Evolution Bio 109 Midterm 2014 Flashcards


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1

What is evolution?

-1st biological use of "evolution" was by the embryologists in the 18th century
-"change"
-darwin: "descent with modification"
-individual organisms do not evolve
- biological evolution occurs at the population level by the differential survival and fecundities of individual organisms that result in the replacement of one genetic character for another
-genetic change, time, populations

2

How does the study of evolution differ from other areas of biology? (2)

1) Method of study: inference based on the "comparative" vs "experimental" method

2) Types of questions asked:

3

1) Method of study

1) Method of study: inference based on the "comparative" vs "experimental" method

-scientists: something is true is it is consistent w/ available evidence or more consistent than some competing hypothesis
-extent at which theory is accepted as fact: # of times it withstood attempts to refute it (FALSIFICATION is critical to accepting a theory-biological evolution has and is occurring has not been disputed)
-darwin used: HYPOTHETICO-DEDUCTIVE method->gather facts/observations, generate hypothesis to explain observations, conduct experiments, gather more evidence to test hypothesis, modify if observations don't mesh w/ original hypothesis, test again
-strengths of hypothetico-deductive method: encourages new theories, more observations, and new types of experiments
-evolutionary biology uses "comparative method" that has developed from this method. experimentation is generally not possible, but there are experiments that can provide evidence favoring evolutionary hypothesis

4

2) Types of questions asked

2) Types of questions asked: "proximate" vs "ultimate" causations

-proximate questions: "functional biology" (i.e. physiology, biochem, molecular bio)
-begins with "how"

-ultimate questions: evolutionary biology
-begins with "why"
-no structure or function that cannot be fully understood b/c organisms are products of long evolutionary histories

-ex) why do birds migrate: proximate->temp change, ultimate->birds that did survived & reproduced better
-one type of question is not "superior" to the other; both are required for a complete understanding of any biological phenomenon.

5

What is HIV?

-originally, Darwin thought natural selection happened too slowly to observe directly but he was wrong (ex: HIV)
-a retrovirus (RNA-based) w/ 9 genes & is a diploid (2 copies of each RNA strand): copies its RNA into DNA, dumps genome into host, leaves body after infected, lots of fast replications
-infects key play of immune system: "helper T cells" (w/ protein CD4 on cell surface through which HIV enters)-> the destruction of these CD4 helper T cells is what lowers immune systems and causes the body to no longer be able to ward off bacterial and fungal pathogens (AIDS is the manifestations of these secondary infections)

-T helper cells are important b/c they are responsible for:
-"cell-mediated response": stimulates killer T cells to kill off infected T cells AND
-"humoral response": stimulate B cells that secretes B cells that bind to free virus particles and destroys them

-by infecting T cells, we lower our immune system by destroying our whole T cell population over time (~10-15 years) and AIDS develops

6

Natural Selection and the HIV virus

-AZT is a "base analog"-> an AIDS drug, works by poisoning the replication of the virus
-it is incorporated into a growing DNA strand and halts replication (new bases cannot be added past this point)
-only effective for 1-2 years b/c HIV evolved a mutant RT (reverse transcriptase) that has a low affinity for AZT and allows effective replication in AZT environments
-the population of viruses present in an infected individual evolve over time to become
predominated by AZT-resistant genotypes.
-this is an example of ADAPTATION BY NATURAL SELECTION
-natural selection favoring AZT-resistant RTs has occurred repeatedly in ~every patient treated with AZT
-also a case of "parallel evolution": evolution of similar traits in closely-related species (or
populations in this case) in response to the same selective agent

7

But how did HIV achieve such a high evolutionary response?

1)high mutation rate: no "proofreading" function to correct mistakes of RNA to DNA
-most mutations decrease viral fitness but a small portion will be advantageous

2)short generation time: 1 year ~300 generations

3)extremely large population size of HIV virions replicating in host
-more chances of advantageous mutations appearing (so large population sizes undergo faster rates of adaptive evolution)

8

Phylogenetics

-tracing the evolutionary history of organisms
-objective: reconstruct evolutionary histories of “taxa” to produce phylogenetic tree

9

HIV-1 and HIV-2

1)both closely related simian immunodeficiency viruses (SIV’s) and only distantly related to infectious viruses isolated from other mammals, so we know that HIV viruses evolved from primate ancestors

2)the pattern of viral evolution does not closely mimic the pattern of primate evolution
-two HIV-1 human strains are very similar to an SIV from the common chimpanzee, suggesting that HIV-1 “jumped” to humans from chimpanzees
-the inter-species transfer of infectious diseases like HIV are known as zoonoses
-studies of 4 distinct clades of SIVs have been co-evolving w/ subspecies of chimps for a long time
-by tracing origin of all 3 principal groups of HIV-1, viruses cluster within the P. t. troglodytes subspecies clade, furthermore, the origin of HIV-1 in west-central Africa coincides perfectly with the geographic distribution of P. t. troglodytes but not any other subspecies telling us that P. t. troglodytes was the source of the HIV-1 currently spreading through human populations

-how did these zoonoses occur?
belief: recent slaughtering and eating of chimpanzee meat is responsible for
the “jump” of HIV from chimps to humans. unfortunate b/c it may prevent us from learning more about virus in its previous host and
using this information to halt the epidemic

10

First theories of origin of life

-by Greek philosophers, share common belief:
1) they resulted from the generative powers of nature (not actions of a God)
2) they were nonteleological (i.e., without an underlying design or goal)
-Anaximander belived humans suddenly appeared from fish-like creatures->example of SPONTANEOUS GENERATION, not a theory of evolution

11

3 aspects of Aristotle’s writing that thwarted evolutionary thinking

-first great naturalist, studied "life histories", and believed all structures and biological activities had a meaning ("adaptive significance")

1) all species are fixed and eternal (so organisms changing or evolving was not possible)
2) the philosophy of essentialism: the belief that all species have an eternal or perfect "essence" or "eidos" (form) so variation was imperfections and unimportant
3) the “scala naturae” or “great chain of being”: linear progression of organisms from the most simple to the most complex (slime molds to humans)->over time, this was believed to reflect the action of a creator

12

Why has evolutionary thinking been so difficult to develop?

