Biology Exam 3 Lecture Notes

Front 1

Geographic splitting of a population followed by evolutionary divergence of the separated parts. = "allopatric speciation"- geographic isolation of the populations precedes evolution of species-level differences

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Multiplication of Species

Front 2

a reproductive community of populations (reproductively isolated from others) that occupies a specific niche in nature

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Biological Species Concept (Mayr)

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temporal (seasonal), ecological, behavioral, mechanical, genetic (prevent formation of zygote btwn diff. species) (pre-marital rituals don't match anymore) (physical/ mechanical genetalia may not fit)

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prezygotic (reproductive barriers)

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hybrid inviability, hybrid sterility, hybrid breakdown (mating occurs --> zygote problems --> death)

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postzygotic (reproductive barrier)

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does selection on hybrids with postzygotic barriers lead to prezygotic reproductive isolation? (for _________________ to occur you must have second contact btwn 2 species that used to be the same, but they evolved)

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reinforcement

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the hybrid can reproduce, but when 2 hybrids mate (or F1 seeds are replanted) it doesn't work well...offspring are maladapted

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hybrid breakdown

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problems with Biological Species Concept

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1. sexual forms only
2. no temporal dimension
3. often not a single unit of evolution/evolutionary
4. often not practically testable

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a linage of ancestral-descendant populations diagnosably distinct from other such lineages (time dimension is explicit), does not limit to sexual reproduciton only it includes budding/ asexual

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phylogenetic species concept (Cracraft)

Front 9

a branch of lineage to form a new species initiated by geographic barriers

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allopatric speciation

Front 10

subdividing formerly continuous habitat-a strong barrier emerged that had not already existed

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vicariance

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rare dispersal across pre-existing barrier--Galapagos Islands--> went over Pacific Ocean pre-existing barrier to make new population son island ...higher rate of colonization of same species btwn islands than mainland

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founder event

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splitting of populations to form diff. species generated by an ancestor in a single undivided geographical location

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sympatric speciation

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evolutionary change occurs in small increments--accumulation of small, quantitative, changes leads to qualitative change (biological transposition of Lyell's ________)

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gradualism

Front 14

large phenotypic change in a single generation (hopeful monster)

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contrasting theory to Gradualism (Richard Goldschmidt is a proponent)

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the raw material for evolving novel forms and species

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intraspection variation

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a population-based mechanism of evolutionary change invoked to explain "adaptation" (NOT RANDOM PROCESS) has Five Observations and Three inferences

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Natural Selection

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variation is produced at random with respect to an organisms needs aka mutational variation in organism

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random component

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organisms with favorable traits have higher rates of survival and reproduction, causing populations to accumulate the most favorable variants and to discard the less favorable ones

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nonrandom component

Front 19

evolution by natural selection has no pre-set goal or direction (adherence of Malaria in populations with hemoglobin S gene)

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(Darwin's Theory) opposes teleology

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Natural populations normally do not increase exponentially but remain fairly constant in size (ie. Alien migrants/invasion in a new area)

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Observation 2 (of Natural Selection)

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organisms have great potential fertility which permits exponential growth of populations

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Observation 1 (of Natural Selection)

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natural resources are limited

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Observation 3 (of Natural Selection)

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variation occurs among organisms within populations

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Observation 4 (of Natural Selection)

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variation is heritable

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Observation 5 (of Natural Selection)

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a struggle for existence occurs among organisms in a population

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Inference 1 (from the first 3 observations of natural selection)

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varying organisms shows differential survival and reproduction favoring advantageous traits (=natural selection)

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Inference 2 (from inference 1 and observations 4 and 5)

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natural selection, acting over many generations, gradually produces new adaptation and new species

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Inference 3 (from inference 1 and observations 4 and 5)

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later forms are superior to earlier ones in a general sense

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progressive adaptation

Front 29

reproducing population with heredity and variation --> variation need to give some indvls. w/ advantages over others

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substrate neutrality (from Dennett's Algorithmic formulation)

Front 30

no teleology

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underlying mindlessness (from Dennett's Algorithmic formulation)

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feeds on randomness to produce order

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guaranteed results (from Dennett's Algorithmic formulation)

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a trait that evolved by natural selection for a particular biological role

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adaptation

Front 33

a trait adopted by natural selection for a role incidental to the trait's origin

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exaptation

Front 34

identify essential aspects of reality and remove distracting elements (1st step of constructing mathematical models)

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abstraction and simplification

Front 35

minimum # of summary variables- combines relevant information of many parameters at lower levels

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sufficient parameters

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unreal conditions used to facilitate study (non overlapping generations is ____ed)

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assumptions

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three conditions in good mathematical models

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reality, generality and precision(repeatability of measurements) BUT remeber!!! no model can fully represent all of these well so it usually focuses on two.

