Labs Flashcards
Great Lakes fishery populations
- overexploitation and invasion by exotic species has placed severe stress on native fish species
- many commercially valuable species have been eliminated/reduced
what evolutionary forces have had a significant impact on the genetic variation of Great Lakes fishery populations?
- selection forces of humans reduce genetic diversity (eg size-selective fishing gear, habitat elimination, alteration of prey species, pollution stresses)
- gene flow; the greater the rate of gene flow, the more homogeneous two populations become. any activity which changes the population densities affects the distance between populations
- genetic drift
what did managers have to do to combat the Great Lakes problem?
- stock the lakes with fish that would eventually begin to reproduce and replenish species
- cultivated in hatcheries
issues with cultivating fish in hatcheries then releasing them into the wild
- genetic diversity is low
- locally adapted populations may be replaced with genetically homogeneous populations which limits adaptive potential
- may increase competition or introduce diseases
why are traditional Mendelian methods of making crosses/scoring phenotypes insufficient for a detailed estimate of genetic variation within a population?
- restricted primarily to phenotypic characters
- too time consuming to wait for future generations
- does not always yield precise information on genotype (homozygous dominant vs heterozygote)
- too many gene loci in most organisms for this process to yield reliable estimates of genetic variation
protein electrophoresis
- tissue sample homogenised to release enzymes
- drop of each sample placed in a straight row near the edge of a rectangular sheet of cellulose acetate gel
- electrodes attached to filter paper wicks soaked in buffer solution at the end of each gel
- electrical current applied across the gel for 20/30 mins
- gel stained for a particular enzyme by pouring over it a solution containing a substrate along with a dye that precipitates where the reaction occurs
- dark bands appear
why do different allonyms move through the gel at different rates?
enzymes of the same size and shape move at a rate determined largely by the ratio of positively charged to negatively charged amino acids
allozymes
differ in their amino acid sequence and are the product of a single genetic locus
diagram for allozyme gel analysis
monomeric enzyme
produces one polypeptide chain which is a fully functional protein
dimeric enzyme
single polypeptide chain is produced by each allele, but these remain inactive until they form dimers
it is necessary to screen at least —— enzyme loci to get a representative sample of the variation in populations
12 to 15
two measures of genetic variation
polymorphism (P)
heterozygosity (H)
variation as measured by the average heterozygosity represents
the adaptive potential of the species and is a powerful evolutionary mechanism
two statistics to quantify genetic differentiation between populations
- genetic identity, I, which estimates the proportion of genes that are identical in the two populations being compared
- genetic distance, D, which estimates the accumulated number of gene differences per locus that have occurred over evolutionary time
advantage of statistical measures of genetic differences
- they apply to any population, whether they be haploid, diploid, tetraploid or selfing
- definitions depend solely on allele frequencies rather than on the genotype frequencies used in the HW equation
look over the method for the experiment
aim of the experiment
to analyse differences in allosyme variation between two species using electrophoresis
zebra mussels
benthic (live on the bottom of the lake)
sessile (fixed to a substrate)
bivalves (mollusc with two shells)
males and females can only be distinguished based on microscopic examination of gonad tissue
phylogenetic systematics
- method for reconstructing evolutionary relationships
- clusters organisms into groups based on modified characters that are shared by members of the group
3 characteristics of the method of phylogenetic systematics
quantitative (characters can be enumerated), reproducible (data are not subjective), and testable
assumptions of phylogenetic systematics
- evolution occurs
- there is a singly phylogeny of life, a result of evolutionary descent
- characters are passed from generation to generation, modified or unmodified, during evolutionary descent
steps in constructing a phylogenetic tree
- identify homologous characters
- code the characters as ancestral or derived and construct a matrix
- group by shared derived characters to produce a phylogenetic hypothesis
character
observable trait of an organism
character reversal
a form of homoplasy, where a species re-evolves the ancestral character state
unique vs shared derived character
unique - found in one taxon
shared - found in more than one taxon
