BIOL 114 Discussion Test
What is the basic formula for probability (p)
# of defined (or desired events)/# of total events A number between 0 and 1 0 indicates impossibility while 1 represents certainty
Mutually exclusive events
(Those that are dependent) Events that cannot happen at the same time. For example, an individual cannot get a head and a tail during a single coin flip The joint probability of mutually exclusive events occurring is their individual probabilities added together. Therefore, the probably of getting heads or tails, is equal to 1
Homoplasy
The similarity of traits in unrelated groups meaning it is not due to a common ancestor
Degrees of freedom for a chi squared test
1 (# of alleles - 1)
What assumptions did we make during the "Evolution by Natural Selection" lab?
1. Assume that our 4 types of prey are equally successful at competing for resources within their environment and that the level of predation they incur affects the survival of the prey' 2. All survivors are equally capable of reproducing and thus their frequency in succeeding generation is the same as their frequency among survivors 3. Assume that the predator frequencies in succeeding generations are direct reflections of the efficiencies of the predators in capturing prey (If a predator only captures 20% of all prey captured then that predator will represent only 20% of total predators in the next generation
In the "Genetics III: Population Genetics Hardy Weinberg Equilibrium" lab, what were the objectives?
1. Expand our use of probabilities to understand what happens at the population level 2. Test whether populations are in Hardy-Weinberg equilibrium 3. Test the effects of violating the assumptions of the Hardy-Weinberg model 4. Practice data analysis to determine if the Hardy-Weinberg hypothesis has been violated
How many generations did we look at during the "Evolution by Natural Selection" lab?
5 generations (all with 2-minute foraging periods) Graph the number of individual types of prey through successive generations (line graph) 1 paragraph conclusion about pattern of change and is this a valid simulation of process of natural selection?
In "Conservation of Small Populations", what were the objectives?
1. To learn about effective population size 2. To calculate inbreeding and variance effective population sizes 3. To use inbreeding and variance effective population sizes to form recommendations regarding species survival
In the "African Rhino Management" lab, what were the objectives?
1. To learn and use the 50/500 rule 2. To estimate inbreeding and variance effective population sizes for rhino populations 3. To create a management plan for a population of endangered rhinos
In the "Mendelian Inheritance Patterns in Maize Genetics" lab, what were the objectives?
1. To test Mendel's hypotheses using maize 2. To solidify data analysis using Chi- square
In the "Measuring Variation Within a Population" lab, what were the objectives?
1. To understand that almost all traits vary to some degree across a population 2. To practice measurement and data collection
In the "Genetics I: Mendel's Law and Probability" lab, what were the objectives?
1. To work with and understand the basic mathematics of probability 2. To work with and understand Mendel's Laws
Foraging period during "Evolution by Natural Selection" lab
2-minutes for each student to pick up as many beans as possible
What is evolution?
A change in gene frequency, in a population, over a number of generations
Extinction vortex
A downward population spiral in which inbreeding and genetic drift combine to cause a small population to shrink and, unless the spiral is reversed, become extinct.
What is frequency?
A measurement of what proportion or percentage of the total number of alleles at that one locus exists within the population Therefore, if one were to blindly select an allele from that locus from the population, the probability that any one allele will be selected is equal to its frequency in the population. For example, if p = 0.75, there is a 75% chance that that allele will be chosen when an allele is selected at random from the population
What did the test cross allow us to do in the "Mendelian Inheritance Patterns in Maize Genetics" lab?
Allowed us to determine the genotype of parental strains directly
Punnet Square
Allows one to determine the probabilities for each randomly generated genotype in the next generation by using the laws of probably we discussed above
What is the Lotka-Volterra model
As prey populations increase, so should predator populations. Due to increasing predator population size, fewer prey survive. As prey numbers decrease, predators have a difficult time finding prey, and they too begin to die off. Once predator numbers are low enough to allow it, prey numbers start to increase again
What did we do during the "Evolution by Natural Selection" lab?
BEANS and UTENSILS Evolution game to demonstrate principles of evolution Explored the process of natural selection through a simulation of predator-prey interactions These relationships inevitably lead to natural selection Prey that are unsuccessful at avoiding predators are killed and predators that have traits that make them less successful at capturing prey will also be less successful at passing their traits to offspring
Null hypothesis with probability
Basically, the null hypothesis is a statement of "no difference" or "randomness"
What two species of rhinos did we study?
