BIOLOGY 201- Exam 2 With complete verified solutions + Rationales

Assortative Mating

when individuals tend to mate with the same genotype or phenotype. ex: inbreeding

Disassortative Mating

when individuals tend to mate with individuals with different genotypes or phenotypes

Inbreeding

when individuals mate with genetic relatives, a type of assortative mating.

Inbreeding Depression

when the offspring of genetic relatives have reduced fitness

What is the distinction between A1 alleles that are identical by descent versus those that are identical by genetic sequence?

Identify by descent entails that two individuals both have the same alleles because of a common ancestor. Identical by genetic sequence means that they just so happened to have the same alleles, but they have no common ancestor.

Give an example of an extreme form of inbreeding

selfing: when an individual fertilizes its own gametes. Flowers and plants do this.

What happens to the frequency of homozygotes and heterozygotes in selfing?

Homozygotes will tend to increase because they only produce homozygotes and heterozygotes form a 1:2:1 ratio which adds to the homozygote population.

How are allele frequencies affected by a population that self-fertilizes?

They aren't affected

What is inbreeding depression?

when the offspring of genetic relatives have reduced fitness.

Gene Flow

the transfer of genes from one population to another.

How does migration affect allele frequencies in populations?

introduces new variations of genes, which cange

Genetic Drift

the process of random fluctuation in allele frequencies due to sampling effects in finite populations.

Sampling Effect

the diversity of a population are due to the greater chance of one or few dominant, high bio=mass species being present within a population.

Selectively Neutral

when alleles have no fitness difference between them

Heterozygosity

the reaction of individuals in the population that are heterozygous at the given locus.

Census Population size

the number of individuals that you can count in a population

Effective Population size

a smaller portion of a population that shows the same dispersion of allele frequencies of the larger population.

Divergence

differences in allele frequencies and ultimately the fixation of different alleles.

Bottleneck

when a small population separates from a larger population and the allele frequencies change dramatically due to random selection of alleles.

Founder Effect

the change in allele frequencies that result from the sampling effects that occur when a small number of individuals from a large population initially colonize a new area and found a new population.

What does the graph of genetic drift look like with population on the y-axis and the frequency of the A alleles on the x-axis.

both are distributed where there is fixation either at 0 or 1.

Heterozygosity Calculation

You take the frequency of Heterozygotes in the population and add them to the others and divide them by the total.

Heterozygosity After Generations Calculation

Ht = (1-(2N))^tHo

Ht-heterozygosity after t generations

N=consensus population size

Ho=original population size (typically won't solve for this)

When causes genetic variation to be lost in a population

Reproductive issues and when the sex ratio of breeding individuals is not 50:50.

Effective Population Size (Ne)

Ne = (4(males)(females))/(males + females)

Then you can plug this number into the Heterozygosity calculation.

Deleterious recessive alleles are usually at low frequency, so in a randomly mating population most are found in ____________ but, inbreeding increases the proportion of homozygous recessive individuals, so ___________________.

heterozygotes; the expression of the recessive form increases

How is no inbreeding depression observed in self-fertilization?

Deleterious recessives have been eliminated via selection in the past

How would inbreeding alter the speed with which selection acts to reduce the frequency of deleterious recessive alleles?

the curve of the inbreeding would decrease more sharply that the random mating curve--because it increases the homozygous recessive individuals.

How is the contribution of genetic drift to the reproductive defects observed in Florida Panthers?

there is fixation of the alleles that is for bad breeding.

Migration Calculation. @equilibrium?

∆Pi = P'i-Pi

∆PI = m(Pc-Pi)

F(A) = (Ni(PI) + Nc(Pc))/Total

Pc - frequency of the A allele on the continent

Pi - frequency of the A allele on the island

P'i - frequency of the A allele on the island after 1 generation

m - proportion of island population that are migrants

∆Pi = 0

Pc-Pi = 0

Pi = Pc

Advantages vs. Disadvantages of introducing Texas Cougars to Population Florida Panther Population

Advantages: increases genetic variation, add backs normal alleles at loci where recessive disease alleles are fixed or at a high frequency

Disadvantages: alleles might not be of use from the cougar population in the Florida Panther population

Overall: it's good.