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#1 Abstract Molecular Basis of Evolution (Mathematical Models)--3 properties of DNA

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1. DNA can replicate
2. DNA can mutate and recombine
3. DNA encodes RNAs/proteins that interact with environmental conditions to influence phenotype

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replication without mutation in DNA--refers to alleles and associated phenotypes

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Identity by Descent

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all copies of homologous DNA trace back to a common ancestral molecule

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coalescence

Front 41

autosomal. One can be heterozygous for this.

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Apoprotein E gene region

Front 42

why is yeast good to test generations from one to another?

Back 42

you can freeze it and look at generations that are years apart at the same time!

Front 43

set of identical haploid genomes for a specific unit of measurement

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haplotype (aka allele)

Front 44

synonymous for "allele" for measurements taken at the DNA/ chromosomal level NOT GENE level

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haplotype

Front 45

branches represent lineal descent of copies of homologous DNA from parents to offspring

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gene tree

Front 46

branches denote mutational events in evolutionary history of homologous DNA

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haplotype tree

Front 47

a transport protein that carries cholesterol through the blood stream

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Apoprotein E

Front 48

refers to a local population of reproducing individuals that has physical continuity over time and space (this is the lowest level that can evolve) (characterize it by measuring genotype frequencies)

Back 48

deme

Front 49

True or False? Demes with the same allele can have very different Genotype Frequencies

Back 49

TRUE

Front 50

population of gene copies collectively shared by indvls. of a deme

-or population of potential gametes that can be produced by the individuals of a deme.

Back 50

gene pool

Front 51

Ratio Dominant: Recessive

Back 51

p^2 + 2pq : q^2

Front 52

selection equilibrium; mutation produces lethal alleles

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mutation

Front 53

removes lethal alleles

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selection

Front 54

mutation rate

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(# newly mutated copies)/ (total # copies of homologous DNA)

Front 55

Hardy-Weinberg equilibrium (5 Assumptions)

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Mendelian inheritance does not cause evolutionary change (not realistic)
Assumes:
1. population infinitely large
2. random mating
3. no mutation
4. no migration
5. no natural selection

Front 56

Rate of elimination of lethal allele =

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q^2

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rate of creation of lethal allele

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= mu (at equilibrium mu = q^2)

Front 58

How does one calculate Hardy-Weinberg degrees of freedom ?

Back 58

H-W degrees of freedom = # of alleles

Eg. 3 alleles = 3 degrees of freedom

Front 59

any measurable trait--- can be either discrete or continuous

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phenotype

Front 60

- 65% heritability
- affects 30% of the population
- no discrete phenotypes
- the correlation between the parent and the offspring having this trait is 1/3.

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coronary artery disease

Front 61

2 major features of most genetic traits

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1. complexity of genotype/phenotype relationships represent interactions among multiple genetic and environmental factors
2. Confoundment of frequency and apparent causation in complex systems

Front 62

has glutamine at aminoacid position 6

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HbA

Front 63

has valine at aminoacid position 6

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HbS

Front 64

Why is the heterozygous genotpye better than the homozygous recessive in malarial conditions for the hemoglobin gene?

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heterozygous can be better because spleen will remove bad cells, but also the malaria parasite cells

Front 65

one of the two or more contrasting states of homologous gene factors that segregates from each other during gamete formation; usually identified by different phenotypes

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allele

Front 66

a multisite haploid genotype at two or more polymorhpic sites on the same chromosome in a defined DNA region; set of identical haploid genomes for a specific unit of measurement

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haplotype

Front 67

True or False? causes of variation of a phenotype (population-level phenomenon) does not equal cause of a phenotype (organismal phenomenon)

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TRUE. Eg. Does cigarette smoking cause lung-cancer?

Front 68

Two ways for discrete genotypes to yield continuous phenotypes:

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1. polygenic inheritance--Ronald Fisher
2. Environmental variation

Front 69

What type of genotype for a mother with PKU needs to go on low phenylalanine diet during pregnancy?

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p/p

Front 70

True or False? PKU is a dietary disease where as scurvy is a genetic disease?

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FALSE...vice versa

Front 71

set of phenotypes associated with a particular genotype in interaction with a variety of environmental conditions and genetic backgrounds

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Norm of Reaction

Front 72

data available for norms of rxn for each diploid genotype at a locus

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measured genotype approaches

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average of expected values of x

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mean (mu)

Front 74

average squared deviation of x from the mean

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variance

Front 75

analysis of genetic variance for continuously varying phenotype within a population

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quantitative genetics

Front 76

Two questions in quantitative genetics:

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1. How much phenotypic variance is associated with genotypic variation at a population in a given generation? (genetic variance vs. environmental variance)

2. How much of the genetic variance can be transmitted through gametes to influence phenotypic variation in the next generation? (additive vs. nonadditive genetic variance)

Front 77

square root of variance

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standard deviation

Front 78

mean phenotype of the genotype minus mean phenotype of the population

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genotypic deviation

Front 79

genetic variance plus unexplained variance

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phenotypic variance (according to Fisher)

Front 80

True or False?an indvls. phenotype can have variance and mean due to genotype and environmental factors?

