BIO120 - FINAL EXAM - LABS

True

T/F: Forces of stress in great lakes are of human origin

The closer organisms are, and the less barriers there are, the more likely they are to exchange individuals and alleles

How does geography relate to gene flow?

• Creates homogeneity

How does gene flow affect populations?

• Tissue sample is homogenized (ground) or blood is drawn from each individual

• Drop of sample from each individual placed in straight line near cellulose acetate gel

• Electrodes attached to filter paper soaked in buffer solution at each gel, and electric current is applied across the gel for 20-30 minutes

• Protein molecules in the sample move through cellulose acetate in response to electric field

• Gel is ‘stained’ with a solution containing enzyme substrate alongside a dye

• Dark bands are created, revealing enzyme position

• If enzyme in an individual has a different amino acid substitution (ex. a mutation), the enzyme will have a different charge, thus moving at a different rate than the rest

  • Called allozymes

• Alleles are distinguished by “fast” and “slow” (further from banding pattern vs. closer to banding pattern)

  • Can distinguish individuals as homozygous fast, homozygous slow, or heterozygous F/S

Explain Electrophoresis.

Cellulose acetate, Starch, Polyacrylamide, Agarose

What are the four types of electrophoresis?

An enzyme that produces one polypeptide chain

Define Monomeric

Two light bands, 1 F 1 S

How do heterozygotes appear in electrophoresis?

A structure formed when two monomers interact with one another

What is a dimer?

12-15 to get a good representation of the overall population

What is the minimum amount of enzyme loci we must screen?

False, arbitrary cutoff of f = 0.95 prevents it from being such

T/F: Polymorphism is a good descriptor of genetic variation

True

T/F: Heterozygosity is a good indicator of genetic variation

Taking the frequency of heterozygotes at each locus, averaging frequencies over all loci

How is heterozygosity of a population obtained?

Under certain conditions, allele frequencies do not change between generations:

• Population is large enough such that stochastic changes have no effect

• There is no gene flow

• No mutations occur, mutational equilibrium

• Reproduction is random, and independent of genotype

• Natural selction is not acting on a particular phenotype

Explain Hardy-Weinberg Equilibrium.

True, but only such that it does not exist (ex. we can observe that there is some evolutionary force at play)

T/F: Hardy-Weinberg equilibrium can be used to measure genetic variation

Using allozyme data

• Genetic identity/similarity (I) (proportion of identical genes)

• Genetic distance (D) (estimated number of gene differences occuring per locus over evolutionary time)

  • If gene substitutions per year is near-constant, genetic distance is linearly related to evolutionary time

How is interpopulation genetic variation measured?

D = -ln(I)

How is genetic distance related to genetic identity?

The study of diversity of organismsWhat

What is systematics?

Both arrange groups of organisms according to evolutionary relationships

What is the similarity between taxonomy and systematics?

• Willi Hennig in 1950s

• Method for reconstructing evolutionary relationships

What is phylogenetic systematics? Who created it?

• Evolution occurs

• There is a single phylogeny of life with a single common ancestor

• Characters are passed from generation to generation during evolutionary descent

What are the assumptions of phylogenetic systematics?

Observable trait of an organism (phenotype, usually)

• Morphological, molecular, developmental, physiological, behavioural, ecological

Define a ‘character’

true

T/F: Characters for analysis must be homogenous

Convergent evolution (different structures resemble each other as a result of selection, character reversal (species re-evolving an ancestral state)

What are the two major causes of homoplasy?

A character, either modified or unmodified, being passed from an ancestor to a descendant

• Modified = derived

• Unmodified = ancestral

Define ‘character state’

A character that is either present or absent (0, 1)

What is a binary character?

A character that has more than two different states (0, 1, 2)

What is a multistate character?

• Ordered: follow a logical evolutionary path (ex. growing beak size)

  • Unordered: No logical path (ex. color of fish)

What is the difference between ordered and unordered multistate?

• First, find the outgroup, and set all of the ancestral states to 0

• Set any trait in each other organism that differs from the outgroup to 1

• Group them based on changes into character trees

• Make sure to mark off, add the character transformation! Ex. wings: 0→1

  • Ancestral state of being absent to derived state of being present

How does the outgroup comparison method work?

