Lecture 10-11: Population Genetics and Mechanisms of Evolution
Terms in this set (53)
An Introduction to Population Genetics
in earlier lectures, learned that natural selection acts upon the individual, buts its results (evolution) are measured at the population level. until now, we have been concentrating on the state of inheritance and variation at the level of the individual.
in this part, we focus on how things occur at population level - meaning, how genes/alleles change in a population over time, how species are created, and how populations grow.
key question to be answered - how do we know when the genes of a population have changed? How do we know evolution has taken place?
Let's start back with the monohybrid cross... What does the mating of two purebred individuals consist of and result in? What is the result when the F1 offspring mate?
The mating of two purebred individuals having a trait that is caused by 2 alleles within a population yields an F1 generation of heterozygous individuals.
The crossing of these hybrids (F1 generation) yields an F2 generation of individuals that have one of two phenotypes, but three distinct genotypes.
Draw a punnett square of all of the crossings.
How would the alleles be represented in the previous question, if they didn't come from a single organism and were randomly selected in pairs? Basically, what are the resulting genotypes?
If the alleles in question (R and r) did not come from a single organism (as in our previous work) but were randomly selected in pairs from a pool of independently occuring alleles within the population, the resulting genotypes would be represented by:
(R x R) + (r x R) + (R x r) + (r x r) = 1.0
combined to: R^2 + 2Rr + r^2 = 1.0
Why are the allele frequencies multiplied together?
The allele frequencies are multiplied together (e.g., (R + r) x (R + r)) b/c the alleles are independently passed from one generation to the next (Mendel's Law of Independent Assortment!)
What does the total accumulation of the genotypes mentioned previously equal? And why?
The total accumulation of these genotypes equals 1.0, b/c they represent the entire (100%) population
What does the equation R^2 + 2Rr + r^2 = 1.0 represent?
the equation is a representation of the frequency of the different genotypes within the generation created by the hybrid parents
Why are the letters p and q significant? What do they represent
p = frequency of one allele in the gene pool
q = the frequency of the second allele in the gene pool
If there are only two alleles in the gene pool, what is the sum of their frequencies?
If there are only two alleles in the gene pool, the sum of their frequencies must equal 100% of the alleles.
What does p + q = ? and how are their combined genotypic frequencies expressed?
p + q = 1.0
the combined genotypic frequencies of p and q are expressed as:
p^2 + 2pq + q^2 = 1.0
What is p^2 + 2pq + q^2 called?
this equation is called the Hardy-Weinberg hypothesis.
What happens if there are more than 2 alleles present in a population (what is their sum of there are more than 2?)
If more than 2 alleles are present in a population, their combination is still a product of the sums of the alleles.
i.e. if there are 4 alleles (p,q,w,z) p + q + w + z = 1.0 and (p+q+w+z) x (p+q+w+z) = 1.0
the resulting genotypic frequency is:
p^2 + 2pq + 2pw + 2pz + q^2 + 2qw + 2qz + w^2 + 2wz + z^2 = 1.0
What did we think prior to the hardy-weinberg hypothesis?
Before H-W, we thought:
1. dominant traits would eventually go to fixation in a population and recessive traits (unless they were selected for) would go away.
2. Or alleles would get distributed equally (50/50 in a 2 allele set)
3. And/or the only way alleles change frequency was through sexual reproduction
What does the Hardy-Weinberg Hypothesis say?
1. p is always the same generation after generation.
2. q is always the same generation after generation
i.e. if 2 alleles at one locus are A and a
A = p = 0.7 and a = q = 0.3 and p + q = 1.0
3. the genotypic frequency of pp in the NEXT GENERATION is 0.49 (=p^2), qq = 0.09(=q^2) and pq = 0.42 (=2pq)). meaning, the genotype pp is 49% of the available allelic combinations in this population
the allele frequencies in this generation are p = 0.49 + 1/2(0.42) = 0.7 and q = 0.09 + 1/2(0.42) = 0.3
0.49 (or 0.09) b/c 100% of those gametes come from homozygous individuals will contain just p (or q) plus half the gametes from pq will be p (or q)
Assumptions of the H-W Model:
1. random mating
2. no mutation
3. no migration
4. infinite population size
5. no natural selection
Things to keep in mind about the assumptions of the H-W model:
1. assumptions are with respect to particular alleles at locus in question.
