evo bio exam #4

Mechanisms of divergence: (Darwinian) natural selection

(Darwinian) natural selection: Selection for habitat or resource use is expected to differ after isolation, and can lead to divergence. There is an abundance of evidence for this.

What are the disadvantages of the phylogenetic species concept (PSC)?

- Arbitrary - Would cause a large increase in number of named species (though whether this is a drawback is debated)

What are the advantages of the morphologic species concept?

- Can be applied for species that are sexual and asexual - Widely applicable to macro-organisms - Useful for both extant and extinct species

What are the disadvantages of the morphologic species concept?

- Can be arbitrary - Not useful in species with few morphological traits (microbes) - Species can be morphologically cryptic: not distinguishable without other, non-morphological information: color, behavior, habitat use

Ecological triggers of adaptive radiation:

- Dispersal and colonization - Extinction of competitors - Both situations involve expansion into empty niches. - Individuals spread and colonize empty niche space, move into new habitats and selection acts on individuals to increase fitness in those habitats which can result in speciation

3rd step of the speciation: secondary contact and its outcomes

- Populations that have diverged in allopatry can come into contact with one another again (for example due to a change in the physical landscape). - What happens next depends on the fitness of the hybrids relative to the parentals.

Antagonistically pleiotropy at a gene that affects two traits:

- Preference for one host and fitness on the other host. - This contributes to genetic isolation.

Antigenenic drift

- Process of immune evasion. - Shifts since the start of modern virology. They usually result in pandemic influenza

Possible outcomes of hybridization between species

- Reinforcement or selection against hybrids - Selection favors hybrids in novel habitat not occupied by parental species - Selection favors hybrids in transitional habitats

TWO POSSIBLE CAUSES OF TRADEOFF in antibiotic resistance

- Resistance due to loss-of-function vs. direct cost of loss - Resistance due to gain of function vs. metabolic cost

What are the disadvantages the ecological species concept (ESC)

- Usually not useful for extinct species. - Connection between definition and evolutionary history is less strong than PSC, BSC.

Hypothesis for pattern of blue-surface and red-deep water cyclid fish in Lake Victoria

- Water molecules absorb red light: most light near the surface is blue. - Blue light is selectively absorbed by sediment particles in the water's surface. By a few meters down, most light is red. - Darwinian natural selection favors individuals most sensitive to ambient light conditions. - Because females have evolved to see better at location -specific wavelengths, males are under selection to develop location-specific coloration. - This sexual selection driven by female choice causes divergence between shallow and deep water fishes.

What are the advantages of the phylogenetic species concept (PSC)?

- Widely applicable to macro- AND micro-organisms. - Useful for both extant and extinct species. - Testable - Able to distinguish cryptic species

Define Adaptive Radiation

Adaptive radiation occur when a single ancestral species rapidly diversifies into a large number of species and a variety of different adaptive forms.

Example of Experimental Evolution of Ribozymes

After 10 generations/rounds of this process the rate at which this reaction was catalyzed increased by a factor of 30. Researchers could ID which mutations increased in frequency.

Physical mechanisms of isolation lead to ...

Allopatric speciation physical mechanisms: Dispersal and vicariance.

Trade-off Hypothesis The balance between transmission and virulence

Although it was widely believed that pathogens should evolve to be benign towards their hosts as they are dependent on their survival for transmission (back in the 1960's and 70's) Theory and data not demonstrate that virulence can be selected for if it increases the rate of transmission.

Define the evolutionary species concept

An evolutionary species is a single lineage of ancestor-descendant populations of organisms which maintains its identity from other such lineages.

How can antibiotic resistance be achieved?

Antibiotic resistance can be achieved either by a loss of function or by a gain of function mutation - regardless of the mechanism the resistance generally comes at a cost of reduced growth. Therefore, antibiotic resistant strains should only have higher fitness in the presence of antibiotics. The percent of the Pneumococcus cases that are resistant to penicillin declined after a public health campaign to reduce the use of this antibiotic.

