Evidence for Evolution Examples:

Tuberculosis Resistance

MRSA: Methicillin Resistance Staph Aureus

Selection for smaller animals due to trophy hunting (overharvesting)

1. drop in bighorn sheep horn size

2. decline in cod size at sexual maturity

Pepper moths and Industrial revolution

Why bacteria evolve rapidly:

Examples include:

Selection for change in morphology (shape/form)

   i.e. leg bristle number in Drosophila

Selection for change in behavior

   ie. selection for running behavior in mice

Examples include:

Dog domestication (wolves --> dogs)

Crop domestication

    1. teosinte --> maize

    2. Brassica oleracea (diversification into many different species, like cauliflower, broccoli, cabbage, kale, brussels sprouts)

Examples include:

Transitional forms:

1. fish to tetrapods (Tiktaalik roseae)

2. dinosaurs to birds (Archaeopteryx - more dinosaur-like, Gansus yumenensis - more bird-like)

3. land mammals to marine mammals/Cetaceans (Ichthyolestes)

Examples Include:

Molecular Biology and Genomics

1. Shared DNA sequences: degree of similarity (more similarity = more recent divergence)

2. Shared non-coding DNA sequences: nucleotide divergence

3. Homologous Structures: five digit limbs in different proportions in mammals (similar morphology, different function)

4. Vestigial Structures: salamander non-functional eyes in dark caves, hind Limb Buds in fetal whales, tail in human fetuses

5. Biogeography: similarity of species correlated to geographical proximity, similarities between mockingbirds on Galapagos Islands

Hypothesis: proposition, conjecture (may or may not be well supported)

Fact: hypothesis supported by a large body of accumulated evidence, NO CONTRADICTORY EVIDENCE

Theory (in science): not synonymous with hypothesis: integrated set of ideas, based on well-supported hypotheses, that together provide a coherent explanation for a wide body of observations (like gravity, atomic theory, thermodynamics)

idea that creatures had one perfect form, but all the creatures we saw were imperfections, deviations from the perfect form

(variation = imperfection)

Aristotle's 'Great Chain of Being' (Scala Naturae)

Medieval Great Chain of Being

all species arrayed along a single axis

less complex organisms at the bottom (plants/trees)

most complex at very top (humans)

Medieval Great Chain:

theologians added "perfection" to the vertical axis

(up --> God)

angels and God added to the chain, above humans

Biblical literalist's interpretation

1. Each species was created independently as part of God's perfect, ordered creation

2. Species are unchanging

3. Everything is recent - young Earth creationism (about 6000 years old)

calculated Earth to be more more than 6000 years old using geneologies in the Bible

scholarly pursuit to find the age of the world

Irish Protestant Church

Father of Modern Classification: Taxonomy

To him classification in terms of similarities was describing God's great creation

Type Specimen: The specimen that has all characteristics of that species, representing ideal (mindset of essentialism.)

However this ignores variation within species.

evidence that species are not perfectly designed, imperfect but workable solutions

Recurrent Laryngeal nerve in giraffes: This nerve is unnecessarily long, very inefficient

Rabbit Digestion: Bacterial fermentation of ruminant is past the large intestine. Rabbits have to re-ingest the excreted matter to absorb nutrients. ID would have placed the fermentation before the stomach.

1. World no longer believed to be an unchanging place

2. Heresies voices (Copernicus, Galileo, etc.)

3. Discovery of fossils

extinct species

implied changes since Creation, gaps in Great Chain

fossils were ancient: was Earth older than biblical account?

Darwin not the 1st to propose evolution of species

mechanism as inheritance of acquired characteristics

ex: giraffes stretching their necks to eat from trees would pass on stretched necks to offspring

doesn't actually work.

gradual, everyday processes over time (instead of catastrophism) can create major geological features (gradual erosion, deposition, can form canyons, mountains)

current processes are the same ones in the past

heretical because it negated the cataclysmic events of biblical creation

Voyage of HMS Beagle in 1831-1836 to Galapagos Islands (local variation in small geographical area)

Came up with descent from common ancestor: all species originated from one parent species (but no mechanism)

Notice the correlation between geographical proximity and phenotypic similarities (see biogeography)

Influenced by Thomas Malthus (the economist): resource limitation gives rise to competition

exponential growth of populations

resource limitation gives rise to competition

traits with competitive advantage become differentially represented in the population

All species have potential to reproduce exponentially; all species therefore face limited resources.

