Evolution Exam 1

Question 1

Biological evolution

Answer 1

changes in lineage of organisms over successive generations, descent with modification

Question 2

Nonoverlapping magisteria

Answer 2

two worldviews that are not necessarily exclusive from one another

Question 3

How do pathogens serve as evidence for evolution?

Answer 3

Antibiotic resistance occurs via a process of rapid evolution of pathogens. Some evidence that supports this is that the prevalence of resistant bacteria is correlated with the amount of antibiotic use

Question 4

What are some reasons why resistant mutations for pathogens evolve quickly?

Answer 4

There is a rapid generation time since bacteria quickly reproduce, have a high mutation rate, and a large population size. Plasmid exchange can also occur between bacteria which further accelerates resistance

Question 5

What are some incidences that serve as evidence of evolution in response to human activity?

Answer 5

In bighorn sheep human hunting is correlated with a smaller body size at sexual maturity

In an alpine plant commercial harvesting is correlated with increased incidence of camouflage

Elephants tracked over time were shown to lose their tusks with poaching pressure

Peppered moth developed camouflage (either as light grey or black) as urban areas developed. A single and recent mutational origin was identified and became prevalent due to gene flow

Question 6

What are some examples of laboratory breeding experiments that serve as evidence for evolution? What about outside the lab?

Answer 6

Selection for change in morphology can show an upwardly selected line and downwardly selected line (more leg bristles in drosophila were downwardly selected)

Selection for change in behavior can be used to identify control lines and selected lines (female selection)

Domestication and crop domestication can be used to look at trends outside the lab

Question 7

What are some examples of evidence showing a shared and common ancestry of present day species?

Answer 7

Fossil records can show transitional forms such as a tetrapod which was a transitional species between fish and limbed vertebrates. It had fish like characteristics (gills, scales, fins) and tetra pod like characteristics (shoulder, elbow, wrist, mobile neck).

Developmental genetics was also used to identify Hox genes which are expressed in both the paws of mice and fins of fish, and this points to a common ancestor

DNA sequencing can be used to look at the degree of shared genetic information between species and look at if that matches expected evolutionary relationships due to shared ancestry. Both the coding and noncoding regions of the genome can be used and the % of nucleotide divergence in any gene is proportional to how long ago the two lineages diverged

Homologous structures can also reflect a shared common ancestry

Biogeography can be used to find correlations between geographic distance and phenotypic similarities which reflect speciation from a shared ancestor from particular area

Question 8

Essentialism

Answer 8

Also known as the platonic ideal. This is the Pre-Darwinian worldview that posits that everything in the universe has a single ideal form which is unchanging and “perfect” and that humans see the variable and “imperfect” earthly manifestations of that ideal. Under this notion variation = imperfection

Question 9

How was the idea of essentialism applied to species?

Answer 9

Aristotle posited that each species has a single ideal form and that species can be arrayed along a single axis from the “lowest” or least complex to the “highest” or most complex on the “Great Chain of Being”

This was then incorporated into a biblical worldview known as “special creation” which posits that each species is created independently as part of a divine Creation and that species are unchanging

Question 10

Thomas Malthus

Answer 10

Posited that resource limitation is an inevitable consequence of exponential growth and that all species, especially humans, produce more offspring than can survive

Question 11

What was Darwin’s theory on evolution?

Answer 11

Darwin posited natural selection, where all species have the potential to exponentially reproduce but all species have limited resources. This means that there is always competition for resources within species and the best competitors differentially survive and reproduce. Credited Malthus for this

Darwin additionally posited that heritable traits that make some individuals better competitors will be disproportionately represented over successive generations causing gradual shifts

Worked with Alfred Russel Wallace to present to the Royal Society of London and Darwin published the Origin of Species a year later

Question 12

What are five theories of evolution in the Origin of Species?

