes
      • in statistical terms, the mean of the phenotype is not affected but the standard deviation is (it should decrease)
    • Directional
      • when a new, fitter phenotype originates or arrives through migration, the population will move from the older, less fit phenotype to the newer phenotype over time
      • This will change the mean value of that over time but need not affect the standard deviation

Fitness

  • For natural selection to occur, there must be a correlation between phenotype and fitness, so lets look closer at fitness
  • Fitness is the overall success in reproduction that can be ascribed to an individual, gene, or group
    • This has many components:
      • Survival of the individual, the individuals carrying the gene, or the group
      • Speed of development
      • Mating success
      • Production of offspring (number, size, condition)
    • Fitness considerations do not stop when the offspring are born, as a parent is only successful if its offspring are also successful (and their offspring, ad infinitum)

Absolute Fitness

  • So, is there a measure that will combine all components
  • Yes, there is.  It is called r (or, as in the book, R (really R0), a related measure that is easier to explain), the intrinsic rate of natural increase
    • When referring to a gene or lineage (can't apply to individuals, only the lineage to which they belong) the letter "m" is often substituted for "r", especially in the older literature
  • r comes from ecology and we will not develop the theory to use it here, so we will conform to the book's use of R0,  the symbol for the replacement rate
    • For asexuals, is the number of individuals in the next generation for ever  individual in the present generation
      • if R0 is greater than 1, the population is growing
      • if R0 equals 1, the population size is stationary
      • if R0 is less than 1, the population is decreasing
    • We can apply this idea to a portion of the population, say those with the A allele at locus A, so if A has an R = 1.4, then there are 1.4 copies of that allele in the next generation for each copy in the present generation
  • R0 (or r) is a measure of absolute fitness because it literally indicates how many copies of a gene there will be in the next generation
    • Absolute fitness is useful but can be hard to measure and hard to work with when modeling evolution

Relative Fitness

  • Relative fitness is often preferred as a measure of fitness
  • The fittest genotype (in absolute fitness terms) in a generation is the reference fitness
  • All other genotypes will have a fitness less than the reference, and so they will be a fraction between 0 and 1 if we simply divide the absolute fitness of each genotype by the absolute fitness of the reference fitness, the maximum absolute fitness
    • notice that the denominator is always at least as large as the numerator and will usually be larger, giving us the 0-to-1 range of relative fitnesses defined above

Mean relative fitness

  • This is a measure of the difference between the actual population fitness and the theoretical maximum
    • The rate of genetic change in a population due to selection will depend on the magnitude of the difference between actual and maximal fitness
  • calculated by multiplying the relative fitness of each genotype by its frequency in the population, then summing up all of the products
    • If absolute fitness (R0) of A1A1 is 1.6, is 1.36 for A1A2 and 1.2 for A2A2,
    • then the relative fitness (Wi) of A1A1 is 1.0, is 0.85 for A1A2 and 0.75 for A2A2
    • Now suppose that half of the population is A1A1 and the other half is equally split between A1A2 and A2A2
    • Then the mean fitness of the population (W-bar) is
    • (0,5 * 1.0) + (0,85 * 0.85) + (0.25 * 0.75) = 0.5 + 0.2125 + 0.1875  =  0.9

Coefficient of Selection (often s)

  • measures the selective disadvantage of a genotype relative to the most fit genotype
  • calculated as   s =  1.0 - W (using the relative fitness of a particular genotype)

One additional and important advantage of using relative fitnesses

  • The rate of genetic change under selection depends not on the absolute fitnesses but on the relative fitnesses
    • So, it doesn't matter if the R0's are 1.6, 1.36, and 1.2 or 8, 6.8 and 6 or 0.5, 0.425, and 0.375 (this last for a declining population), evolution will proceed in the same manner and speed because the relative fitness of all three scenarios is 1.0, 0.85, and 0.75.
  • Note that it does not matter if the population is growing or not, evolution will proceed as expected