1) an appreciation of "deep time": difficult to envision/grasp 4.5 BYA
2) a rudimentary understanding of biological inheritance: Darwin knew the importance of genetic variation among individuals of a species (natural selection)
3) a basic understanding of ecology and other areas of biology (development, comparative anatomy, biogeography, etc.)

13

How did evolutionary thinking develop?

-it happened very slowly
1) The scientific revolution (astronomy-heliocentric, geology-age of earth, physics/math/chem/bio-challenged biblical account)
2)The discovery of new faunas (undermined Noah's ark story)
3) Extinction
4) The microscope: multicellular organisms (further supported spontaneous generation, although wrong, undermined biblical beliefs of one creation)
5) The development of systematics: branch of biology that aims to classify individual species into phylogenetic groups that reflect their evolutionary histories (developed by Linneaus dramatically undermined the “scala naturae”

14

Lamarck

-first to formulate a biological theory of evolution
-he thought "change in form of a lineage" happened very slowly: GRADUALISM (he studied fossil molluscs)

15

Lamarck recognized two causes of evolutionary change

1) life has an innate potential to acquire greater and greater complexity (“orthogenesis”)

2)organisms “reacted” to their environments, changed form, and then transmitted these
changes to their progeny-certain parts are used more or less (“inheritance of acquired characteristics” or “soft inheritance”)

-NEITHER OF THESE MECHANISMS IS CORRECT

16

Darwin

-two objectives for writing "the origin": evolution had occurred, and to provide a mechanism for how evolutionary change occurs
-evidence provided by comparative anatomy, embryology, the fact of extinction, behavior, the fossil record, vestigial organs, biogeography (i.e., the distributions of various plant and animal groups), and the experience of plant and animal breeders active in his day

17

Darwin's Five Theories

1) evolution per se: change
2) common descent: theory that every group of organisms descended from a common ancestor (so, all species can ultimately be traced to a single origin of life on earth)
3) multiplication of species (speciation causes biological diversity)
4) gradualism: evolutionary change by gradual genetic change
5) natural selection: was the mechanism for evolution

18

Similarities b/t Lamarck and Darwin (3)

1) evolution was occurring (lineages change)
2) a continually changing world drives evolutionary change
3) the rate of change is slow ("gradualism")

19

Difference b/t Lamarck and Darwin (6)

1) inheritance (L: soft, D: hard)
2) extinction (L: no, D: yes)
3) orthogenesis (L: yes, D: no)
4) common descent (L: no, D: yes)
5) speciation (L: no, D: yes)
6) environment (L: creates variation, D: sorts variation)

20

The Darwinian Revolution (6)

-challenged beliefs of his day
1) the belief in a constant world of limited age (world hasn't changed much since its creation)
2) the belief that the world was designed by a wise and benign creator
3) the belief in the immutability of species (fixed and unchanging)
4) the belief of man being unique
5) the belief of essentialism (variation IS actually important)
6) the belief in natural "laws" of science (like in physics or chemistry)

21

Darwin's formation of the principle of NATURAL SELETCIONG

-example of syllogism (form of reasoning where conclusion is drawn from given assumptions)
-5 facts, 3 inferences (only 2 inferences were discovered by Darwin)

FACTS:
1) Natural populations have large excess reproductive capacities.
2) Population sizes generally remain stable.
3) Resources are limiting.

Inference 1) A severe struggle for existence must occur among individuals of a species in
nature.

4) An abundance of variation exists among individuals of a species.
5) Some of this variation is heritable.

Inference 2) Genetically superior individuals outsurvive and outreproduce others.
Inference 3) Over many generations, evolutionary change must occur in the population

22

Evolution by natural selection

-“Changes in the relative frequencies of different genotypes (genes) in a population because
of differences in the survivorship and/or reproduction of their phenotypes”.
-what persists over evolutionary time are genes, not organisms
-natural selection favors more “efficient” gene transport machines b/c individuals that do not efficiently transport genes into subsequent generations will quickly be displaced by individuals possessing genes that do

23

Important principles of natural selection (4)

1) Natural selection acts at the level of individuals, not populations
-a genotype may produce a # of diff phenotypes depending on environmental conditions, so selection acts directly on phenotype and indirectly on genotype
2) Populations, not individuals, evolve
3) Natural selection is retrospective and cannot predict the future
4) Natural selection is not necessarily progressive (chance plays impt role-like environment)

24

Fitness

-Darwinian fitness: the number of gene copies a phenotype places into the next generation
-relative fitness: a phenotype’s Darwinian fitness relative to other phenotypes

-relative fitness more relevant to understanding natural selection: what matters is how well a genotype does relative to the rest of the population