- always competition for resources within species

- best competitors will differentially survive and reproduce

Variation among individuals within species

- heritable traits that make some individuals better competitors will be passed to future generations

- over successive generations, change in the proportion of individuals with that trait

(evolution - change in mean characteristics of species)

Five theories of evolution:

(1) Evolution as such

species evolve

idea not new or unique to Darwin, quickly accepted by contemporaries

species change over time

Ex:

1. similar anatomy between contemporary and extinct sloths,

2. fancy pigeons bred with ridiculous feathers (domestication/selective breeding)

Five theories of evolution:

(2) Common descent

shared common ancestors; all life has one common ancestor

evidence: all organisms have L-amino acids; same chirality in R-DNA/RNA

supported by lots of paleontological, morphological data

quickly accepted by contemporaries

Five theories of evolution:

(3) Gradualism

evolutionary change through small incremental steps

not quickly accepted by contemporaries

To think that the world came about in miracles (large leaps of species transformation) is to leave of science

(- Darwin)

challenged again in late 20th C. with punctuated equilibrium

Five theories of Darwin:

(4) Species diversification

Divergence from common ancestors creates multiplication of species

Other side of common descent: looking from top-down

provides evolutionary explanation for biodiversity

(speciation is inherently a branching process)

Within species: evolution occurs by changes in the proportion of individuals in a population that have a trait

Accepted by contemporaries

Five theories of Darwin:

(5) Natural selection

Differential survival and reproduction of some individuals over others in a population due to phenotypic differences

if heritable, traits will be differentially represented in next generation

initially not accepted widely by contemporaries - mechanism of inheritance unknown

widely accepted as part of the Modern Synthesis

Every: Evolution as Such

Car: Common Descent

Goes: Gradualism

So: Species Diversification

Nicely: Natural Selection

Microevolution

Population Genetics

Population

Microevolution: evolutionary change within species (often defined specifically as genetic change over successive generations)

Population genetics: biological discipline that studies microevolutionary processes

Population: group of individuals of the same species living in geographical proximity and potentially having reproductive interactions.

all measurable traits where variation may affect survival and reproductive process

results from genotype and environmental interactions

Discrete (Mendelian) variation

Discrete variation:

qualitative traits, either/or trait

Ex: cyanogenesis in clover (either cyanogenic or not, no in-between)

- 2 compounds required: enzyme, substrate

- presence/absence of allele for cyanogenic glucosides (substrate)

- presence/absence of hydrolyzing enzyme

easily followed, easy to use as candidate gene for molecular analysis

Continuous variation: quantitiative traits

Ex: human height, disease risk, dermal ridges in fingerprints

- large, continuous variation with everything in between two extremes

- more common than discrete variation, typically polygenic

Examples:

1. Genetically similar plants under different wavelengths of light grow to different heights

2. Sex ratio in reptiles depend on temperature

Determing whether a trait has a genetic basis

(Super Party Cart)

1. Segregation of trait variation in crosses:

examine genotype and phenotype ratios & if they are Mendelian ratios

Issues:

Time-consuming

traits usually not Mendelian (not applicable to all traits)

not feasible with humans

2. Parent-offspring correlations:

plotting value of offspring trait as function of parent trait

Issues:

correlations from similar environment (maternal effect)

Maternal effect: nongenetic effect of a mother on offspring's phenotype; reflects environment offspring were exposed to during gestation/rearing. (Hydrangea and soil pH)

3. Common garden experiments

Collecting organism from different environments and rearing them in the same environment (control for the environment)

Issues:

seeds (maternal effects)

difficult to test a complex trait (ie. disease susceptibility)

1. genes/alleles defined by phenotypes they produced,

defined as units of inheritance:

e.g. "Eye color gene" (red eye allele, white eye allele)

2. can also define genes/alleles at the molecular level,

defined in terms of genetic basis as units of transcription

[image]

Allele at the DNA level

In haplotypes:

1. point mutation

2. indel - ie. Huntington's Disease

In genes:

1. synonymous substitution - no a.a. change

2. nonsynonymous substitution - a.a. change

3. frameshift 

4. microsatellites (SSRs) - usu. in noncoding areas; high mutation rate due to replication slippage (easy for polymerase to err with many repeats); used as genetic markers

5. recombination - crossing-over

on avg, << 1x10^-6 mutations per bp per generation

(sufficient for evolutionary significance)

e.g.  How many mutations per zygote?

mutation rate = humans ~2.5x10^-8

haploid human genome ~3.5x10^-9 bp

25 x 3.5 = ~87.5 new mutations/gamete

~175 new mutations/zygote

if 2.5% of genome expressed, .025 x 175 =

~4 mutations/zygote

polymorphism as a function of divergence - amount of variation in the time since divergence

With respect to genomic location: No, hotspots and coldspots

(more mutation at telomere, less at centromere)

With respect to whether it is advantageous for the organism: Yes

Ex. Lederbergs replica plating - only colonies that were already resistant showed resistance in the presence of antibiotic; disproves Lamarckian evolution

gene geneology

unrooted - don't know which haplotype is oldest

info on movement between populations in a species

(buffalo are migratory but impala are not - haplotype change pattern is isolated)

Six assumptions of Hardy-Weinberg equilibrium

What happens when any of these assumptions are violated?

1. Random mating (panmixia)

2. Infinite population size (no sampling effects)

3. No migration (gene flow)

4. No new mutation

5. No segregation distortion (meiotic drive)

6. No natural selection: all genotypes have equal survival/reproduction

Violation of these assumptions leads to a change in allele frequencies in the next generation = Evolution.

Natural selection: differential survival and/or reproduction of individuals in a population due to phenotypic differences.

Fitness (W): a way to quantitatively compare the competitiveness of one phenotype relative to others

    Most fit allele/genotype: W = 1

    Less fit alleles/genotypes: W = 1 - s

    (s: selection coefficient = difference in the fitness of

         a given genotype relative to the most fit genotype)

What equation is used to determine what happens when the fitness of the heterozygote (W_A1A2) is exactly halfway between the fitness of the homozygotes?

(see bottom slide, page 3 of 9/15/2010 lecture)

Δp = (spq)/[2(1-sq)]

Remember this equation!

As long as there's a non-zero Δp, there's a change in allele frequencies = Evolution!

1. Strength of selection (how unequal is W?)

2. Initial allele frequency

3. Degree of dominance (W differences between homozygotes and heterozygotes)

Viability: probability of survival to reproductive age

Mating success: sexual selection (factored into fecundity when calculating fitness)

Fecundity: viable offspring per female

*Sometimes viability and mating success are at odds!

Example: water striders favor larger females (more eggs, better fecundity) BUT those larger females are more likely to be eaten (worse viability)

Given the viability component of fitness (viability W) and the fecundity component of fitness (fecundity W):

                  A₁A₁    A₁A₂    A₂A₂

viability W:    1.0    0.92   0.97

fecundity W:  0.80   0.75    1.0

then the relative fitness is:

(1.0)(0.8)    (0.92)(0.75)    (0.97)(1.0)

   (0.97)          (0.97)            (0.97)  <--standardize

                                                     by highest value

W: 0.82            0.71                1.0

1. Heritable phenotypic variation (differential fitness)

2. Genetic change over successive generations (Δp ≠ 0)

Note: Natural selection is one mechanism that can lead to evolution. It is not evolution!

Evolution can also occur by violating the other H-W assumptions.

Hypothesis: different beaks developed to help birds eat different foods (seeds, insects, etc.)

Discovery: the birds all ate the same kind of plentiful seed!

However! This was observed during a rainy year, when food was plentiful. During drought seasons, birds with larger bills were favored. The small plentiful seed became scarce and the remaining seeds were rock-hard. Large-billed birds were better able to eat the hard seeds and were more likely to survive the drought.

Loggerhead shrikes (a type of bird) eat horned lizards.

Shrike flies lizard up a tree, sticks lizard to a branch by its horns, then eats the body. Selection for horn length occurs in the lizard: larger horns help it fend off the attacking shrike.

Significance: It's often difficult, if not impossible, to examine which phenotype was selected against in a population because they have already died off. Due to the killing method the shrike uses on horned lizards, we know what the horn length phenotype of the selected-against individuals were.

Modes of selection

(1) Directional selection

Directional selection favors higher or lower value of a character.