What is the law of large numbers and why does it matter for the H-W model and assumptions about population size?

states that the size of a random sample increases, the realized frequencies—those frequencies that we actually observe—usually will be very close to the expected frequencies.

What effect does genetic drift have on allele frequencies?

1. In a finite population, allele frequencies fluctuate over time, even in the absence of natural selection.

2. Some alleles are fixed, others are lost, and the fraction of heterozygotes in the population decreases over time.

3. Separate populations diverge in their allele frequencies and in terms of which alleles are present.

Explain how genetic drift affected New Zealand snapper. What is an effective population size and what was it for the snapper?

the large commercial fishing of the New Zealand snapper caused a decrease in heterozygosity among the population. The effective population represented the same allele dispersion as the census population (3 million fish), and it was 200 fish.

What causes the effective population size to be smaller than the census (actual) population size?

when populations reach small numbers.

Explain what circumstances led to reduced heterozygosity in northern elephant seals.

the bottleneck in the population. Other options were skewed distribution of reproductive success.

What evidence was used to determine that a bottleneck effect caused the reduced genetic variation?

Why was it important to use museum examples to make a final determination? If the museum samples had not existed, could we have reached the same conclusion? Why or why not?

-They took mitochondrial DNA from bone and dried skin of animal samples taken before the bottleneck.

-They had to look at the genetic details of the species before the bottleneck.

-No because they couldn't have observed any genetic differences.

Does natural selection tend to increase or decrease standing variation in a population?

natural selection could increase because their is more genetic variation for the selective force to choose from.

Does mutation tend to increase or decrease standing variation in a population?

it increases standing variation in a population. "Provides a continual supply of new genetic variation."

Does migration tend to increase or decrease standing genetic variation in a population?

increases

Does inbreeding tend to increase or decrease standing genetic variation in a population?

decreases

Does genetic drift tend to increase or decrease standing genetic variation in a population?

decreases

selective neutrality

allelic differences in organisms that have no fitness consequences. Ka/Ks = 1

synonymous substitution

substitutions of the genes of an organism that do not alter the amino acid sequence of an organism.

nonsynonymous substitutions

substitutions of the genes or an organism that do alter the amino acid sequence.

purifying selection

a type of selection that maintains the currency common allele despite occasional deleterious mutations. There are more synonymous mutations than nonsynonymous mutations. Ka/Ks < 1

positive selection

a type of selection where the nonsynonymous mutations occur more than the synonymous mutations. Ka/Ks >1

Ka/Ks Ratio

occurrence of nonsynonymous mutations (Ka) over synonymous mutations (Ks)

Polymorphism

the occurrence of several different members of a population in a Ka and Ks sense.

Divergence

fixation to just two types of genotypes.

Molecular Clock

selectively neutral mutations arise at similar rates in different taxa and they should also be fixed at similar rates because substitution rates at neutral loci do not depend on population size or other demographic parameters.

why was the discovery that molecular variation such a conundrum for scientist?

because it went against the notion that natural selection was the only force in play with the genetic variation.

What are the two major tenets of the Neutral Theory of Molecular Evolution? How do these two tenets differ?

--Most of the variation present within a population is selectively neutral

--Most of the changes in DNA or amino acid sequence over time—and thus many of the molecular differences between related species—are selectively neutral.

--Different in that the first applies to a population and the second applies to a single organisms DNA.

What is the difference between a mutation and a substitution?

a substitution occurs due to a mutation and it is subsequently fixed into a population and is neutral, but there are several types of mutations that don't necessarily imply a substitution.

What is the difference between a polymorphism and a substitution?

A mutation is defined as any change in a DNA sequence away from normal. This implies there is a normal allele that is prevalent in the population and that the mutation changes this to a rare and abnormal variant. In contrast, a polymorphism is a DNA sequence variation that is common in the population.