Back 80

FALSE ( only populations can have variance)

Front 81

Fisher's Analysis of Variance (What are the steps of calculation?)

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1. calculate the mean
2. calculate the genotypic deviation
3. calculate genetic variance

Front 82

proportion of the phenotypic variance within a population that results from genetic differences among indvls.

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broad-sense heritability

Front 83

the proportion of the phenotypic variance that results from the additive effects of different alleles on phenotypes

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narrow-sense heritability

Front 84

dominance variance for more than 2 one-locus model; dominance and epistatic variance for a 2+ locus

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non-additive genetic variance

Front 85

used to measure heritability without measure genotype approaches; ___________= .5 times additive variance

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covariance between parents and offspring

Front 86

standard covariance that varies from -1 to +1

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correlation coefficient

Front 87

When did the Pioneer Fund began and who started it?

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1937 by Wickliffe Draper

Front 88

locus whose variation contributes to populational variation of a continuously varying phenotype

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quantitative trait locus (QTL)

Front 89

List the steps in a quantitative genetics analysis

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1. Find genomic regions of interest
2. Find base substitutions affecting the disease phenotype

Front 90

saturated, genome-wide linkage mapping, SNP markers every 10 cm throughout; genome pedigree analysis of disease and SNP state

Population must have: 1. high incidence of disease phenotype
2. high levels of linkage disequilibrium

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genome scan

Front 91

use haplotype tree to test individual SNP sites for influence on the disease phenotype

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tree scan

Front 92

True or False? Linkage disequilibrium causes disequilibrium from 1 generation to the next.

Back 92

FALSE... it does not cause it just allows it to persist

Front 93

Fisher's analysis of Variance

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phenotypic variance = genetic variance + unexplained variance

Front 94

genotypic deviation

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= mean phenotype of the genotype- mean phenotype of population

Front 95

genetic variance

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= sum of H-W frequencies x (genotypic deviations)^2

Front 96

Name 2 sources of Allopatry

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Vicariance and founder event

Front 97

Heritability

Back 97

characteristics of offspring are correlated with those of their parents in a population.

Front 99

Lowest biological level that can evolve

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Deme

Front 100

Connects deme to gene pool

Back 100

Meiosis

Front 101

How do you explain why autosomal recessive lethal genetic diseases cannot be efficiently eliminated by natural selection.

Back 101

Hardy-Weinberg Equilibrium explains that autosomal recessive lethal genetic disease cannot be efficiently eliminated by NS unless it's in its homozygous form.

Front 102

Bonellia

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marine worm

Front 103

How is a female Bonellia made?

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unfertilized Bonellia larvae

Front 104

How is a male Bonellia made?

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If the Bonellia larvae is engulfed by another female worm, it develops into a parasitic male gonad. lolol

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CAD

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Coronary Artery Disease: blockage in vessel so little blood can get through --> Oxygen deprivation in heart --> stroke

Front 106

Enzyme deficiency (of the enzyme dihydropteridine reductase). Accumulation of phenylacetic acid and orthohydroxy

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Phenylketonuria

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p/p with low phenylalanine diet

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normal intelligence

Front 108

p+/p with nomral phenylalanine diet

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mentally retarded

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Vitamin C deficiency

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Scurvy

Front 110

What causes linkage disequilibrium?

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1. Hybridization between populations of contrasting haplotypes
2. Founder Event
3. Genetic Recombination destroys linkage disEQ

Front 111

How to retain linkage disEQ?

Back 111

Requires genetic linkage of the sites that are in linkage disEQ

Front 112

Epistatic variance

Back 112

nonadditive genetic variance at the population-level arising from interactions among genotypes at different loci

Front 113

True/False? Mendelian epistasis is necessary and sufficient for epistatic variance

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False. Necessary but not sufficient

Front 114

protein that binds HDL (good cholesterol)

Back 114

Apoprotein E

Front 115

protein that binds LDL (bad cholesterol)

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Apoprotein B

Front 116

Population-Genetic definition of Evolution

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change in an allele or gamete frequency in the gene pool

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Evolutionary forces in populations

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factors or processes that can change the frequency of an allele in the gene pool

Front 118

causes many small changes

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mutation

Front 119

Random change of allelic frequencies. When there is finite population size.

Back 119

Genetic Drift (Sampling Error)

Front 120

True/False? The smaller the population size, the smaller the effect of genetic drift

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False. The smaller the population size, the greater the effect of genetic drift

Front 121

Average squared deviation (sigma) of xi from the mean (how wide the distribution is)

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variance