Chapter 4 Notes: Population Genetics and Natural Selection



Chapter 4 Notes: Population Genetics and Natural Selection

For Monday: read pp 77-85, 4.1, 4.2, Math in Conservation parts 1-3

Monday: no class

For Friday: read pp 85-97 4.3, 4.4, 4.5, Math in Conservation parts 4-7

Friday: Due – AA 1, Vod 1; Math in Conservation parts 8-11, Vod 2.8-2.9 Q 4-5, Vod 15.1-15.4 Q 3-4

Everything in this chapter depends on understanding 1) Darwin’s theory of evolution by natural selection and 2) the Hardy-Weinberg equilibrium of predicting allele changes over time.

Darwin’s natural selection – 5 rules

1. organisms give rise to others like themselves through sexual reproduction

2. there is natural variation in any given population

3. some of that variation is heritable

4. competition for resources exists

5. because of their traits, some individuals are more likely to survive to reproductive age and/or produce more offspring

The mathematics discovered and worked by Mendel are necessary for completing Darwin’s understanding of genetic changes over time.

Section 4.1: Variation is critical for the process of natural selection.

Clausen, Keck, and Hiesey

studied the growth and development of stinky cinquefoil (P. gladulosa) at three elevations. Plants were transplanted from each site to each of the other two and all nine gardens were observed.

Within clones, differences in growth seen between sites are the result of environmental influence. Between clones at different sites, differences in growth indicate genetic differences

Phenotypic plasticity: variation among individuals in form and function as a result of environmental influences

Ecotypes: locally adapted and genetically distinctive populations within a species, such as the three populations of P. glandulosa.

Q: How do we define a species?

Douglas and Brunner

Alpine fish migration of cold-requiring populations toward headquarters near the Alps created clusters of geographically isolated populations, thus reducing movement between populations (gene flow). Genetic divergence increases variation between populations/species.

Concluded that the Coregonus species are a highly diverse set of populations with a high level of genetic differentiation. They use “evolutionary significant units.” The distinctiveness is sufficient so that they should be managed separately.

Microsatellite DNA: tandemly repetitive nuclear DNA from 10 to 100 bases.

CR4.1.1: Can we be confident that differences in growth within P. glandulosa clones grown at different elevations were not the result of genetic differences?

CR4.1.2: What would you expect to see [as results] in figure 4.4 if alpine, mid-elevation, and lowland populations of P. glandulosa were not different genetically?

CR4.1.3: What is a fundamental evolutionary implication of the large amounts of genetic variation commonly documented in natural populations?

Section 4.2: Hardy-Weinberg

Hardy-Weinberg equilibrium identifies evolutionary forces that can change gene frequencies in populations.

Evolution: changes in gene frequency in a population over time

Mendel’s math – if a population’s genotypes exist at a 1 AA : 2 Aa : 1 aa ratio, the frequency of aa and AA individuals would increase in the population. But, this rule could only apply to self-fertilizing individuals. Mendel was unaware of more complicated population situations

Elytra: wing covers on insects.

Harmonia, Asian lady beetle – over 200 forms governed by more than a dozen alleles.

Homozygous “19-stignata” SS

Homozygous “aulica” AA

Heterozygous SA

SS = 0.81 SA = 0.18 AA = 0.01

Frequency of S =

SS + ½ SA

0.81 + ½ * 0.18 = 0.81 + 0.09 = 0.90

Frequency of A =

AA + ½ * SA = 0.01 + 0.09 = 0.10

Hardy-Weinberg principle: in a population mating at random, with no evolutionary forces, allele frequencies remain constant.

Probability of paired zygotes:

Ss * Se = 0.9 * 0.9 = 0.81

As * Ae = 0.9 * 0.9 = 0.81

Ss * Ae = 0.9 * 0.1 = 0.09

Se * As = 0.1 * 0.9 = 0.09

Note: These are same as parent population.

In more general terms, we can apply these rules to any population using a simple algebraic equation.

p2 + 2pq + q2 = 1

and

p + q = 1

(p + q)2 = (p + q)(p + q) = p2 + 2pq + q2 = 1

where p is usually dominant form, and q is usually recessive form.

Both p and q have to be positive nonzero numbers less than 1

In our example,

p2 = (0.9)2 = 0.81 SS Se * Ss

2pq = 2(0.9 * 0.1) = 0.18 SA Ss * Ae AND Se * Ax (two possibilities, thus 2pq)

q2 = (0.1)2 = 0.01 AA As * Ae

To test, set the full equation to 1, and plug in the calculated frequencies:

p2 + 2pq + q2 = 1

0.81 + 0.18 + 0.01 = 1, true

Therefore, random mating is sufficient to maintain constant genotype and allele frequencies

BUT, in the wild, additional conditions are required because of the inclusion of environmental influences.