25

How do we measure fitness? (4)

1) fitness is a description, not an explanation: measures reproductive success of diff genotypes and quantifies biological differences among individuals that cause differential survival and reproduction
2) fitness is an average property: average probability of survival and/or reproduction of a genotypic class; an individual's probability of survival to a certain age is either 0 or 1
3) fitness is "relative": fitness of a given genotype or individual is measured relative to other genotypes or individuals ("selection coefficient" quantify the magnitude of selection acting against the 2 genotypes that are not fixed at 1, i.e., "s" and "t")
4) Total fitness is comprised of several individual components: an individual’s total fitness is a measure of its ability to transmit genes to the next generation through the production of progeny (included are components due to differential viability, longevity, and fecundity)

26

Forms of natural selection (3)

1) purifying selection: selection acting against deleterious (harmful) alleles
-“mutation-selection balance”: rate of introduction by mutation = rate of removal by selection (in homozygous state)
-purifying selection acts to prevent harmful alleles from becoming common in natural populations (prevent polymorphism)

2) directional selection: opposite of purifying- directional (or positive) selection is when a selectively favored allele is introduced into and sweeps through the population to become fixed (i.e., reach a frequency of 1.0)

3) balancing selection: form of natural selection that lead to active maintenance of genetic variation in natural populations
-at this equilibrium state, alleles are maintained at certain frequencies, determined by the
relative selection acting on the various genotypes, and if the frequencies are perturbed from this equilibrium point, selection will act to return it to this point
-kinds of balancing selection?
a)OVERDOMINANCE: this arises when the heterozygote is more fit than either alternate homozygote (strong advantage of heterozygotes can lead to marked departures from H-W equilibrium)
b)FREQUENCY-DEPENDENT selection: genotypes may use resources differently, such that the fitness of a
genotype is dependent on what other genotypes happen to be present in the population (if the “A” allele is low in frequency, the fitness of the AA homozygote is high, as the “A” allele increases in frequency the fitness of AA will decline)
-this leads to a stable equilibrium state at p = q = 0.50. At this point, the fitness of the
heterozygote is less than either homozygote (this is an example of negative frequency-dependent selection)
c) SPATIALLY- or TEMPORALLY-VARYING selection: produced by variable environments – some
genotypes are more fit than others in some habitats, or under some environmental conditions
(typically different seasons), than others.
-in the absence of gene flow, the “A” allele would be fixed in environment A and the “a” allele
would be fixed in environment B, however, because individuals move between the two areas a polymorphism may result

27

Phylogenetic Inference (2)

1) phylogenetic trees are hypotheses (some w/ very strong support, some w/ very little)

2) gene trees are not always the same as species trees (species trees-> speciation of the group; gene trees->show the evolutionary relationships among DNA sequences for a locus

-spp. A is more closely-related to spp. B than it is to spp. C = spp. A and B share a more recent common ancestor than either does with spp. C
-inferring the phylogeny of a group is thus simply a matter of determining the branching pattern
that describes these ancestral relationships
-in the context of phylogenies, we deal with “characters”.
-characters can be morphological, behavioral, physiological, or molecular
-characters can be either ancestral or derived

28

(2) assumptions about the characters used to construct phylogenies

1) they are independent

2) they are homologous (a character shared by two species because it was inherited from a common
ancestor)
-if a similar character or trait is possessed by two species but was not possessed by all the
ancestors intervening between them, it is said to exhibit “homoplasy”
- homoplasy can result from convergent or parallel evolution, or from evolutionary reversals (reversals are very common at the DNA sequence level because there are only four nucleotide
bases)

29

Difference between convergent and parallel evolution

1) convergent: involves distantly-related species.
-similar adaptation results from different genes and/or developmental pathways (ex: convergent evolution between placental and marsupial mammals)

2) parallel: involves closely-related species (or sometimes populations of the same species).
-similar adaptation results from the same genes and/or developmental pathways (ex: evolution of lactose tolerance in humans has evolved independently at least 3 times)

30

Monophyletic, paraphyletic, polyphyletic groups

-monophyletic: derived from a single ancestral species and includes all descendants (ex: mammals)

-paraphyletic: derived from a single ancestral species but does not include all descendants (reptiles b/c they do include birds)

-polyphyletic: derived from more than one ancestral species and omits the most recent common ancestor (e.g., pachyderms including both elephants and rhinoceros on the basis of their thick skins)

31

Pheneticists vs. Cladists

-Pheneticists (or "Distance methods/trees"):
1. reflect overall degree of similarity
2. *be based on as many characters as possible*
3. minimize the overall distance between taxa
-a strange feature is that arriving at the true phylogeny is not an explicit objective
-the tree produced (sometimes called
a phenogram) also imparts information through its branch lengths->short branches between taxa: high genetic similarity, long branches: more distant relationships

-Cladistics:
1. reflect the true phylogeny
2. be based exclusively on synapomorphies (characters that are shared and derived)
3. be rooted by one or more outgroup taxa.
- the outgroup is chosen to reveal the ancestral states of characters (picked from fossil evidence, so, it belongs to a genus or family that
existed prior to the ingroup upon which the phylogeny is based)
-unlike distance trees, the tree produced (called a cladogram) carries no information in its branch lengths
-one problem in evaluating cladograms is the large # of possible trees to be considered (the # of possible trees increases dramatically with the number of taxa) How to decide best tree? Two approaches:
1)maximum parsimony: the best tree is that which minimizes the number of evolutionary steps (i.e., changes among characters)
-the smaller number of changes required, the better the tree
-this is Occam’s razor: simpler explanations should be preferred over more complicated ones
2)maximum likelihood: the best tree is that which has the highest likelihood, or highest probability, of being produced (obtaining this set of DNA sequences)
-maximum likelihood tends to perform better than maximum parsimony but is computationally intensive

