Bio 286 Exam 1 Thought Q's (credit to Dilanya_Moonesinghe on quizlet)

What does it mean for biological entities to be hierarchically organized? What levels of the hierarchy are typically involved in ecological studies?

In order to study the relationships ecology focuses on, we must understand how individual organisms fit in with their environments and the world. That is why hierarchy organization is so important. Organism, species, population, community, ecosystem, and in some cases biosphere are all hierarchies typically examined. Levels: ecosphere,ecosystem, communities, populations, organisms.

What are the steps of the scientific method? Why can they be applied to questions addressing adaptations or natural selection?

The steps of the scientific method are observation, hypothesis, measurements, results, and conclusion.

What distinguishes a scientific hypothesis from a scientific theory?

A scientific theory is an explanation of related observations or events from multiple hypotheses that have been supported multiple times.

What is the difference between proximate and ultimate levels of causation? Be able to provide an example for each.

Proximate causation is the direct effect of stimuli from the environment, like temperature, diet, or stress hormones affecting fur color in snowshoe hares.
Ultimate causation is the evolutionary factors that led to the appearance of certain traits. An example is selective pressure from a predator.

What are Tinbergen's four questions? How do they inform our understanding of proximate and ultimate levels of causation? What is ontogeny?

Tinbergen's four questions include causation (what causes this trait to happen), ontogeny (how has this trait developed in the individual), evolution (how has this trait evolved from previous species), and survival value (how has this trait increased fitness). They help in our understanding of proximate and ultimate levels of causation by allowing us to observe the specific evolutionary causes and effects of external influence on the trait.

The changes that have occurred in the horse lineage over 60 million years constitute macroevolutionary changes. How do these relate to microevolutionary changes?

Macroevolutionary changes are changes that are not just allele frequencies. Microevolution changes tend to become more pronounced over time resulting in macroevolution. They have a major phenotypic change big enough to have a change in lineage. In horses this occurred when they evolved from a Eocene leg to now having a Pleistocene Leg.

What factors influence how rapidly different organisms may evolve?

Rates of environmental change
Genetic variation within the species
Size of the population
Generation time

What contributions did Charles Darwin make to our understanding of biological diversity?

Darwin developed a scientific theory of biological evolution that explains how modern organisms evolved over long periods of time through descent from common ancestors

What is the unit of evolution (what evolves)?

population

What is the relationship between genetic information flow and evolution? How are genes related to evolution?

Genetic information flow directs development, which plays the key physiological role connecting the heritable genotypes, passed from one generation to the next, to the phenotypes that are made available for selection.

Genetic variations can arise from gene mutations or from genetic recombination. If a trait is advantageous and helps the individual survive and reproduce, the genetic variation is likely to be passed to the next generation. Over time, as generations of individuals with the trait continue to reproduce, the advantageous trait becomes increasingly common in a population, making the population different from the ancestral one.

What factors are responsible for producing a phenotype?

Genotype + environment = phenotype

What is natural selection?

Organisms better adapted to their environment tend to survive and reproduce more leading to more of the population having those adaptations.

What is artificial selection? How is it similar and how does it differ from natural selection?

Artificial selection is the process in which humans specifically breed organisms with specific phenotypic features to increase the frequency of the phenotype. It is similar to natural selection because it can cause an evolutionary change in the species. It differs from natural selection because it is not influenced by the environmental factors a population typically deals with.

Why can evolution occur with or without selection?

Evolution is simply a change in allele frequency so bottlenecking, founder effect, or genetic drift could all cause evolution w/o selection.

What is an adaptation? Why are 'adaptations' not necessarily adaptive across time or environments?

Adaptation - trait that provides enhanced survival and/or reproductive success (fitness) in a given environment relative to individuals in the population that don't possess the trait

What is fitness? Why is fitness a relative measure?

Fitness is the genetic contribution of an individual to successive generations. It is a relative measure because it compares the individuals to other individuals in the environment with different phenotypes. The success of these individuals can vary based on the environment.

What does it take for a trait to evolve by natural selection (e.g. what are the prerequisites)? Why is each important? For any trait, be able to explain how each of the prerequisites must be met in order for that trait to have evolved by natural selection.