Geographic isolation through vicariance - Panama

Approximately 3 million years ago, Panama rose and cut off/ formed Pacific and Caribbean populations. Using morphospecies concept, Tree shows pairs of sister species: each was "split" when the land-bridge between North and South America was formed. C & P populations also showed little interest in mating with each other and almost no females produced viable offspring

Which of the following are NOT one of Stuart Levy's guidelines for limiting the development of antibiotic resistance? A) To avoid contracting food-borne bacteria, consumers should wash fruits and vegetables and avoid raw eggs and undercooked meat. B) Consumers should always use antibacterial soaps and cleaners, even when no perceived bacterial threat is present. C) Patients should not request antibiotics for viral infections, such as colds or flu. D) When they take antibiotics, patients should complete the course of treatment. E) To avoid spreading infections from patient to patient, physicians should wash their hands thoroughly between patients.

B) Consumers should always use antibacterial soaps and cleaners, even when no perceived bacterial threat is present.

What is the basic principle of Pathogen Evolution: Antibiotic Resistance ?

Basic principle - when you apply or put a toxic agent into an environment, it exerts a very strong selection pressure. Antibiotic treatment sorts bacteria into two groups - susceptible and resistant. Widespread use or misuse can lead to the rise and spread of antibiotic resistant bacteria

How do you define an "outgroup" for life?

Build gene trees for families of genes. Gene families that arose through ancient duplications provide an molecular outgroup

Experiment to prove trade off hypothesis

Bull et al. Using E. coli and phage f1 the researchers allowed phages to be transmitted vertically (mother-daughter) or horizontally (between cells). Measured virulence (cell growth rate) & phage reproduction rate. Two predictions: 1. Phage growth rate would be correlated with virulence. 2. Cultures subjected to 8-day transmission phase would evolve lower virulence.

The strongest factor in speciation events is ________. A) genetic drift B) sexual selection C) natural selection D) the bottleneck effect

C) natural selection

1) From simple inorganics to the building blocks of life: how?

One possibility: an extraterrestrial source. Meteorites have been shown to contain amino acids of non-earth origin. Did the building blocks of life entering the atmosphere on meteors or as dust?

Oparin-Haldane Model

Oparin & Haldane developed a theory of how cellular life could have come about from simple molecules. It is similar to Darwin's idea of a "primordial soup". There are problems with it, but no stronger alternative at this time. Step 1. Formation of biological building blocks. Step 2. Polymers assemble that can store information (genotype). Step 3. Polymers express phenotype that leads to the direction of biological structures.

fitness of hybrids < fitness of parentals Outcome? Reinforcement that occurs?

Outcome: Hybrid zone is narrow and short live. Reinforcement occurs: response to natural selection that results in assortative mating. Differentiation of parental populations continues and can result in full speciation.

fitness of hybrids > fitness of parentals (Difference is on a gradient) Outcome?

Outcome: Hybrid zone is stable (persists long term) Parental populations remain separated but limited gene flow between the two populations continues.

fitness of hybrids = fitness of parentals Outcome? Parental populations coalesce

Outcome: Hybrid zone is wide and long lived. Parental populations coalesce: Differentiation of parental populations decreases, and they can reintegrate to a single population through gene flow.

fitness of hybrids > fitness of parentals (Difference is in a discrete habitat) Outcome?

Outcome: Speciation; third species is formed.Gene flow among all three stops eventually.

Origin of Pandemic Flu Strains

Pandemic strains emerge when two separate influenza strains co-infect the same host and recombine. The result is a unique combination of genes with very low immune response across populations.

What is the 2nd major result of LUCA?

Perhaps knowing the shape of the tree would tell us more about the characteristics of LUCA. Other studies constructed trees using a wide variety of conserved "housekeeping" genes.

Postzygotic barriers

Postzygotic barriers: reduced hybrid viability, reduced hybrid fertility, and hybrid breakdown. (H) Hybrids have very low fitness and may not survive. (I,J,K) Hybrids may be vigorous/healthy but cannot produce fertile offspring. (L) Hybrid breakdown: some first generation hybrids may be viable and fertile, but when they mate with either parent species, offspring produced are feeble or sterile.