Black rhinoceros (Diceros bicornis) - with 3 subspecies, hooked triangular upper lip that allows you to browse shrubs effectively The white rhinoceros (Ceratotherium simum) - square mouth which allows you to graze grasses and other low-growing herbs better Both hear and smell very well with poor eyesight
What did the F2 generation consist of in the "Mendelian Inheritance Patterns in Maize Genetics" lab?
Both purple and yellow kernels at a ratio of approximately 3:1 (monohybrid cross) or 9:3:3:1 for a dihybrid These will serve as the null hypothesis
How to calculate the following generation of prey in "Evolution by Natural Selection" lab?
Calculate the percent total survivors represented by each prey type and multiply by 400 These represent the amount available in the next generation Only place this amount in the dish
What populations did we study in the "Conservation of Small Populations"?
California Condor (Gymnogyps californianus)
Who made the modern taxonomic system?
Carolus Linnaeus It is a hierarchical system since organisms are grouped into ever more inclusive categories from species up to kingdom
3 sisters of Iroquois legend
Corn, beans, and squash
Calculations for "Conservation of Small Populations"
Data given for 5 years Calculate an arithmetic mean for the population Calculate an inbreeding effective population size for this population. What does this value mean? Calculate a variance effective population size for this population. What does this value mean? How do these numbers compare to the arithmetic mean?
Ways to represent probability
Decimals, fractions, percentages, and ratios
What did we do during the classification lab?
Develop a taxonomic classification and phylogenetic tree for a group of imaginary organisms called Caminalcules after the taxonomist Joseph Camin who devised them 14 "living" and 58 "fossil" species The purpose of this lab is to illustrate the principles of classification and some of the processes of evolution (e.g. convergent evolution). Created a phylogenetic tree and a table for kingdom, phylum, class, order, family, genus, species (King Phillip Came Over For Good Spaghetti)
What is variation?
Differences that exist between individual organisms in their structures, functions, and behaviors
What shows variation?
Different phenotypes and genotypes which are selected for or against over the course of generations
What did we do in the "Mendelian Inheritance Patterns in Maize Genetics" lab?
Examine the Mendelian inheritance of traits in Zea mays (maize or corn) Each kernel is a seed representing an offspring of the parent corn plant. Thus, a corn cob represents a sizeable sample of offspring derived from specific crosses
Calculations for H-W using p^2 +2pq +q^2 = 1.0
First find amount of A alleles and a alleles Divide these amounts by the total to find allele frequency (should add up to 1) which will give you p and q respectively Can plug this into H-W equation to see if it is in H-W equation
Calculations during the "Evolution by Natural Selection" lab
For your group only: Prey Record number of prey captured and the number of survivors of each prey type Total the amount of survivors Calculate the percent of the survivors For the whole class: Predator Record number of prey each utensil captured Total prey captured Percent of prey captured by each species of predator
Hardy-Weinberg as a null hypothesis
Hardy weinberg is the null hypothesis Ex. Chi squared = 3.3 and is less than the 3.84 which isrequired to reject our null hypothesis (the H-W model). Therefore, we should conclude that our observed data are only different from the expected numbers by chance alone. As a result, we can conclude that the population is in HardyWeinberg equilibrium
Darwin
On the Origin of Species, 1859 Convincing evidence that life had evolved through the process of natural selection Indicates that all organisms descended from a common ancestor As a consequence of Darwin's work it is now recognized that taxonomic classifications are actually reflections of evolutionary history
Sampling
If an entire population is available for measurement, then very accurate data may be obtained (e.g., mean, variance, etc). However, scientists rarely have access to entire groups of organisms, nor, most times, is it even practical to try to gather data on an entire population. Therefore, data are collected on a smaller sample of the larger population.