32

Evaluating tree support by bootstrapping

Step 1) randomly select one of the positions to be the first position of the re-sampled data (say, site 7)
Step 2) randomly select a second base to be the second position (say, site 4)
Step 3) generate a complete data set of 500 base pairs long (sampling the original data with
replacement)
Step 4) construct a tree from this data and record if the groupings match those seen in the original tree
Step 5) repeat this process a large # of times (say 1,000)
-phylogenetic trees with BOOTSTRAP SUPPORT VALUES below 70 have minimal support for percentage of groupings seen in the original tree and should be viewed with caution
-tree is accurate if > ~90

33

Mutation (4)

-mutations represent “raw material” for the evolutionary process

1) point mutations
2) “Copy-number” mutations
3) chromosomal mutations
4) Genome mutations

34

1) Point mutations

1) Point mutations: simplest types of mutations occur at single base positions of DNA
- four categories of point mutations:

1. transitions: A to G, C to T
2. tranversions: T to A, C to G
3. insertions
4. deletions

-within coding regions point mutations can involve silent (or synonymous) or replacement changes (or nonsynonymous->alter AA sequence).
-insertions/deletions occurring within coding regions of DNA give rise to frameshift mutations
whereby the correct reading frame is disrupted.
-transitions outnumber transversions (b/c they are easier mistakes to make) and silent changes outnumber replacement changes

35

2)“Copy-number” mutations

2) “Copy-number” mutations: these mutations change the numbers of genetic elements

-gene duplication events->a single gene is duplicated, typically results in the new gene copy being close to the progenitor copy
-over time, this process may lead to the development of gene families where a number of copies are physically clustered in chromosomes (the mechanism responsible is unequal crossing over)

-a “retrogene” (rare) is a gene duplicated and copied into diff chromosomal regions and has an identical exon(coding region) structure to the ancestral gene but lacks introns

-transposable elements (TE’s): AKA jumping genes b/c they can move about the genome, copying
themselves and inserting into diff places (a process called replicative transposition
-three major classes of TE’s:
1. Insertion sequences (700-2600 bp)
2. Transposons (2500-7000 bp)
3. Retroelements
-TE effects include: altering gene expression, increasing mutation rates, and causing chromosomal rearrangements

36

3) Chromosomal mutations

-2 major types: inversions and translocations

1) inversions (common in insects): a piece of a chromosomal flips around and becomes integrated in the opposite direction
-causes suppression of recombination, so, the genes locked within an inversion can coevolve to function optimally as a concerted group giving rise to what are called coadapted gene complexes

2) translocations: a piece of chromosomes breaks off and moves to a new region
-may affect transcription

-“Robertsonian fusions and fissions”: mutations affecting the karyotype

37

4) Genome mutations

-at the "highest" lever, the entire genome may be duplicated (these are called polyploidization events)
-ex) diploid (2N) species -> tetraploid (4N) species
-polyploidy has played a major role in the evolution of plants (due to self-fertilization)

38

How do genes with novel functions evolve?

-having data from complete genomes can determine how different classes of genes evolve and diverge over evolutionary time
-the major mechanism is gene duplication followed by acquisition of novel function
- the evolution of complex structures (like eyes or wings) is very poorly understood because they lack clear correspondence to earlier features
-ex) treehoppers: developed helmets from bilateral buds and shares a number of features in common
with wings (first time in 250 MY of insect evolution that a group has evolved the ability to express wing-like structures from the first thoracic segment!)

39

The Hardy-Weinberg-Castle Equilibrium

-if mating is "random" the frequencies of matings among different genotypes are determined simply by their frequencies
- p^2 + 2pq +q^2 = 1
-p & q: frequencies
-p^2 and q^2: proportions

-3 conclusions from HWE:
1)Allele frequencies will not change from generation to generation
2) Genotype proportions will occur according to the “square law”
-two alleles: (p + q)^2 = p^2 + 2pq + q^2
-three alleles: ( p + q + r)^2 = p^2 + q^2 + r^2 + 2pq + 2pr +2qr
3) HWE occurs independently of allelic frequencies

Assumptions of HWE:
1. Random mating
2. Infinite population size (no genetic drift)
3. No migration (no gene flow)
4. No mutation
5. No selection

-HWE states that allele frequencies in populations will not change unless some evolutionary process is acting to cause a change, therefore, HWE predicts that no evolution will occur unless one of the above assumptions is violated
-so, microevolution is largely concerned with understanding the conditions under which the above assumptions are violated.
-it involves determining the relative importance of random drift, migration, mutation, and
natural selection in affecting the frequency of genetic polymorphism in natural populations

40

Testing for HWE

1) Estimate genotype frequencies
2) Estimate allele frequencies (check that p+q=1)
3) Estimate expected genotype frequencies under the assumption of HWE
-Expected # of A1A1= p^2 x N
-Expected # of A1A2= 2pq x N
-Expected # of A2A2= q^2 x N
4) Compare observed and expected numbers of genotypes
-we can test if the proportions differ significantly by performing a Chi-square test (if they are then an assumption may be being violated)

-what is we had a mixed population? Wahlund effect: a deficiency of heterozygotes
-there will be a marked departure from HWE due to the violation of the random mating assumption.