Prezygotic Barriers to reproduction are?

Prezygotic barriers: habitat isolation, temporal isolation, behavioral isolation, mechanical isolation, and gametic isolation. Prezygotic barriers block fertilization from occurring. (A,B) Species may have limited contact with each other due to spatial differences in their habitat range. (C,D) Species vary temporally as well with respect to their breeding seasons or times- species that breed during different parts of the day or year will generally not mate. (E) Courtship rituals can also form a barrier to reproduction as even closely related species may not know the behavior. (F) Morphological differences between two species can prevent successful mating (G) Gametic Isolation: sperm and egg will not fuse

Kimura 1968: Neutral Theory of Molecular Evolution

Proposes that neutral mutations that rise to fixation by genetic drift vastly outnumber beneficial mutations that are fixed due to natural selection. Therefore: 1. Most of the molecular variation with a population is selectively neutral. 2. Most of the fixed substitutions in a genome are selectively neutral.

What if the fitness of the parentals and hybrids depends on location? (Experiment example)

RECIPROCAL TRANSPLANT EXPERIMENT - Wang et al (1997) put plants from all three elevations into all three types of sites. - Experiments showed that the hybrid plants did best in the transitional environment. - We might otherwise expect it to be intermediate.

What hypothesis answers what the first living thing was ?

RNA-first & Metabolism-first Hypotheses

Assessing the cost of antibiotic resistance

Resistance comes at a cost, however compensatory mutations can arise that reduce or nullify the cost of the resistant phenotype. Schrag et al. looked at the evolution of compensatory mutations. Top figure shows the resistant strains were outcompeted by sensitive strains - cost to resistance After experimentally evolving resistant bacteria for a # of generations and repeating the experiment, resistant bacteria now had a higher fitness.

Mechanisms of Divergence: Sexual selection

Sexual selection: Changes in mate-choice promote divergence because they directly affect gene flow. They therefore cause rapid divergence.

What is the Phylogenetic Species Concept (PSC)

Species are the smallest (highest level) monophyletic groups on a tree.

What is the morphological species concept?

Species defined based on morphological similarity

Prezygotic barriers to reproduction

Temporal isolation Not physical- geographical separation but the mating seasons, period of activity, timing between two species is out of sync, so they tend to not share genes or mate with each other. There is little gene flow between apple and hawthorn flies because the time at which these flies mate does not overlap.

Q: How would the presence of apple trees have contributed to reproductive isolation of Rhagoletis?

If flies that develop on hawthorn, look for mates and lay eggs on hawthorn, they may not frequently exchange genes with flies 300 yards away that are carrying out their life cycle on apple trees.

Trade-off Hypothesis: Making the best of the situation

If hosts are plentiful and short-lived, and/or you can only be transmitted horizontally, maximizing transmission is the best option. If hosts are rare, live a long time and/or you can be passed from parent to offspring, minimizing virulence is the best available option. This optimum could be shown with the same kind of graph as the optimal reproductive strategies

RNA World hypothesis

In 1982, Cech and Altman discovered an enzyme composed of RNA - the first enzyme that was not a protein. Chicken or the egg - Did proteins or DNA arise first? Resolved à Catalytic RNA (ribozymes) possess both a genotype and a phenotype.

What are the limitations to the RNA world hypothesis?

In the artificial selection experiment, proteins were used to replicate ribozymes, but in the RNA world these proteins would not have existed. Catalytic RNA's have not been found to replicate themselves. So, ribozymes have many properties that would be sufficient for life, but without the ability to self replicate they are not living organisms.

Example of Natural selection and infectious disease in human populations

Individuals with the mutant CCR5- 32 allele are nearly immune to HIV infection. This allele is almost exclusively found in Caucasians. Positive selection in response to smallpox during the middle ages likely led to positive selection of this allele

Biotic Replacement: Is there evidence for competitive replacement in the fossil record?

