PCB4674 Midterm 1 Concepts

Provide a definition of evolution through tree-thinking.

Evolution is a process of branching, highly focused on the sequence of events over time and the origin of traits and evolutionary relatedness.

What is essentialism?

The idea that all individuals in a population will meet the same criteria

Provide a definition of evolution through population-thinking.

There is variation among individuals in a population, and this variation allows for gradual change to occur. Eventually this results in speciation and evolution of separate species.Traits show this variation and can covary.

What evidence did Darwin have of evolution and how did they support his theory?

A fossil record showing other species lived in the past and transitional steps between species groups, which questioned the constancy of species. Homology, where organisms shared similar characteristics suggesting a common ancestor. Convergence, where species shared similar traits due to environmental pressure and selection acting on their ancestors. Biogeography showing unique new and old world plants with specific dispersions. Artificial selection

Homologous structures

where organisms shared similar characteristics suggesting a common ancestor

Convergent evolution

species shared similar traits due to environmental pressure and selection acting on their ancestors

Vestigial structures

traits that are homologous to traits of other organisms but no longer serve a purpose

How has biogeography shaped the distribution of organisms, and supports descent with modification?

The shifting of tectonic plates and splitting of land masses caused indirect dispersal of some organisms, and allows better predictions of the existence and speciation of certain species based on their location.

What organisms are on oceanic islands?

More recently evolved organisms that have dispersed there, possibly endemic species that had evolved entirely on the island.

What organisms are on continental islands?

Very similar to mainland organisms due to proximity.

What organisms are on plate fragment islands?

Organisms from ancient groups that are not good dispersers, may have gone extinct elsewhere on mainland.

What are modern (Post-Darwin) examples of evolution?

Mendelian genetics and the inheritance of alleles, molecular genome mapping, comparative embryology

Explain how a trait can be both homologous and convergent at the same time.

The homologous structure could be retained in a forelimb, but the specific task of digging resulted in convergent spade-shaped paws for moles.

Why is genetics needed for natural selection to lead to evolution?

Natural selection allows heritable traits that increase odds of reproduction to occur more and more frequently in a population

Describe the Grants’ work on Darwin’s finches

Showed rapid evolution in beak size/shape due to environmental changes (e.g., drought).

What are difficulties in estimating heritability in a field study?

Genetic effects are difficult to separate from environmental influences, and human error in field measurements can result in inaccurate conclusions.

Describe the process of natural selection and differentiate it from evolution.

Natural Selection: Process where advantageous traits increase in frequency.

Evolution: Broader, includes all mechanisms of genetic change over time.

What are examples of evolutionary ideas present in ancient cultures?

In Taoism, Zhuang Zhou’s proposed speciation (300 B.C.). In Islam, Book of Animals discussing struggle for existence by Al Jahiz (9th century). In Ancient Greece, Anaximander proposed humans evolved from non-human species, and Plato & Aristotle proposed a static view of the universe and chain of being (600-300 B.C.)

How did the influence of Aristotle and Plato led to resistance of evolution in western thought?

Fossils were thought to be remains of organisms still living elsewhere, perfection of creation and chain of being, “why should things change if they’re already perfect?”

What is Uniformitarianism & how did it affect evolutionary thought?

Proposed that the Earth was very old, & the geological processes occurring now operated similarly in the past, which challenged the idea of the constancy of the Earth.

What did Lamarck contribute to the history of evolution?

Proposed organisms evolve new traits through a combination of environmental pressure and acquired characteristics.

What did Lyell contribute to the history of evolution?

Published the Principles of Geology that explained uniformitarian ideas about the geological events on Earth.

What did Darwin and Wallace contribute to the history of evolution?

Wrote and proposed their theory of natural selection (Darwin wrote the Origin of Species), which was initially rejected bc of the common theory of blending.

What did Fisher/Haldane/Wright contribute to the history of evolution?

Set up a mathematical framework to allow us to predict evolution under certain conditions, using genetics

What is the modern synthesis and its impact on evolutionary thought?

Integration of genetics with Darwin’s theory to propose that evolution occurs from small changes during natural selection (microevolution) which results in the origin of new species (macroevolution).

What is methodological naturalism, and how did it impact evolutionary thought?

The only hypotheses and explanations for natural phenomena that are accepted are ones involving strictly natural causes, because they believe no other higher power exists.

What is irreducible complexity, and how did it impact evolutionary thought?