The prerequisites for a trait to evolve by natural selection are -
Phenotypic variation: This is important because without variation in the phenotypes there would not be any differences in traits to select. Everything would be the same
Differential survival or reproductive success with certain phenotypes: Similarly to the first reasoning, if all phenotypes had the same amount of success, no traits can be selected.
Individual capacity to overproduce is limited by environmental resources
Trait heritability: If the trait can't be inherited, it will not be passed down through a population.

What is heritability and why is it important for natural selection to act on a trait? What is one simple way it can be estimated?

Heritability is the proportion of variance among individuals in a train that is attributable to differences in genotype. It is also the degree of trait resemblance between parent and offspring. It is important for natural selection because traits must be able to be passed on to the next generation to see changes in a population. It can be estimated using a slope regression.

We discussed the heritability of human height in class. What data would suggest that human height was not a heritable trait?

Environmental factors, such as air quality and nutrition, can affect height. Heritability can be determined through a regression slope.

What is a mid parent?

A mid parent is the average trait of both parents.

What is phenotypic plasticity? Polyphenism?

Phenotypic plasticity is the ability of a genotype to exhibit different phenotypes under different environmental conditions. This can create polyphenism which is the development of multiple phenotypes from a genotype due to the different environmental conditions.

What is a reaction norm? What is the usefulness of reaction norms for studying phenotypic plasticity?

A reaction norm is a plot of the phenotypic values across environments. The slopes can tell us the degree of plasticity. A steep slope means there is high plasticity whereas a flat slope means there is low plasticity.

What are the three patterns of selection? Be able to explain them in terms of average trait value, population variability, and fitness. Be able to plot them graphically. Based on our discussion so far, be able to provide examples of the first pattern, with explanation.

Directional selection is when the favored trait shifts the frequency of the phenotype toward one of the tails of normal distribution.
- Leads to shift in mean trait value but variance may be unaffected
- eg. beak depth of Geospiza fortis and those that survived subsequent year drought

Stabilizing selection puts individuals in both tails of the curve at selective disadvantage.
- Maintains mean trait value and reduces trait variation
- eg. human birth weight

Disruptive selection occurs when tails of the distribution are favored over the intermediate phenotype
- Increases trait variance, produces bimodal distribution of traits
- eg. Mimulus luteus (yellow flowers) in Chile

How can rainfall patterns on the Galapagos Islands act as a selective pressure on finch beak morphology? What are the ultimate rainfall effects on beak phenotype?

Beak depth of Geospiza fortis and those that survived after a drought period experienced directional selection toward deeper beaks.

More rainfall> small seeds> small beaks; Low rainfall> hard caltrops>large beaks. Directional

What are the ways, other than selection, that can lead to microevolutionary changes? How do they relate to natural selection?

Genetic drift - random changes in allele frequencies in a population over time
Important for moving between the peaks of an adaptive landscape
- Can drive population up or down peak, whereas natural selection will only drive population up

Gene flow - the net gain or loss of certain alleles by movement of individuals resulting in changes in allele frequencies in a population over time
- Immigration of new individuals into populations introduce new alleles
- Emigration of individuals out of populations may lead to loss of alleles
- Can counteract genetic drift and/or natural selection

Mutation pressure - the evolutionary change resulting from new mutants which lead to changes in allele frequencies in a population over time
- Natural selection will select for favorable mutation in a changing environment (eg. pesticide resistance)

How do mutations relate to evolution? Be able to explain using a real-life example.

New alleles introduced into the population due to change in DNA sequence. A good example is sickle cell hemoglobin. Because of this mutation cells hemoglobin form a crescent shape. This impairs the amount of oxygen the hemoglobin cancontain. This mutation also causes clotting. Mutations can also introduce new, potentially adaptive traits to a population which can be selected, leading to evolution.

Be able to explain how parasitoid wasp and bird foraging behavior act as a selective pressure on the size of fly-induced goldenrod galls, and what the resulting pattern is.

If the fly larva is too big, woodpeckers will peck into the larger galls in order to get the larva inside. If the galls are too small the wasps can oviposit. However, Ovipositors cannot deposit eggs into large galls. This causes stabilizing selection where the intermediate sized galls are selected for.

