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Mechanisms of Microevolution. Reading:Freeman, Chapter 24, 25. Microevolution vs. Macroevolution. The term “ microevolution ” applies to evolutionary change within a lineage It occurs continuously.

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Mechanisms of microevolution

Mechanisms of Microevolution

Reading:Freeman, Chapter 24, 25


Microevolution vs macroevolution
Microevolution vs. Macroevolution

  • The term “microevolution” applies to evolutionary change within a lineage

    • It occurs continuously.

    • Depending upon the organism and the circumstances, it can transform a lineage. dramatically over time.

    • Alternately, a lineage may appear to remain the same over time-this is called stasis.

  • Macroevolution is the origin and extinction of lineages.

    • It can happen gradually, or slowly.

  • Both processes are essential to evolution. Microevolution is probably better understood, and better documented, because in some organisms it takes place on timescales we can study directly by experiment and direct observation.

  • Ironically, in “On the Origin of Species” Darwin lays out a theory of microevolution…he assumed macroevolution would inevitably result from microevolution.

    • It would be 100 years later that Ernst Mayr, and others, would develop a scientific theory of speciation.

    • The replacement of one species by another (as opposed to the replacement of one allele by another), by the way, is an ecological process..it is not evolution in the usual sense, though this phenomenon usually leads to extinction of some species and diversification of others.


The population is the basic unit of microevolutionary change
The Population is the Basic Unit of Microevolutionary Change

  • The genotype of an individual is, essentially, fixed at birth.

  • The population is the smallest unit where evolutionary change is possible.

    • Unlike individuals, populations permit the origin of new alleles through mutation, and the change in the frequency of alleles through selection, genetic drift, etc..

  • Individuals do not evolve, populations and species evolve.


Population genetics
Population Genetics

  • Population genetics refers to the study of evolution via the observation and modeling of allele frequencies and genetic change in populations of organisms.

  • There are three parameters to keep in mind:

    • allele frequency: the proportion of a specific allele at a given locus, considering that the population may contain from one to many alleles at that locus.

    • genotype frequency: the proportion of a specific genotype at a given locus, considering that many different genotypes may be possible.

    • phenotype frequency: the proportion of individuals in a population that exhibit a given phenotype.


  • Consider a population of N organisms.

  • Two phenotpyes, yellow and tan.

  • Suppose that they are diploid and reproduce sexually.

  • Consider one gene with two alleles, A and a.

  • The possible genotypes are therefore:

  • AA, Aa, and aa.


  • Phenotype Frequencies

  • To calculate the frequency of a phenotype, count the number of individuals with that phenotype, and divide by the total. Therefore, the frequency of the yellow phenotype in the population below is 4/10=.40


  • Genotype Frequencies-

  • To calculate the frequency of a genotype in the population, find the total number of individuals in the population with that genotype, and divide by the population size, N.

    • f(AA)= #(AA)/N

    • f(Aa)= #(Aa)/N

    • f(aa)= #(aa)/N


  • Question: What are the frequencies of the AA and Aa, and aa genotypes in the population below?

Aa

Aa

aa

aa

AA

Aa

aa

Aa

aa

AA


Aa

Aa

aa

aa

AA

Aa

aa

Aa

aa

AA


  • Allele Frequencies- freq(aa)=4/10=.40

    • By convention, the frequency of the dominant allele is called p, thus the frequency of the recessive allele, q=1-p.

  • To calculate the frequency of an allele in the population, add the total number of homozygotes for that allele to half the heterozygotes, and divide by the population size, N.

    • p= ((#AA) + (1/2)(#Aa))/N

    • q= ((#aa) + (1/2)(#Aa))/N

  • If you already know the genotype frequencies,

    • p=f(AA)+(1/2)f(Aa)

    • q=f(aa)+(1/2)f(Aa)


  • Question: freq(aa)=4/10=.40 What are the frequencies of the A and a alleles in the population below?

Aa

Aa

aa

aa

AA

Aa

aa

Aa

aa

AA


Aa

Aa

aa

aa

AA

Aa

aa

Aa

aa

AA


Evolutionary change is a consequence of changes in allele frequencies
Evolutionary Change is a Consequence of Changes in Allele Frequencies

  • This is the genetic definition of evolution…a synthesis between Mendel’s and Darwin’s theories.

  • All of the evolutionary change between our single-celled ancestors and ourselves can be described as the sequential origin of new alleles, their replacement of old ones, and occasionally the origin of new genes through duplication..


Evolution as change in allele genotype frequency
Evolution as Change in Allele/Genotype Frequency Frequencies

  • Microevolutionary change is inherent in the change in the frequencies of alleles over time.

  • To be able to see if evolution IS occurring, we need to consider what we would expect if evolution is NOT occurring.

  • Once we know that, then if we see a departure, we know that evolution is occurring.


The hardy weinberg equilibrium
The Hardy-Weinberg Equilibrium Frequencies

  • Hardy-Weinberg Equilibrium is defined as the situation in which no evolution is occurring. It is a genetic equilibrium.

  • It was the solution to a nineteenth century misconception-the notion that the dominance or recessiveness of an allele alone could cause evolutionary change (it can’t).

  • The Hardy-Weinberg Equilibrium refers to a particular locus: one locus may be undergoing rapid allele-frequency change, while other loci are in equilibrium.


Assumptions of the hardy weinberg equillibrium
Assumptions of the Hardy-Weinberg Equillibrium Frequencies

  • A locus with two or more alleles will be in Hardy-Weinberg Equilibrium if five assumptions are met. These are:

    • 1. infinite population size (there are infinitely many individuals in the population.)

    • 2.there is no allele flow (i.e., no movement of individuals from population to population.)

    • 3.there is no mutation (no biochemical changes in DNA that produce new alleles.)

    • 4. there is random mating (this means that with regard to the trait we're looking at, individuals mate at random they don't select mates based on this trait in any way.)

    • 5. No Selection: the different genotypes (for the genetic trait we're studying) have equal fitness.


  • Consider a population of diploid, sexually reproducing individuals. Imagine a gene with two alleles, A and a, so there are three genotypes, AA, Aa, and aa.

    • Assume this population meets the five assumptions of Hardy-Weinberg Equilibrium.

    • Because mating is random, alleles mix together at random.