The idea that structures only make sense in their final form & are too complicated to form gradually over time in less than ideal forms, anti-evolutionary thought.

What is a taxonomy?

naming of organisms grouped into progressively more inclusive sets (heirarchy)

What is phylogenetic systematics?

naming based on evolutionary relationships with a tree-based classification (often with clades)

What is a node?

the most recent common ancestor between two groups that show a point of divergence

What is a sister taxa?

Two groups that share a unique common ancestor not shared with other groups, that are the closest relatives to each other

What is a monophyletic group?

a group, or clade, that includes a common ancestor and all of its descendants

What is a paraphyletic group?

a group that includes a common ancestor but not all of the descendants of that ancestor

What is a polyphyletic group?

A group that contains species with no common ancestor

What are synapomorphies?

A homologous, shared, derived trait between species that identify monophyletic groups. Associated with branch points on a phylogeny.

What is homoplasy, with examples?

The independent appearance of a character state in more than one place on a phylogeny, such as convergently derived characters or a return to an ancestral state/loss of a derived trait. Creates similarities between groups other than common ancestry.

What is parsimony?

The theory that the most “parsimonious,” or easiest, evolutionary pathway is the most likely pathway to have occurred

What is maximum likelihood?

The calculated probability of the data given a theoretical phylogenetic tree, using the branch lengths and the model, used to compare to other likelihoods of other trees

What is neighbor joining?

The calculation of an unrooted phylogenetic tree using an initial star phylogeny and genetic distances of species to show divergences, eventually rooted into a true phylogeny

What is Bayesian Inference?

The calculation of phylogenetic trees using software that is provided multiple species in a population, which then simulates multiple phylogenetic trees and estimates their likelihood of aligning with the population. The more a possible tree appears in a simulation, the more likely it is.

What is bootstrapping?

A calculation that can be used to validate phylogenetic trees developed through any other method. Instead of having to collect more data, it simulates “replicate” data sets from the original data and compares the trends between trees to find the majority/common trends.

What are the advantages and disadvantages of molecular data for constructing trees?

Molecular data gives us a lot of data to work with, but there are issues with homoplasy, issues with unambiguous character states, and it’s difficult to retrieve DNA from fossils.

What are the advantages and disadvantages of morphological data for constructing trees?

Morphological data provides helpful information on convergence, but it is difficult to code traits and isn’t very useful for prokaryotes and small eukaryotes

What can branch length represent in a phylogeny?

Branch length can represent the amount of genetic change between other species in a phylogeny (ex: 1 mm of length = 1 nucleotide change in DNA)

What are the three sources of phenotypic variation?

Genetic variation, environmental variation, and genetic by environment variation

What is genetic variation in a population?

Different alleles within the genome are responsible for different phenotype presentations

What is environmental variation in a population?

The degree of phenotype expression depends on the stress of the environment (such as daphnia armor for predators) even when the same alleles for a phenotype are present

What is genotype x environment variation in a population?

Different genotypes (alleles) respond differently to environmental cues, resulting in many varying phenotype presentations

What is a reaction norm, and how does it relate to variation?

A reaction norm is the range of phenotypes an organism can develop in response to different environmental conditions, given a particular genotype. It illustrates how gene expression can be influenced by the environment. Reaction norms contribute to phenotypic variation within populations by allowing individuals with the same genetic makeup to exhibit different traits based on environmental factors.

How can mutation add variation into populations for evolutionary change?

Mutations introduce new genetic variations by altering DNA sequences. These changes can create new alleles, modify gene function, or affect gene regulation. Over generations, mutations accumulate, providing a genetic basis for adaptation and evolutionary change. Beneficial mutations may confer advantages that increase an organism's fitness, allowing them to spread through the population via natural selection.

Why are most mutations expected to be harmful?

Most mutations are harmful because biological systems are finely tuned by natural selection, meaning random changes are more likely to disrupt functional genes rather than improve them. Harmful mutations can lead to loss of function, structural deformities, or reduced survival and reproduction.

What is a point mutation?

The smallest possible mutation, where one nitrogenous base in DNA is substituted for another. It can cause transition or transversion mutations, where purines and pyrimidines are substituted as well.

What is a silent/synonymous mutation?

The amino acids in protein produced from the RNA/DNA are not changed, so the mutation goes unnoticed

What is a replacement/synonymous mutation?

The amino acids in protein produced from the RNA/DNA are changed

What is a gene duplication?

Another copy of a gene is produced onto the DNA, resulting in new genes that can maintain the original function, gain a new function from mutation/selection, or become functionless

What is a genome duplication?