Answer 12

Species evolve over time, this idea was quickly accepted by Darwin’s contemporaries

Species have shared common ancestors, this was supported by paleontological, anatomical, and biogeographical data. In July 2016 more evidence was found supporting an origin of life in hydrothermal vents. Accepted by contemporaries

Gradualism where evolutionary change occurs through small, incremental steps. This was challenged by contemporaries including T. H. Huxley. Darwin believed sudden transformations of species were unscientific and gradual shifts did not invoke a supernatural element

Species diversification where divergence from common ancestors creates a multiplication of species. This means that speciation is a branching process and accounts for why there is a wide variety of species, explanation for biodiversity. Accepted by contemporaries

Natural selection which is the differential survival and reproduction of some individuals over others in a population due to phenotypic differences. This leads to favored traits being differentially represented in the next generation if they are heritable. Required integration with Mendelian genetics and population genetics before being accepted by contemporaries in 1940s

Question 13

What are some misconceptions about natural selection?

Answer 13

Natural selection can lead to evolution but it refers to the differential survival and reproduction in one generation, does not look at successive generations

Natural selection does not create perfectly adapted organisms, it can create clumsy but workable solutions that reconcile trade offs (melanoma in fish results in increased sexual selection, long necks in giraffes means long nerves)

Evolution does not “progress” to any goal or purpose and there are no lower or higher species. No “missing links” since a great chain doesn’t exist. No species wild type since variation

Question 14

Microevolution

Answer 14

Evolutionary change within a species, lots of focus on genetic changes over successive generations

Question 15

Population genetics

Answer 15

Biological discipline that studies microevolutionary processes

Question 16

Population

Answer 16

Group of individuals of the same species that live in geographical proximity and reproduce

Question 17

Phenotypes

Answer 17

Measurable traits where variation may affect survival and reproductive success

Question 18

Mc1r

Answer 18

Gene responsible for pigment variation in geese, jaguar, lizards, etc. Partially responsible for red hair phenotype in humans and other phenotypes such as anesthesia susceptibility

Question 19

Discrete variation

Answer 19

Also known as Mendelian variation, refers to phenotypic variation that occurs in discrete classes. Qualitative traits such as a flower with 2 or 3 distinct colors are examples. Tends to be associated with simple inheritance and more uncommon in nature but is usually the focus of early genetic studies

Color of a clover plant corresponds to whether or not cyanide is produced from tissue damage (cyanogenesis). This is controlled by the Ac gene expression (substrate) and Li gene expression (hydrolyzing enzyme). If there is at least one dominant allele for both genes cyanogenesis results, it is an either/or scenario so falls under the discrete variation category

Question 20

Continuous variation

Answer 20

Tends to fall along a normal distribution, quantitative traits such as human height and disease risk are examples. These are typically polygenic with complex genotype and environment interactions, tend to be more common in nature

Question 21

What are some scenarios where phenotypic variation reflects the surrounding environment?

Answer 21

Ratio of red to far-red light wavelengths affects the height in plants where an ambient r:fr ratio results in elongated plants and a high r:fr ratio results in suppressed, shorter plants

In some turtle and alligator species, the temperature of egg incubation affects the sex determination and proportion of males in a clutch of eggs

Question 22

What are some methods to determine whether a trait has a genetic basis?

Answer 22

Crosses can be constructed to segregate trait variation for discrete traits

Correlations between traits of parents and offspring can be observed, but there are often confounding variables in these traits since parents and offspring tend to be in similar environments. Additional data is often needed to make stronger conclusions such as carrying out observations in a controlled, standard environment

Common garden experiments in controlled, uniform environments, sometimes occurs in nature where samples are collected from similar environments

Question 23

Genes

Answer 23

Previously defined as units of inheritance since genes and alleles were solely identified based on the phenotype they affect. Currently defined as units of transcription since some transcribed molecules are not translated such as ribosomal RNA

Question 24

Haplotype

Answer 24

Allele at the DNA sequence level. For diploid organisms 2 alleles are present for gene and haplotypes may be identical (homozygous) or different (heterozygous)

Question 25

What are common sources of variation between genes?

Answer 25

Single nucleotide polymorphisms (SNPs) result from point mutations

Insertions and/or deletions (Indel)

Within exons synonymous substitution can occur where a point mutation results in no amino acid change

Nonsynonymous substitutions can occur where a point mutation results in an amino acid change, this may not have a major effect on phenotype

Frameshift mutations result from insertions/deletions, often results from premature stop codons

Microsatellites are SSRs or simple sequence repeats. These are commonly used as genetic markers and determining biological diversity since there is a high mutation rate due to replication slippage and they result in high allelic variation in a population

Recombination due to meiosis

Question 26

Linkage disequilibrium

Answer 26

Nonrandom associations in the inheritance of alleles at different loci, can be quantified with the term D, looks at patterns of genetic recombination in larger populations

Question 27

What is the difference between linkage and linkage disequilibrium?