2. if any of these assumptions are violated, then H-W does not apply.
3. if the allelic frequency does not match from one generation to the next, then something is happening to the population.
4. points to one or more of the assumptions as the culprit
How do we tell when there is change in a population over time? H-W as a Null hypothesis
HW as Null hypothesis:
1. the HW equilibrium hypothesis acts as a null hypothesis for the sake of determining whether genetic changes are taking place within a population. if you detect change in a population (and HW says you shouldn't) you must assume that HW does not fit your population (you reject it) and that something is causing the changes (likely a violation of one of the assumptions)
2. Your job then becomes one of finding out what it is that is causing the change (which is more fun aspect of pop. ecology)
3. typically, researchers do not go through the process of testing first whether HW is violated. they usually see what they think is a change, hypothesize what is causing the change, develop an experiment to test it, and form conclusions. researchers use the genetic change in a population as evidence that one of the violated assumptions is causing a change in the population.
bottleneck - one of the ways populations change, violating HW hypothesis:
a bottleneck is where a gene pool is significantly reduced for some reason and a relatively small allele diversity remains.
1. i.e. imagine a population has the alleles A a B b C c D d E e in it at one locus. if something happens that eliminates some of the alleles at that locus (fire destroys that part of the population with those alleles, few members with one or two specific alleles migrate away, etc), the population is left with a smaller diversity of alleles in the gene pool. as a result of the lower allele diversity, the population may be more subject to environmental changes.
What do cheetahs have to do with bottleneck violation of HW?
it is thought that cheetahs have gone through 2 bottlenecks in their history. these bottlenecks have caused them to directly violate 2 of the assumptions of the HW hypothesis. they have non-random mating, and small population sizes. as a result, their populations are experiencing severe genetic problems (see interbreeding depression below) and are declining significantly.
Define Genetic drift
genetic drift - ALWAYS causes DECREASE in VARIATION (ALLELE DIVERSITY)
genetic drift - the constant changing of allele frequencies (that percentage of all alleles any one, or more, allele occupies in a population) in a population over time, due to random mating.
genetic drift caused by randomness in sexual reproduction and most influential in bottlenecks (b/c fewer individuals, fewer genes) minor changes in allele frequencies over course of generations.
founder effect - separate from rest of population and start new - single individual seed launched far away from population, creates own seeds and so forth.
smaller population = bigger impact change
genetic drift effect is much more in small populations
What does random mating do in regards to genetic drift?
random mating has the effect of changing how frequently an allele is found in a population. For example, imagine a population consisting of allele A at 60% (frequency 0.6) and allele a at 40% (frequency 0.4). if by random chance many of the aa individuals do not mate, the next generation may have a different allele frequency distribution, say 70% of the alleles are A and 30% of alleles are a. in the next generation, by chance, some of the individuals with A die off (and thus have no offspring). the resulting offspring may have a new allele frequency, say 55% A and 45% a
Keys to understanding genetic drift
1. genetic drift is RANDOM
2. any change in allele frequency is DUE TO CHANCE.
3. allele frequencies are CONSTANTLY DRIFTING up and down over time.
4. allele changes are NOT ADAPTIVE.
5. drift is most effective in SMALL POPULATIONS (KNOW BOTTLENECKS AND FOUNDER EVENTS/EFFECTS)
6. drift can LEAD TO THE FIXATION OR LOSS OF ALLELES
7. genetic drift DOES NOT INCREASE ALLELE FREQUENCY DISTRIBUTION in a population. DRIFT CANNOT INCREASE THE DIVERSITY OF ALLELES IN A POPULATION, only the RELATIVE ABUNDANCE OF EXISTING ALLELES within a population.
1. gene flow - the movement of individuals and their alleles from one population to another. gene flow - think migration - variation from each other b/c genetic drift.
What does gene flow result from, and what does it do to populations and allele frequencies?
gene flow typically results in equilibrating allele frequencies between populations. that is, flow makes the populations look more alike genetically.
More info about gene flow
Gene flow into a population is one of two ways in which allele frequency distribution (i.e., allele diversity) increases. Although it may cause a decline in allele diversity in the population that the individuals are emigrating from. The other way to increase allele diversity is mutation.