Chi squared rulings
If your chi-square calculated value is greater than the chi-square critical value, then you reject your null hypothesis. (not just due to chance) If your chi-square calculated value is less than the chi-square critical value, then you "fail to reject" your null hypothesis
Hardy-Weinverg principle
In the absence of evolution, the allele frequencies of a population will stay constant from generation to generation The state of unvarying genetic and allele frequencies within a population is referred to as Hardy-Weinberg equilibrium
Nei
Inbreeding effective size Size of the population that would experience the same impacts of inbreeding as the actual population t/(1/N(0)+... 1/N(t-1)) Include founders
Effects of inbreeding
Increases homozygosity Decreased offspring success then leads to population decline Described with delta F The negative effects of inbreeding in such a small population will cause the population to enter an extinction vortex, because any individuals that encounter issues from homozygosity of alleles represent a much larger portion of their population than those same individuals would in a larger population
Fundamental insight of Mendelian genetics
Inheritance is particulate Genetically determined traits are inherited as indivisible units that are not diluted from one generation to the next Mendel's Laws clearly spelled out the fact that inheritance of many traits involves all-or-none transmission governed by the laws of probability
Predators in the "Evolution by Natural Selection" lab
Knife, fork, spoon Variations of the species Knifis forkspoonus
Mendel's Second Law
Law of Independent Assortment states that alleles of one gene are passed to the next generation independently of alleles of another gene, and that the process obeys the rules of random probability. A mathematical graph called a Punnet Square allows one to determine the probabilities for each randomly generated genotype in the next generation
Mendel's First Law
Law of Segregation states that in diploid organisms two alternate alleles segregate from each other in the germ-plasm and are passed separately without dilution in gametes to the next generation Alleles separate and go independently into separate gametes
Types of beans in the "Evolution by Natural Selection" lab
Lima beans, kidney beans, navy beans, and lentils Beanus beanii Started with 100 of each
Maximum capacity of predator and prey in the "Evolution by Natural Selection" lab?
Maximum capacity of each foraging environment is 400 indiv. beans in any combination Max number of predators in each foraging environment is 4 students
Definition of mathematical probability?
Measure of the frequency of occurrence, or likeliness of a given or desired event When the measure is used to describe events that have already occurred or pertain to a population, the term "frequency" is commonly used
Calculations for H-W chi squared
Multiply p^2 and q^2 x(total number of individuals) to get expected number of genotypes
How to calculate the following generation of predator in "Evolution by Natural Selection" lab?
Multiply the % total prey captured of each utensil by the total number of predators in the class
Processes of evolution?
Natural selection - requiring differential survival and differential reproduction due to some heritable variation (**Principal mechanism by which evolution occurs**) Genetic mutations Recombination Genetic drift
Mechanisms that bring about change
Natural selection, mutation, genetic drift, and gene flow Hardy-Weinberg principle is used to explain how these four mechanisms affect population genetics
What did the F1 generation consist of in the "Mendelian Inheritance Patterns in Maize Genetics" lab?
PP x pp (homozygous) All purple
Ways of showing evolutionary relationships
Phylogenetic tree Physical attributes: Generally, the greater the resemblance between two species, the more recently they diverged from a common ancestor
Sample classification of Caminalcula
Phylum, Class, Order, Family, Genus, Species
Degrees of freedom with probability
Possible outcomes - 1
Dominant allele of corn
Purple color, PP Pp will also express this color
Carrying capacity of rabbits and coyotes
Rabbits: 100 Coyotes: 75
Conditions of H-W equilibrium
Random mating, large breeding population, no mutations, no migration, no natural selection
What does a sufficient sample size depend on?
Sampling technique, knowing enough about your organism of choice to account for known variation, time, space, and resource availability
Homology
Similar appearance due to a recent common ancestor
What did we do during the "Coyotes and Rabbits: A Predator-Prey Simulation" lab?
Simulated the Lotka Volterra model The aim of this exercise is to give you first-hand experience of how this pattern works. During this exercise, you will play the parts of predator and prey, and keep track of their population sizes across 20 generations. Work in pairs for this exercise, maintaining this partnership from this week to next week.
What are the two categories of genetic diversity that are both important for the conversation of ecosystems?
Species richness Genetic diversity within a species (greater allele diversity within a population) Both making a population more resistant to environmental pressures
Steps for the simulation of the "Coyotes and Rabbits: A Predator-Prey Simulation" lab?
Start with 5 coyotes and 5 rabbits Basically played battleship To find the pop. rabbits for the next population: Take the total rabbits from the previous generation and subtract the number of overlaps (rabbits eaten). Now multiply this number by 3 To find the pop. coyotes for the next population: Take the amount of rabbits eaten subtract 1/3 of that number and then add the amount to that sum
Alternative hypothesis with probability
The alternative hypothesis is generally the opposite of the null (i.e., there is a difference). Sometimes the alternative hypothesis can be more specific (depending on the test you are performing), but it does not need to be
What did we do during the "Measuring Variation Within a Population" lab?