Individuals within a species compete for resources, similarly individuals in different species compete for resources. Not really, and abundant and broadly distributed species would likely be very difficult to drive to extinction. However, following a mass extinction if the species is able to survive, it may be able to thrive & diversify on this new playing field.

Infectious disease in human populations

Infectious pathogens are arguably among the strongest selective forces that act on human populations. Host genetics strongly influences an individual's susceptibility to infectious disease. Pathogens that diminish reproductive potential, either through death or poor health, drive selection on genetic variants that affect resistance; this is more clear/pronounced for pathogens that have had a long standing relationship with humans. Natural selection leaves distinctive signatures in the genome, as genetic variants that improve survival and reproduction increase in frequency, and detrimental variants vanish.

Issues and questions regarding Oparin-Haldane model: From simple inorganics to the building blocks of life: How?

It was thought that early earth had a reducing atmosphere in which methane and ammonia were dominant. Under those conditions, Miller showed in 1953 that simple organic molecules (amino acids) could form (with lightning as energy source). BUT it is now thought that the early atmosphere was not so reducing, and under the currently-believed conditions it would be much more difficult for organic molecules to arise.

What drives diversification?

Key ingredient is reproductive isolation, and differential selection. In a heterogeneous environment. Different selective pressures in each environment drive diversification Imagine each shape and color presents a different abiotic environment.

Why do phylogenetic trees with other conserved neutrally evolving genes look different?

LATERAL GENE TRANSFER had a large influence on early genomes.

Where we stand with the origin of life: Where did the building blocks come from?

Miller's simple organic molecules

Effect of menstrual cycling on breast cancer

Monthly menstrual cycling can influence the risk of cancer as the combination of estrogen and progesterone stimulates cell division in the lining of the milk ducts- more cell division more risk of cancer. Strassman 1999 - observed the Dogon of Mali and estimated that the average woman had 100 menstrual cycles during her lifetime, less than 1/3 the average. Women with a similar # of menstrual cycles have a much lower rate of breast cancer.

Morphological triggers of adaptive radiation:

Morphological innovation can lead to adaptive radiation by allowing species to exploit new habitats or resources.

What are the 4 species concepts?

Morphospecies Concept Biological Species Concept Phylogenetic Species Concept Ecological Species Concept

How natural adaptation drives adaptations to different habitats and an example.

Natural selection drives adaptation to different environmental conditions. The monkey flower displays two unique ecotypes. Diverging life history strategies based on environmental conditions. A chromosomal inversion was also at play here, which limits cross over during meiosis and could contribute to speciation.

What are other hypothesis regarding what the first living thing was?

The Ring-of-Life Hypothesis The Chronocyte Hypothesis The Three Viruses, Three Domains Hypothesis

what are the conclusions regarding LUCA?

The last universal common ancestor was a "community" that regularly traded genes (i.e there was lots of LGT). Three main branches of life emerged from this community.

What 3 major domains of life were the results of LUCA? (last universal common ancestor)

bacteria, archaea, and eucarya

Catalytic RNA molecules (RIBOZYMES) are a possible to have both of what in one step?

genotype and enzyme

Is virulence in vector-borne pathogens symmetric or asymmetric?

highly asymmetric

What is the most important mechanism promoting divergence between populations

natural selection

What is the essence of speciation? (what do they all have in common)

the absence of gene flow between two populations that are in contact with each other.

The species concept defined as a group of organisms that are capable of interbreeding to produce fertile offspring is ________.

the biological species concept

Define virulence

the harm done to a host by a pathogen during the course of an infection.

Species

the smallest evolutionarily independent unit.