Consider the example of prairire lupine from mount st. helen from lecture and Great tits on pg 447-448 in text
Define non-random mating
non-random mating - the HW model is based on mates being selected at random. however, random mate selection is not the norm in insects, vertebrates, and many other animals. even in organisms that broadcast gametes, population mixing is not entirely homogenous.
for example, grasses are pollinated by wind carrying pollen from plant to plant. a particular plant is more likely to be pollinated by a plant nearby compared to one farther away. this is not random with respect to the population interbreeding.
mating is not random - all exist in matter of space and time. i.e. clam lets out eggs hoping opposite gametes get them. population may span for miles, but ones that are local/nearby each other will mate with each other, not the clams that are miles away. this is considered nonrandom mating.
nonrandom mating includes inbreeding, which increases homozygosity(dom/recessive) and decreases heterozygosity.
recent common ancestor - differs on species in question
does not cause evolution since allele frequency DOES NOT CHANGE
causes inbreeding depression - decreased overall fitness (# offspring produced throughout lifespan)
alot of traits do better heterozygote alleles - if you increase homozygosity, there is higher chance of inbreeding depression.
What are the three different ways in which non-random mating occurs?
1. Assortative mating
3. sexual selection
Define assortative mating
assortative mating - an individual is more likely to mate with another that is similar in phenotype to itself.
plants- plants who create flowers early mate with other plants who flower early, those who flower late mate with other late bloomers.
blister beetles - blister beetles mate with those of similar size. females choose male thats 10% larger results in 25% reduction in charge. male reproductive parts don't fit. females fitness will go down.
humans - same religion, same ethnic background, same educational background.
assortative mating - tendency organism to mate with someone similar to itself
inbreeding - inbreeding is the mating of individuals that share a recent common ancestor. "recent" means relative to the organism in question, and the intent to introduce novel alleles into the offspring, or maintain allele frequency distributions the way they are. as an example, consider the cheetahs from earlier in the notes. the species as a whole is so similar genetically that almost any mating between two cheetahs might be considered inbreeding, even if the two mates and their ancestral lines have been separated for many generations. the resulting offspring may exhibit inbreeding depression. those that are involved in trying to increase the numbers, and species health of cheetahs keep strict records of genetic lines and who mates with whom, so as to maximize genetic diversity in resulting offspring.
alternatively, an ancestral line of pea plants may be able to interbreed parent to offspring for multiple generations without seeming much of an effect.
inbreeding - mate with individual with same ancestor. depends on species specifics - what causes problems.
1. increases homozygosity (dominant or recessive), decreases heterozygosity - increase in homozygosity there is a higher chance of inbreeding depression.
recessive alleles - referred to as 'loss of function' allele where dominant allele usually carries function. double rr = loss function entirely.
heterozygosity - strongest for disease fighting, etc. many traits do better as heterozygote alleles
define inbreeding depression
inbreeding depression - individuals are likely to share alleles they inherited from their common ancestor, causing inbreeding depression.
inbreeding depression is the loss of fitness as homozygosity in resulting offspring, future generations, and the population increases and heterozygosity decreases. evolution does not occur here since allele frequency does not change. only the genotypes do! SEE FIGURE 25.12 TABLE 25.4 - INBREEDING DEATHS - individuals who have offspring with cousin have a higher chance of offspring dying than nonrelated parents.
Why is homozygosity a problem?
1. inbreeding examples from humans (table 25.4)
2. inbreeding example of Cardinal flowers (figure 25.13)
cardinal flower - munoecius - both male and female parts, can self fertilize
unrelated parents have high fitness
self fertilizing have low fitness (but adaptation if no other plants are near to mate with)
3. outbreeding example of Austrian and Turkish ibex.
sexual selection - special case of natural selection that favors individuals with traits that increase their ability to obtain mates.
What gender does sexual selection act upon the most?
sexual selection acts on males more than females because females are typically the higher investment sex. since females invest so much in their offspring, they should be choosy about what males they mate with. they should choose males that appear the most healthy, wealthy, and/or wise. males invest little. therefore, they should be willing to mate with any female. therefore, females of many species look less showy/huge.