- The mean value of the trait is shifted (if heritable)

- Decreases variation

Examples:

- bacterial antibiotic resistance

- maize oil content (selected by humans)

- Drosophila bristle number (lab)

- level of activity in mice (lab)

Modes of selection

(2) Stabilizing selection

Stabilizing selection selects against phenotypes that deviate in either direction from the optimal value for a character.

- The mean value of the trait is maintained

- Decreases variation (if heritable)

- predominant selective force for many traits

- often involves 2 opposing directional selection forces

Examples:

- human birth weight (percent mortality goes up for very heavy or very light infants)

- gecko body size (gain territory/mates vs. exposure to owls)

- gall size in gall flies (wasps prey on smaller galls, birds prey on larger galls; selection favors middle ground)

Modes of selection

(3) Diversifying (disruptive)

Diversifying selection selects for two or more modal phenotypes and against those intermediate between them.

- Increases variation (if heritable)

- Mean value of trait may not change

- The only one of the three modes that increases variance.

Example:

- Black-bellied seedcracker (finch in E.Africa) feeds on sedge seeds, which have a large/small size dimorphism. Large-beaked and small-beaked birds are favored over birds with mid-sized beaks.

Possibilities:

1. Balance between new deleterious mutations and selection: bad mutations always popping up, but not so bad that they are not viable.

2. 'Fisher's Fundamental Theorem' hypothesis: lots of great new mutations constantly arising! This creates genetic variation.

3. Diversifying selection, and/or selection favoring different traits in different times or places.

Frequency-dependent selection

(1) Negative frequency-dependent selection

Negative (inverse) frequency-dependent selection:

the rare phenotype is favored.

Examples:

- frequencies of left-mouthed and right-mouthed scale-eating cichlids vary cyclically over time, depending on when the host fish "wise up" to which phenotype is more common at the moment

- self-incompatibility alleles in plants prevent inbreeding, so a rare allele can fertilize more plants - until it becomes common

maintains/increases genetic variation

Frequency-dependent selection

(2) Positive frequency-dependent selection

Positive frequency-dependent selection: the common phenotype is favored, fixed.

Different populations may become fixed for different phenotypes.

Example: Müllerian mimicry: several unpalatable species share a similar warning pattern (butterflies). Transplant experiments show that survival rate goes down if a butterfly is moved to a region where it does not look like the majority.

expect to lose variation.

Selection with environmental heterogeneity

(1) Spatial heterogeneity

Individuals vary between different environments.

Two types of spatial heterogeneity:

1. Fine scale (within population) - example: copper tolerance in bentgrass near a mine

2. Large scale (across multiple populations or species range) - example: frequency of cyanogenesis in clover decreases with colder temps (polymorphism may be maintained due to resource allocation trade-offs, favored in different environments)

Selection with environmental heterogeneity

(2) Temporal heterogeneity

Different phenotypes are favored at different seasons

Example: Darwin's finch beak size in drought vs. wet years (large beak favored in drought years)

Heterozygote fitness exceeds homozygotes

- active maintenance of variation occurs; no longer expect fixation of one allele.

Example: sickle cell anemia in humans

A_AA_A: no anemia, susceptible to malaria

A_AA_S: slight anemia, resistance to malaria

A_SA_S: severe anemia and early death

W values for these genotypes, from top to bottom, are: 0.89, 1.0, 0.2 (in Africa, where malaria is common)

People with cystic fibrosis lack functional CFTR protein (found in lungs and intestinal tract), are susceptible to Pseudomonas bacteria (lung infection), early death

However! Heterozygotes are protected against Salmonella typhi (typhoid fever) infiltration in the gut: 86% fewer bacteria.

Thus, across 11 European countries, severity of typhoid outbreaks is correlated with frequency of ΔF508 in the next generation. (Allele is favored during times of typhoid outbreak.)

Genetic drift will ultimately cause the fixation of one allele and loss of the other (loss of genetic variation). Breaks H-W assumption of infinite population size and no sampling effects.

Drunkard's walk metaphor: as he staggers crookedly down the train platform, he will eventually fall off one side (fixation) or the other (loss). Rare alleles are more likely to be lost; the drunkard is more likely to fall off one side of the platform if he starts walking at a point closer to that side than the other.