    • Because the population is infinitely large, the probability of getting a gamete with a particular allele in it is simply the frequency of that allele.

    • Similarly, determining the probabilities of getting particular genotypes will tell us thefrequencies of those genotypes in the population.


  • To get individuals. Imagine a gene with two alleles, A and a, so there are three genotypes, AA, Aa, and aa. AA, you need an egg with allele A, with probability p, and a sperm with allele A, also with probability p.

  • The probability of getting both of these is p2

  • Similarly, for aa, the chance of a sperm with an "a" allele is q and the chance of an egg with an "a" allele is also q, so: q2


  • There are two ways of getting the heterozygous genotype, Aa. These are:

  • 1.an "A" bearing sperm and an "a" bearing egg

  • 2.an "A" bearing egg and an "a" bearing sperm

  • The probability of an "A" bearing sperm is p; the probability of an "a" bearing egg is q, so the probability of the first way of getting an Aa is (p)(q) = pq.

  • Similarly, the probability of aA (a sperm, A egg) is also (p)(q)=pq.

  • So to get the probability of getting the Aa genotype, we add together the probabilities of the two ways of getting this genotype. So: The genotype frequency of Aa is pq+pq=2pq


  • With a little more math, it can be demonstrated that: These are: As long as the conditions of the Hardy-Weinberg equilibrium are met, allele frequencies will remain constant.

    • After one round of random mating, there will exist a stable, mathematical set of genotype frequencies for any given allele frequencies.

  • This relationship will hold as long as the conditions of the Hardy-Weinberg equilibrium are met.

    • This means that if you know allele frequencies, you can solve for expected genotype frequencies.

    • If you know the frequency of a recessive genotype, you can usually infer the expected frequency of the recessive allele as well.


These apply under hardy weinberg equilibrium
These apply under Hardy-Weinberg equilibrium These are: :

Freq(AA)=p2

Freq(Aa)=2pq

Freq(aa)=q2

p2+2pq+q2=1


  • So-Without the HW equilibrium, you can do thus: These are:

  • Allele frequencies from numbers of individuals

    • p= ((#AA) + (1/2)(#Aa))/N

    • q= ((#aa) + (1/2)(#Aa))/N

  • Genotype frequencies to allele frequencies

    • p=f(AA)+(1/2)f(Aa)

    • q=f(aa)+(1/2)f(Aa)

  • To go from allele frequency to genotype frequency, you must assume HW equilibrium

    • If this is not the case, there may be many potential genotype frequencies for a single allele frequency.

    • For instance, 500AA 0Aa 500aa, and 1000Aa both have p=.5, q=.5

  • If HW is the case, use the following to go from genotype frequency to allele frequency, but remember these are estimates (and expected values of each would be these estimates times the total population size), not the true values:

    • Freq(AA)=p2 Freq(Aa)=2pq Freq(aa)=q2

  • If you have the frequency of a recessive phenotype, its frequency is q2, thus, take the square root and get q. Get p from there, etc.


Question
Question: These are:

  • The albino color in rabbits is caused by a recessive allele. Aa and AA individuals are normally pigmented, and aa individuals are albino.

  • Imagine a population with 9999 normally pigmented rabbits, and a single albino rabbit.

  • What is the frequency of the recessive phenotype? What is the frequency of the (aa) genotype?

  • Under Hardy-Weinberg equilibrium, what are the expected frequencies of the dominant and recessive alleles? What is the expected frequency of the (Aa) genotype?


Answer
Answer. These are:

  • Freq Recessive phenotype 1/10000=.0001

  • Freq (aa) genotype, 1/10000, .0001

  • q2=.0001, therefore q=(.0001)1/2 q=.01

  • p+q=1, so p=1-.01=.99

  • 2pq=(.01x.99x2)=.0198

  • Note that while 1 in 10,000 rabbits is an albino, approximately one in fifty individuals carry the allele. This is a fairly common situation for a recessive allele which is selected against.


  • We can define five different ways in which evolution occurs based on the situations in which these five assumptions are NOT met. These are:

  • 1.genetic drift is change in allele frequency by random chance. It occurs if a population is not infinite in size. In populations that are not infinitely large, there will be random error in which alleles are passed from generation, and allele frequencies will change at random. Since no population is really infinitely large, there is always some genetic drift occurring; however, the effect is very small in large populations. The effect of genetic drift is larger in small populations.


  • 2. based on the situations in which these five assumptions are NOT met. These are: Allele flow is change in allele frequency that occurs because individuals move among populations. If there are different allele frequencies in different populations of a species, then when individuals move to a new population, they will change theallele frequencies in the new population.


  • 3. based on the situations in which these five assumptions are NOT met. These are: mutation is biochemical change in DNA that one allele into another and creates alleles. It not a common event (typical mutation rates are about one mutation in a million genes passed from generation to generation ); as a result, evolution through mutation is extremely slow.

  • Mutation is very important for evolution because, ultimately, mutation is the source of genetic variation. Other forms of evolution on cannot occur without genetic variation.

  • With regard to the fitness of alleles, mutation is random -- it may produce alleles that result in high fitness (rare) or low fitness (much more common), and the probability of a mutation is independent of an evolutionary “need” for the mutation.


  • 4. based on the situations in which these five assumptions are NOT met. These are: non-random mating is evolution that occurs because individuals select mates based on their characteristics.

  • 5.natural selection is evolution that occurs because different genotypes have different fitness. More about this later.


You can test to see whether a population is in Hardy-Weinberg equilibrium, if you have the numbers of individuals of each genotype.

-The Chi-Square test is ideal for this:

-Generate expected values from HW expectations and compare them to observed values.

-The “null hypothesis” in this case is that the population IS in HW equilibrium, and thus, no evolution is ocuring at that locus at the moment.

-A violation might signal that some force of evolution is at work.


  • For instance, imagine that you had a population of river grapes Vitis riparia.

    • There is an enzyme locus you find interesting,(could be anything, superoxide dismutase for instance).

    • It has two codominant alleles, SODF, for fast (because DNA fragments of it migrate rapidly on a gel), and SODS for slow, because DNA fragments migrate less quickly on a gel.

    • You don’t actually know much about evolution in this species, and you want to know if this locus is evolving.

    • You census 1000 individuals (at least you think so, they are grapes).

