Biology Exam 3-Larson

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Substrate Neutrality

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The power of the procedure is a result of its logical structure, not the materials that happen to be used in carrying it out. Long division works equally well with pencil or pen, paper or parchment, neon lights or skywriting, using any symbol system you like

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Underlying Mindlessness

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Although the overall design of the procedure may be brilliant, or may yield brilliant results, each constituent step is utterly simple. The recipe requires no wise decisions or delicate judgments on the part of the recipe reader

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Guaranteed Results

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Whatever it is an algorithm does, it always does it, provided the algorithm is executed with out misstep. An algorithm is a foolproof recipe.

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haplotype

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the multisite haploid genotype at two or more polymorphic sites on the same chromosome in a defined DNA region

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transmission genetics

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concerned primarily with genetic processes that occur within individuals and how genes are passed from on individual to another

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molecular genetics

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interested largely in the molecular nature of heredity: how genetic information is encoded within the DNA and how biochemical processes of the CELL translate the genetic information into influencing phenotype

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population genetics

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applies the principles of transmission genetics to large group of individuals, focusing on the transmission processes at one or a few genetic loci--applies Mendelian Principles and math

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quantitative genetics

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also considers the transmission of traits simultaneously determined by many genes--applies Mendelian Principles and math

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Mendelian Population

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group of interbreeding individuals who share a common set of genes

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gene pool

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the genes shared by Mendelian population

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principle aim of populations genetics

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to study and understand evolution

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Hardy--Weinberg law

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states that in a large, randomly mating population and assuming there is no mutation, no migration, and no natural selection, allele frequencies will not change and the genotype frequencies stabilize after one generation

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true of false genotypes have continuity over a period of time

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False-- only alleles do because they are passed to the next generation through gametes

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genotype frequencies

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at a specific locus, we count the number of individuals with one particular genotype and divide this number by the total number of individuals in the population

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allele frequencies

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can be calculated in two equivalent ways: from the observed numbers of different genotypes at a particular locus or from the genotype frequencies

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Part 1 of Hardy-Weinberg Law

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(Assumptions): In an infinitely large, randomly mating population, free from mutation, migration, and natural selection

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Part 2 of Hardy-Weinberg Law

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the frequencies of the alleles do not change over time where p is the allele frequency of A and q is the allele frequency of a; and

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Part 3 of the Hardy -Weinberg Law

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he genotypic frequencies remain in the proportions p^2 (frequency AA), 2pq (frequency of Aa), and q^2 (frequency of aa). The sum of the genotype frequencies equals 1 (that is, p^2+2pq+q^2=1)

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random mating

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mating between genotypes occurring in proportion to the frequencies of the genotypes in the population

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What genotypic proportions qualify a population to be in Hardy-Weinberg Equilibrium

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p^2 : 2pq: q^2

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the 2 reasons why the standard deviation is 1 in a Chi Squared analysis for Hardy-Weinberg

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1. subtract one for every parameter (p in this case) that must calculated from the data

2. and another for the fixed number of individualts

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allele frequency cline

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when allele frequencies change in a systematic way across a geographic transect

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polymorphic loci

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is any locus with more than one allele present within a population

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neutral theory

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acknowledges the presence of extensive genetic variation in proteins but proposes that most of the variation is neutral with regard to natural selection....meaning though the genetic sequences of something maybe different the physiological function is still the same (proteins on gel)

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synonymous changes

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nucleotide changes in DNA that do not alter the AA sequence

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DNA length polymorphism (620)

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when a number of nucleotides differs between two equal genes

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short tandem repeats

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small base sequence that is repeated

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PKU

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phenylketonuria, mutation on long arm chromosome 12 (must be homozygous to show symptoms)--mutation for gene phenylalanine hydroxylase so cant convert AA phenylalanine to AA tyrosine essential amino acid (67)

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Guthrie Test

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tests for PKU by placing blood on culter with bacteria and a chemical to inhibit bacterial growth--if phenylalanine is present bacteria will grow (the test just shows a child has high levels of phenylalanine not necessarily PKU)

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Albinism

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autosomal recessive mutation; a gene for tyrosine is mutated...tyrosine converts to DOPA which the brown pigment melanin derives...two pathways so two affected parents can produce normal children if the type of albinism carried by each is different

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Kartagener Syndrome

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sterility, sinus and lung abnormalities; autosomal recessive; genes involved with mutations effect dynein motors of flagella and cilia

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Tay-Sachs

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chromosome 15 gene on long arm; higher in Ashkenazi Jews, mutated gene is HEXA and encodes for an enzyme in the lysosome (69)