Hardy-Weinberg Equilibrium: constant frequencies in a population, regardless of what other forces are or are not present.

HWE requires:

1. random mating

2. no mutations

3. large population/gene pool

4. no immigration or emigration

5. no competition for resources

For each requirement that is not met, evolution is more likely.

Q. What overlap do you see between the requirements to maintain a HWE and Darwin’s rules of natural selection?

HW – 1908

Darwin – 1860s

CR4.2.1. Why is genetic drift more probable in small populations than in large populations?

CR4.2.2. How does highly selective mating by females (see fig 8.10 – females choose mates based on nuptial offerings) affect the potential for HWE?

CR4.2.3. How might immigration oppose the effects of genetic drift on genetic diversity in a small population?

4.3 Natural Selection distribution curves

Natural selection: differential survival and reproduction within a population due to phenotypical differences

Can lead to or impede change; can increase or decrease diversity

Stabilizing selection: conserves characteristics, acts against extreme phenotypes and favors the average forms.

Q: if the potential for change is high, due to violations of HW, why are there not more obvious evolutionary changes?

Q: is the lack of apparent change just as evolutionarily consequential as apparent change itself?

Fitness: number of offspring or genes contributed to future generations

Stabilizing selection happens when average individuals are already best adapted to a given set of environmental conditions. SS maintains the match between prevailing environmental conditions and the average phenotype.

Directional selection: favors one extreme phenotype over any others, extreme or average

In directional selection, population shifts from average to one extreme. The favored extreme becomes the new average over time, and the most common.

Disruptive selection: average phenotypes are selected against, making them least common, and two or more extreme phenotypes are selected for. NOTE: must be more than one phenotype selected for, to create a dip in the distribution curve (see fig 4.9, p. 86)

CR4.3.1. If you observe no changes in gene frequencies in a population over several generations, can you conclude that the populations is not subject to natural selection?

CR4.3.2. Why is rapid human-induced environmental change a threat to natural populations?

4.4 Evolution by Natural Selection

Heritability is essential for natural selection. We can determine if a trait is heritable by knowing its variance.

Heritability = h2 = VG/VP

where VG = variance due strictly to genotypic differences and VP = variance due to phenotypic differences

BUT,

VP (phenotypic variation) can be either variation due to genotype, or due to environment, and is often a combination of the two, SO

VP = VG + VE

Substitute this for VP in the original equation:

h2 = VG/(VG + VE)

Meaning, heritability of a particular trait depends on the relative sizes of genetic vs environmental variance.

Heritability increases with increasing genotypic variance, and decreases with decreasing environmental variance. (check that this makes logical sense)

IF all phenotypic variation is the result of genetic differences and none is due to environment, trait is 100% heritable:

VE = 0, so h2 = VG/VG = 1

OR IF none of variation is due to genetic differences, trait is 0% heritable:

VG = 0, so h2 = 0/(0 + VE) = 0

But, variation in a trait often falls somewhere between those two extremes.

An example = Stabilizing selection for egg size among ural owls, Kontiainen, Brommer, Karrell, Pietiainen

Q asked: How much of the variation in egg size is the result of genetic differences among females (mothers) and how much is environmentally controlled?

Ural owls are “site tenacious,” but their primary prey, a vole, populates in cycles. The abundance or lack of voles is an example of a potential environmental influence on variation. Behavioral responses to environmental factors can lead to differences in phenotype.

Researchers measured 3000 owl eggs laid during different vole cycles and found an h2 = 0.60, trait is subject to natural selection, leading to stabilizing selection. That is, very small and very large eggs hatch at a lower rate than intermediate sized eggs. Further, females who produce eggs at extreme sizes have shorter reproductive lives.

Another example = Directional selection in soapberry bugs, Carrol and Boyd

Q asked: Has beak length in bugs changed as new food choices were introduced?

Bugs must break through the fruit wall to capture the seeds. Fruit size varies greatly between populations and species. Beak length should be under strong selective pressure.

After the introduction of new plants, bugs shifted to introduced species.

A: as fruit radius increase, beak length does too.

Q asked: are the differences developmental responses? Are they due to pre-existing differences among populations, or are they environmentally influenced?

A: differences in beak length in field bugs feeding on plants were retained in bugs that developed on the alternative hosts. Differences were likely the result of natural selection. Bugs show reduced reproduction and survival when forced to live on alternative hosts.

h2 = 0.60

Another example = Disruptive selection in Darwin’s finches

On one island, finches either have small beaks or large. Any medium beaked birds either die or leave, either because of lack of appropriate food, or competition loss.

“Individuals in the population with small beaks mate preferentially with other small beaked birds, while large choose large”

Any disruptive selection is reinforced by nonrandom mating to produce genetic differences, h2 = 0.62

CR4.4.1. Can a trait with h2 = 0 evolve?