    • You get:

      • 460 SODFSODF

      • 23 SODFSODS

      • 517 SODSSODS

    • Is the population in HW equilibrium?


  • So, there is no dominant locus, but we will call the frequency of SODF p.

  • p=(460+11.5)/1000=.47, thus q=.53

  • Observed Expected

    • 460 SODFSODF 221 SODFSODF

    • 23 SODFSODS 498 SODFSODS

    • 517 SODSSODS 281 SODFSODS

  • Thus Chisquare=approximately 910

    • There is only one degree of freedom here (crazy, I know it seems, but we generated three expected values from just p and q, so df=1)

  • This is much lager than the critical value, so the locus is not in HW equilibrium.

  • Why?

  • A statistical test cannot answer that…but there are not enough heterozygotes. This (as you will learn later) is the signature of inbreeding, and grape plants self-fertilize.

  • Alternately, since grapes reproduce asexually as well as sexually, this could be the differential success of two genotypes, both homozygotes, at reproducing asexually.


The mechanisms of evolution
The Mechanisms of Evolution frequency of

  • Mutation

  • Allele (gene) flow

  • Selection

  • Genetic Drift

  • Nonrandom mating

    • each one is, in essence, the result of a violation of one or more of the assumptions of the Hardy-Weinberg equilibrium


Mutation
Mutation frequency of

  • A mutation is a change in the organism’s DNA.

    • Mutations may affect somatic (nonreproductive tissue), or they may affect the germ line (reproductive tissue). Except in clonal organisms, somatic mutations cannot generally be passed on.

    • Evolutionary biologists are interested in heritable mutations, the kind that can be passed on to the next generation.

  • A heritable mutation changes one allele into another, sometimes creating an allele that is not already present in the population.


  • Some mutations create dominant alleles, some create recessive or codominant alleles.

  • Some mutations are harmful or lethal, many are totally neutral-they have no effect, a few are favorable.

  • Whether a mutation is harmful, neutral, or favorable, depends upon its environment


Some types of mutations
Some types of mutations. recessive or codominant alleles.

  • Substitution: one nucleotide is substituted for another, frequently this causes no change in the resulting organism, sometimes the change can be dramatic.

  • Insertion: DNA is inserted into a gene, either one nucleotide or many. Sometimes, entire genes are inserted by viruses and transposable elements.

  • Deletion: DNA bases are removed.

  • Small insertions and deletions can inactivate large stretches of a gene, by causing a frame shift that renders a gene meaningless.

  • Duplication: an entire gene is duplicated.

  • Transposition: DNA is moved to a new place in the genome, frequently this happens because of errors in meiosis or transposable elements.


Cat mutations
Cat Mutations recessive or codominant alleles.


Songbird mutations
Songbird mutations recessive or codominant alleles.


  • Mutations are random events recessive or codominant alleles.: their occurrence is independent of their selective value - i.e., they do not occur when they are needed any more often than they would otherwise.

  • Mutations at any single locus are rare events: mutation rates at a typical locus are about 1 in 106 gametes.


  • Since each individual has thousands of alleles, the cumulative effect of mutations is considerable:

    • Consider that each of us has about 3.5x104 loci, and the mutation rates are about 1x10-6 per locus, thus, about 1 in 30 of our gametes has a new mutation somewhere in its genome. That means about 7% of us are mutants, more or less. YOU could be a mutant.


Mutations are the ultimate source of genetic variation
Mutations are the ultimate source of genetic variation cumulative effect of mutations is considerable:

  • Mutations are the only source of new alleles (other than the occasional transfer of alleles by viruses).

  • Mutation is thus the ultimate source of genetic variation…it creates the raw material upon which natural selection acts.


Example an interesting mutation
Example-an interesting mutation: cumulative effect of mutations is considerable:

  • In humans, one interesting mutation is called the CCR-d32 allele (the locus is named CCR, it is one of many alleles at that locus)

    • This allele codes for a 32 base pair deletion that makes the protein nonfunctional.

    • Lacking this protein on the surface of their blood cells, homozygous individuals (it is effectively codominant) are essentially resistant to HIV-HIV cannot infect their cells.

  • This mutation did not arise because of HIV, best we can figure, it predates the evolution of HIV by hundreds or thousands of years, and was neutral (or possibly maintained by selection induced by the bubonic plague) until HIV entered out species!


Genetic drift
Genetic Drift cumulative effect of mutations is considerable:

  • Genetic drift is the change in allele frequencies that occurs by chance events. In essence, it is identical to the statistical phenomenon of sampling error on an evolutionary scale.

  • It is a random (stochastic) process.

  • Because sampling error is greatest in small samples and smallest in large samples, the strength of genetic drift increases as populations get smaller.


Effects of genetic drift
Effects of Genetic Drift cumulative effect of mutations is considerable:

  • Does not generally result in adaptation.

  • In a large population - it has little effect unless enormous spans of time are involved.

    • (if vast spans of time ARE involved, the cumulative effects of drift on any species can be considerable-genetic drift is the primary mechanism for the substitution of neutral alleles over time, which is the mechanism of the molecular clock used in systematics.)


  • In a small population cumulative effect of mutations is considerable:

    • alleles can be lost (usually the rare ones)

    • other alleles are fixed-their frequency reaches 1.0

    • genetic variation is lost, resulting in at population can become homozygous at many loci


Founder effect
Founder Effect cumulative effect of mutations is considerable:

  • The founder effect is genetic drift that occurs when when a few individuals, representing a fraction of the original allele pool, invade a new area and establish a new population.


  • Examples: cumulative effect of mutations is considerable:

    • California Cypress-a very large population was established from a small number of individuals.

    • Founder effect occurs in many introduced species.

    • Amish-a religious minority, which is essentially an isolated population, established from a relatively small number of individuals.


Bottlenecks
Bottlenecks cumulative effect of mutations is considerable:

  • Bottlenecks are periods of very low population size or near extinction. This is another special case of genetic drift.

  • The result of a population bottleneck is that even if the population regains its original numbers, genetic variation is drastically reduced


  • Examples: cumulative effect of mutations is considerable:

    • Cheetahs -nobody knows exactly why it occurred, but cheetahs underwent an extreme population bottleneck several thousand years ago. As a result, they have very little genetic variation.