A Model of Selection

  • Since the purpose of this model is to understand how selection will effect evolution, we will ignore genetic drift (and mutation, migration, and mating)
    • this is only a simplification and more realistic models incorporate both
  • We will also simplify by focusing on a single locus with only two alleles present in the population
  • From the Hardy-Weinberg equation, we will borrow p and q (the frequency of the A and A alleles, respectively) and the starting point for our population
Genotypes
A1A1
A1A2
A2A2
Frequency of Genotypes at Birth
p2
2pq
q2
Fitness of Genotypes
w11
w12
w22
  • The model predicts what the allele frequencies will be after selection operates on this population
  • Since we know the initial frequencies of each genotype and their fitnesses, we can calculate the mean population fitness at birth as (this is useful later):

  • We will use the change in allele frequency as our measure of the effect of selection and, for consistency, we will always predict the change in p, the frequency of allele A1

  • Logically, if p increases, then q, the frequency of the A2 allele, must go down

  • The general solution is (see book for derivation):

  • But this equation can be simplified if we make some assumptions about dominance and the fitnesses

A1 dominant and advantageous (A2 disadvantageous)

  • First, and for all of the equations below, we will express the relative fitnesses in terms of selection coefficients and then present the algebraic simplification that results from substituting them into the general equation above (all five cases are simplifications to predict the outcome in specific situations)
 
w11
w12
w22
Fitness
1
1
1-s

  • This says that p will increase (the right side of the equation is positive and so delta-p is positive), which makes sense as A1 is the most fit of the two alleles

A1 dominant but A2 selectively advantageous

 
w11
w12
w22
Fitness
1-s
1-s
1

  • Here delta-p is negative (look at the right side) and so A1 is being lost from the population, as is should if A2 is more fit than A1

Incomplete Dominance with the heterozygote fitness between the advantageous dominant homozygote and the disadvantageous recessive heterozygote

  • In this case, the heterozygote must have a higher fitness than the homozygous recessive genotype and one way to do that is to multiply s by a second fraction, h
  • h will increase w because, as h is between 0 and 1, the product of h and s will be smaller than s and this smaller product is subtracted from 1
 
w11
w12
w22
Fitness
1
1-hs
1-s

  • This equation predicts that the change in p is always positive, so the endpoint arrives when A1 is fixed in the population
  • Note that this equation differs from the text's equation (equation A3 on page 274).  I could not derive the equation presented in the text but, when I graphed the equation, it did not behave as described there.  So, I am presenting my derivation, which does behave as predicted (and as makes sense because w11 is the fittest genotype and should move A1 to fixation)

Incomplete Dominance with Heterozygote advantage

  • The heterozygote has the fittest genotype but we will allow each of the homozygotes their own selection coefficient
 
w11
w12
w22
Fitness
1-s
1
1-t

  • The change in p will depend on its frequency: it will be positive below a particular value of p and negative when p is over that value (change = 0 when p is at that value)
  • This scenario produces a Balanced Polymorphism, a stable equilibrium (stable because when not at the equilibrium point the value of p moves toward equilibrium so that the system returns to equilibrium)
  • This situation is called Heterosis

Incomplete Dominance with Heterozygote disadvantage

 
w11
w12
w22
Fitness
1+s
1
1+t

  • The outcome here is also an equilibrium but an unstable equilibrium
  • When the value of p is not at the equilibrium point the change in p will not move it toward the equilibrium point but away from it (toward either fixation or loss of the A1 allele, depending on the value of p)

A special case - A1 is dominant and A2 is a recessive that is lethal when homozygous (harmless when heterozygous due to the dominance effect)

  • In this case, we see that dominance can protect the heterozygote but every generation, the homozygous recessive individuals are lost before they can reproduce (or even before they can develop)
 
w11
w12
w22
Fitness
1
1
0

  • Notice something about the equation above
    • As q, the frequency of the lethal allele (A2) decreases, as it should (after all, its lethal in the homozygous condition), the rate of change for p is smaller and smaller (it depends on q2, which is a smaller and smaller numerator)
    • Thus, the rate of loss of the lethal slows to a trickle and it persists in the population for many generations
  • This makes sense because, when there are very few A alleles present, the chance of an individual carrying A mating with another rare carrier of A is very small and that is the only way to get homozygous individuals that will be lost