Large-scale mutation where entire chromosome sets get duplicated, seen in a lot of genetically modified fruits/vegetables today

What is an inversion?

A mutation where a portion of chromosome breaks, flips, and reattaches, resulting in entirely different nucleotide sequences

What is allele frequency?

The frequency of an allele in a population, used to measure the genetic variation in a population

What is heterozygosity?

Individuals with two different alleles for a particular genotype, as opposed to two of the same alleles

What is heritability?

Heritability is the proportion of total phenotypic variation in a population that is due to genetic differences among individuals. It is measured on a scale from 0 to 1, where 0 means no genetic influence and 1 means all variation is genetic.

What is the significance of Hardy Weinberg in population genetics?

The Hardy-Weinberg principle provides a mathematical model for predicting allele and genotype frequencies in a population that is not evolving. It serves as a null hypothesis to detect evolutionary forces such as selection, mutation, genetic drift, non-random mating, and migration.

Why is modeling selection in a diploid system more complicated than in a haploid system?

In a diploid system, selection acts on genotypes rather than directly on alleles, meaning dominance and recessiveness affect how alleles are expressed and inherited. In contrast, haploid organisms express all alleles directly, making selection more straightforward.

What are the effects of selection on recessive and dominant alleles?

Dominant alleles can spread quickly but are easier to eliminate if they are harmful, as heterozygotes still express the trait. Recessive alleles take longer to increase in frequency because they must reach a high enough level for homozygous individuals to appear and be selected for. Harmful recessive alleles can persist in heterozygotes, making them difficult to remove.

Why is selection not effective on recessive lethal alleles at low frequencies?

At low frequencies, most recessive lethal alleles are hidden in heterozygous carriers, where they do not affect survival or reproduction. Since selection only acts on expressed phenotypes, these alleles are not effectively removed from the population.

What will allele frequency look like in a heterozygote advantage vs. a heterozygote inferiority?

Heterozygote Advantage (Overdominance): Both alleles are maintained in the population, leading to balanced polymorphism (e.g., sickle cell anemia and malaria resistance).

Heterozygote Inferiority (Underdominance): One allele will eventually become fixed, and the other lost, depending on initial frequencies and selection pressures.

What is frequency dependent selection? Provide an example

Frequency-dependent selection occurs when the fitness of a phenotype depends on its frequency in the population. Positive frequency dependent selection would be aposematic coloration to warn predators, because more individuals with the warning colors means it is more likely for the predator to already be familiar with the warning. Negative frequency dependent selection would be multiple grazing strategies evolved in a deer species, and the more deer that graze on bushes, the less bushes there will be to eat for all deer.

What is the importance of mutation for evolution?

Mutation is the ultimate source of genetic variation, introducing new alleles that natural selection, genetic drift, and other evolutionary forces can act upon. Without mutation, evolution would eventually stagnate as variation is lost.

How could migration of populations alter a Hardy-Weinberg equilibrium?

Migration (gene flow) introduces new alleles into a population or changes allele frequencies, preventing genetic isolation and potentially counteracting local adaptation or genetic drift.

What is FST? How is it calculated?

FST (Fixation Index) measures genetic differentiation between populations. It is calculated as:

FST = (variation between populations - variation within populations) / variation between populations

Higher FST values indicate greater genetic differentiation.

When is genetic drift powerful, and what does it do within and between populations?

Genetic drift is most powerful in small populations because random fluctuations in allele frequencies have a greater effect.

Within populations: It reduces genetic variation by randomly fixing or losing alleles.

Between populations: It increases genetic differentiation as different alleles become fixed in different populations.

What is effective population size?

Effective population size (Ne) is the number of individuals in a population that contribute genetically to the next generation. It is often smaller than the actual population size due to factors like unequal sex ratios, variation in reproductive success, and population fluctuations.

What is nonrandom mating? How does it differ from other evolutionary forces?

Nonrandom mating occurs when individuals choose mates based on certain traits rather than randomly.

Unlike natural selection, it does not directly change allele frequencies but affects genotype frequencies (e.g., increasing homozygosity with inbreeding).

Unlike genetic drift, it is not random but instead structured based on mate choice.

Why does inbreeding result in higher homozygotes in the population, and why is it generally negative on fitness?

Inbreeding increases homozygosity because relatives share alleles, making it more likely that offspring inherit two copies of the same allele. This can expose deleterious recessive alleles, leading to inbreeding depression, which reduces fitness due to increased genetic disorders and reduced adaptability.