    • Northern Elephant Seal-underwent an extreme population bottleneck resulting from fur hunting in the nineteeth century.

    • Ashkenazic Jews-a religious minority in Central Europe that has rebounded from attempted genocide.

    • Endangered Species


  • Genetic drift contributes to evolution in a number of ways cumulative effect of mutations is considerable:

    • by decreasing genetic diversity, it can put the population at risk of extinction

    • its random nature increases the genetic differentiation between two or more populations

      • this may lead to speciation if one or more populations become reproductively isolated.

      • Genetic differentiation caused by genetic drift may change the genetic background against which new mutations act. If there is epistasis, a new mutation may be favorable in some populations and unfavorable in others. (Wright’s shifting balance theory)


The neutral theory of molecular evolution
The Neutral Theory of Molecular Evolution. cumulative effect of mutations is considerable:

  • One of the most interesting breakthroughs in evolutionary biology in the 1960’s-1990’s, has been the development of the neutral theory of molecular evolution.

  • It was introduced by the Japanese theoretician Motoo Kimura, in the late 1960’s.

  • It is a theory of evolution that Darwin never could have anticipated (evolutionary biology does not begin and end with Darwin).

  • It runs in parallel with Darwinian evolution by natural selection, though its effects are most noticeable and easiest to understand on loci for which there are no differences in fitness between alleles (thus, it is called the neutral theory).

  • It causes change over vast spans of time, at a more-or-less constant rate, when averaged over many loci.

  • For that reason, it can be used to develop a “molecular clock”..to tell how long it has been since two lineages have diverged.


  • In the 1960’s techniques of observing genetic variation in natural populations became available, and were pioneered by researchers such as Richard Lewontin.

    • It was discovered that, in natural populations, many selectively neutral genetic polymorphisms exist.

  • Kimura based his theory upon this.

    • Thus, he hypothesized that much of genetic variation is actually neutral

    • He also asserted that most evolutionary change is the result of genetic drift acting on neutral alleles.

    • New alleles originate through the spontaneous mutatation of a single nucleotide within the sequence of a gene.

      • In single-celled organisms, or asexuals, this immediately contributes a new allele to the population, and this allele is subject to drift.

      • In sexually reproducing, multicellular organisms, the nucleotide substitution must arise within the germ line that gives rise to gametes.

    • Most new alleles are lost due to genetic drift, but occasionally one becomes more common, and by random accident, replaces the original.

    • The chance of this is small, but over time, it happens occasionally, at a predictable rate.

  • In this way, neutral substitutions tend to accumulate, and genomes tend to evolve.

    • Many of the polymorphisms we see may be “transient”-one allele is in the process of replacing another.


  • *Stolen from a great site natural populations became available, and were pioneered by researchers such as Richard Lewontin.nitro.biosci.arizona.edu/.../Lecture47.html

  • In the scematic diagram above, you can see that some alleles are lost over time, but occasionally, one becomes fixed, and replaces the other, all by random genetic drift.


  • *Stolen from a great site natural populations became available, and were pioneered by researchers such as Richard Lewontin.nitro.biosci.arizona.edu/.../Lecture47.html

  • Although its importance, relative to Darwininan evolution, is debated, this theory is farily well supported by now.

  • Rates of molecular evolution vary among proteins, and among organisms. Some proteins allow much less neutral variation, and evolve more slowly.

  • Interestingly, population size is not that important for rates of molecular evolution (it cancels out in the math, small populations drift faster, but have fewer mutants per generation)


Population structure
Population Structure natural populations became available, and were pioneered by researchers such as Richard Lewontin.

  • Most species do not exist as many populations, which are isolated from each other to some extent.

    • Populations occasionally exchange members.

    • Most populations are spatially structured; individuals tend to cluster in areas of suitable habitat.

      • These local aggregations, called subpopulations, regularly exchange members.


Allele flow
Allele Flow: natural populations became available, and were pioneered by researchers such as Richard Lewontin.

Allele flow (or gene flow) is an evolutionary force that results from migration of individuals or the dispersal of seeds, spores, etc.

Allele flow can potentially cause evolutionary change, provided that:

1) the species has multiple subpopulations.

2) there are differences in allele frequency among populations, or among subpopulations within populations.


Effects of allele flow
Effects of Allele Flow natural populations became available, and were pioneered by researchers such as Richard Lewontin.

  • Even small amounts of allele flow can negate genetic drift.

  • If natural selection favors certain alleles in some populations, and different alleles in others, allele flow can oppose natural selection and prevent the evolution of genetic forms suited to each environment.

  • If sufficiently strong allele flow will cause allele frequencies in different populations to converge on a single, population-wide mean.


Allele flow v s genetic drift
Allele Flow v.s. Genetic Drift natural populations became available, and were pioneered by researchers such as Richard Lewontin.

  • When does allele flow negate the effects of genetic drift?

  • Let us consider a whole bunch of semi-isolated populations, that exchange occasional migrants with each other; exchange of migrants is random

  • Let m=the proportion of migrants exchanged per generation.

  • Let N=the number of individuals in each population.


  • I will spare you the proof, although famous, it runs several pages….

  • Allele flow will negate the effects of genetic drift if m>(1/(2N)).

  • This is a very small number, one migrant every other generation is sufficient to prevent genetic drift from causing evolutionary differences among populations of a species, or subpopulations within a populations of a species.


Allele flow and selection
Allele flow and selection pages….

  • Note that allele flow can also oppose selection.

  • On the edge of the range of a species, there might be local populations adapted to special conditions.

  • Allele flow from a large, central population adapted to a different environment might swamp the effects of natural selection, by causing an influx of less fit alleles every generation to counterbalance the unfit alleles lost to selection.


Nonrandom mating
Nonrandom Mating pages….

  • Two important patterns of nonrandom mating affect evolution:

  • 1) Inbreeding, or mating between relatives (selfing is a form of inbreeding)

  • 2) Assortative Mating


Inbreeding
Inbreeding pages….

  • Inbreeding, including selfing, is common in many species. Inbreeding was formerly common in humans, before the advent of increasingly sophisticated forms of transportation.

  • High levels of inbreeding lead to the loss of the heterozygous genotype, although allele frequencies are not necessarily changed.

  • Inbreeding exposes recessive alleles to selection, since they are more likely to be present in the homozygous state if the population is inbred.