What is fetal macrosomia and how does it impact newborn survival?

Fetal macrosomia is a newborn that weighs more than the average and the mortality rate is significantly higher. This is a baby born significantly larger than the average. This decreases the likelihood of the infant's survival. The complications with this are birth asphyxia, trauma, and low blood sugar.

Why are small populations more vulnerable to genetic drift?

There are less alleles when a population is small. It is easier to lose all variation.

What does it mean for an allele to go to fixation?

This means the allele is 100% prevalent in the observed population.

What is the role of the individual when genetic drift is occurring versus natural selection?

Natural selection occurs at the level of the individual, whereas genetic drift occurs at the level of a population.

What is the relationship between genetic drift and natural selection? Which is likely to be more directional? Why?

Genetic drift is more likely to be directional, as it is a random change in allele frequencies in a population over time. Genetic drift typically occurs in small populations, where alleles can more easily become fixed or lost over time. Fixation or loss is inevitable but unpredictable.

What is the adaptive landscape? On what axes is it plotted? Who proposed it?

The adaptive landscape is a 3D representation of fitness, plotted on the y-axis, of different genotypic combinations, plotted on the z and x-axis. It was proposed by Sewell Wright, a population geneticist, part of the Modern Synthesis.

How does the selective landscape integrate concepts of drift and selection?

Drift can drive a population up or down the y-axis, whereas selection will only drive a population's fitness up. Genetic drift is important for a population to move between peaks in the adaptive landscape.

What is the Modern Synthesis and what is its importance to Darwinian evolution?

- introduction of mathematical models to evolution demonstrated that natural selection operating on Mendelian variation could lead to rates of evolutionary change that explain historical patterns of evolution, as theorized by Darwin
- Allowed the examination of the forces of evolution on populations to predict how the genetic composition of a population will change over time
- Gave birth to new scientific discipline called population genetics

How can gene flow enhance natural selection? How can it oppose it?

Gene flow can enhance natural selection by introducing new alleles, that may or may not be advantageous, to a population. Emigration of individuals out of populations may lead to loss of alleles. Gene flow can reinforce or oppose the changes caused by natural selection and drift. If the same genes entering the population are those that are increasing randomly within the population by genetic drift, the effect of drift will be more pronounced. Gene flow has an important impact on evolution by selection: the more
isolated the population, the less gene flow and the more effective natural selection can be.

In addition to mutation, how can an organism acquire new genetic variation?

An organism can acquire new genetic variation through horizontal gene transfer (HGT), gene flow, recombination, epigenetics, genetic drift, and selection.

What is the Malaria Hypothesis? Is it supported, and why?

The malaria hypothesis states that the potentially lethal genetic mutation for sickle cell anemia does not diminish by the process of natural selection because of its advantage in protecting against malaria. Carriers of sickle cell hemoglobin allele have increased resistance to malarial infections, an example of how the adaptive value of trait varies among different environments. This is supported by a sickle cell gene proliferation chart with global data showing the sickle cell gene is predominantly found in regions of high incidences of malaria.

What are genetic duplications and trinucleotide repeats? Why may they be deleterious?

Duplications are repeats of all or a segment of a chromosome. An example of the mutations deleterious effects are evident in the cause of exertion-related sudden cardiac arrest in Amish children homozygous for the mutation.

What is Huntington's disease?

Individuals have an increase in the number of CAG repeats in the first exon of the huntingtin protein gene, which is involved in signaling, cell contact and transport in CNS neurons.

What is genetic recombination? How does it differ from mutation?

Genetic recombination is the exchange of DNA between other individual cells whereas mutation is a change in the gene structure that occurred randomly.

Why are influenza strains characterized by a letter (A, B, or C) and H and N values? Why are vaccines targeted to different strains each year?

Influenza is classified in three types based on proteins that form spikes in the coat surrounding genetic material.
- Hemagglutinin (H) protein helps virus enter host cell
high mutation rate
- Neuraminidase (N) helps virus exit cell after it has replicated
- Vaccines target different combinations of H and N proteins

Approximately how many people died from the 1918-19 influenza pandemic?

The 1918-19 influenza pandemic is estimated to have killed at least 50 million people worldwide, and was caused by A(H1N1).