Maintaining Allelic Variation

  • Many of the predicted outcomes from selection predict the loss of less fit alleles, which should decrease genetic variation
  • In the face of loss of alleles through selection (and genetic drift), what maintains genetic variation
    • Migration can re-supply alleles
    • Mutation can re-supply alleles
      • This is only true for mutations that recur (i. e. that are not unique events) like point mutations (and, to a lesser extent, indels)
      • Mutation pressure produces an equilibrium that depends on the ratio of the mutation rate to the selection coefficient

    • Balancing Selection
      • I disagree with the book on the equivalence of the terms "Heterozygote Advantage" and "Overdominance"
        • Heterozygote advantage is measured in terms of fitness (heterozygotes have the greatest fitness)
        • Overdominance refers to the phenotype of the heterozygote
          • when the phenotype of the heterozygote lies outside of the range between the two homozygotes
      • Why is this confounded in the book (and by many)?
        • If you consider fitness a phenotypic measure, then it is a case of overdominance
        • however, an overdominant phenotype need not be the most fit (which seems to imply that fitness is not, in actuality, a phenotype but a measure of success linked to a phenotype)
    • Antagonistic Selection
      • when a phenotype affects more than one fitness component, selection of one component may oppose selection of another component
      • Malaria-linked anemias
        • heterozygotes experience lowered viability and homozygotes often have very low viability, which selects against the recessive (anemia-producing) allele
        • when malaria is present, heterozygotes do not support the parasite as well as homozygous dominant, giving the heterozygote the greatest fitness
      • so the anemia-producing alleles are not favored unless malaria is present
    • Selection that varies over Time or Space (Multiple-Niche Polymorphisms)
      • polymorphism can result:
        • if one allele is favored part of the time and the other allele is favored the rest of the time  OR
        • if one allele is favored over part of the habitat and the other allele is favored in the rest of the habitat
      • often detected when older individuals' phenotypes are distributed bimodally but not so at birth
      • Chiricauhua chromosome in Drosophila pseudoobscura (favored part of the year, disadvantageous the rest of the year)
    • Frequency-Dependent Selection
      • Inverse frequency-dependence
      • selection advantage is inverse to allele frequency
      • produces a stable polymorphism
      • Sex-Ratio is an example of inverse-frequency dependence

Multiple Outcomes

  • Some situations are unstable equilibria
  • here, both fixation of an allele and its elimination are both possible
  • Adaptive Landscapes
    • Here, the average fitness of a population is mapped
    • The length and width represent phenotypes
    • The vertical dimension is fitness, so going up a hill means increasing fitness and down decreases fitness
    • Top of each hill is an Adaptive Peak
    • populations cannot leave as all directions are down
    • multiple hills (peaks) represent multiple stable outcomes

Detecting Selection in the Gene

Background:

  • Recombination:
    • All nucleotide positions along a gene are subject to point mutations
      • Each position is a separate "locus" and recombination can occur within the sequence of a gene
    • However, the probability of recombination between any two points along a chromosome depends on the distance between those points
    • Since no gene is that large, the distances between any two nucleotides is very small and so is the chance of recombination
      • Even with such tight linkage between positions within a gene, over sufficient time recombination should occur
      • Recombination "breaks" linkage between sites along a chromosome
  • Selection and Hitchhiking within the Gene
    • When a mutation occurs a particular site, it has a chance of becoming fixed
      • For neutral mutations, the probability of fixation and time until fixation depend on the population size
      • For advantageous (in terms of selection) mutations, the mutation will become fixed and the time until fixation will depend on the selection coefficient
      • Advantageous mutations should be fixed in less time than neutral mutations in large populations (in small populations, there may be no great advantage when the selection coefficient is not very large)
    • Due to tight linkage, when an advantageous mutation is fixed, so are most (if not all) of the neutral mutations that happened to be near the mutant position on the particular gene sequence bearing the advantageous mutation (another case of hitchhiking)
      • Selective Sweep
        • The fixation of an advantageous point mutation carries a set of neutral mutations to fixation as well, "sweeping away" the variation that was present in the population at each of the proximal nucleotide sites along the gene
      • Balanced Polymorphism
        • Once a balanced polymorphism hits the equilibrium frequency for each allele, each lineage is preserved (will not become fixed due to genetic drift) if the population is large
        • This prevents "selective sweeps" affecting variation within that gene