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sickle-cell anemia

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affects hemoglobin (oxygen transporting protein in red blood cells), shape of blood cell becomes sickled--they break, less flexible, clog--so blood circulation is impaired and tissues are oxygen deprived (research on this helped to prove that genes control protein structure)

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discontinuous traits

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a heritable characteristic that exhibits a small number of distinct phenotypes, which commonly are determined by variant alleles at a single locus

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penetrance

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the frequency with which a dominant or homozygous recessive gen is phenotypically expressed within a population

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expressivity

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the degree to which a particular gene is expressed in the phenotype. A gene with variable expressivity can cause a range of phenotypes

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pleiotropic

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referring to genes or mutations that result in multiple phenotypic effects

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epistasis

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interaction between two or more genes that controls a single phenotype. For instance, the expression of a gene at one locus can mask or suppress the expression of a second gene at another locus

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norm of reaction

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range of phenotypes produced by a particular genotype in different environments

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quantitative traits

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a heritable characteristic that shows a continuous variation in phenotype over a range (aka continuous trait)

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quantitative genetics

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study of inheritance of complex characteristics that are determined by multiple genes

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Wilhelm Johansen

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published a study demonstrating that quantitative variation in seed weight in beans had both environmental and genetic determinants.--helped define multifactorial traits

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multifactorial traits

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a characteristic determined by multiple genes and environmental factors

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polygene

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two or more genes who additive effects determine a particular quantitative trait

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polygene hypothesis for quantitative inheritance

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the hypothesis that quantitative traits are controlled by many genes

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Nilsson-Ehle

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crossed true-breeding lines of red kernal plants with white....1:4:6:4:1 for discrete shades of red and 1 white....the products of two genes affect the same trait

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contributing alleles

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an allele that affects the phenotype of a quantitative trait (functional)

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noncontributing alleles

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an allele that has no effect on the phenotype of a quantitative trait (non functional)

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population

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group of ultimate interest

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sample

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used to give us an estimate of the population

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frequency distribution

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summary of a group in terms of the proportion of individuals that fall within a certain phenotype range

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normal distribution

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bell-shaped

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mean

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tells where the center of the distribution of the phenotypes from a sample is located

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variance

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a measure of how much the individual observations spread out around the mean

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sample variance

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s^2 is calcualted by first subtracting the sample mean from each individual measurement. The difference is then squared and all squared values are totaled. The sum is divided by (n-1)

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standard deviation

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square root of sample variance

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correlation coefficient

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a statistic that measures the strength of the association between two variables in the same experimental unit, which in genetics is usually an individual

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covariance

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a measure of how much variation is shared by an individual for both traits

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true of false: two variables can be highly correlated and yet have different values

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true

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regression

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a statistical analysis assessing how changes in one variable are quantitatively related to changes in another variable

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regression line

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a mathematically computed line that represents the best fit of a line to the data values for two variables plotted against each other...the slope of the regression line indicates the change in on variable (y) associated with a unit increase in another variable.

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regression coefficient

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the slope of the regression line drawn to show the relationship between two variables

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the slope indicates....

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how much of an increase in the variable on the y axis is associated with a unit increase in the variable on the x axis

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analysis of variance (ANOVA)

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a series of statistical procedures for determining whether differences in the means of a variable in two samples are significant and for partitioning the variance into components...the probability that the difference in means of the two samples results from chance

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Rollins Emerson and Edward East

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started their experiments with two pure-breeding strains of corn, each of which displayed a little variation in ear length p.660 for rest of experimental results

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Four Observations that Apply Generally to Quantitative Inheritance Studies that Incorporate Crosses between genetically differentiated individuals or populations

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1. The mean value of the quantitative trait in the F1 is usually intermediate between the means of the two true-breeding lines
2. The mean value for the trait in the F2 is usually approximately equal to the mean for the F1 population
3. The F2 almost always shows more variability around the mean than the F1 does.
4. The extreme values for the quantitative trait in the F2 extend closer to the two parental values than do the extreme values of the F1, and may sometimes even surpass the parental values

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heritability

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the proportion of a population's phenotype variation that is attributable to genetic factors

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phenotypic variance

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Vp a measure of all variability for a trait

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genetic variance

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V(G)= gene contribution to phenotypic variation

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environmental variance

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V(E)= additional variation often results from environmental differences experienced by the individuals

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Vp=

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V(G)+V(E)

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COVg,e

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phenotype-by-environment interaction G x E

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dominance variance V(D)