Analysis of the 1918 and 2009 flu epidemics reveals that the most likely scenario was that ________.

the virus ultimately arose in birds, jumped to pigs, and then was able to switch to humans

Breast cancer as a viral disease in mice

•Mice carry a virus MMTV that causes the equivalent of breast cancer in mice •Wang looked for the presence of a MMTV gene in normal and cancer tissue Found that incidence of breast cancer is higher in western Europe

Rhagoletis pomonella life cycle

1.The female lays fertilized eggs in the fruit. 2.Maggots (larvae) emerge from the egg, feed on the fruit, and grow through several molts. 3.Healthy maggots drop from the tree with the fruit and burrow in the soil. Pupation takes place in the soil. 4.Adult maggot flies emerge from the soil and fly back to fruit trees, where they mate on the surface of the fruit. (repeat cycle)

Coincidental Evolution

A trait that is selected for in some other part of the pathogen's life cycle has a by-product that increases virulence in the host. Legionella pneumophila evolved a number of traits to resist predation by protozoa/amoebae. These traits coincidentally result in virulence in humans because macrophages and amoebae have similar phagocytic mechanisms. Infection in humans is a dead end - the bacteria are not transmitted between individuals so virulence in humans has no selective advantage

The biggest issue facing the successful production of influenza vaccines is that ________.

A) flu virus populations evolve rapidly B) flu vaccines can take months to prepare C) researchers must successfully predict which flu strain(s) will survive from among the existing strains to become the next season's epidemic All of the above are serious issues.

What are the advantages of the ecological species concept (ESC)

-Widely applicable to macro- AND micro-organisms. - Sometimes testable - Able to distinguish cryptic species

Define vicariance events

Can be slow (movement of continental shelves) or fast (lava flow, change in a riverbed). Ex: Albert's squirrel and Kalibab squirrel became geographically isolated about 10,000 years ago due to formation of the Grand Canyon

The Neutral Theory as a null model:

... when purifying (negative) selection eliminates deleterious nonsynonymous changes, the ratio of dN/dS is less than 1 dN < dS and so, dN/dS < 1 ... when positive selection is pushing beneficial nonsynonymous changes to fixation, the ratio of dN/dS is greater than 1 dN > dS and so,dN/dS > 1

Mechanisms of isolation- what is the 3 step process of speciation?

1)Reproductive Isolation 2)Divergence 3)Secondary contact and its outcomes

What are the 2 possibilities that the breast cancer rate in North America?

1. Breast cancer is caused by a pathogen 2. Breast cancer is a disease of civilization

What 2 predictions does the dispersal and colonization hypothesis make?

1. Closely related individuals should be located on adjacent islands 2. Sequence of branching should correspond to island formation

Issues to address with origin of life (first living thing)

1. Inorganic to organic building blocks 2. Polymerization - building blocks into proteins and nucleic acids 3. Genotype/phenotype - ability to store information and catalyze reactions 4. Compartmentalize - separate internal/external environment 5. Evolving via non-Darwinian processes

What are 2 assumptions from the neutral theory of molecular evolution?

1. Population size is not a factor. 2. Sequence evolution by N.S. is so rare that it is insignificant.

What are the 3 reasons that RNA is an early life form?

1. The ribosome is the most conserved and universal component of information transfer. Ribosomes are built on an RNA frame and use RNA adaptors to function. 2. RNA portion of ribosome carries out catalytic function. 3. Basic currency for biological energy is ribonucleoside triphosphates - ATP & GTP

What 3 things should a good species concept be?

1. be mechanistic (imply the process by which one species becomes two). 2. be testable. 3. accurately reflect evolutionary history.

Where did the first living thing (RNA) come from/ 4 issues that need to be addressed

1.Information-containing biomolecules are composed of simple inorganic compounds - Where did these compounds come from? 2.Chemical rxns to construct larger molecules must be favorable and have a source of energy. - What are these reactions? 3.Building blocks must be able to polymerize. How? 4.Larger biomolecules need to be protected from harsh environmental conditions. How?

3 models to explain the evolution of virulence:

1.The coincidental evolution hypothesis 2.The shortsighted evolution hypothesis 3.The trade-off hypothesis

The species concept that relies most heavily on the criterion that species are evolutionarily independent units that are isolated by gene flow is ________. A) the morphospecies concept B) the phylogenetic species concept C) the biological species concept D) This criterion is common to all of these concepts.

D

What is the "Holy Grail" of the RNA World hypothesis?