What are the most prevalent flu strains affecting humans this flu season?

A (H1N1), (H3N2) and B Victoria and Yamagata lineages

What type of viruses are coronaviruses? How can new infectious strains be produced?

Coronaviruses are RNA viruses. New infectious strains can be produced from high rates of recombination and mutation.

Based on the analyses by Anthony et al., what are the most common reservoirs for coronaviruses?

The most common reservoirs for coronaviruses are bat species

What is horizontal gene transfer (HGT) and how may it occur?

HGT is when genes from one species are introduced into another species and it occurs through transduction, transformation and conjugation.

How can horizontal gene transfer affect evolutionary rates?

Horizontal gene transfer may allow organisms to rapidly acquire new traits.

What is the coffee berry borer and what adaptation did it acquire through HGT?

The coffee berry borer is a small beetle native to Central Africa. It can feed exclusively on coffee beans by digesting the coffee bean polysaccharide galactomannan due to production of mannanase from HhMAN1 gene acquired through HGT from bacteria.

What phenotypic variation could you observe in the Mexican tetra (Astyanax mexicanus)? What is a proximate mechanism responsible for this phenotypic variation and what is an ultimate mechanism responsible for this phenotypic variation?

Cave-dwellers are blind and lack eye pigment, whereas river-dwellers have vision and eye pigment. Proximate mechanisms include loss of eye pigment due to genetic drift and arrest of eye development by natural selection. An ultimate mechanism responsible for this phenotypic variation is that the energetic costs to maintain vision tissue is too high.

What is epigenetics? Two examples are histone acetylation and DNA methylation. How could these affect the genotype? The phenotype?

- Epigenetics is the process that changes gene expression (such as due to histone acetylation or DNA methylation) without a change in DNA sequence.
- Histone acetylation causes DNA (negatively charged) to reduce its affinity for acetylated histones, making it more accessible for transcription factors (TF), so gene expression INCREASES.
- DNA methylation of a gene's CpG island (upstream CG-rich regions) represses gene expression because transcription factors cannot bind to promoters
- Epigenetic traits may be heritable (passed from one generation to the next)

How can epigenetic changes be involved in evolutionary changes within a population?

Epigenetic traits may be heritable (passed from one generation to the next). In the example of the Mexican tetra, reduced eyes may be due to selection on epigenetically silenced genes.

What is Lake Tanganyika and why are its fish inhabitants of interest to evolutionary biologists?

Lake Tanganyika has high cichlid fish diversity. Cichlids are bony fish (Osteichthyes) that have tremendous phenotypic and behavioral diversity.

Why would fish eat the scales of other fish?

Fish scales are a source of protein and calcium.

What are scale-eating cichlid fish and what striking phenotypic variation do they exhibit?

Scale-eating fish are parasitic fish that consume the scales of other fish. The populations have two morphs: mouth parts twisted to the left, enabling it to eat scales off its victim's right flank, or, in contrast, mouth twisted to the right, enabling it to eat scales off its victim's left flank.

What is frequency dependent selection? Why are the scale eating fish a good example of frequency dependent selection?

Frequency-dependent selection is when the fitness of a genotype varies with its frequency in the population. Scale-eating fish are a good example of negative frequency-dependent selection, which is when fitness increases with RARENESS of genotype in the population. Parasitized fish learn to look to the right or the left to avoid the parasitic scale-eating fish, thus variation is maintained by favoring rare genes.

Be able to distinguish between positive and negative frequency-dependent selection and provide an example of each.

negative - genotype rareness increases fitness (fish). positive- genotype prevalence increases the fitness (batsean mimickry)

In terms of the Hardy-Weinberg theorem, what do p and q represent? What do p2, 2pq, and q2 represent?

p= frequency of dominant alleles (A)
q= frequency of recessive alleles (a)
p2= homozygous dominant (AA)
q2= homozygous recessive (aa)
2pq= heterozygous (Aa)

What does the Hardy-Weinberg theorem predict? What does it assume?

Hardy-Weinberg theorem serves as a null hypothesis for whether evolution is occurring in a population.