How could most polymorphism and substitution be neutral if most mutations are deleterious?

because polymorphisms and substitutions are fixed or common in a population and a deleterious mutation become eradicated due to natural selection.

What is the distinction between synonymous and nonsynonymous substitution? If substitutions are neutral, why is the rate of the former usually higher than the rate of the latter?

-synonymous mutations do not change the amino acid sequence because it is on the third nucleotide

-nonsynonymous mutations do change the amino acid sequence.

How can the Neutral Theory useful as a null model even when it is not strictly true?

"The natural theory makes predictions about the amount of variation expected in a population, the reactive rates of synonymous an nonsynonymous substitution and other population genetic quantities... we can investigate whether these quantities are consistent with what we would expect under a neutral model. If they are not, we might expect that some other process, possibly natural selection, is operating."

How does the saturation of substitutions complicate applying the molecular clock?

because further substitutions can't be detected by comparison with an ancestral sequence. This is because a substitution may occur two or more times at a sight and you can't really go back from there to see what the original nucleotide was if you don't know how many times it was substituted.

Why would you choose different molecules or sites if you wanted to use the molecular clock to date short-term versus long-term events?

because looking at the differences in certain sites of sequence that have changed can give insights on both short-term and long-term events and how much they have changed.

polymorphism

difference between individuals in populations

what is a polymorphic site

any codon position where there is a difference in genetic sequence

Graph of frequency vs. time for deleterious, neutral and beneficial mutations

- deleterious: once they are introduced, they fall right back down.

- neutral: Could affect polymorphism but probably won't.

- beneficial: smooth line where a lot of polymorphism could occur.

what is substitution in terms of a phylogenetic tree?

- a mutation that went to fixation in a population

What is divergence in terms of a phylogenetic tree

- differences between populations, which happens fast because of coevolutionary reactions.

how do you calculate dS and dN when observing a Codon Chart and what do they mean?

dS = # synonymous substitutions/#synonymous sites

dN = # non-synonymous substitutions of/#non-synonymous sites

- whatever number is higher is what is more likely to fix than the other.

what is the difference between divergence and polymorphism?

?

What are the expected contributions of deleterious, neutral, and beneficial mutations to polymorphism and divergence?

most are neutral

Using the neutral expectation as our null model, what can we infer about the nature of selection acting on no-synonymous sites when:

dN < dS = Neutral synonymous substitution is more likely to fix

dN = dS = non-synonymous mutations are neutral and evolve by genetic drift

dN > dS non-synonymous mutations are often more likely to fix because they are sometimes beneficial because selection acts to fix mutations, "positive selection"

Phenetic species concept

drawing species boundaries around clusters of phenotypically similar individuals or populations.

Biological species concept

groups of actually or potentially interbreeding populations which are reproductively isolated from other such groups.

phylogenetic species concept

the smaller monophyletic group distinguished by a shared derived character.

allopatric speciation

the process of speciation takes place in populations that are geographically isolated from one another.

parapatric speciation

two adjacent populations diverge into separate species in the absence of a geographic barrier to dispersal.

sympatric speciation

occurs when no geographic boundary separates diverging populations.

vicariance

an initially large population is subdivided into new populations that are themselves still relatively large.

divergence

created when mutation, genetic drift and/or selection causes species to change.

cline

a spatial gradient in the frequency of phenotypes or genotypes. In Parapatric speciation.

hybrid zone

where there is gene flow between diverging populations exists somewhere along a cline.

ring species

individual live in one of a series of populations that are connected to one another in a ringlike fashion; however as time proceeds and the species meet at the other end of the barrier to complete the ring, there is no longer any gene flow between the species.

resource competition

when species have to compete for resources and are possible separated through sympatric speciation due to a specific difference or quality.

reproductive isolation

refers to the situation where different species may live in the same area, but properties of individuals prevent them from interbreeding.

prezygotic mechanisms

- potential mates live in the same place but do no encounter one another, due to either: habitat isolation and/or temporal isolation (by time of day or time of year).