Answer 27

Linkage looks at the location of two genes on a chromosome in an individual, linkage disequilibrium looks at the degree of association between the inheritance of genes by measuring the level of recombination between two linked genes in a population

Question 28

Pleiotropy

Answer 28

Single gene with multiple phenotypic effects

Question 29

Epistasis

Answer 29

Interaction between different genes such that allelic variation at one gene affects the phenotypic expression of the other

Question 30

Haplotype genealogy

Answer 30

Since mutations generate allelic variation, haplotypes can be sequenced to track mutations at a specific haplotype across generations

A rooted haplotype tree can be generated if we know which mutations arise first. But if haplotypes are sampled from a population and we don’t know the root of the tree, patterns of relationships can be inferred with an unrooted haplotype tree

Question 31

What kinds of information can haplotype trees provide?

Answer 31

They can help provide information about movement between populations in a species. Species with large migration patterns tend to have haplotypes that differ from one another and species that live closer together tend to have more overlapping haplotypes

Question 32

What assumptions are made when using the Hardy-Weinberg model and what are some violations in real life populations?

Answer 32

Random mating (assortative and disassortative mating are violations, non-random mating with relatedness to individuals is also a violation)

Infinite population size (random genetic drift occurs when a finite population size is present)

No migration (migration leads to gene flow where migrant individuals contribute new alleles)

No new alleles via mutation (mutations do occur in populations but mutations themselves are a weak evolutionary force)

No segregation distortion (retinoblastoma is a disease that occurs due to segregation distortion in humans where a large tumor forms in the eye, occurs since sperm that carry diseased allele are more likely to survive so there is a differential transmission of disease allele >80%)

No natural selection, all genotypes have equal survival/reproduction (ignores natural selection as an evolutionary force)

Question 33

Evolutionary change

Answer 33

Anything that causes a change in allele frequencies from one generation to another, occurs when Hardy-Weinberg assumptions are violated

Question 34

Natural selection

Answer 34

Differential survival and/or reproduction of individuals in a population due to phenotypic differences. If we assume phenotypic differences reflect heritable variation then natural selection reflects unequal fitness among phenotypes

Question 35

Fitness

Answer 35

Average contribution of an allele to the next generation compared with that of other alleles

Most fit allele has W = 1 since relative fitness is standardized to 1, Less fit alleles have a selection coefficient (s) of 1 - W

Can be used to predict how much allele frequency changes in comparison to Hardy-Weinberg

Question 36

What does the rate at which the favored allele is fixed depend on?

Answer 36

The strength of selection, the initial allele frequency, and the degree of dominance for the trait affecting fitness (between homozygotes and heterozygotes)

Question 37

What phenomenon occurs when all HW assumptions are met except for natural selection when fitness between homozygotes and heterozygotes varies?

Answer 37

In a model where the fitness of a heterozygote neither exceeds nor is less than the fitness of both homozygotes, the allele that is present in the most fit homozygote will always increase in frequency every generation until it reaches fixation where p=1

Question 38

What causes the rate at which a favored allele is fixed to vary?

Answer 38

Strength of selection (how unequal W is), the initial allele frequency, and the degree of dominance for the trait affecting fitness

Question 39

Darwin’s Finches

Answer 39

Natural selection favored larger bill size in drought years where small seeds are scarce, during a drought population majorly decreased

BMP4 was identified as a factor that controlled beak morphology

Haplotype variation at the ALX1 gene was also a major factor determining beak morphology

Question 40

Flat-tailed horned lizards

Answer 40

researchers can directly tell which lizards experienced predation and which did not due to their horns, determined horn length as a proportion of head size is ~10% greater in survivors. Even though there was differential survival of a phenotype, there was no evidence of heritability for horn length meaning evolution by natural selection was not occurring

Question 41

What is some evidence of selection favoring the evolution of pesticide resistance in insects?