  • Inbreeding can cause a dramatic decline in the fitness of a population, possibly extinction, because many species harbor numerous deleterious recessive alleles that are effectively hidden from selection (i.e. the Florida Panther), although other species are unaffected by inbreeding (i.e., certain groups of parasitic Hymenopetera).


Assortative mating
Assortative Mating population, possibly extinction, because many species harbor numerous deleterious recessive alleles that are effectively hidden from selection (i.e. the Florida Panther), although other species are unaffected by inbreeding (i.e., certain groups of parasitic Hymenopetera).

  • Assortative mating occurs when individuals choose their mates based on their resemblance to each other at a certain locus or a certain phenotype.

  • Positive assortative mating occurs when like genotypes or phenotypes mate more often than would be expected by chance.

  • Negative assortative mating occurs when similar genotypes or phenotypes mate less often than would be expected by chance.


Examples of assortative mating in humans
Examples of assortative mating in humans population, possibly extinction, because many species harbor numerous deleterious recessive alleles that are effectively hidden from selection (i.e. the Florida Panther), although other species are unaffected by inbreeding (i.e., certain groups of parasitic Hymenopetera).

  • Dwarfs: very high positive assortative mating, individuals with achronoplastic dwarfism pair up much more often than would be expected by chance

  • IQ: slight positive assortative mating

  • Height: slight positive assortative mating

  • Redheads: moderate negative assortative mating-red haired individuals pair up less often than would be expected by chance.


Natural selection
Natural Selection population, possibly extinction, because many species harbor numerous deleterious recessive alleles that are effectively hidden from selection (i.e. the Florida Panther), although other species are unaffected by inbreeding (i.e., certain groups of parasitic Hymenopetera).

  • What is it? Natural selection is the differential survival and reproduction of individuals with certain traits.

  • It acts on phenotypes.

  • Because most phenotypes are, in part, determined by an organism’s genotype at one or several loci, natural selection has the potential to cause change in the frequency of alleles through time.


  • Any allele that affects the ability of an organism to survive and reproduce will be subject to natural selection.

  • In populations, natural selection operates whenever individuals in the population vary in their ability to survive and reproduce.

  • Natural selection causes evolutionary change whenever there is genetic variation for traits that affect fitness.


  • For Natural Selection to Operate: survive and reproduce will be subject to natural selection.

  • 1) there must be variation

  • 2) some of the variation must affect survival and reproduction of individuals

  • For Natural Selection to Cause Evolutionary Change

  • 1) there must also be allelic variation for characteristics that affect fitness.


What is fitness
What is Fitness? survive and reproduce will be subject to natural selection.

  • Fitness is the ability of an individual to survive and make copies of its alleles that are represented in the next generation.

    • The fitness of an individual organisms is essentially the same as its lifetime reproductive success. The fitness of a genotype is the average fitness of all the individuals in the population that have that genotype.


  • It is NOT physical performance. survive and reproduce will be subject to natural selection.

  • Differences in fitness may be due to differences in survivorship, differences in fecundity, or both.


Absolute fitness vs relative fitness
Absolute fitness vs. relative fitness. survive and reproduce will be subject to natural selection.

  • An organism’s absolute fitness is the total number of surviving offspring that an individual produces during its lifetime (its lifetime reproductive success).

    • some things that contribute to fitness are: its chance of living to a certain age (age specific survivorship), its number of offspring during a certain time interval (age specific fecundity).

    • These are called components of fitness.


Relative fitness
Relative Fitness survive and reproduce will be subject to natural selection.

  • For mathematical purposes, absolute fitness is standardized to get relative fitness.

  • Imagine there are several genotypes, each codes for a different phenotype. The genotype with the highest absolute fitness has a relative fitness of 1.0

  • For every other genotype, their relative fitness is: absolute fitness of that genotype/absolute fitness of fittest genotype


Example
Example survive and reproduce will be subject to natural selection.

  • A beetle is polymorphic for color, it comes in black, brown and yellow color morphs. Birds and lizards prey upon them, so that, due to differences in survivorship, the fitnesses of the color morphs differ.

  • CBCB=black 67% chance of survival to adulthood

  • CBCY=brown 93% chance of survival to adulthood

  • CYCY=yellow 11% chance of survival to adulthood

  • QUESTION: Assuming they have identical numbers of offspring, what is the relative fitness of each genotype?


Answer1
Answer survive and reproduce will be subject to natural selection.

  • The relative fitness of brown is the highest, so w(CBCY)=1

  • the fitnesses of black and yellow are:

  • .67/.93=w(CBCB)=.72

  • .11/.93=w(CYCY)=.12

    • Note how we designate fitness as w, to avoid confusing it with frequency.

    • Also note that survivorship is a component of fitness, it is necessary to assume fecundity is identical in the three morphs to calculate relative fitness.



Directional selection
Directional Selection fitness of a genotype between its own value, and the ideal of 1.0.

  • Most extreme phenotype is the most fit. When applied to a single locus, that means one allele becomes more common until it reaches fixation (I.e., frequency 1.0)

    • Directional selection tends to eliminate genetic variation over time. If directional selection is to proceed for a long time, new mutations must replace lost genetic variation.

    • In laboratory experiments, directional selection causes rapid change in phenotypes, followed by a plateau, caused by the loss of genetic variation.


Directional fitness of a genotype between its own value, and the ideal of 1.0.

Selection


Example of directional selection the peppered moth biston bettularia
Example of Directional Selection: The peppered moth, fitness of a genotype between its own value, and the ideal of 1.0. Biston bettularia

  • One of the best known cases of directional selection is the evolution of “industrial melanism” in this species.

  • It has two forms: dark (melanic) and light.

  • Controlled by a single locus with two alleles.

  • Melanic is dominant, so that MM and Mm are dark, mm is light

  • the moth rests on trees during the day, and uses crypsis as protection from predation by birds.

  • Kettlewell (1955) showed that the two forms differ in their suceptibility to bird predation.


  • The melanic form was rare in 1848. When it was first reported outside Manchester, it was visible against the lichen-covered trees and often eaten by birds.

  • Museum collections indicate that by 1898, the melanic form had increased from <1% to >98% of the population

  • Soot had darkened the trees, making the light form most visible.

  • In rural areas with no soot, the melanic form was still rare.