-example of directional selection: use equations and calculate relative fitnesses (w1, w2, wbar)

41

Mean population fitness (wbar)

-natural selection acts to maximize mean population fitness
-natural selection favors, and ultimately fixes, an advantageous allele (during directional selection)
-natural selection will prevent less fit genotypes from invading a population

-2 conclusions:
1) natural selection results in a maximization of mean population fitness at the equilibrium frequency of the A and alleles (if the frequencies are perturbed from this point, then overdominant selection will return them to this equilibrium point)
2) the population never realizes its highest possible fitness (i.e., that of the
heterozygote = 1) but is maintained at a reduced level because of the maintenance of the polymorphism (this is a type of GENETIC LOAD
incurred by the population)

42

Shifting balance theory

- the concept of an adaptive landscape: a multidimensional representation of mean population fitness as a function of allele frequencies at multiple loci
- this surface was covered by many peaks separated by valleys of reduced fitness
- under this model, natural selection would act to push populations up to local adaptive peaks but
not necessarily the highest “global” peak
- once at a local peak, the population would be stuck, its ability to move across a saddle of
lower fitness to reach a higher adaptive peak would be prevented by selection
- Wright argued that random genetic drift could act to move populations off local peaks, across valleys, and on to higher adaptive peaks
-for this process to occur, however, natural populations must be small (so the effects of drift are large) and experience little gene flow.
-large controversy as to how feasible this model is b/c natural populations are too large

-example where a population can get "stuck" on a lower fitness peak: sickle-cell case HbC->has the highest fitness (1.3) but can't invade the population at the stable equilibrium point for the A and S alleles b/c it would have to traverse a valley of reduced fitness (the AC and SC heterozygotes)-natural selection will act to oppose any movement off the local AS peak (fitness of 1)
-the population could get onto the higher CC peak if inbreeding results in the production of CC
homozygotes in a small isolated population, or if random drift happened to cause a higher
frequency of the C allele

43

Mutation

-the process that fuels evolution
-w/o mutations into natural populations, genetic variability will eventually be lost and the population will become monomorphic, but is very inefficient b/c it only causes evolutionary change at individual loci within natural populations
-so, the rate of change due to mutation pressure is exceedingly small
-despite this fact, mutation rates are sufficient to generate large pools of genetic variation in
natural populations, b/c there are many loci capable of mutating and there are typically many individuals in a population in which these new mutations can occur

44

Migration/gene flow

-gene flow is the movement of gametes or individuals among populations
- unlike selection, drift, and mutation that occur within single populations, gene flow refers to a process that occurs among populations
- gene flow, if unopposed by other factors (i.e., selection, drift, or mutation) will lead to the
homogenization of different populations of a species
- this means that allele frequency differences that existed among the populations will be
eliminated by gene flow
- gene flow is thus the most important process determining population structure

45

How rapidly does gene flow occur?

-the magnitude of gene flow is determined by m
m= the proportion of genes entering a population in individuals immigrating from other populations
-∆p = m(p2 - p1)
-this tells us that the relative change in frequency in population 1 is determined by the
allele frequency difference between population 1 and population 2 and by the level of gene
flow
-allele frequency differences among populations can be rapidly eliminated
-if unopposed by selection, gene flow will always result in the elimination of genetic
differences between populations

46

Random genetic drift

-drift is now realized to play an important role in evolution, especially at the molecular level
-random genetic drift may be defined as random changes in the frequencies of neutral alleles from generation to generation caused by “accidents of sampling” (random events that result in mistakes in the transmission of genes across generations- these accidents of sampling arise because populations are finite in size

47

Random genetic drift: How can alleles be neutral?

1)Mutations in non-coding DNA regions (most point mutations in most non-coding DNA sites are likely to be neutral in their phenotypic effects)

2)Mutations involving silent, or synonymous, changes (no amino acid substitution)
-however, CODON BIAS (the nonrandom usage of codons specifying the same amino acid) at some genes in bacteria, yeast, and Drosophila suggests that even silent mutations may not be entirely neutral; this only happens in genes expressed at high levels

3)Mutation among very similar amino acids (change too small to be significant)

48

Random genetic drift: How does it occur?

-the magnitude of random drift is more prevalent in small populations (red and white balls)
-the smaller the population, the greater the chance that sampling error will result in allele
frequency
-random fluctuations in the transmission of genes will tend to “even out” in very large populations by the law of large numbers.
-therefore, the magnitude of random genetic drift is simply inversely proportional to the effective
population size
-each generation, a population will lose variation in proportion to the term 1/2Ne, where Ne is the
effective population size

49

Random genetic drift: Some properties (5)

1) Magnitude inversely proportional to effective population size (Ne)
2) Ultimately results in the loss of variation from the population
3) The probability of fixation of a neutral allele equals its frequency in the population
4) Random drift will cause isolated populations to diverge genetically
5) Is accentuated during population bottlenecks and founder effects

50

Random genetic drift: What is effective population size?