What are quantitative traits and how are they inherited?

Quantitative traits are traits influenced by multiple genes (polygenic) and often affected by the environment, showing continuous variation (e.g., height, weight, intelligence). They follow a normal distribution and do not follow simple Mendelian inheritance.

What is genetic variance, and how does it differ from environmental variance?

Genetic variance (Vg): Variation in a trait due to genetic differences among individuals.

Environmental variance (Ve): Variation in a trait due to environmental factors.

The total phenotypic variance (Vp) is the sum of both

How is heritability calculated?

Heritability (h²) is the proportion of phenotypic variance due to genetic variance: h² = Vg/Vp. It ranges from 0 (no genetic influence) to 1 (all variation is genetic) and is estimated using twin studies, parent-offspring regression, or breeding experiments.

What is a selection differential? What is it used for?

The selection differential (S) measures the strength of selection on a trait:

S = Mean trait value of selective individuals - mean before selection

What is a selection gradient? What is it used for?

A selection gradient (β) quantifies the strength of selection on a trait relative to its effect on fitness:

β = Fitness/Trait

It is used in studies of natural and artificial selection.

What is a QTL? How are they detected?

A Quantitative Trait Locus (QTL) is a genomic region associated with variation in a quantitative trait. QTLs are detected using linkage mapping and GWAS (Genome-Wide Association Studies) by analyzing genetic markers and phenotypic traits in populations.

What are the different mechanisms for maintaining genetic variation?

Mutation: Introduces new alleles.

Heterozygote Advantage: Maintains both alleles in a population (e.g., sickle cell trait).

Frequency-Dependent Selection: Rare alleles have a fitness advantage.

Gene Flow (Migration): Introduces new alleles from other populations.

Variable Selection Pressures: Selection varies across time or space.

Why can trade-offs alone not maintain variation?

Trade-offs involve fitness costs and benefits (e.g., high reproduction vs. short lifespan), but they do not actively maintain genetic variation unless selection fluctuates over time, is frequency-dependent, or heterozygote advantage is present. Without such mechanisms, one trait variant may still become fixed over time.

For each mechanism, what are the evolutionary and genetic effects?

Selection: Decreases phenotypic variation, promotes divergence

Mutation: Increases genetic variation, promotes divergence

Migration: Could increase OR decrease genetic variation, prevents divergence

Drift: Decreases genetic variation, promotes divergence

Non-random Mating: Leads to increased homozygous genotype allele frequencies, could lead to or prevent divergence

What does the Stickleback fish speciation study address?

Stickleback fish live in coastal waters with access to freshwater habitats. Saltwater species have more armor due to a greater predation risk, which freshwater species have lost this armor over evolutionary time. Example of speciation.

What does Grant’s work on Darwin’s finches address?

Grant’s work showed how natural selection alongside heritability is necessary for evolution to occur, following species of finches on the galapagos islands.

What does the PTC taste receptor study address?

An example of genetic variation, where in humans there are two alleles for a taste receptor: PAV and AVI. PAV/PAV individuals taste PTC most intensely because their receptors are shaped well to fit the PTC molecule, AVI/PAV individuals can taste it but not intensely, and AVI/AVI individuals taste it least intensely or not at all.

What does the Daphnia Environmental Variation study address?

Daphnia grows more armor in habitats where predators are present (= inducible defense). Exposure to predator olfactory cues triggers the development of armored structures compared to genotypically identical controls, suggesting there is no underlying genetic variation, but rather phenotypic variation is dependent on environmental cues.

What does the Leopard geckos GxE study address?

Leopard geckos have temperature dependent sex determination. At high and low temps, eggs will become female. At 30-32C, eggs are mostly male. The GxE interaction is shown in graph (c). % male offspring varies depending on genotype of the father.

What does the Tobacco hornworm caterpillars (Suzuki & Nijhout 2006) study address?

Tobacco hornworm caterpillars are normally green. Suzuki & Nijhout (2006) worked with a line of caterpillars that were normally black, unless they were exposed to high temps (heat shock) before molting. They found that some individuals were more sensitive to heat shock than others. Suzuki & Nijhout (2006) created three lines of caterpillars, those with high or low plasticity, and an unselected line. They bred these lines for many generations then compared their reaction norms = the measure of a trait against environmental cues for different genotypes The high plasticity line varied widely in its response to temperature The low plasticity line was consistently black regardless of temperature

What does the University of Illinois corn oil study address?