Founder effect: The principle that the founders of a new colony carry only a fraction of the total genetic variation in a population.

- Amish community founded by about 200 individuals; greater frequency of Ellis-Van Creveld syndrome

Bottleneck: Instances in which populations are greatly reduced in size for one or more generations.

- population of Pohnpei descended from 20 survivors of 1775 typhoon; extremely high incidence of congenital achromatopsia (complete color blindness if homozygous for mutant allele)

- elephant seal population bottlenecked due to overhunting for blubber; population growth from ~10-30 to >175,000; no variation in 24 allozyme loci

Genetic drift leads to a loss of genetic variation:

# alleles/locus

# polymorphic loci (through fixation)

Heterozygosity frequency = 2pq

Average loss of heterozygosity frequency from genetic drift per generation:

H_t1= H_t[1-(1/2N)]

For multiple finite populations, all with allele A₁, at frequency p, we expect that a proportion p of the populations will be fixed for A₁

i.e. the allelic frequency reflects the fixation

if p has frequency of 0.4 we expect that 0.4 of the populations to be fixed for the allele.

Describe the setup of the experiment:

Buri 1956 and bw⁷⁵/bw Drosophila

In this experiment, the author had 106 populations, each with 16 individuals (N=16)

Randomly picking 8 males and 8 females from each of the parent generation the author showed that genetic drift reduced the frequency of heterozygotes in each population, they were becoming fixed for either the bw⁷⁵ or the bw allele

The predicted frequency of heterozygotes did not match with allele frequency: heterozygote frequency curve

Y axis: = 2p(1-p)

X axis = p where p is the allele frequency

The actual decline of heterozygous frequency matched more closely to smaller population

-Heterozygotes were counted by orange eye color as the phenotype was under incomplete dominance

-Under other types of Mendelian genetics like complete dominance, heterzygotes would be tougher to count

N_e: The effective population size

Census Population Size

N_e: The size of the theorectical (ideal) population that producesa the level of genetic drift observed in a real population

Census Population: The actual recorded population size based on the level of genetic drift

Reasons why N_e < census population size

3 reasons

1. Variation among individuals in contribution to the next generation

-Unequal sex ratios

-Fitness variation

2. Fluctuations in population size (N_e is predicted by harmonic mean, not arithmetic mean, since drift is stronger in smaller populations)

3. Overlapping generations (reduce heterozygosity by combining identical offspring and parental alleles)

Patterns of genetic differentation among populations of a species

This includes:

- Quantification of population structure and genetic diversity within populations

- Interaction with gene flow

- Interaction between genetic drift, gene flow, and selection

Example: Collared lizards

F_st and how to calculate it

Standard variance in allele frequencies amoung populations

Measures the degree of genetic differentiation among populations

F_st: 0 means that all the populations are genetically identical(same alleles and frequencies)

F_st: 1 means that all populations are fixed for one allele or another (complete divergence)

F_st = (H_T - H_s)/H_T

H_T = heterozygous frequency (2pq) calculated for allele frequencies pooled across  Total populations

H_s = heterozygous frequency from each individual subpopulation

Sample problem:

In population 1: In one population 60 alleles are A₁ and 40 alleles are A₂. In another population 160 alleles are A₁ and 40 alleles are A_2. What is the F_st between the two?

Ans: 0.046

p₁ = 0.6

q₁ = 0.4

2p₁q₁ = 0.48

p₂ = 0.8

q₂ = 0.2

2p₂q₂ = 0.32

H_s = [(100)*0.48 + (200)*0.32]/(100 + 200) = 0.373

H_T = 2p_Tq_T = 2[(160 + 60)/300 + (40 + 40)/ 300] = 0.391

F_st = (0.391-0.373)/ 0.391

Why F_st is not a measure of overall genetic diversity

Given two species, each with five populations

Species 1 Each population may be fixed for either one of two alleles

diversity is low (only two alleles) but: high F_st

Species 2 Each population has the same five alleles present at the same frequencies

diversity is high but: low F_st

How to measure genetic diversity in a population

2 ways

1) Measure expected heterozygosity for all alleles

2) Calculate genetic diversity at the nucleotide level

-Takes into account the amount of nucleotide divergence among haplotypes

How to calculate the expected heterozygosity for all alleles

Sample problem: If alleles A₁ A₂ A₃ A₄ have frequencies

0.8, 0.08, 0.1, 0.02, what is the measure of expected heterozygosity  

H_e = 1 - Sigma (p²_i)