-the effective population is roughly equivalent to the # of breeding individuals in the population; this will always be lower than the current # of individuals present in the population (this is the CONTEMPORARY effective size)
-EVOLUTIONARY effective size: strongly influenced by the longer-term history of a population (that is largely responsible for its standing levels of genetic variation)

- 3 factors strongly effect effective population size:

1)Fluctuations in population size
-if populations fluctuate in size over time, the effective size = the harmonic mean of the
actual population numbers (which can be strongly influenced by the smallest population sizes-pulls the mean down to make it look like the current effective population size is a lot smaller)

2)Unequal #s of males and females
-the sex which contributes a lower # of gametes will experience a “bottleneck” and thus be subject to genetic drift

3)Variance in reproductive success
-if there is a large variance in the # of progeny produced by individuals the effective population size is further reduced below the census size

- all of these factors contribute to making effective population sizes considerably lower than what we may think from current population sizes

51

Genetic Bottlenecks and Founder Effects

Genetic Bottlenecks: severe reductions in population sizes->may dramatically reduce genetic
variation through pronounced genetic drift
-ex: elephant seals hunted until near extinction, rebounded but now no genetic variation, and cheetahs who must have gone through at least 2 severe bottlenecks b/c of their little genetic variation
-the loss of genetic variation by population bottlenecks is a direct cause of genetic drift
-the DURATION of the bottleneck (i.e., the # of generations spent at a reduced population size) is more important in determining the loss of
genetic variation by genetic drift than the actual population size itself; if short->little heterozygosity is lost, if long-> then random
drift can greatly accelerate the loss of alleles
-genetic bottlenecks also cause an increase in inbreeding in the population, inbreeding does not actually cause alleles to be lost from the population but simply shifts the distribution of genotypes to have more homozygotes than expected under random mating which will typically result in the expression of deleterious recessive alleles in homozygous state leading to the phenomenon of INBREEDING DEPRESSION

Founder Effects: the reduced genetic diversity that results when a population suffers genetic bottlenecks

52

1) gene flow vs random drift
2) gene flow vs selection
3) selection vs random drift

1)gene flow vs random drift: for neutral alleles, random drift and gene flow will act in opposition to each other
-random drift leads to the genetic divergence of populations
-m (strength of migration) and N (the effective population size) dictate magnitude of random drift
- if Nm > 1, gene flow overrides drift, populations are will remain genetically identical
- if Nm < 1, gene flow is too low, random drift can lead to genetic divergence

2)gene flow vs selection: gene flow and selection can act in opposition if selection favors different alleles in different populations
- s (strength of selection) and m (magnitude of gene flow)
-if m > s, gene flow can overpower the affect of selection in local populations (no genetic change)
- if s > m, then selection can override the impact of gene flow and result in “local adaptation”

3)selection vs random drift: random genetic drift and natural selection will act in opposition when population sizes become too small for the selective process to operate
-strength of selection (determined by the selection coefficient, s) and the effective population size (that will determine the extent of random drift)
- if Ns > 10, selection controls the fate of the allele
- if Ns < 1, drift will overpower the effect of selection
-when population sizes become too small the random fluctuations caused by drift exceed the deterministic selective trajectory, therefore, the same allele with the same selective advantage will be selected in a large population yet behave as if it is neutral in a small population (because random drift will override the effect of selection).
- in the first case (large population), directional selection will always result in the fixation of the allele
- in the latter case (small), the allele may drift to either fixation or loss

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“Classical” vs. “balanced” views of genome structure

-began w/ 2 schools of genetics: naturalists (who studied natural pops) and Mendelians (whose research was exclusively in the lab)
-gave rise to: “Classical” and “Balanced” schools
of genome structure

1)classical (Mendelians): viewed the genome as homozygous for "wild-type" alleles, interspersed throughout w/ deleterious recessive alleles (-) present at low frequencies

2)balanced (naturalists): believed that natural populations harbored large amounts of genetic variation
-developed the view that there was no such thing as "wild-type" alleles – the majority of loci possessed two or more alleles and the most fit state was heterozygous not homozygous

-adaptation&speciation: C->difficult, B->easy (lots of raw material available for natural selection)
-selection primarily for: C->purifying (remove deleterious alleles from populations risen from mutation), B->balancing
-population variation: C-> inter>intra, B-> intra>inter (so much variation within populations)
-polymorphism: C->shortlived (mildly deleterious or neutral alleles wander through populations by random drift, eventually being lost or going to fixation), B->longlived (polymorphisms are balanced)

-discovery of abundant protein polymorphism vindicated the balanced school, however, the classical school had a very simple way to explain this excess variation - it is "neutral" in its effect on the phenotype and since it has no effect on fitness, most loci have the equivalent of homozygosity for wild-type alleles

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What led Kimura to propose the neutral theory? (2)

1)segregational load: refers to if balanced polymorphisms (large amounts of variation) are maintained in a species population then each generation's less fit genotypes are maintained, reducing the population fitness
-Segregational load = st/(s + t)
-for the sickle-cell polymorphism, the load is ~11%, in other words ~11% of the population dies every generation because of this polymorphism!
-if balancing selection is incapable of maintaining large #s of loci at polymorphic equilibria, then the only viable alternative is that the majority of polymorphic loci are neutral in their
effects on the phenotype

2)the molecular clock: many proteins (observed from fossil records) exhibited a constant rate of amino acid divergence over evolutionary time, they followed a “molecular clock”.
- the “clock” was observed to “tick” at different rates for different proteins – some evolved very
quickly (e.g. alpha-globin) compared to others (e.g., histones)
-however, Kimura believed that the rate of evolutionary change is more dependent on the properties of the molecule than the environment- he though the constant rate of amino acid substitutions per year was more easily explained by the fixation of neutral mutations rather than natural selection/environment