Answer 41

Evolved resistance is behavioral (avoidant behaviors), cuticle permeability, toxin excretion, detoxification

Organophosphates also lead to diverse detoxification mechanisms such as altered protein conformation and increased production of proteins that can degrade pesticides

Question 42

Components of fitness

Answer 42

Vitality is the probability of survival to a reproductive age

Sexual selection or mating success

Fecundity is the viable offspring per female (reproductive success)

Differences between allele frequencies between a population at birth and as adults can be used to calculate relative fitness. Since viability is the only fitness component that varies among genotypes, relative viabilities = relative fitness. Fecundity fitness can also be calculated so relative fitness is the product of the two W components

Question 43

What are some examples of trade-offs between vitality and fecundity?

Answer 43

In bullfrogs an evolutionary trade-off is present since larger female bullfrogs are more fecund but also more subject to predation

Question 44

Modes of selection

Answer 44

used to describe the action of natural selection on phenotypic distributions for quantitative traits

Question 45

Directional selection

Answer 45

favors the higher or lower value of a character, beak size, maize oil content, drosophila bristle number, and mouse behavior are all cases where selection moves in a direction favoring a higher or lower value. If trait is heritable mean tends to change and variation tends to be reduced

Question 46

Stabilizing selection

Answer 46

occurs when selection against phenotypes that deviate in either direction from the optimal value. A narrowing of a distribution tends to occur where a mean value of a trait is maintained and standard deviation/variation decreases. Human birth weight and gecko body size are examples. If heritable mean may not change but variation tends to decreases

Question 47

Which HW assumption does natural selection violate? Why is this significant?

Answer 47

Violates the HW assumption of equal fitness for all genotypes/phenotypes. If no other HW assumptions are violated we can exactly predict change in allele frequencies per generation (Δp) from the allele frequencies and fitness for all genotypes

Question 47

Disruptive or diversifying selection

Answer 47

occurs when the selection in favor of two or more modal phenotypes occurs and against the intermediate phenotypes occurs. If the trait is heritable mean may not change but variation tends to increase

Question 48

Why is there still heritable variation for traits directly correlated with fitness?

Answer 48

A balance between new deleterious mutations and selection may occur, a lot of genetic variation is deleterious/maladaptive but not so deleterious that it is immediately purged

New favorable mutations may be constantly arising, creating genetic variation for fitness-related traits, enzyme evolution is an example of this where new favorable mutations make an enzyme more refined but other favorable mutations are possible leading to variation

Disruptive selection can occur or selection can favor different traits either at different times or places (temporal and spatial heterogeneity occurs where selective pressures change across space and time), leading to the maintenance of phenotypic and genotypic variation, best documented

Question 49

Frequency dependent selection

Answer 49

fitness depends on phenotype frequency, one way natural selection maintains the variation within species

Question 50

Negative frequency-dependent selection

Answer 50

occurs where fitness is directly tied to how rare a phenotype is. One example is scale eating cichlid where fish bites larger fish and two different mouth shapes are present, right and left mouth. Allele frequency for right and left mouth oscillates as larger fish become more primed to target whichever phenotype is more common and rarer type becomes favored

Gametophytic self-incompatibility is a classic example where the pollen’s genotype at the S. locus must differ from ovule’s genotype at that allele in order for fertilization to occur (mechanism to avoid inbreeding), this means a rare allele can fertilize more plants until it becomes more common. This leads to all S alleles oscillating in frequency, and oscillation has a value of 1/k where k = no. alleles

Question 51

Batesian mimicry

Answer 51

convergent evolution where nonvenomous species evolve to mimic more venomous species, classic example is how non-venomous king snakes evolve to look almost identical to venomous coral snakes

Shine et al paper argues that Batesian mimicry in sea snakes is dependent on Negative FDS since phenotype is only favorable if the Batesian mimicry is rare

Question 52

Positive frequency-dependent selection

Answer 52

scenario where the common phenotype is favored until the phenotype becomes fixed

Since the expected outcome is that the favored phenotype will be rapidly fixed, this is tricky to detect in most cases. In cases where different geographically isolated populations happen to be fixed for different phenotypes (likely based on whatever started out as a high frequency), positive FDS can be documented