1 - the frequency of homozygotes

Note that for two alleles it boils down to 2pq

2pq = 1 - (p² + q²)

1 - (0.8*0.8) - (0.08*0.08) - (0.1*0.1) - (0.02*0.02)

= 0.3432

How to calculate genetic diversity at the nucleotide level

Sample problem

[image]

Find the genetic diversity of these sequences

Nucleotide diversity: π = the average number of nucleotide differences pet site site between 2 sequences sampled at random

π = Sigma [p_ip_jπ_ij]

p_i = frequency of allele 1

p_j = frequency of allele 2

π_ij = average change = number of pairwise differences/number of nucleotides

A₁ = 0.5

A₂ = 0.25

A₃ = 0.25

Sample question

π = A₁*A₂*(# difference nt/total nt) +

      A₁*A₃*(# difference nt/total nt) +

     A₂*A₃*(# difference nt/total nt) +

π =

(0.5)(0.25)(1/10) + (0.5)(0.25)(2/10) + (0.5)(0.5)(1/10)

= 0.04375

Breaking the assumption of H-W that there is no migration

Also define this term

This introduces gene flow: incorporation of alleles into a population from another population

This acts against genetic drift to homogenize the populations

note: Not all migrations lead to gene flow as an animal may migrate but fails to survive and add to the gene pool

Example: Dispersal of pollen grains and seeds

Gene flow and evolution: What influences the potential for gene flow to cause evolution

2 terms

The power of gene flow to cause evolution depends on:

1) The rate of gene flow (m): porportion of alleles derived from migrant parents

2) Amount of initial genetic differentiation between populations. The large the genetic difference between the two the less powerful gene flow is

Gene flow counteracts genetic drift; there is an inverse relationship between the two.

F_st = 1/(4Nm +1)

Where Nm = effective gene flow or the number of migrants contributing alleles per generation

Name three models of gene flow and which model corresponds to the ideal inverse relationship with genetic drift

1) Island Model: Each population is equally distant from another and connected to one another

This model is assumed in the ideal inverse relationship as each population contributes equal gene flow

2) Isolation by distance: Each population is connected to one another but not by equal distances. Hence some populations contribute more to gene flow to others

For many species this is the realistic model

3) Stepping stone model: Populations are only connected to the neighbouring population, gene flow does not occur outside of these two populations

How can F_st be used as a tool for identifying genes evolving under natural selection

We assume that most allelic varaition is most genes is not under selection. For these genes, F_st and inferred Nm reflect only genetic drift and gene flow

Outlier genes reflect selection on that gene

Direct methods: For example, mark and recapture species

Use marker traits/alleles

-Migration does not equal gene flow

-May not represent other populations, seasons, environments

-Ignores rare, long distance events most difficult to detect

Indirect methods: Infer gene flow from level of genetic differentiation

-Assumes F_st reflects current gene flow: One can calculate gene flow for species that have been completely isolated but in the past were connected

-Assumes island model of gene flow; unrealistic for many species. Isolation by distance is more realistic

-Genetic markers are not under selection: selectively neutral; when tracking animals and where they end up using genetic markers if that genetic marker is under natural selection this will skew their results as it will affect F_st

            High F_st will result if favoring different alleles in different populations (+the genetic marker) is selected for

           Low F_st will result if selection for the same allele (our genetic marker) is favored for in each population

*This can be used to identify traits under natural selection

How can gene flow facillitate evolution by natural selection (2 ways)

Mitigate loss or rare alleles by genetic drift

Spread favorable alleles among populations

   -example a rare allele for pollen grain recognition that allows for self fertilization

Example 1: Wind blowing metal resistant grass seeds to non-metal areas hence preventing fixation of the metal resistant allele and non-metal allele

Example 2: Northern water snake; the gene flow between populations leads to large-scale heterogeneity, and thus no fixation

There could be a climate threshold below which acyanogenesis would be fixed if there is no gene flow.

Imagine that since herbivores are more common in warmer temperatures, cyanogenosis is costly in colder temperatures were there are fewer herbivores.