Consequences:

  • When we sequence genes, we can sequence many examples of the gene from different individuals in the population
  • If we count the number of variable sites along the gene by comparing all of the sequences, we can get an estimate of the time since the previous "selective sweep"
  • We can detect selection by looking for regions with exceptionally little variation (directional selection causing selective sweeps) and exceptionally great variation (balancing selection preserving particular alleles)

Conflict and Cooperation

Review the discussion of Levels of Selection (Lecture 05 and Chapter 11), Kin Selection (Lecture 05 and Chapter 11), and Frequency Dependent Selection (Above and Chapter 12)

Conflict between individuals and between alleles is well documented (we will see more instances in the additional material on sexual selection presented below)

Cooperation is harder to document and sometimes has also been harder to understand because of the possiblity of cheaters who receive cooperative benefits but do not bear cooperative costs

  • Group selection is one explanation but it has not been extensively researched
    • Cheaters are hard to discourage in group selection
    • Structure of groups not obvious

So, the stress has been on finding reasons for cooperation that do not depend on group selection and there are four general types of explanations

Four general types of explanation of cooperation that do not rely on Group Selection

  1. Kin Selection - when the organism donating the resource is donating it to kin who will indirectly spread the donor's genes
  2. Direct Individual Advantage (note "direct" added to the book's terminology) - when the cooperation is not a cost but a direct benefit (or the benefits outweigh the costs) for the individual performing the altruistic act (in this case, the behavior is only apparently altruistic)
  3. Manipulation - when the organism donating resource is forced ("manipulated") to donate
  4. Reciprocation (a specific example of the Transactional Model of Reproductive Skew) - when cooperation brings just enough added reproductive opportunity to subordinates that the do better than if they did not cooperate
    • if the interaction is not between dominant and subordinate individuals, then this interaction is called Reciprocal Altruism, where individuals donate if they are also getting benefits (for foraging flocks of birds, those watching for predators (sentinels) will warn others of their approach and expect the same from others who watch when the current sentinels are eating)
      • notice that, in this case, there need be no close familial relationship between the members of a flock
      • when there is no relatedness, the benefits for both sides are equal for both
    • as the degree of relatedness increases, the immediate benefits may become more and more skewed (one member of the transaction gets most of benefits or pays less of costs)
      • This is because the donor gets not only some direct benefits, but also will get indirect benefits when the recipient of the benefits reproduces and passes on some of the donor's genes because the donor and recipient are related
      • Kin Selection is really a case of the Transactional Model when relatedness is close and Reciprocal Altruism is at the opposite end of the spectrum (no relatedness)

Evolutionary Stable Strategies (ESS)

This is a situation (really not appropriate to call it a strategy as this implies a goal and is teleological) in which no mutant can increase its frequency due to natural selection alone