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when dominance is present, the individual effects of the alleles are not strictly additive

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additive genetic variance V(A)

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adding effects of alleles at a certain locus to the effects of alleles at other loci that might influence same phenotype

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interaction variance

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V(I)presence of epistasis adds another source of genetic variation

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general environmental effects

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V(EG) = different phenotypes because of different environments over time

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special environmental effects

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V(ES) = immediate transient changes in phenotype do to the environment

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family environmental effects

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V(ECF) = environmental effects shared by family members

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maternal effects

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V(EM) = (a) the phenotype established by expression of maternal effect genes in the oocyte before fertilization (b) an influence derived from the maternal environment

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broad-sense heritability

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the proportion of phenotypic variation in a population attributable to genetic differences among individuals (heritability ranges from 0 to 1)

= V(G)/V(P)

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narrow-sense heritability

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the proportion of the phenotypic variance that results only from additive genetic variance (more important usually)

= V(A)/ V(P)

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limitations of heritability

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1. broad-sense heritability does not define the complete genetic basis of a trait
2. heritability does not indicate what proportion of an individual's phenotype is genetic
3. heritability is not fixed for at trait
4. high heritability for a trait does not imply that differences between populations for the same trait are genetically determined
5. traits shared by members of the same family do not necessarily have high heritability

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What does the slope of the regression line for mid-parent values and mean offspring phenotypes tell you?

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information about the magnitude of the narrow-sense heritability

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evolution

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genetic change that takes place over time within a group of organisms

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natural selection

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differential reproduction of individuals in a population resulting from differences in their genotypes

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artificial selection

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process for deliberating changing the phenotype traits of a population by determining which individuals will survive reproduce

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selection response R

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the amount by which a phenotype changes in one generation when natural or artificial selection is applied to a group of individuals

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selection differential s

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natural and artificial selection, the difference between the mean phenotype of the selected parents and the mean phenotype of the unselected population

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phenotypic correlation

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between two quantitative traits can be computed by measuring the two phenotypes on a number of individuals and then calculating a correlation coefficient for the two traits

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genetic correlations

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phenotypic correlation due to genetic causes such as pleitropy or genetic linkage

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quantitative trait loci (QTL)

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individual loci that contribute to a quantitative trait

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QTL identification

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an exercise in finding segments of the genome associated with phenotypic differences between individuals

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another aspect of Hardy-Weinberg Law

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a population that is large, randomly mating, and free from mutation, migration, and natural selection, then whatever variation there is in the populations will remain at the same frequency forever

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gene mutations

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can alter frequencies of alleles within a population--it consists of heritable changes in the DNA that occur within a locus, usually converts one allele form of a gene to another

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_____________is the source of all new genetic variation

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gene mutations

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forward mutation

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A to a mutation (rate= u)

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reverse mutation

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a to A mutation (rate = v)

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random genetic drift

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random change in allele frequency due to chance (usually can only occur in small populations)(p624)

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sampling error

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chance deviations from expected proportions arise from a general phenomenon called..

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effective population size

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equals the equivalent number of adults contributing gametes to the next generation (not necessarily every person in the population)

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Ne= effective population size

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(4 x Nf x Nm)/(Nf +Nm) p. 625

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Wright-Fisher Model

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considers the changes in allele frequency each generation as a binomial sampling, but at each successive generation the allele frequency can change, so the binomial parameter (in this case, the allele frequency) changes each generation

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founder effect

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can also lead to genetic drift, a founder effect occurs when a population is initially established by a small number of breeding individuals

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bottleneck effect

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form of genetic drift that occurs when a population is drastically reduced in size

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the second effect of genetic drift

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reduction in genetic variation within populations

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the probability of fixation by genetic drift is equal to....

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the current frequency of the allele

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genetic drift is greater in small or large populations?

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small

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infinite alleles model

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each mutation that occurs in a gene is assumed to generate a novel allele; also assumes that random genetic drift occurs by the repeated sampling (629)

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The probability of coalescing in the previous generation

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1/(xNef) x= the ploidy level Nef= population of the breeding size

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The probability that 2 genes did not coalesce in the previous generation

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1-(1/(xNef))

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nonsynonymous changes

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the diversity at nucleotides that change the resulting AA sequence of the protein

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RFLP

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Restriction fragment length polymorphisms:
different patterns on the gel that indicate that the DNA sequences of the 2 individuals differ. Are inherited like normal alleles are, except that they do not produce any outward phenotypes; their phenotypes are the fragment patterns produced on a gel when the DNA is cut by the restriction enzyme.