  • (Since the passage of clean air laws in Britain, the trend has reversed, and the light form is more common once again.)


  • Many laboratory experiments have documented evolutionary change by imposing directional population on strains of laboratory organisms.

    • For instance, by imposing directional selection on Drosophila melanogaster, researchers, such as Michael Rose and Brian Charlesworth, have documented changes in body size, sternopleural bristle number, and life history characteristics such as age at reproduction.

    • Selection in laboratory populations often produces dramatic change, quickly, followed by a plateau, as genetic variation is exhausted.

www.biology.duke.edu/rausher/lec11.htm


Stabilizing selection
Stabilizing Selection change by imposing directional population on strains of laboratory organisms.

  • Intermediate phenotypes, somewhere close to the mean are most fit. When applied to a single locus, it implies that the heterozygous genotype is most fit, and is called Balancing Selection.

    • Generally, stabilizing selection maintains the mean value for the trait, and decreases the variation for the trait (thus, it usually decreases genetic variation). In the special case of balancing for a single locus, genetic variation is actually preserved, since both alleles will be maintained.


Stabilizing change by imposing directional population on strains of laboratory organisms.

Selection


Examples of stabilizing selection
Examples of Stabilizing Selection change by imposing directional population on strains of laboratory organisms.

  • Stabilizing selection is probably common in nature.

  • Birth Weight in Humans: It is well known that early mortality is highest for extreme birth weights. Both very small and very large infants suffer high mortality.

  • Clutch Size in Birds and Parasitoids: Females that lay intermediate numbers of eggs have the highest reproductive success. Too many, and the offspring all starve. Too few, and the mother could have laid more. Called the Lack optimum, it applies to many birds, also to parasitoids.


Example of Balancing Selection, and of the Differing fitness of an Allele in Different Environments: Sickle Cell Anemia in Humans

  • Sickle cell anemia in humans is caused by an allele that causes hemoglobin to deform under low oxygen conditions, causing the red blood cell to “sickle”.

  • Homozygotes for normal hemoglobin Hb+ Hb+ have no illness.

  • Homozygotes for the sickle allele HbSHBShave a very serious genetic disease.

  • Heterozygotes HbS Hb+ appear normal, but occasionally their blood cells sickle under stress. This is not particularly debilitating.


  • In countries without malaria: of an Allele in Different Environments: Sickle Cell Anemia in Humans

  • There is strong selection against homozygotes for the sickle cell disease, w(HbSHBS)=0, because, they rarely survive long enough to have many offspring.

  • The other two genotypes have a the same relative fitness w(Hb+ Hb+)=w(HbS Hb+ )=1, because carriers are essentially indistinguishable from those possessing normal hemoglobin.

  • There is thus directional selection against the sickle cell allele.


  • In countries WITH malaria: of an Allele in Different Environments: Sickle Cell Anemia in Humans

  • Heterozygotes for the sickle cell allele have some limited resistance to malaria, because the cells sickle and kill plasmodium within.

  • The heterozygote is most fit w(HbS Hb+ )=1, w(Hb+ Hb+)=.90, w(HbSHBS)=0.

  • Selection acts to balance maintain both alleles because the heterozygote is favored, this is an example of balancing selection.

  • This explains why the original distribution of the sickle cell allele roughly matches the worldwide prevalence of malaria.


Disruptive or diversifying selection
Disruptive or Diversifying Selection of an Allele in Different Environments: Sickle Cell Anemia in Humans

  • Two or more phenotypes are most fit, but the intermediates have low fitness.

    • Not particularly common in nature. In most cases, it increases the variance for a trait, while not affecting the mean. Combined with assortative mating, it has the potential to form a polymorphic population.


Frequency dependent selection
Frequency-Dependent Selection of an Allele in Different Environments: Sickle Cell Anemia in Humans

  • Selection can be frequency-dependent

  • + frequency dependent selection: most common type is the most fit

  • - frequency dependent selection: least common type is the most fit.

    • Example-Eye-eating cichilids in Lake Victoria.

    • Example-Color polymorphism in elderflower orchids. Interesting case studied by Luc Gigold et al.


  • Elderflower orchids have two colors, yellow and purple. of an Allele in Different Environments: Sickle Cell Anemia in Humans

  • Populations typically have both color morphs, generally with the yellow morph being slightly more common.

  • Bumblebees are the primary pollinator.

    • Like many orchids, elderflower orchids are deceptive. They advertize to bees, but offer no nectar reward.

    • Bumblebees learn to recognize the most common morph, and learn to avoid it, giving an advantage to the least common morph.



  • Natural Selection has been documented and studied in nature many times.

    • Despite Darwin’s intuition, many documented examples of natural selection in the natural world show rapid evolution and a dramatic response to natural selection, rather than slow, gradual change.

    • Interstingly, since the environment changes, selection in the real world often reverses direction and is not consistent over time and from one location to the next.

    • The best know study of natural selection in the wild was the study of Galapagos finches by Rosemary and Peter Grant, and their colleagues.

    • They documented dramatic changes in finch populations, in response to strong natural selection imposed by drought.


The environment affects the fitness of alleles
The Environment affects the Fitness of Alleles many times.

  • Alleles may have different fitnesses in different environments. An allele that is favored in one environment may have a disadvantage in another environment.

  • For systems of epistasis, the genetic environment may affect the fitness of an allele.

  • The frequency of an allele may also affect its fitness.

  • Examples: Sickle cell anemia, the Lap locus in mussels, color patterns in Heliconia butterflies, chromosomal inversions in Drosophila.


  • Environmental change may reverse the effects of selection. many times.

    • Over evolutionary time, this seems to be the rule rather than the exception.

  • Selection has no memory, no plan, and no goal.

    • There was no special driving force in evolution to produce human beings, or anything like us. This does not exactly make us an “accident:”, more precisely, it makes us one species among billions of potential evolutionary outcomes.

  • Selection does not act for the good of the species, nor for the good of the planet.


Selection is weak against rare recessive alleles
Selection is weak against rare recessive alleles many times.

  • As you can see from the preceding equation, as recessive alleles become rare, selection against them becomes weaker and weaker, because most copies are likely to exist in the heterozygous state

  • Likewise, selection in favorable of new mutations is very weak if that mutation is recessive. Favorable, recessive mutations can be lost by genetic drift before they have a chance to spread by selection.