Classic example is Mullerian mimicry where multiple unpalatable species convergently evolve the same warning coloration that predators learn to recognize and avoid. Shared warning coloration phenotypes among two different species (H. melpomene and H. erato) are found in particular geographical regions but are distinct between the same species in different regions. Positive FDS was demonstrated via transplant experiments and noted that butterflies transplanted to locations with different pattern are attacked but butterflies moved to location with same warning coloration do fine

Question 53

Selection with environmental heterogeneity

Answer 53

Spatial heterogeneity can occur where selective pressures change in different regions. One classic example is copper tolerance in bentgrass where in a mine adults have a higher metal tolerance than seeds and downwind a mine seeds have higher metal tolerance than adults. Seeds with metal tolerance in a nonmetal region are selected against (possible resource allocation trade-off). Cryogenic plants are also favored in different environments within a species’s range, frequency of cyanogenesis also decreases with colder temperatures

Temporal heterogeneity also occurs where selective pressures change with different environmental conditions (Darwin’s finch beak size in drought vs wet years)

Question 54

Cline

Answer 54

gradual change in a genotype/trait over a geographical continuum

Question 55

Heterozygote advantage

Answer 55

occurs when heterozygote fitness exceeds the fitness of one allele meaning that the fixation of one allele does not occur, classic example is sickle cell where homozygotes have disease phenotype but heterozygotes are less susceptible to malaria so fixation of healthy allele does not occur

Question 56

Methods for documenting natural selection

Answer 56

Longitudinal studies where a group of individuals are followed for some or all of their lives and variation in phenotypes/genotypes along with fitness is observed (Darwin’s finches)

Experimental manipulation (transplants, mark and recapture) where the aim is to look for associations between phenotypes/genotypes and fitness in different environments, Mullerian mimicry transplants allowed researchers to identify positive FDS

Comparison among age classes where shifts in phenotypes/genotypes can be documented. One example is the heavy metal tolerance in grass and eelpout fish were classified at two different life stages where phenotypic variations of neonates were compared to variations in adults

Observational studies of phenotypic distributions over many generations (fossil records and Darwin’s finches)

Environmental perturbations (artificially or naturally), some examples are observing the Celtic mine sites and how species have adapted to altered conditions, also observing how species have adapted to the Galapagos drought

Correlations between environment and phenotypes/genotypes (cyanogenesis clines), important to keep in mind that correlation is not always causation so a good follow up experiment could be a transplant experiment

Question 57

How does population size affect genetic drift?

Answer 57

Smaller populations means stronger genetic drift, probability of fixation of a newly arisen allele in a diploid population is 1/2N, average time to fixation if a newly arisen allele does become fixed is estimated at 4N generations

Allele frequencies fluctuate randomly and eventually one allele is fixed, probability of fixation is determined by initial allele freq and is inversely correlated with population size, genetic drift can sometimes overpower other forces of selection

Question 58

Founder effect

Answer 58

principle that founders of a new colony carry only a fraction of the total genetic variation in a population, hard to document

Classic example is how Amish community came from a small amount of founders and inbreeding resulted causing multiple inbreeding associated syndromes so founders can lead to genetic consequences

When SSR loci were used to classify allelic diversity and subsequent founding events were associated with less allelic diversity in birds

Question 59

Bottleneck

Answer 59

phenomenon where population is greatly reduced in size for one or more generations through a random event and then eventually rebound

Question 60

What is the association between serial founder events and genetic diversity?

Answer 60

Serial founder events are associated with decreased genetic diversity systematically as a function of geographical distance due to migration from origin in human populations and also the increase of deleterious mutations, since genetic drift is a stronger force in smaller populations, selection is less effective at removing deleterious alleles in smaller populations

Question 61

Genetic Drift

Answer 61

Ultimately causes the fixation of one allele and loss of the other leading to a loss of genetic variation within a population

Probability of fixation is determined by the initial allele frequency where rare alleles tend to be lost more often

Genetic drift is also the strongest in smaller populations, and it can even potentially override selection and lead to the loss of a selectively favored allele

Leads to a loss of genetic variation where number of alleles, polymorphic loci, and level of expected heterozygosity are decreased

H = 2pq

H = H0[1 - 1/(2Ne)], effective population size fits more for reduction of heterozygosity than ideal population size

Question 62

Why is the effective population size generally smaller than the census population size?