Female Choice - How does a female choose a good mate (how does she know he has good alleles)?
males that have a healthy body can "afford" to have bright feathers/beaks, long tails, colorful bodies. those that are not healthy spent their energy in body maintenance, and cannot develop such "extras". females choose mates that are brighter, showier, larger, or have more resources.
sometimes they choose mates on other criteria, like a willingness to provide resources, care for young, defend territories, etc.
male-male competition - sometimes males compete with one another for mates. typically, the biggest and strongest are the ones that get the mates. often, this is interpreted as females choosing the biggest and strongest mates (i.e. female choice). however, the traits that are being selected for here are sorted out by the males, not the females. i.e. white tailed deer
males compete with each other to see who gets majority of matings in population. females NOT selecting, being given that b/c it's individual who won. females just get the winner.
other males - sneaky males - after alpha male preoccupied, sneaky males mate with whoever else is left over. sneaky male fish - look like female - gets in between male and female mating, sneaky ends up mating with female and other male doesn't fertilize as many eggs as he should have.
What is sexual dimorphism? Which form of sexual selection causes it
both forms of sexual selection (male-male competition, female choice) can lead to sexual dimorphism - the tendency of the two sexes of a species to look different. careful, not all species that exhibit sexual dimorphism are that way due to sexual selection
In class notes about Cheetah
fewer than 12,000 left in wild
so far and so spread apart, live in small sub populations, seldomly intermix.
little genetic variation (can have 100% organ transplant fine with cheetahs)
cheetahs don't breed in captivity - ones that do have birth defects and odd behavior, so captive cheetahs not a solution.
define extinction horizon
extinction horizon - prediction of how much longer species will last. for cheetahs, 15 years left (meaning last of cheetahs being born in 15 years)
not ALWAYS humans faults, its just fall of the cheetah
Notes on HW and bottleneck concept
Punnett Squares are based on RANDOMNESS of 2 allele distribution
Back to Cheetahs:
2 bottlenecks - restriction over time of how many alleles can get from one generation to next
think literally of a drawing of a bottle on its side, with all different alleles in there - not all can fit through the opening. only a very small sample of alleles actually get through.
glaciers - came down and reach down into cheetah population. glaciers destroy everything, destroy habitat and change resulting habitat
population isolation also b/c of glaciers, b/c habitat changed so dramatically, sub populations of cheetahs. lots of problems, can't keep population from getting sick, same sub populations went extinct.
lots of alleles going extinct HURTS GENETIC DIVERSITY.
cheetahs also had to compete for food issues - had to compete with humans
existing cheetah population exceptions to HW
1. non-random mating
2. small population size
another problem - cheetahs make good pets, they never associated humans as a threat, esp. young cheetahs. so 3 problems in total - loss of habitat, food competition, and cheetahs as pets.
cheetahs aren't good meat, fur is useless (besides for decoration) also do not eat unless chase and then kill prey. many cheetah keepers used to have thousands of cheetahs at once, like Akbar the Great, who had 1000+ cheetahs in his palace.
Genetic Drift - Experiment on Genetic Drift, Page 445
Kerr and Wright started with large lab population of fruit flies that contained a GENETIC MARKER - a specific allele that causes a distinctive phenotype. in this case, the marker was the morphology of bristles. fruit flies have bristles on their bodies that can either be straight or bent. this differences in bristle phenotype depends on a single gene. Kerr and Wright's lab pop. contained just two alleles - normal (straight) and "forked" (bent).
the researchers set up 96 cages in their lab
they placed four adult females and four adult males of the fruit fly Drosophilia melanogaster in each
they chose individual flies to begin these experimental populations so that the frequency of the normal and forked alleles in each of the 96 starting populations was 0.5.
the 2 alleles do not affect the fitness of flies in the lab environment.
b/c of this, Kerr and Wright confident that if changes in the frequency of normal and forked phenotypes occured, they would not be due to natural selection.
after these first generation adults bred, Kerr and Wright reared their offspring
in the offspring (f1 generation) they randomly chose four males and four females - meaning that they simply grabbed individuals without regard to whether their bristles were normal or forked - from each of the 96 offspring populations and allowed them to breed and produce the next generation
they repeated this procedure until all 96 populations had undergone a total of 16 generations
the ONLY evolutionary process in this experiment = GENETIC DRIFT
Result of Kerr and Wright Fruit fly experiment on genetic drift
after 16 generations, the 96 populations fell into three groups. forked bristles were found on all of the individuals in 29 of the experimental.