Mutation selection balance
Mutation-Selection Balance many times.

  • Imagine that allele A mutates into disadvantageous allele a at rate u.

  • u is usually very small, on the order of 10-8.

  • Selection will reduce the frequency of a to a low level, but selection is weak against uncommon recessive alleles.

  • A mutation-selection balance will be reached where

  • q*=equilibrium frequency of allele a=(u/s)1/2


  • This result has enormous significance to medicine. It provides an explanation for the continued existence of alleles which, when homozygous, cause severe hereditary illnesses….most of these are in mutation-selection balance.

  • Alleles which occur in unexpectedly high frequencies in some populations, such as sickle cell anemia, thallassemia, or cystic fibrosis, may have been subject to balancing selection in the past.

    • The agent of selection for Sickle Cell Anemia, and for thallasemia (Mediterranean populations of humans), was probably malaria, for CF, it was most likely typhus.

  • Alternately, it is possible that genetic drift has caused them to become more common that would be expected under this model.

    • This may be the mechanism causing Tay Sachs disease to be unexpectedly common in certain Jewish populations.


  • Behavioral Ecology provides an explanation for the continued existence of alleles which, when homozygous, cause severe hereditary illnesses….most of these are in mutation-selection balance. is the science of the ultimate, evolutionary causes for behavior.

  • It brings together three sciences; ecology, animal behavior, and evolutionary biology.

    • It is a very new science, resulting from the intersection of ideas by several influential schools of thought

    • These include; David Lack, who pioneered the comparative approach, W.D. Hamilton, who pioneered the concept of kin selection, and E.O. Wilson, who pioneered sociobiology.


  • Behavioral Ecology has 2 basic themes: provides an explanation for the continued existence of alleles which, when homozygous, cause severe hereditary illnesses….most of these are in mutation-selection balance.

    • Natural selection maximizes the ability of an organism to survive and reproduce. Individuals (in essence, temporary vehicles for genes and alleles) should behave in ways that maximize inclusive fitness.

    • The so called “optimal” behavior needed to maximize inclusive fitness will depend on both the behavior of other individuals & ecological circumstances.



  • Possible 'obstacles' to optimal behavior & fitness: But, will behaviors always be optimal?

    • Mutation-many mutations produce individuals with lower fitness.

    • Linkage - genes beneficial in some way may be very close on a chromosome to a gene that tends to reduce fitness. So, to get the benefit of one gene, an organism must withstand the liability of the other.

    • Pleiotropy-Alleles have multiple effects. So, if an allele influences traits X, Y, & Z, with X being an optimum phenotype, there's no reason to assume Y & Z are also optimum

    • Variable environments - difficulty of achieving optimal behavior varies in proportion to variability of the environment

    • Evolutionary lag-individuals adapted to past conditions are not necessarily adapted to present conditions

    • Phylogenetic inertia-evolutionary baggage'; resistance to acquisition of adaptive characteristics due to prior evolutionary history (e.g., flightless birds on many islands)


The comparative method
The Comparative Method But, will behaviors always be optimal?

  • The comparative method: comparing species in divergent lineages, to see if there is a pattern of convergent evolution, where lineages that enter particular ecological niches evolve certain behaviors or structures, is widely used in evolutionary biology.

  • By comparing different species, behavioral ecologists can link behavior and social organization to ecological factors.


The comparitive approach is good for making inferences about evolutionary trends
The Comparitive Approach is Good for Making Inferences About Evolutionary Trends.

  • For example, why is male mortality greater than female mortality in some species?

  • For instance, once reproductive maturity has been reached, male mortality is much greater than female mortality in orcas.




Criticisms of optimality models
Criticisms of Optimality Models care. Natural selection favors increased lifespans for males in species where males provide parental care.

  • The major criticism of optimality models is that they appear to test the animal to see whether it is behaving perfectly according to the model.

    • It is important not to loose sight of the fact that the model is being tested, not the animal.

  • The inherent assumption of optimality theory, that animals behave in a way that maximizes their fitness, is not likely to be met all the time.

    • Thus, if the animal’s behavior does not match the model, is the animal flawed or is it the model?

    • One of the best approaches is to see whether animals that behave according to the model have higher fitness than animals that deviate from it.


Ecological game theory
Ecological Game Theory care. Natural selection favors increased lifespans for males in species where males provide parental care.

  • One of the most interesting things about natural selection for a behavior is that the behaviors of other individuals in the populations may affect the fitness of an individual.

  • Some behaviors, such as stealing from another individual’s nest, may be favored by selection when they are uncommon (thieves are rare and the population is naïve). When they become common, however, they may be selected against (in a population where everyone is stealing from everyone else, there is nothing left to steal)

  • Axelrod, Hamilton, John Maynard Smith, and others brought the economic science of game theory over into behavioral ecology to explain how these systems work.


Example of an ecological game stealing in digger wasps
Example of an Ecological “Game”, Stealing in Digger Wasps

  • The great golden digger wasp (Sphex ichneumoneas) is a close relative of the species Fabre studied.

  • It digs a burrow in the ground and stocks it with paralyzed crickets.



  • The second strategy has advantages when it is rare. strategies.

    • It is easier to take over a burrow, it takes less time and involves less wear and tear to the wasp.

  • As this behavior becomes more common, however, disadvantages accumulate.

    • With more wasps looking for pre-existing burrows, there are no “empty” ones left over when wasps die, and most of the time the individual has to fight a wasp for the nest. This is time-consuming and potentially deadly.


  • Ecological game theory predicts that the two behaviors should be “balanced” in the population by natural selection, so that they both have equal fitness.

    • If one has a higher fitness, it will become progressively more common until its fitness drops enough to equal the other one.

    • Wasp fitness is relatively easy to measure: by counting cocoons (the larvae eat the cricket and spin a cocoon), it is possible to assess how many offspring they have produce

    • Thus, by observing wasps in nature, it should be possible to test this prediction.


  • Brockmann and Grafen tested the prediction by observing the wasp over the course of several seasons.

    • Their result; the two strategies have roughly equal fitness (though a wasp will switch from one strategy to the other-thus the behavior is not strictly encoded by genes, but genes presumably determine a flexible strategy where individuals change tactics based upon their environment to maximize their fitness)


  • Altruism wasp over the course of several seasons. is behavior that benefits another individual at the expense of one’s self.