it is —— —— —– that are used to infer evolutionary relationships
shared derived characters
binary vs multistate characters
binary: present or absent (coded 0 and 1)
multistate: in more than two different states (coded as 0, 1, 2)
multistate characters can be considered to be
ordered or unordered
ordered characters
follow a logical evolutionary path (eg small size beak to medium to large)
unordered characters
do not follow any logical evolutionary progression (eg colour of coral reef fishes)
go through the process of making a phylogenetic tree
parsimony
a principle in phylogenetic which forces one to accept the shortest tree that explains all the character states
polytomy
an unresolved group of three or more taxa
measurement error
reflects the discrepancy between our repeated measurements and the true value of the object being measured
precision
the repeatability of the measurement
accuracy
the tendency for the measured value to be close to, or approximate, the true accepted value
sample size is abbreviated by
n
population size is abbreviated by
N
title for a graph
placed at bottom of a graph
interpolation
a line of best fit through the data that allows you to predict values of the dependent variable for which you do not have actual data points
extrapolation
the process of extending the line beyond the existing data, maintaining the trend shown by interpolation, and provides a basis for prediction
bar graph
used for discrete quantitative variables which are similar but not necessarily related
histogram
used exclusively for showing the distribution of data that are continuous
statistics of location
describe the position of a sample along a given dimension
- most common statistics of location are the mean, median and mode; these are called measures of central tendency
statistics of dispersion/variability
describe the distribution of observations.
- simplest is the range, and most common are the variance and standard deviation and standard error
variance
measure of how much scatter there is around the mean
(n-1)
degree of freedom. adjustment to have an unbiased estimate of the variance from a sample
standard deviation, s
average size of the deviation from the mean
standard error
measure of how reliable the sample mean is as an approximation to the population mean
test of significance
evaluates the probability of rejecting the null hypothesis when it is actually true
student’s t-test
statistical test that compares the means of two samples and assesses whether or not they differ enough to represent samples from different populations
significance level
the probability of mistakenly rejecting the null hypothesis when it is true
draw graph for t test acceptance/rejection region
chi square test / goodness of fit /contingency
used to test a hypothesis in an experiment in which the data are frequency data rather than continuous date
- tests difference between observed and expected frequencies and is used for data that can be arranged into classes such as habitat, genotype, percentage
assumptions of a chi square test
- data must consist of samples taken at random from a large population
- for each sample taken there is a restricted number of outcomes that can be divided into distinct categories
- probabilities for each of the outcomes are independent from each other and do not change from one sampled individual to another
draw graph for acceptance/rejection region for chi squared distribution
when would you use a 2 x 2 contingency table?
when an analysis is concerned with two variables
what did Hardy and Weinberg realise?
that the genotype frequencies of a population could be predicted from the frequency of the alleles, represented as p and q, using the binomial equation:
p^2 + 2pq + q^2
the above equation describes a single locus with two alleles
what is necessarily true for the HW equation?
frequencies of the two alleles (p + q) must equal 1 and the frequencies of the genotypes (p^2 + 2pq + q^2) must also equal 1.
two functions of HW equation
- calculate genotype frequencies of a pair of alleles at a gene locus
- predict genotype frequencies of the next generation as long as there have been no changes in the gene pool
when there have been no changes in the gene pool, genetic equilibrium will only occur when:
- population is large enough to be unaffected by random gene changes (i.e. genetic drift)
- there is no gene flow (immigration or emigration)
- no mutations occur or there is mutational equilibrium
- reproduction is random (independent of genotype)
- natural selection is not acting on a particular phenotype
why is the concept of genetic equilibrium an important concept if in natural populations all of the conditions are almost never met?
significant deviations from the expected HW values provide evidence that some evolutionary force is in action. We can think of the expected HW values as a null hypothesis (no evolutionary force is acting on the population)