The idea in phylogenetics that forces one to accept the shortest possible tree explaining all character states

Define Parsimony

Unresolved group of 3+ taxa

Explain ‘polytomy’

HIV-1 origins

What was the case study performed in class?

Humans came incontact with SIV when hunting primates, became infected with a mutated variant called HIV through zoonotic transmission

Explain the Hunter Hypothesis

• Similarities in genome organization

• Plausible routes of transmission

• Co-occurrence in geographic location

• Two viruses are closely related

  • Virus is prevalent in wild host

What evidence must there be to explain zoonotic transmission?

HIV-1 and SIV have identical genome organization

What was the evidence for similarities in genome organization for zoonotic transmission?

Historical evidence of humans hunting chimpanzees

What was the evidence for plausible routes of transmission for zoonotic transmission?

Humans live within the geographic distribution of P. Troglodytes

What was the evidence for occurrence in the same geographic region for zoonotic transmission?

HIV-1 groups M and N are closely related to SIV from captive P troglodytes - however, this was initially only confirmed in captivity

What was the evidence for virus relatedness for zoonotic transmission?

• Beatrice Hahn collected stool samples in Cameroon

  • Found that only stool samples of P. Troglodytes interacted with HIV antigens, isolated 16 strains of SIV

How did they determine the geographic region similarity in wild hosts?

Through phylogenetic observation, found that HIV-1 M and HIV-1 N are more related to SIV than each other

How did they determine virus similarity to original strain in wild hosts?

HIV Groups M and N arose from two separate zoonotic transmissions and are not directly related

What was the conclusion that arose from the results of phylogenetic analyses for SIV?

Group M

Which group of HIV-1 is responsible for most infections?

• Precision: Repeatability of the measurement (how close it is to other measurements)

• Accuracy: How close it is to the accepted true value

What is the difference between precision and accuracy?

sample size: n

population: N

How is sample size and population denoted?

Interpolation

What is using a line of best fit to predict data called?

Extrapolation

What is the process of extending the line beyond the data called?

bar graphs: Discrete quantitative variables

Histograms: Continuous quantitative variables

In what cases are histograms used instead of bar graphs?

Mean (average, x with overhead line), median (middle value, or average of two middle values), mode (most frequently appearing value) - measures of central tendancy

What are the three statistics of location? What is their usual name?

Variability

Range, variance, st. dev, standard errorW

What are the common statistics of dispersion? What are they also called?

difference between largest and smallest values in a sample

What is the range of a sample?

Measure of scatter around the mean, denoted as s²

measurements denoted as x

What is the variance of a sample?

The square root of variance (s) - average size of deviation from the mean

What is the standard deviation?

How reliable the sample mean is in reference to the population mean (denoted as SE)

What is standard error?

Compares two samples’ means - denoted as t

• State null hypothesis

• Calculate observed t-value

• Calculate degrees of freedom (denoted as df) → Corrected sample size of analysis

• Decide probability level of test (significance level) → usually 5%

• Find critical t value (corresponds to df of analysis)

• Outside of +- t critical is rejection region

What is the student’s t-test? How does it work?

Tests hypothesis in which experiment is frequency data instead of continuous data

What is the chi-squared test? how does it work?

• Samples are from population at random

• Each sample has restricted # of outcomes

• Probability of outcomes are independent of one another

What are the assumptions of x² test?

• Null hypothesis

• Check if assumptions of x² are met

• Define expected values for each category

• O is count observed for i categories

• E is count expected for i categories

• x² sum

• Find degrees of freedom (i - 1, where i = # of categories)

• Compare observed and critical values for null hypothesis assessment

What are the steps of the x² test?

• Sums of each category

• Horizontal categories will have equal amounts assuming independence

What is a contingency table? when is it used?

p² + 2pq + q²

Can make a 2×2 table out of it [p²][pq]/[pq][q²]

Can calculate genotype frequencies

p², 2pq, q² are genotype frequencies, p, q, are allele frequencies

hardy weinberg acts as null hypothesis

use chi squared test

What is the hardy-weinberg equation? How do we use it?