    • From an evolutionary standpoint, the trouble with altruism is that if an altruistic behaviour is costly ­ for example, dying for someone else ­ then the genes that promote it should quickly disappear from the population.

    • Yet examples of self-sacrifice abound in animal societies. The most conspicuously selfless are the social insects, the ants, bees and wasps in which most individuals work tirelessly for the good of the colony and never reproduce themselves. How can such behavior be explained?


  • W.D. Hamilton argued that such extreme altruism is most likely to evolve if, by sacrificing themselves, individuals increase their "inclusive fitness"­that is, the proportion of their genes carried by others in the population. "Hamilton's rule" is the mathematical formulation of this; put crudely, it amounts to the idea that you can die for close kin and still spread your genes, since close kin have many genes in common with you.


Kin selection
Kin Selection likely to evolve if, by sacrificing themselves, individuals increase their "inclusive fitness"­that is, the proportion of their genes carried by others in the population. "Hamilton's rule" is the mathematical formulation of this; put crudely, it amounts to the idea that you can die for close kin and still spread your genes, since close kin have many genes in common with you.

  • Some behaviors have evolved to increase the fitness of an organism’s close relatives.

  • Individuals with certain heritable traits might have genotypes that code for behaviors that help close relatives raise more offspring than they would without help.

  • These alleles would be favored by selection, provided that their close relatives are likely to have copies of the same heritable traits.



  • Relatedness even if the allele does not confer an increase in fitness to the individual in question.is the probability that a particular allele, present in one individual, is also present in another individula because of descent form a common ancestor.

  • r=the coefficient of relatedness, is a mathematical expression of that probability.

  • It is easy to calculate r, given that you know how two individuals are related.

    • EXAMPLES:

      • Identical twins - r = 1 Unrelated individuals - r = 0 Parent & offspring - r = 0.5 Full siblings - r = 0.5 Half siblings - r = 0.25 Uncles/aunts & nieces/nephews - r = 0.25 Cousins - r = 0.125


Hamilton s rule
Hamilton’s Rule even if the allele does not confer an increase in fitness to the individual in question.

  • A behavior that helps a close relative’s fitness, even though it harms one’s own fitness, should be expected to evolve provided that:Br>C

  • Where:

    • B is the benefit to the relative (in terms of increased fitness)

    • r=the coefficient of relatedness

    • C= the cost of that behavior in terms of one’s own fitness.


  • An organism’s even if the allele does not confer an increase in fitness to the individual in question.inclusive fitness is a function of one's behavior on their own survival and reproduction, as well as the effect of one's behavior on all relatives (with the importance of each relative valued in proportion to degree of relatedness).


Example multiple foundresses in polistes
Example; multiple foundresses in even if the allele does not confer an increase in fitness to the individual in question.Polistes.

  • Polistes sp. are a genus of paper wasps.

    • Any female has the potential to be a queen, though those born at the end of the year are larger and more dominant.

    • Small females born in the middle of the summer are always workers, though one of them will potentially take over if the queen dies.


  • These large females mate and overwinter. In spring, they emerge and;

    • found their own nests

    • join females that have already founded nests.

  • Females that “join” usually get bullied into the subordinate, worker role.

    • Thus, their personal fitness is close to zero (they occasionally sneak a few of their own eggs in).

    • Thus, C is the number of offspring their colony would have produced if they did not join another female’s nest.


  • In the worker role, they increase their own inclusive fitness by helping the queen.

    • Nests with multiple foundresses are more likely to survive and produce more males and potential queens at the end of the year (fitness for a colony of social insects must be measured by counting males and queens, since workers do not reproduce their genes).

    • Thus, B is the increased number of offspring a colony will have when it has the extra foundress.


  • Kin selection theory predicts that wasps should join if Br>C fitness by helping the queen.

    • Thus, unrelated females (r=0) should not work together because there is no benefit to the female who does not become queen.

    • Wasps have a special genetic system, so that sisters are particularly closely related. r between wasp sisters is between .75 and .50, depending upon whether they share the same father.

  • Various researchers have studied this system (and others, including the related wasp Mischocyttarus) to see if Hamilton’s rule is supported.


  • Studies of fitness by helping the queen. Polistes support Hamilton’s rule.

    • Unrelated sisters do not generally cooperate (at least not after the issue of who will become queen is settled)

    • Lone females have a low chance of colony survival.

    • The first female who joins her sisters and acts as a “worker” definitely increases the chance of colony survivorship (thus, B is greater than zero).

      • It is tough to measure B exactly, and one of the reasons females join is to possibly take over the nest from the female who founded it, thus there is an element of game theory to the system.

      • Accounting for the fact that the female that looses the battle would have very low fitness if she went off on her own, because she would be a late-starter (thus, C is small), Br>C.


  • Extra helpers after the first “joiner” help the colony less

    • (thus, B is low for the second joiner, lower still for the third joiner).

  • In Northern North America, you rarely see more than two Polistes females working together.

  • In environments where there is competition for nest sites, or colony founding is particularly dangerous, more queens will work together, because B is larger (reflecting the extra need for help) and C (reflecting the smaller sacrifice in fitness because going it alone is so risky) is smaller.

    • Thus, several Mischocyttarus (Caribbean species) females work together, and hundreds of Polybia (closely related genus, Central American) females may work together to found a nest.


Three less Mischocyttarus females

at a new nest, these are probably

original foundresses.

The first true “workers” are in

the cocoons.

This Polybia nest

was probably founded

by a dozen or more females


  • How does an organism 'know' its relatives (and, if known or recognized, the degree of relatedness)?

    • In some cases, the biology of the organism facilitates close relatives living in close proximity.

    • In other cases, there are mechanisms of kin recognition.

    • Kin recognition is sometimes accomplished by smell, sometimes it is a function of cognition and memory, sometimes it is biochemical.

      • Social insects, such as Polistes, generally use smell. Colonies have a distinctive “colony odor”. Thus, sisters can smell each other.


Example-tunicates recognize each other by chemical signals (MHC genes, the same chemicals that enable our bodies to reject foreign organs) on their skin. Kin colonies of tunicates grow together. Non-kin colonies form a “zone of death” between each other.


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