What does it mean if Hardy Weinberg predictions are not upheld? Be able to explain how a violation of each of the Hardy-Weinberg assumptions produces a mechanism of evolution.

If H-W predictions are not upheld, that means evolution has occurred

What are quantitative traits? Be able to provide examples.

Traits that vary in regard to size, volume, or otherwise numerical values relating to certain characteristics of an organism. (Height, Blood pressure, risk of disease etc.)

What is the selection differential and how can it be calculated using trait values?

Selection differential is the phenotypic value of individuals that breed distinguished from population mean. S=us-u, where us=avg trait value of breeders in population u=average trait value in population

What is the response to selection and how can it be calculated?

Response to selection (or R) is the change in population average trait value after selection. It is calculated as R=h^2*S H^2 is the heritability coefficient and S is the selection differential

How can you use the response to selection to predict how a particular phenotypic trait in a population will change over time?

Traits with high R (due to high heritability) will respond to natural selection more rapidly and therefore be more prevalent

Quantitatively, what is the difference between absolute and relative fitness?

absolute fitness: the survivorship and reproduction of each genotype in a population
relative fitness: the ability of one genotype to survive and reproduce relative to the best genotype

How is absolute fitness calculated?

divide number of individuals of each genotype after selection by number of individuals of each genotype before selection

How is relative fitness calculated?

divide each absolute fitness value by the highest absolute fitness value

How do you use relative fitness to calculate the selection coefficient? What does the selection coefficient mean biologically?

s = 1 - relative fitness

What is inbreeding? How can it lead to inbreeding depression?

The mating among organisms that are genetically closely related. It can cause a shortage of heterozygotes with higher fitness or an increase in homozygotes for deleterious recessive alleles

What is hybrid vigor? Why does it occur?

The tendency of a crossbred individual to show qualities superior to those of both parents, occurs because the combination of the phenotypes may have a better outcome than the parental phenotypes.

What is a population bottleneck and now does the genetic diversity of the population following the bottleneck compare with that preceding it? Why is this important?

Evolutionary event in which a large portion of the population is lost or prevented from breeding, genetic make-up after bottleneck may not represent the diversity that was present before the bottleneck, which could cause more issues within the population.

Cheetahs demonstrate some of the effects of a population bottleneck. What additional factor(s) threaten their population persistence?

Low reproductive success due to highly abnormal sperm and low sperm count

What is a founder effect? How might it influence the genetic differentiation of a population relative to its source population?

when a new population is founded by a small number of individuals, drift from founder effect can enhance population differentiation

What are neutral alleles? How can they be used to assess genetic drift?

genes that are selectively neutral, any changes in gene frequencies of neutral alleles between populations are caused by genetic drift

What is the difference between the censused and the effective population size? Why might they differ?

Censused population: what can be actually counted
Effective population: the size of an ideal population that has the same rate of inbreeding or loss of genetic diversity by drift as the actual population being studied

Be able to calculate effective population size if given the formula. What factors can reduce effective population size, and why?

- unequal number of males and females
- not all of individuals reproduce
- the number of offspring produced differs from random expectations
- mating is not random
- number of breeders changes from one generation to the next

What is the relationship between Ne and genetic drift? How are these potentially related to population persistence?

Ne: if the proportion of population that is actually randomly mating (cause)
Genetic drift: change in allele frequency by chance (effect)

What is the difference between an endangered and threatened species? How does effective population size inform that status?

Endangered: any species that is in danger of extinction throughout all or a significant portion of its range
Threatened: any species that is likely to become an endangered species within the foreseeable future throughout all or a significant portion of its range

What does it mean for a threatened or endangered species to have critical habitat?

critical habitats are geographic areas that contains features necessary for the conservation of an endangered or threatened species and that may require special management and protection

For grizzly bears in Yellowstone National Park, how do census and effective population size values compare? What is the current status of Yellowstone grizzlies?

removed from threated species list, however Ne<Nc
Yellowstone grizzlies are currently threatened

Generally, for any trait to be selected for, what has to be true about the benefits of the trait relative to the costs of the trait?

Benefits should be higher than the costs

What is the approximate average heritability of behavioral traits?

0.235

What is altruism? Why have some species evolved the behavior of potentially sacrificing individual survivorship for reproduction? What is an example?

