Evolutionary Biology Exam 2

A population of a finite size N (diploid or haploid depending on formulation) in which each generation is formed by random sampling of gametes or chromosomes from the previous generation

What does the Wright-Fisher model describe?

Random fluctuations in allele frequencies when we sample to form finite populations

What is genetic drift?

Fixation

Regardless of population size, drift eventually leads to the _____ of one of the alleles in the two-allele system

It describes a theoretical state where genetic variation remains stable if individuals pair by chance, there are no mutations, no migrations, and no natural selections, basically the absence of evolutionary forces.

What does the H-W model describe?

The proportion of individuals in a population that are heterozygous at a given locus

Describe observed heterozygosity (Hₒ)

Also called gene diversity, it is the probability that two randomly chosen alleles from the population are different

Describe expected heterozygosity (Hₑ)

It measures the number of individuals effectively passing genetic material to the next generation, often used as a better predictor for genetic drift and long-term evolutionary potential, and especially inbreeding

What does effective population size describe?

Drift

_____ leads to an increase in variation among populations of a species

A sharp reduction in population size, normally caused by natural disasters or disease, that causes a permanent loss of genetic diversity because the surviving individuals carry only a random subset of the original gene pool

What does a genetic bottleneck describe?

On smaller islands or isolated regions, relatively small numbers of individuals may have different allele frequencies than the population as a whole. Because of this, drift will be stronger in the new population at the beginning.

What does the founder effect describe?

Much higher levels of genetic variation that are prominent in DNA/amino acid sequences but are not observable under normal conditions

What does cryptic molecular variation describe?

New mutations in non-functional or synonymous DNA regions, mutations in functional regions with no fitness effect, and genetic changes via recombination or gene conversion

What are the three main ways by which selectively neutral alleles arise?

A point mutation where one nucleotide is replaced by another, but the resulting codon still specifies the same amino acid

What is a synonymous substitution?

A point mutation that alters the amino acid sequence of a protein by changing the codon to one that specifies a different amino acid

What is a nonsynonymous substitution?

Strong

Genetic drift has a ____ relationship with selectively neutral alleles.

The number of nonsynonymous substitutions at nonsynonymous sites

What does Ka measure in the Ka/Ks ratio?

The number of synonymous substitutions at synonymous sites

What does Ks measure in the Ka/Ks ratio?

When comparing similar genes between species or between populations of a single species, synonymous substitutions tend to occur more frequently than nonsynonymous substitutions in many genes

What does the Ka/Ks ratio show?

Selection for nonsynonymous changes that act to maintain the less important alleles

What is positive selection?

Occurs when selection acts to maintain the allele that’s currently most common in the population

What is purifying selection?

When nonsynonymous substitutions equal the rate of synonymous substitutions, meaning mutations are neither clearly beneficial nor harmful

What is neutral selection?

The number of new alleles that become fixed in a population per unit time. They are not affected by natural selection, but their fate is determined solely by genetic drift

What is the substitution rate of neutral alleles?

If selectively neutral mutations arise at a similar rate across species with a similar fixation rate, then the number/proportion of differences in nucleotides between species can be used as an indirect measure of the time since the species had a common ancestor

What does the molecular clock describe?

As time goes on, the number of sites that can have substitutions can plateau, so that any new substitutions may not be detectable

Explain the issue of saturation in the molecular clock

A theory that takes selection, mutation, and drift and predicts that population size has a stronger influence on outcomes, unlike neutral theory, where population size is much less important

What does the nearly neutral model of molecular evolution describe?

If the only selective force is operating, it will eventually lead to fixation of one allele at a locus, which leads to a loss of heterozygosity

How do mutations interact with drift in a nearly neutral model?

Drift

If population size is small and/or the selection coefficient is small, then ______ primarily determines changes in allele frequency

Natural selection

If population size is large and/or the selection coefficient is large, then ______ primarily determines changes in allele frequency

The gene copies present in the current population and work their way backwards in time showing gene copies in previous generations

What do gene trees show?

By going back in time, we can find that two gene copies eventually originate from a single gene copy

What does coalescence describe?

When many traits are affected by the actions of multiple genes

What is a polygenic trait?

Interactions between two or more genes that are nonadditive, which may show the action of one gene masking or provoking the action of one or more other genes

What is epistasis in the term of polygenic traits?

Refers to hidden genetic or phenotypic differences that remain unexpressed under normal conditions but can be altered when there is a change in environment or genetics

What does latent variation describe?

A set of alleles, one from each gene that affects our trait of interest, like ABCD, AbcD, aBcd, abCD, etc

What does a haplotype describe?

False

True or False: Haplotype frequencies can be predicted by allele frequencies

When there exists some type of association (non-independence) between the gene copies (alleles) found on two loci

What does linkage disequilibrium describe?

When like alleles tend to be found closer together more often than expected

What does the type of linkage disequilibrium coupling describe?

When two different alleles tend to be found closer more often than expected

What does the type of linkage disequilibrium repulsion describe?

Mutation, natural selection, migration, genetic drift, and nonrandom mating

What causes linkage disequilibrium?

The absence of any major evolutionary forces causes a decline

How does linkage disequilibrium change over time?

If an allele goes to fixation due to natural selection, it can carry along with its nearby genes/loci

What does a selective sweep describe?

A new beneficial mutation arises and nearby loci are fixed along with it

What does a hard selective sweep describe?

A formerly neutral allele becomes beneficial, and nearby loci are fixed along with it

What does a soft selective sweep describe?

It is directional instead of random and generally independent of population size

What is the makes genetic draft different from genetic drift?

Strongly selected alleles should show longer stretches near them of similar haplotypes, while the unselected alleles should have shorter stretches

How can hitchhiking be used to determine if an allele is under positive selection?

Clonal interference

When multiple beneficial mutations appear, it is called ______

Parent-offspring regression and selection experiments, which can be measured by the breeder’s equation

What are the two ways you can estimate narrow-sense heritability?

Genotype space should map to phenotype space, with influences of the environment, like climate change or new predators/competitors, that can shift some or all of the landscape

What is an adaptive landscape?

Domain, kingdom, phylum, class, order, family, genus, and species

What is the order of the Linnaean classification scheme?

A diagram that shows evolutionary relationships among groups of organisms, which are based on characters of organisms, such as morphological, genetic, behavioral, ecological, or physiological

What does a phylogeny describe?

Contains an ancestral node and all descendant taxa

What is a monophyletic clade?

Includes taxa that do not share a common ancestor

What is a polyphyletic clade?

Some, not all, descendants of a common ancestor

What is a paraphyletic clade?

Character states found in an ancestral node

When building trees, what do plesiomorphies describe?

Derived trats that have evolved from ancestral traits

When building trees, what do apomorphies describe?

A derived trait that is shared between two or more taxa and is the result of common ancestry

When building trees, what is a synapomorphy?

Two descendant species share a trait, but it has evolved separately in each species

When building trees, what is a homoplasy?

An ancestral trait shared by two or more descendant species

When bulding trees, what is a symplesiomorphy?

A trait that has arisen in only one species of descendants from a common ancestor

When building trees, what is an autapomorphy?

Bottleneck

____ event, a large population is reduced to a very small size in a short period of time

Narrow-sense heritability

The breeder’s equation is used to calculate ________

More rapidly in a small population than in a large population

Fixation of an allele via genetic drift will occur _______