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Neutral Theory

1)The rate of protein evolution is roughly constant per site PER YEAR
2)Rate of substitution of neutral alleles equals the mutation rate to neutral alleles
-this rate is unaffected by population size!
3)Heterozygosity levels are determined by the “neutral parameter”, 4Neu
-if 4Neu >> 1 then heterozygosity is high, if 4Neu is << 1 then heterozygosity is low
-in species with large, stable effective population sizes the amount of polymorphism can, in principle,
approach 100%
4)Rates of protein evolution vary with degree of selective constraint
- “selective constraint” represents the ability of a protein to “tolerate” random mutations
- for highly constrained molecules, most mutations are deleterious and few are neutral (slow rate of evolution)
- for weakly constrained molecules, more mutations are neutral and few are deleterious (fast rate of evolution)
- functionally less important molecules,thus evolve at faster rates than more important ones

-neutral theory predicts that polymorphism is simply a transient phase of molecular evolution as
neutral alleles wander aimlessly through populations by random drift and ultimately produces fixed differences b/t species
-it also predicts that the dynamics of silent and replacement polymorphism should be similar
-the degree of constraint dictates the level of polymorphism observed and also the rate of
evolution
-the proportion of replacement to silent changes that are polymorphic within species
should be similar to the proportion of replacement to silent changes that are fixed between species

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Neutral theory: Positive selection

-when a protein’s rate of nonsynonymous substitution exceeds its rate of synonymous substitution, this suggests that most amino acid changes are beneficial and have fixed by natural selection
- positive selection reflects the long-term outcome of repeated selective sweeps
-ex) "arms race" host-pathogen interactions, and reproductive genes (antagonistic coevolution)
-Conclusion: Natural selection may be more important in directing molecular evolution than
previously believed!

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Sexual and asexual reproduction

-2 features that distinguish sexual from asexual reproduction: meiosis and syngamy
1)meiosis: the process by which a diploid organism produces haploid gametes
2)syngamy: the fusion of two haploid gametes to produce a diploid zygote

-meiosis-> each gamete, while possessing
half of the parental genotype, carries a unique combination of parental genes
-therefore, sexual reproduction is capable of generating a wider variance of phenotypes

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How and why did sex evolve?

-in many species, sexual reproduction is associated with the evolution of anisogamy (the presence of large eggs and small sperm)
-phylogenetic evidence clearly shows that anisogamy evolved from isogamous organisms (ex:yeast and algae) where cells of the same size unite if they belong to different mating types (i.e., + and -)
-anisogamy can evolve if one genotype (female) is
favored because the large size of its gametes enhances the survival of its offspring
-another genotype can then be favored by virtue of its making many small gametes (male)
-recombinants formed between these “parental” forms are expected to be less fit

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Linkage disequilibrium

-Linkage equilibrium: occurs when the genotype present at one locus is independent of the genotype at a second locus

-Linkage disequilibrium: occurs when genotypes at the two loci are not independent of another
-if alleles at a gene controlling gamete size, G, (alleles for small size, S, and large size, L) enters a population in which two alleles already exist at a mating type locus, M, (+ and -), then selection will favor the two loci to become tightly-linked, causing linkage disequilibrium

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Linkage disequilibrium: What causes it? (3)

1)Natural selection: this may occur either by a selective sweep (directional selection favors a beneficial mutation) or by epistatic natural selection (the fitness of a genotype at one locus depends on its genotype at another locus)
- when directional selection favors a beneficial mutation, it will “drag” along with it other tightly linked mutations
- this process is called genetic hitchhiking

2)Random genetic drift: this is much less effective than selection in creating disequilibrium.
- sizable disequilibrium can only occur from large genetic bottlenecks or founder effects
- however, in a large population random drift is too weak to cause measurable nonrandom associations of genotypes

3)Population admixture: the mixing of 2 differentiated groups will create disequilibrium only if they possess different frequencies of chromosomes
- can be as important as selection in creating disequilibrium

-What eliminates linkage disequilibrium? RECOMBINATION!

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Why sex?

-sex: large intrinsic advantage
-asexuals represent less than 0.01% of all species
-phylogenetic distribution of asexual species suggests that they do arise continuously from
sexual species
-asexual species are observed at the tips of phylogenetic trees, suggesting that these asexual lineages flourish for relatively short periods of time but typically become extinct long before closely-related sexual groups

Q: Why then do asexual species only occur on the tips of phylogenetic trees?
A: Because of the short term advantages of asexual reproduction lose out to the long-term
benefits of sexual reproduction

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Costs of sex (4)

1)The cost of producing males (AKA the “two-fold cost of sex”): if females reproduced asexually, eventually there would only be females and no males

2)The costs of finding mates (may not be able to find one if pop density is low or if on isolated "island")

3)The costs of mating: risky, lots of time&energy->courtship (vulnerable to predation), mating, stds

4)The cost of recombination: recombination not only leads to the production of unique gene combinations, it also breaks them apart.
-therefore, genotypes with unique combinations of genes favored in one generation in one particular environment will not be conserved in the next generation
-this may be viewed as a cost but must obviously be weighed against the benefits provided by
recombination

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Benefits of sex (3)