CR4.4.2. What must have been true in the soapberry bugs before the new plants were introduced?

CR4.4.3. There is genetic evidence that mating between G. magnirostris and G. fortis (fig 13.8, p 287) may have helped establish sufficient genetic variation in the populations of G. fortis at El Garrapatero for the distribution of beak sizes at that site (fig 4.13) to emerge under the influence of disruptive selection. Explain.

Section 4.5: Change Due to Chance

Random processes, like genetic drift, can change gene frequencies in populations (especially smaller ones)

Chihuahua spruce live at mountain peaks in northern mexico in small, highly fragmented populations separated by valleys.

Ledig, Hodgkiss, Jacob-Cervantes, Eguiliz-Piedra

Q asked: Has ch spruce lost genetic diversity as an effect of reduced population size due to separation by global warming?

Q asked: Is reduced genetic diversity contributing to continuing decline of the species?

Alloenzymes: various forms of an enzyme

They determined the number of alleles present in 16 enzyme systems. A greater number of alloenzymes indicates higher genetic diversity.

A: smallest populations have lower genetic diversity. This supports HWP; genetic drift is more effective in smaller populations.

Frankham observed extinction rates are higher for island vs mainland populations and hypothesized that because lower genetic variation indicates lower potential for evolutionary responses to environmental changes, lower variation on islands may be responsible for higher extinction rates.

Q asked: do island populations have lower genetic diversity? Do endemic?

Endemic: populations of species that live in one isolated area and nowhere else. i.e., a species consists entirely of a single populations

He found a trend exists: higher genetic in mainland populations vs island populations of the same species. Trend is even stronger in endemic populations vs their closely related species

Genetic factors cannot be eliminated as a contributor to higher extinction rates on islands. This finding supports the validity of a link, but does not demonstrate a specific connection.

Hanski, Kuussaari, Nieminen studied Melitaea butterflies. Population size increases with size of meadow. Small populations in small meadows are more likely to go extinct. Inbreeding is also higher in small popualtions. Combined with already low genetic variation, opulations w lowerst heterozygosity and high inbreeding have highest extinction, smaller larvae, pupate longer, have less hatching eggs, and less survival to reproductive age.

CR 4.5.1: Why do managers of breeding programs and reintroduction programs for endangered species try to maintain high levels of genetic diversity?

In small populations, even common alleles can be lost to chance. Lower genetic diversity indicates less potential for an evolutionary response to environmental changes. Inbreeding can increase, which can lead to problems, and extinction is more likely.

CR 4.5.2: What is the ecological significance of Frankham’s finding in lower genetic variation in smaller isolated island populations? Lower genetic variation in small populations can lead to extinction.

Chapter 4 Review Questions

1. Contrast the approaches of Darwin and Mendel to the study of populations. What were Darwin’s main discoveries? What were Mendel’s? How did the studies of Darwin and Mendel prepare the way for the later studies reviewed in Chapter 4?

2. How did the studies of Douglas and Brunner complement he earlier studies of Clausen, Keck, and Hiesey?

3. What is the HWE equation? What conditions are required?

4. What parts represent gene frequencies? What elements represent genotype frequencies and phenotype frequencies? Are genotype and phenotype frequencies always the same? Use a hypothetical population to specify alleles and allelic frequencies as you develop your presentation.

5. What is genetic drift? Under what circumstances do you expect it to occur? Under what circumstances is genetic drift unlikely to be important? Does genetic drift increase or decrease genetic variation in populations?

6. Suppose you are direction for a captive breeding program for a rare species of animal, such as Siberian tigers, which are found in many zoos around the world but are increasingly rare in the wild. Design a breeding program that will reduce the possibility of genetic drift in captive populations.

7. How might the distribution of beak sizes in the population differ from that shown in figure 4.13, if mate choice in the population was random with respect to beak size?

8. How did the studies of Scott Carroll and his colleagues demonstrate rapid evolutionary adaptation to introduced soapberry plants? What advantages do a group of organisms, such as soapberry bugs, offer to researchers studying natural selection compared to larger organisms such as Chihuahua spruce?

9. Ho do classical approaches to genetic studies, such as common garden experiments, and modern molecular techniques, such as DNA sequencing, complement each other? What are the advantages and disadvantages of each?

Vocabulary

Adaptation

Agriculture

Allele

Allele frequency

Allozyme

Artificial selection

Directional selection

Disruptive selection

Ecotype

Endemic

Evolution

Fitness

Genetic drift

Genetic engineering

Genetically modified organisms

Hardy-weinberg principle

Heritability

Inbreeding

Loci

Microsatellite DNA

Natural selection

Phenotypic plasticity

Population genetics

Range

Rhizome

Stabilizing selection

Standard deviation

Variance

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