  • It is the optimal phenotype for the conditions affecting fitness
  • ESS is derived from game theory and has been mostly used to compare possible sets of behaviors
    • Prisoner's Dilemma is often used as an example
      • From Wikipedia:  "Two suspects are arrested by the police. The police have insufficient evidence for a conviction, and, having separated both prisoners, visit each of them to offer the same deal.  If one testifies (defects) for the prosecution against the other and the other remains silent, the betrayer goes free and the silent accomplice receives the full 10-year sentence.  If both remain silent, both prisoners are sentenced to only six months in jail for a minor charge.  If each betrays the other, each receives a five-year sentence.  Each prisoner must choose to betray the other or to remain silent.  Each one is assured that the other would not know about the betrayal before the end of the investigation.  How should the prisoners act"
      • It pits the costs and benefits from cooperating versus those from "defecting" - i. e. refusing to cooperate.
        • In the simplest cases, defecting is the best strategy
      • There are countless variations on this game (look to the book's explanation of the famous Hawks and Doves situation for an example of a case where a mixed strategy is an ESS)
    • Iterated Prisoner's Dilemma alters the game by running it again and again and assessing the long-term return from each strategy (ESSs differ if, for instance, the game is for a pre-determined number of iterations or if the number of iterations is not known at the outset or if there are infinite iterations)
      • In these games, total cooperation has the best payoff is there is no defection (ESS is called a Pareto optimum)
      • If cheaters are present, the iterated form of the game allows one to identify and punish cheaters and allows for may possible mixed strategies
      • Tit-for-tat (respond to others as they have responded to you - cooperate with cooperators and defect from defectors) is an example of a mixed strategy that can be an ESS under some conditions

Conflict and Sexual Selection

Review the discussion of Sexual Selection (Lecture 05 and Chapter 11)

  • Mating Conflict
    • One sex produces large few gametes and the other many, small ones
    • A male has more gametes than a female and can mate with more females than a female can mate with males
    • Leads to greater variation in male mating success than female mating success
    • Asymmetry in mating opportunities sets up contests between males for matings and successful fertilizations (sperm competition)
    • Can lead to changes in male phenotype to increase success
    • Antagonistic selection can occur if the altered phenotype increases mating success but bears a selective cost from lowered ecological performance
  • Mate Choice
    • Sex with fewer gametes chooses mates from among available, competing mates
    • Choice often depends on possession of extreme phenotypes in chosen sex
    • Once again,  antagonistic selection may occur if exaggerated phenotype is beneficial for mating but carries ecological costs
    • Reasons for mate choice
      • Sensory Bias
      • Some trait or traits that possess the ability to provoke positive mating responses from females may explain the origin of choice in some cases
      • This is a kind of "preadaptation" in which the preference develops before the male trait appears
      • Direct Benefits
      • If both parents contribute to the post-fertilization welfare of the offspring, choice of a good provider provides a direct benefit
      • Since the chooser cannot perceive the ability or willingness to provide directly, choice must be made on a character that is correlated with the desired traits
      • Indirect Benefits
      • If one mate only contributes its gametes to the next generation, then any benefits of choice will be through increased fitness of the offspring, not benefits directly experienced by the other mate
  • Runaway Sexual Selection
    • This model begins with two alleles for a male trait that can be used as a means of choice by females
      • T1 is the normal allele and T2 is a slightly exaggerated version (the exact details of the model will differ depending on the dominance relationship between T1 and T)
      • The frequency of T1 is t1 and the frequency of T2 is t2
    • Originally, there is no genetic basis for choice by females but a mutation occurs at locus P that encourages P2P2 and (if the system works quickly) P1P2 females to prefer males with T2 phenotype
      • The frequency of P1 is p1 and the frequency of P2 is p2
    • The appearance of mating preference has two consequences:
      • t2 will start to increase as males with T2 phenotype will get more matings because P1P1 females will not distinguish between T1 and T2 males and will mate with them with a frequency equal to their gene frequencies (t1 and t2)
      • P2 females will choose T2 males (in the simplest models the choice is exclusive but that is not necessary)
        • So T1 males mate with only P1P1 females and T2 males mate with P1P1, P1P2, and P2P2 females, an advantage that increases t over time
    • P2 will also start to increase but not through direct selection but through hitchhiking
      • P2 females choose T2 males, which violates random mating and, as a result, causes a linkage disequilibrium between the P and T alleles (in other words, assortative mating links the P and T alleles)
      • As the frequency of T2 (t2) increases, so will the frequency of any alleles linked to it - in this case P2 is becoming linked and, so, p2 will increase
    • Further mutation for more extreme phenotypes is favored
      • If a new mutation occurs (T3) that is even more exaggerated than T2, it will most likely be preferred over T1 and T2 by P2 females, which will give it the same advantage over T2 that T2 had over T1
      • If a new mutation occurs (P3) that causes a stronger preference for T2 males, it will be more closely linked to T2 than P2 and p will increase as the result of hitchhiking
    • This is a "run away" system because the male trait gets more and more exaggerated and female choice gets more and more exclusive over time
      • Run away can be prevented by costs associated with either more exaggerated T traits and costs associated with strict choice (bypass a mating today and you are risking finding no mate tomorrow or, for strong choice, never finding a suitable mate)