1)Adaptive evolution is enhanced: with recombination, it is easy to produce a genotype that possesses two or more advantageous mutations (greatly accelerating the rate of adaptive evolution)

2)The Red Queen hypothesis: species populations have to continuously evolve to track
changing environments just to keep even
-if they fail to adapt to the changing conditions, they are liable to go extinct
-predators are becoming better predators, competitors are becoming better competitors, parasites are becoming better parasites
- if a species does not continuously keep up it is likely to be displaced by a competing species

3)Muller’s ratchet: sexual and asexual populations have to deal with harmful deleterious mutations, the most fit clones possess the lowest number of mildly deleterious mutations, but this group is
unlikely to be the most frequent...by chance, this clonal group has the possibility of going extinct by random drift
- when this happens, the fittest genotype has been lost - “Muller’s ratchet” has made another turn
- now the most fit group has one more deleterious mutation than before - the “mutational load” has increased
-there is only one direction for asexual populations to move - towards ever greater loads of
deleterious genes, therefore, asexual populations are expected to gradually decline in fitness

-sexual reproduction breaks the ratchet! when the least mutated class in a sexual population is lost be drift, recombination can recreate the lost mutational class having the highest fitness
-advantageous mutations that drive progressive
evolution have a better chance of being decoupled from deleterious genetic backgrounds
-sexual populations will enjoy a higher rate of adaptive evolution

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Quantitative traits/genetics

-continuous/polygenic variation among individuals
-2 charcteristics:
1)they are influenced by many genetic loci
2)they exhibit variation due to both genetic and environmental effects

-QTLs ("quantitative trait loci"): they possess multiple alleles, exhibit varying degrees of dominance, and experience selection and drift
-some QTLs exhibit stronger effects than others – these are called major effect and minor
effect genes
-the total number and relative contributions of major effect and minor effect genes underlies the
genetic architecture of the trait

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Heritability

-heritability estimates the proportion of the total phenotypic variation that is due to
genetic rather than environmental effects

-"broad sense" heritability:
VP = total phenotypic variance
VG = genetic variance
VE = environmental variance
VP = VG + VE
-then heritability = VG / VP

“narrow-sense” heritability: only incorporates the additive component of genetic variance
-additive (VA), dominance (VD), and epistatic (VI) (or “interactive”) effects
VG = VA + VD + VI
heritability = h2 = VA/VP
-ex) the heterozygote exhibits a phenotype that is exactly intermediate between the two alternative homozygotes (A1A1: 1 bristle, A2A2: 3 bristes, so A1A2: 2 bristles)

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Estimating heritability

-most common is to compare the resemblance between
parents and their offspring
-we can then estimate heritability by regressing the offspring values against the midparent
values (the slope of this regression line is an estimate of heritability)

Midparent-offspring h2
Parent-offspring 1/2h2
Half-sibs 1/4h2
First cousins 1/8h2

- as the groups become less related, the precision of the h2 estimate is reduced
-we can predict the response to selection by the prediction equation (the “breeder’s equation”):

R = h^2S

- here, R is called the response to selection and S is the selection differential
- the selection differential is equivalent to the strength of selection acting on the trait quantified by the difference between the mean of the selected group and the original population
- heritability usually remains constant over a sizable number of generations giving us a
constant and predictable response to selection
-heritability estimates in natural populations are commonly very high

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Selection on quantitative characters (3)

1)Directional selection: increases or decreases the mean of a quantitative character in a consistent
manner over a number of generations
-also reduces the amount of variation in the population, but this depends on the intensity of
selection and the heritability of the trait

2)Stabilizing: most common form of selection
-individuals with intermediate phenotypes have the highest fitness and those with extreme phenotypes the lowest fitness (small gall size attacked by wasps, large by birds, so intermediate size is favored)
-selection thus does not change the mean of the character but reduces its variance

3)Disruptive: extreme values of a phenotypic trait have the highest fitness
-unlike stabilizing and directional, this selection increases the amount of phenotypic variation of the selected trait but may not change the mean
-occurs less frequently than the other two

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Adaptation

-Acclimatization: the physiological adjustment of individual organisms to different
conditions (e.g., temperature, photoperiod)->no genetic change

-to evolutionary biologists, adaptation is used in 2 very different contexts:

1)The process of becoming adapted (AKA natural selection)
-for the process of adaptation to occur, genetic variation and differences in fitness must exist among individuals in the population

2)The state of being adapted
-refers to the end-point of this adaptation process
-individual characters of organisms are viewed as adaptations

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How do we study adaptations? (2)

1)The experimental approach: hypotheses for the adaptive origins of traits are tested by experiments
(ex: wingwaving fly to deter jumping spiders)
-we still have no insights into whether the markings and wavings evolved explicitly for mimicking jumping spiders, or whether both traits evolved for a different reason and then were “co-opted” for this new function

2)The comparative approach: hypotheses for the adaptive origins or traits are tested by:
(a) performing comparisons among species
(b) making observations among individuals within species
-to undertake statistical comparisons it is necessary to correct for lack of independence (bat testes size could be dependent from common ancestors)
-3 steps in carrying out the so-called “adaptationist program”:
1. Observe or describe some organism trait.
2. Formulate an adaptive hypothesis for the evolution of that trait.
3. Test hypothesis by experiment or by collecting additional data
-it is necessary to subject these hypotheses to further tests and consider the likelihood of
alternative explanations, not simply uncritically accept a hypothesis because it is plausible