DUE TO GENETIC DRIFT, the forked allele had been fixed in these 29 populations and the normal allele had been lost.
in 41 other populations, however, the opposite was true: all individuals had normal bristles. in these populations, the forked allele had been lost due to chance. both alleles were still present in 26 of the populations.
the message of the study is startling: in 73% of the experimental populations (70 out of 96), genetic drift had reduced allelic diversity at this gene to zero.
as predicted, GENETIC DRIFT DECREASED GENETIC VARIATION WITHIN POPULATIONS AND INCREASED GENETIC DIFFERENCES BETWEEN POPULATIONS.
define founder effect
founder effect -
when a group of individuals immigrates to a new geographic area and establishes a new population, a founder even is said to occur. If the group is small enough, the allele frequencies in the new population are almost guaranteed to be different from those in the source population - meaning, the population iin the place from which the group emigrated - due to sampling error. a change in allele frequencies that occurs when a new population is established is called a founder effect.
define genetic bottleneck
genetic bottleneck - a sudden reduction in the number of allele in a population. drift occurs during genetic bottlenecks and causes a change in allele frequencies.
gene flow - movement of alleles from one population to another. it occurs when individuals leave one population, join another, and breed.
gene flow usually has one outcome as an evolutionary mechanism: it equalizes allele frequencies between the source population and the recipient population. when alleles move from one population to another, the populations tend to become more alike.
lupines colonize sites and form populations
1981 - one single lupine 4 km away from source population, trace genetic change in species over time.
1. oldest individual in new population had very different allele frequency than source population
b/c seed establishes new population
want seed -> grew -> start reproducing.
source pop (diff alleles - but only taking one set from source pop) ----> new population - allele frequency totally different (b/c its only that one allele frequency that was taken over, and not the others). founder tends to look different overall in resulting offspring from source population.
also found that over time, 2 populations start to look more alike.
why? b/c genes probably get shared back and forth between 2 populations eventually due to animal pollinators, etc.
Out of genetic drift, natural selection, and mutation, which always consistently adds diversity to a population?
genetic drift - ALWAYS CAUSES DECREASE in variation (allele frequency )
natural selection - decrease diversity in alleles in population
only one that CONSISTENTLY ADDS DIVERSITY IS MUTATION.
Natural Selection - include definition, the effect on genetic variation it has, and effect on average fitness it has.
natural selection - certain alleles are favored
effect on genetic variation - can lead to maintenance, increase, or reduction of genetic variation
effect on average fitness - can produce adaptation
Genetic Drift - definition, effect on genetic variation, and effect on average fitness
genetic drift - random changes in allele frequencies, most important in small populations
effect on genetic variation - tends to reduce genetic variation via loss or fixation of alleles
effect on avg fitness - random with respect to fitness; usually reduces average fitness
Gene flow - definition, effect on genetic variation, and effect on average fitness
gene flow - movement of alleles between populations, reduces differences between populations
effect on genetic variation - may increase genetic variation by introducing new alleles, may decrease it by removing alleles
effect on avg fitness - random with respect to fitness, may increase or decrease avg fitness by introducing high or low fitness alleles
Mutation - definition, effect on genetic variation, and effect on avg fitness
mutation - production of new alleles
effect on genetic variation - increases genetic variation by introducing new alleles
effect on avg fitness - random with respect to fitness; most mutations in coding sequences lower fitness
handicap hypothesis - zahavi (think outside box)
if male of species (energetically speaking) can afford to have handicaps b/c must have good genes, b/c otherwise he'd be spending all his energy trying to not get killed and just survive. males who can put themselves @ willing disadvantage must be really strong and have good genes.
Phylogeny and Classification
Carlous Linneaus - swedish botanist, binomial (2 words) nonmenclature (naming stuff)
taxonomic hierarchy (related between individuals)
^ did this b/c felt more he understood about nature and relationships between organisms to get closer to god's wisdom
What are the 5 Kingdoms?
What is the taxonomic hierarchy?
(Genus) Species <- organisms not necessarily descended by species name - every organism described by genus + species name (this is the binomial nonmenclature - 2 latin words)