Mating Systems and Parental Care

  • Parents invest (potentially limiting) resources in their offspring
    • Many animals only invest the cost of gamete production, which is often greater (per gamete and total) for females
    • Some animals invest resources after fertilization (guarding young, feeding young) which increases the cost of each offspring
  • Promiscuous Mating (Polygamy) - no parental care is invested and one or both sexes may mate with multiple partners
    • When females provide care and males do not, the males are promiscuous (Polygyny)
    • When males provide care (some frogs, birds and fish), the females are promiscuous (Polyandry)
  • Monogamy - Some animals (birds and mammals and even some insects) form pair-bonds and generally  mate only with the other member of the pair
    • Extra-pair matings are usually present (strict monogamy is rare)
    • Pair-bonds often only last for a single reproductive season for many long-lived animals (new parings each season)
  • Conflicts arising from Parental Care
    • The asymmetry of costs to parents from reproduction leads to conflict between males and females over which will provide care
      • Since the benefits of successful care are shared equally by both parents, the sex that experiences less of a cost (in terms of lost reproductive opportunity) in providing the care will be the one actually providing it
        • If care is only guarding the young, males may pay less of a price if they can still find opportunities to mate with other females
        • If feeding is also provided, males may desert because they lose the mating opportunities due to the extra time needed to forage for the young
        • If male and female losses are balanced at some intermediate point, an ESS with both sexes providing care may be possible
    • Parent-Offspring Conflict
      • A second asymmetry in parenting is comes from the difference in relatedness between siblings and parents
      • Offspring are completely related to themselves (r = 1.0), usually half related to their siblings (r = 0,5) and half related to each parent (r = 0.5)
        • Thus, when a parent distributes food, there is no reason for favoring any particular offspring based on relatedness
      • Offspring are more related to themselves than to siblings and so their interests are best served if the parent devotes more resource to them than to siblings, even though the parent has no reason to do this
      • This can lead to conflict between parent and offspring about distribution of resources
      • Example -
        • Haplodiploidy means that a female is half related to her female offspring and completely related to her male offspring
        • Haplodiploidy means that female siblings are 3/4ths related but only half related (r = 0.5) related to their male siblings
        • Thus, females will want to devote more resources to male offspring than the workers want, since they are more related to sisters than brothers
    • Paternity - the third asymmetry in parenting that needs attention
    • Females are usually able to identify which young are theirs (carry their genes) but males are often unable to tell this
    • Male behaviors have developed that help ensure the paternity of offspring
      • Mate Guarding - males prevent subsequent matings with other males so that they are guaranteed that a female's eggs are fertilized by their sperm
      • Infanticide of offspring not likely to be their own
      • (not the only reason for infanticide as instances of infanticide occur when parents responsible for care do not have resources for all of the young)
  • Siblicide - to continue the theme from the above, many infants die not as a result of infanticide (adults killing offspring) but through siblicide (sibs killing sibs)
    • When resources are plentiful, sibs benefit one another through inclusive fitness
    • When resources are scarce, in individual will pass on more of its genes that will its sib (normally relatedness is no more than 0.75) and so sibs may compete to the death for the available resources
      • Some sharks eat siblings while still in their mother's uterus, which may be a case of limited resource or it might be an extension of Oophagy (where egg production continues as embryos develop and the developing sharks eat the eggs) as a means of feeding the developing young.
Last updated February 20, 2009