For a molecule or collection of interacting molecules, gaining the ability to self-replicate can be considered a transition to being "life". Researchers are trying to recreate such an RNA molecule or group of molecules.

Issues and questions regarding Oparin-Haldane model: Assembly of Biological Polymers

Chains of amino acids and nucleotides have been made abiotically. But there are still problems explaining how proteins and nucleic acids arose. Chirality: living systems use only one of the two stereoisomers of amino acids and nucleotides. How did that happen? (and why?) Activation: many molecular building blocks need to be activated (charged) before they can be incorporated into polymers. This activation process is hard to explain without a cell membrane. (So when did the membrane come into the picture?) Instability: proteins and nucleic acids break down easily in water (hydrolysis); even if they were formed, they might not last long enough for the next steps to happen. INSTABILITY: The "clay-catalysis" model suggests a way that chains can be formed faster than they are broken down. Early on, there was probably an abundance of energy, so complex metabolism would not have been necessary until much later. The earliest life would have been anaerobic, because Earth did not yet have an oxygen atmosphere.

What are antibiotics?

Chemicals that inhibit the growth or kill microorganisms -originally discovered being produced by other organisms (i.e. other microorganisms). -many different mechanisms of killing -inhibit protein synthesis -prevent cell wall formation Hailed as a miracle cure back in the 1940's, and have saved millions of lives since their discovery.

What types of isolation lead to sympatric speciation?

Chromosomal isolation, e.g. polyploidization (2-4% of plant speciation events). Other genetic forms of isolation e.g. Emergence of a mutant that can use a new resource due to an antagonistically pleiotropic allele. Temporal isolation: e.g. early flowering vs. late flowering host plants. Resource utilization: Discussed in Stroud & Losos.

How do ribozymes evolve by artificial selection?

Created a mutant pool of ribozymes. Incubated ribozymes with DNA for an hour, and then added added to enzymes that would replicate ribozyme if it completed reaction shown in 17.2 B

A disadvantage of the morphologicalspecies concept is ________. A) it can be difficult to apply to organisms with small, difficult to distinguish features B) species definitions may become arbitrary if the concept is not applied carefully C) species definitions applied by different researchers may not be comparable D) All of these are potential problems with this species concept.

D

Hemoglutin definition and its evolution.

Definition: A coat protein that binds to sialic acid on host cells. It is also the primary influenza protein that is recognized by our immune system. Finch: Is hemagglutinin under selection? Sequenced flu strains collected over a period of 20 years and estimated rate of evolution & phylogeny of the sequences. Surviving lineages had a significantly higher fraction of amino acid replacements at antigenic sites.Influenza strains that have novel antigenic recognition sites can evade the immune system. Hemagglutinin is under strong selection by the immune system.

Shortsighted evolution: Within-host evolution of HIV

During the chronic phase this region of the gp120 gene evolves rapidly (under positive selection) to evade the immune system. The rapid evolution under positive selection stops about when the immune system collapses. Eventually HIV evades host immunity so well that it infects and kills host T cells more rapidly than they can be replaced. The host gets sick, greatly decreasing likelihood of further transmission to new hosts.

Example: How many species of African elephant are there? (Answer this using each species concept.)

ESC: They use different resources -- this is the observation that spurred the investigations in the first place. Morphospecies: New analyses suggested forest and savanna African elephants may be different. BSC: Ambiguous, because they do not interbreed as their ranges do not overlap. PSC: ? "Large genetic distance, multiple genetically fixed nucleotide site differences, morphological and habitat distinctions, and extremely limited hybridization of gene flow between forest and savannah elephants support the recognition and conservation management of two African species: Loxodonta africana and Loxodonta cyclotis."

What came first, genetic material or enzymes?

Evidence suggests both -- in the form of catalytic RNA.

What evolutionary mechanism is responsible for most molecular evolution?

Genetic drift (not Natural Selection)

Mechanisms of divergence: (Genetic drift)

Genetic drift: neutral evolution, especially in small, new populations could cause rapid divergence.