Altruism is an action that is beneficial for another but carries a fitness cost. Some species have evolved this behavior in order to increase chance of population's overall fitness
- Eg: Belding's ground squirrel

What does it mean for a behavior to be plastic and heritable?

phenotype can change based on environment and the phenotype displayed can be passed down to offspring

What are stimulus response behaviors and why are they important? How may they be involved in maintaining the integrity of a species?

Behaviors that only occur when a specific stimulus, such as noise or visual cue, occurs. For example certain baby birds have specifically colored markings in the inside of their beaks which can assist in parents feeding the correct young and not an imposter

What sensory modalities may be involved in communication?

visual, auditory, olfactory, or tactile signals

What evidence is there that multiple pieces of information may be conveyed in a communication event?

chickadee alarm calls can warn of presence of raptor and communicate size of potential threat, belding ground squirrels alarm calls differ for aerial and terrestrial predators

What is sexual dimorphism?

Sexual dimorphism is the difference in appearance, physiology, immunology etc between the two sexes of a species

Compare the different investments males and females make in reproduction, on average. What factors generally influence male versus female reproductive success?

- females incur high anatomical, physiological, and energetic costs of reproduction
- female fitness cannot increase indefinitely by increasing the quantity of the progeny
- female fitness increases as a function of the quality of the progeny
- male contribution (sperm) is energetically cheaper than eggs
- male fitness increases with the number of females he inseminates

What is sexual selection?

selection on traits associated with mating success

What is its relationship between sexual selection and sexual dimorphism? Between sexual selection and natural selection?

- the opportunity for sexual selection increases with the degree of sexual dimorphism
- male traits are exaggerated by female choice until their overall fitness cost is too high

According to Bateman's principle, which sex experiences more intense sexual selection, and why?

Males experience greater variation in reproductive success than females do. This is due to males experiencing more variation in their traits brought about by sexual dimorphism, giving females a greater opportunity for selection.

We discussed several mating systems (monogamy, serial monogamy, polygyny, polyandry). Be able to describe each of these, provide an example, and explain how ecological factors have shaped them.

Monogamy: males mate with a single female

Serial monogamy: monogamous relationship lasts for a single breeding season; occurs if successful rearing of the young requires both parents and/or providing parental care is more advantageous to a male than seeking additional copulations

Polygyny: each male mates with more than one female during a breeding season; shaped by spatial distribution of females and spatial distribution of other critical resources

Polyandry: each female mates with more than one male during breeding season

What is the difference between precocial and altricial development?

precocial offspring: born relatively well developed and capable of independent movement
altricial offspring: incapable of independent movement or of taking care of themselves

What is a lek? What is a harem? In mating systems which have these, how are Nc and Ne affected? How would those compare to a monogamous mating system's effects on Nc and Ne?

lek: tradition sites used for male display
harem: a group of females a male defends from other males and has exclusive access to
Ne would be much lower than Nc

What is positive assortative mating? What is negative assortative mating? What patterns of selection would you expect to see in populations associated with each, and why?

positive assortative mating: occurs between individuals of similar phenotypes, positive assortative mating would experience directional selection

negative assortative mating: occurs between individuals of opposite phenotypes, negative assortative mating would experience stabilizing selection

Under what circumstances can selection favor giving up one's life to mate? What are the different reasons this may occur?

cannibalized males copulate longer, fertilize more eggs, and make it less likely that females will be willing to mate with subsequent suitors
cannibalized males could cause females to lay more and larger eggs and cause offspring to have higher survivorship

What are ways other than mating with another individual that plants may use to reproduce? Under what ecological circumstances are these favored?

outcrossing: mating among different individuals
autogamy: self-fertilization
apomixis: asexual reproduction; formation of seed from maternal tissue without meiosis and fertilization

What are at least three costs and three benefits to being social?

Benefits: Increased Vigilance, Increased food finding, decreased probability of being depredated.

Costs: Increased Conspicuousness, increased disease transmission, and decreased food intake per capita.

What is cooperative breeding and why does it occur?

Cooperative breeding is a type of social system in which group members raise young that they can not produce, and may delay their own production. (9% of Birds, Insects, Naked mole rat and the mongoose).