The concept of variation will be illustrated in this lab by measuring traits of you and your classmates and by examining the differences that exist within your class. You will assess the variation of traits within your classmates, and discuss how this sample might reflect the trait within the larger population of B.U. students. Further, you will discuss how these and other variations can act to fuel evolutionary processes. We collected the heights of the different classmates
Effective population size
The effective population size is considered to be "ideal" in that it obeys all the typical assumptions, and, therefore, obeys the rules of, HardWeinberg equilibrium An effective population size is the size of a population that would experience inbreeding or mutation rates to the same degree as the population we are studying
What is taxonomy?
The field devoted to the classification of organisms
Gambler's Fallacy
The mistaken belief that if something happens more frequently than what is considered normal, then it will happen less frequently than normal in the future, even if the observer knows that the independent probability of that event occurring is already established.
50/500 rule
The model provides guidelines regarding minimum population sizes that will allow for population stability The model states that a population with an inbreeding effective population size (Nei) of 50, or less, is at immediate risk of extinction The model also says that populations with a variance effective size (Nev) of 500 or less are at long-term risk of extinction
Effects of genetic drift
The smaller the population gets, the less likely the effects of non-random mating will be balanced throughout the population, and allele frequency changes may be more severe. The accidental loss of alleles due to genetic drift makes the population less able to deal with environmental changes (because of a lack of genetic variation) and risks extinction if no members have the genotype required for survival
Inbreeding coefficient (F)
The value of ΔF is a reflection of how at risk an isolated population is ΔF > 0.6 indicating that the population may be at risk of going extinct in t number of generations A ΔF below 0.6 would suggest that the population is not at particular risk of going extinct in t generations in the future, unless something else unaccounted for happens to the population
Characteristics of a phylogenetic tree
The vertical axis in this figure represents time. The point at which two lines separate indicates when a particular lineage split. The most recent common ancestor shared by mammals and reptiles is indicated by the point labeled A.
Differential reproduction/survival
Those organisms best adapted to a given environment will be most likely to survive to reproductive age and have offspring of their own.
Independent events
Those that are not affected by previous events, nor do the events affect each other. For example, if you were to flip two successive coins, the results from one toss should not affect the results of the other toss The probability of two independent events occurring at the same time is their two independent probabilities multiplied together
What did we do during the "African Rhino Management" lab?
Took population data every 7 generations and estimated their populations Calculated Nei and Nev Describe long term plan for each population
What sample distribution was used as an example in the "Measuring Variation Within a Population" lab?
Tree trunk diameters (in cm) and number of trees of each diameter for all 820 red for all 820 maples in a local forest Mean diameter = 11.0 cm vs. 2 different teams collected data on two different amount of trees Team one had a mean trunk of 8.1 cm and team 2 had a mean trunk of 12.0. Because team 2 had a higher sample size, their results were closer to the true mean
What did we do during the "Genetics III: Population Genetics Hardy Weinberg Equilibrium" lab?
Used different colored cubes (100 indiv.) and picked them with our eyes closed Picked them in pairs (simulation of mating) Blue- homozygous dominant Yellow- homozygous recessive Green- heterozygous Population started at H-W equilibrium (25 blue, 25 yellow, 50 green) Used a punnet square to determine their offspring genotypes Calculated alleles and frequencies, genotype frequencies (squared frequencies), and expected genotype numbers Violated some of the assumptions to determine if this had an effect on H-W
Nev
Variance effective size Size of the population that would experience the same impacts of genetic drift as the actual population t/(1/N(1)+... 1/N(t))
What is the basis of evolution?
Variation
Recessive allele of corn
White or yellow pp
Population trends of black and white rhinos
White rhinos much less endangered than black rhinos White rhinos- 20,000 Black rhinos - 4,800 Data from 2011
Allelic frequency calculations
p+q=1 p = the frequency of an allele in the population q = the frequency of the second allele at the same locus
Equation for all possible genotypes (according to H-W)
p^2 +2pq +q^2 = 1.0
Convergent evolution
resemble each other because they independently evolved similar structures in response to similar environments or ways of life, not because they share a recent common ancestor Distantly related species seem to converge in appearance (become more similar). Examples of convergent evolution include the wings of bats, birds and insects, or the streamlined shape of whales and fish.