Compartmentalization is often left out of early life puzzles, but the question of when it occurred is also a "chicken and egg" story. Explain compartmentalization.

Having an "inside" and an "outside" defines self vs environment: important for natural selection to be able to favor one thing over another. Having a cell membrane makes the reactions necessary for formation of proteins and nucleotides more explainable. But how do you get a membrane without something hereditary to encode it? Some argue that spheres of lipid bilayers may have formed spontaneously and thereby provided compartmentalization. Miller's experiment (Miller-Urey experiment) showed that lipids can form under early-earth conditions, and spontaneous bilayers do form...but the lipids that formed in Miller's experiments were the wrong kind.

Speciation through dispersal and colonization is often seen in groups of endemic species. What is an example of geographic isolation through dispersal?

Hawaiian drosophilids. Estimated 1,000 species - many with their range restricted to a single island. Founder effect & then divergence after the founding population becomes established.

Define the ecological species concept (ESC)

The set of organisms sharing a particular set of resources in the environment à differences in form (morphology) and behavior are often linked to differences in ecological resource exploitation patterns.

Flu strain Out-evolving the immune system

There are 5 antigenic regions of hemagglutinin. These regions are the ones recognized by the immune system. Using the neutral theory as a null hypothesis, researchers were able to show that the excess of replacement to silent substitutions in those regions indicates that positive selection is acting, promoting non-conservative change.

Universal Gene-Exchange Pool Hypothesis

There was rampant LGT. So much so that before a "Darwinian threshold" natural selection could not act at the level of the organism. Suites of genes acting together formed, making genomes cohesive (less modular and swap-able) At that point a lineage passes a Darwinian threshold and evolves by natural selection. At first, lateral exchange of genes was so common that evolution by natural selection could not work. As self replication replaced "assembly" by LGT, common ancestors emerged and natural selection began to act.

What about bacteria and archaea?

These taxa separate reproduction and sex (genetic exchange). Genetic exchange often occurs among taxa that are on average much more distant from one another than eukaryotic recombination associated with meiosis. Gene flow is often unidirectional and involving only a portion (often small) of the genome. Gene flow may trigger divergence in bacterial populations-while the opposite is true in eukaryotes. Traditional: percent similarity based on genome wide DNA-DNA hybridization. Today, few still think this is actually a good idea. Most recently: Gene content (which genes are present) - with the logic that gene content is the link between the genotype and the ecology of the organism.

What are the methods used for a phylogenetic approach?

They sequenced the DNA encoding the small subunit of rRNA (16S subunit). This is a highly conserved gene that is present in all life. It has the same function in all cells.

How can species be separate from one another?

To be separate species, populations must have diverged enough for diagnostic traits to have evolved. The clusters of populations cannot be distinguished phylogenetically and would be same species.

shortsighted evolution

Traits favored within hosts may increase virulence, even though long term they are bad for the population because they decrease transmission between hosts. Polio - polioviruses normally infect the intestinal tract and are relatively asymptomatic. In about 1% of infection, poliovirus can invade the nervous system (harms host) but CNS infections are an evolutionary dead end since transmission from CNS does not occur. Opportunistic pathogens that infect immunocompromised individuals have generalized pattern of host adaptation that leads to chronic infections but low transmission. Traits decrease ability to survive outside of host.

Define Assortative Mating

Traits that influence the way species choose mates. Variation in trait if females prefer certain variations of the trait it can lead to reproductive isolation. Similar idea to the indirect "sexy son" hypothesis.

Mode of Transmission and Virulence

Virulence should be influenced by or correlated to the mode of transmission. Modes of transmission: Vector-borne Sexual/direct contact Waterborne Airborne

Ecological controls on species richness

When a new habitat is first exploited by a group of organisms, and adaptive radiation will occur & many species form rapidly, however as the number of empty niches declines that rate of speciation also declines.

When does evolutionary independence occur?

When the forces of evolution operate on populations separately. Since evolution consists of changes in allele frequencies across generations, species consist of interbreeding populations that evolve independently of each other.