Answer 62

Fluctuations in population size, Ne is predicted by the harmonic mean (using reciprocals) between generations rather than the arithmetic mean since drift is stronger in smaller populations

Overlapping generations where alleles from a parental generation displace some from the next generation and make new genotypes, this reduces heterozygosity since it combines identical offspring and parental alleles

Unequal sex ratios where not all individuals can contribute equally to the next generation

Natural selection can also affect population size where there is an unequal contribution to the next generation caused by fitness variation (leg bristles in male flies

Question 63

What is population structure and how can it be identified in a species

Answer 63

Population structure is a pattern of genetic differentiation among populations in a species

Some ways to measure population structure is to identify genetically differentiated subgroups in a sample of individuals (admixture or Bayesian analysis), quantification of population differentiation (Fst), quantification of genetic diversity within populations, and interaction between genetic drift, gene flow, and natural selection

Question 64

Bayesian analysis

Answer 64

Involves an admixture analysis where distinct genetic subgroups are formed based on the genotypes of multiple loci from many different individuals, K refers to the amount of subgroups that one individual can be mostly unambiguously assigned to

Question 65

Collared Lizards

Answer 65

Isolated populations in Missouri became mostly fixed for one genotype but larger populations had around 7 distinct genotypes

Question 66

How can variance in allele frequencies between populations be measured?

Answer 66

Fst measures the degree of genetic differentiation among the population (Fst = 0 indicates all populations are genetically identical, Fst = 1 indicates all populations are fixed for two distinct alleles)

Question 67

What is the difference between differentiation and diversity?

Answer 67

Differentiation compares two populations and diversity looks at a single population

Question 68

How can diversity in a single population be measured?

Answer 68

Expected heterozygosity can be measured using 2pq for two alleles, and for more than 2 alleles 1-sum(p^2) or 1 - sum of expected homozygote frequencies

Question 69

How can diversity be calculated at the nucleotide level?

Answer 69

This can be calculated from the amount of nucleotide divergence within haplotypes, this can be measured using pi or the average number of nucleotide differences per site between 2 sequences sampled at random from a population

This value tells us that for a given population, 2 sequences sampled at random differ on average by pi percentage of their nucleotides

Question 70

Gene flow

Answer 70

Operates in direct opposition to genetic drift by increasing homogeneity between populations and promoting variation within populations

Occurs via migration, migration can occur in juvenile life stages and also via pollen dispersal and pollination

Strength of gene flow as an evolutionary force depends on the rate of gene flow (m) or proportion of alleles derived from migrant parents and also the amount of initial genetic differentiation between populations, Nm is generally used to describe gene flow

Question 71

Relationship between gene flow and population variance

Answer 71

There is an inverse relationship where Fst = 1/(4Nem + 1), this model assumes an island model where there is an equal gene flow among all populations

Question 72

Models of gene flow

Answer 72

Island model which posits that gene flow among all populations is equal

Isolation by distance model which posits that migration is proportional to distance between populations

Stepping stone model, like fish going upstream or downstream

Question 73

Direct methods of studying gene flow

Answer 73

One direct method is to mark and recapture marker traits and alleles

Some disadvantages is that migration is not the same as gene flow, one observation may not always represent other populations, seasons, or environments, may miss key migration events

Question 74

Indirect methods of studying gene flow

Answer 74

Gene flow can be inferred from the level of genetic differentiation calculated as Fst based on genetic data between populations

One assumption for this is that Fst reflects current gene flow but this may not be completely accurate since completely isolated populations may still have an Fst greater than 1 if they have been connected in the past and there hasn’t been enough time for genetic drift to completely fix different alleles

Another assumption is that an island model of gene flow is assumed, but Fst between populations generally suggests an isolation by distance model rather than an island model

Another assumption is that the genetic markers are selectively neutral and natural selection does not act on them, for most loci across the genome this assumption is okay but selection

Selection favoring different alleles in different populations raises Fst (spatial environmental heterogeneity) and selection favoring the same allele in populations lowers Fst (overdominance, heterozygote advantage, when one high fitness allele spreads across population)