- Potential mates interact but do not mate (behavioral isolation).

- Individuals couplet, but male gametes (sperm or pollen) are not transferred.

- Male gametes are transferred, but the egg is not fertilized (gametic incompatibility).

postzygotic isolating mechanisms

- Zygote dies early in embryogenesis

- F1 hybrids are inviable

- F1 hybrids survive but are sterile

- Backcross or F2 hybrids are inviable or sterile.

What are the advantages and disadvantages of the phenetic species concept?

Advantages

1. Used for statistical analysis for large groups of species and data

Disadvantages

1. Don't know which trait is more important.

2. Makes too many species.

3. Hard to distinguish polymorphism from divergence.

What are the advantages and disadvantages of the biological species concept?

Advantages

1. separates by populations and connects individuals who are able to mate.

Disadvantages

1. To few species

2. Some distinct species can make hybrids

3. doesn't work on asexual or fossil species

4. Hard to test

What are the advantages and disadvantages of the phylogenetic species concept?

Advantages

1. you don't need information about the gene flow.

Disadvantages

1. can't explain groups that have similar characteristics from other species.

2. smaller groups

3. hard to decide which are groups

4. divergence in sequence data may evolve slower than reproductive isolation.

What are the mechanisms of isolation in Allopatry? (Three Spine Sticklebacks)

physical or geographic barriers

What are the mechanisms of divergence in Allopatry? Why? (Three Spine Sticklebacks)

- genetic drift and natural selection

- because fish will adapt to different environments in their different geographically separated areas.

Mechanisms of Isolation in Secondary Contact. Prezygotic or Postzygotic? (Three Spine Sticklebacks)

1. Hybrids may not be viable (postzygotic)

2. adaptations to different environments may prevent matings (prezygotic)

3. inhabit different region of lake (prezygotic)

Mechanisms of divergence for secondary contact? (Three Spine Sticklebacks)

Selection

- competition impose selection for divergent resources or habitat use.

- if hybrids have low fitness, selection will act to reduce production of hybrids.

a. selection would favor mating preference.

Mechanisms of Isolation in Sympatry. (Prezygotic or Postzygotic) (Soapberry Bugs)

- behavioral/dietary isolated (Prezygotic)

- assortative mating (Prezygotic)

- hybrids may have a (Postzygotic)

Mechanisms of divergence in sympatry (Soapberry Bugs)

- selection on back length to match fruit radius.

- competition for resources favors use of introduced small plant leaf where there are no competitors.

What does the fossil record tell us about the rate at which new species were formed across the history of life on earth?

took a long time to form unicellular organisms (genetic makeup of life), but once that happened, there was an (Cambrian) explosion of life.W

What does the Tree of Life, based on 16S rRNA sequences, tell us about the rate at which new species were formed?

quickly with lots of speciation

Difference between punctuated equilibrium trees and phyletic gradualism trees.

- Punctuated Equilibrium: morphological evolution occurs simultaneously with speciation

- Phyletic Gradualism: morphological evolution happens all the time. Not particularly associated with speciation.

What happens when two populations have been diverging from one another in allopatry but are then reunited before reproductive isolation is complete?

Secondary Reinforcement - What happens is that the reproductive isolating mechanisms are sufficiently weak as to allow free interbreeding across the reunited populations, and such matings produce offspring that are not at some fitness disadvantage compared to offspring derived from matings between individuals from within either population, then the process of speciation halts and a single species remains.

Hominin

humans and the extinct species more closely related to humans than to chimpanzees

Hominoid

members of a superfamily know as the hominoid which consist of:

- orangutans (Pongo)

- gorillas (Gorilla)

- chimpanzees (Pan)

- Humans (Homo)

- 4 gibbon generas

Denisovan

the name of a species whose genetic sequence is more closely related to the Neanderthals (Homo neanderthalensis) who are more closely related to modern day humans.