Researchers used artificial selection to increase the oil content of corn kernels. Each year, they measured the amount of oil in the kernels and selectively bred those that produced the most. After 100 generations of selection, the average oil content increased from 4% to 20%. Mutation, recombination, and selection produced a new phenotype

What does the C. elegans mutation accumulation study address?

In studies of C. elegans, researchers created two lines: (1) a control (in which mutants and non-mutants could complete and “weed out” less fit alleles and (2) a mutation accumulation line raised in a very safe and benign environment (no competition, no ENS). They found that the line insulated from ENS accumulated so many mutations that their fitness declined over time, while the control population eliminated those with low fitness.

What does the fruit flies inversions study address?

There is evidence that frequency of inversions in Drosophila chromosomes varies with latitude and climate (= cline). A natural experiment assessed trends of N. American population, which is derived from the S. American population. The N. American population developed the same clines in inversion as those from old population, suggesting that selection acted on inversion rate across latitudes

What does the Cavener and Clegg (181) alcohol dehydrogenase in fruit flies study address?

Goal: to document change in allele frequencies in a lab-based NS experiment using fruit flies (diploid). Four populations: two on food spiked with ethanol, two on control food. Results: AdhF frequency didn’t change much in the control, but increased rapidly in the ethanol populations. Conclusion: allele frequencies change in response to natural selection in diploid populations

What does the Dawson (1970) selection on a recessive allele study address?

Studied a lab colony of flour beetles at the l locus. This locus has two alleles: + and l.

– Individuals with genotype +/+ or +/l genotypes survive. Individuals with the genotype l/ l do not survive. l is a recessive lethal allele.

– Dawson collected heterozygotes from his colony and established two experimental populations. p = q = 0.5 initially.

Prediction: the populations would evolve toward lower and lower frequencies of the l allele, and higher frequencies of the + allele. Dawson conducted calculations to predict how the allele frequencies would change. He found that the changes in allele frequency in the two beetle populations matched what he predicted!

Conclusion: dominance and allele frequency interact to determine the rate of evolution.

What does the Mukai and Burdick heterozygote advantage study address?

Mukai and Burdick set up a study in fruit flies that was similar to Dawson’s. There were two alleles: V (viable) and L (lethal). VV and VL genotypes remained alive, while LL genotypes were dead. They established two populations with p = q = 0.5. If our thinking from Dawson’s experiment holds true, we would predict the V allele will rise in frequency (rapidly, then slowly)— but this didn’t happen! The frequency of V did increase rapidly, but it slowed down long before we expected. The frequency seemed to reach an equilibrium (unchanging) state at a frequency of 0.79. What?! This means the L allele maintained an equilibrium frequency of 0.21. Why? Heterozygote advantage (aka overdominance) = heterozygotes have a higher fitness than either homozygote.

What does the Elderflower orchids frequency dependent selection study address?

Elderflower orchids come in two colors: yellow and purple. Yellow flowers are normally more common in natural populations. Bees (pollinators) visit the flowers but often do not receive any rewards. How can these two deceptive color morphs exist in the same flower orchid population? Frequency-dependent selection!

What does the Lenski et al E. coli mutation study address?

Lenski et al. raised a strain of E. coli in which only mutation was the source of genetic variation. Measured fitness by growth rate, which was related to cell size in most cases. Fitness and cell size increased in dramatic jumps in response to selection

Steplike pattern: A new mutation enabled bacteria to divide at a faster rate, Frequency of mutants quickly increased. Eventually, the mutation reached fixation

What does the Water snakes of Lake Erie study address?

There are mainland and island populations of water snakes. Individuals vary in appearance, ranging from strongly banded to unbanded. Migration of mainland snakes to island populations maintains the banded allele there, counteracting genetic drift/selection.

What does the Giles and Goudet (1997) red bladder campion study address?

They predicted young populations would vary in allele frequencies across loci, intermediate populations would be more homogenous due to migration, and old populations would again vary due to declining migration. For each group, they calculated FST. If allowed to proceed unopposed by any other mechanism of evolution, migration will eventually homogenize allele frequencies across populations

What does the Buri (1956) bw75/bw gene and loss of heterozygosity study address?

Tested the random fixation and loss of heterozygosity in fruit fly populations.

What does the Templeton and colleagues (1990) drift in natural population study address?

Tested predictions about random fixation of alleles in a population of collared lizards.