Evolution Final for real

1855 human health discovery

John Snow maps the cholera outbreak in London and links it to the water

1858 human health discovery

Louis Pasteur develops germ theory of disease

1863 human health discovery

Robert Koch shows disease is caused by Vibrio Cholerae

1990s human health discovery

"Darwinian medicine" applies evolutionary principles to medicine

Sanitation and antibiotics

The battle against TB started with improved sanitation. Antibiotics helped push the disease to local extinction

The case of the flu virus

The flu virus evolves rapidly in response to the host's immune system because

-Large population sizes

- Short generation time

- High mutation rates

When is the evolution of the flu especially rapid?

At antigenic sites on the hemagglutinin protein of flu virus. Evolved at a constant rate since 1965 due to arms race of immune systems.

What causes pandemics?

When strains incorporate mutations at antigenic sites on hemagglutinin

What did they learn from frozen flu samples?

- Almost all strains die out as most mutations are neutral except for antigenic sites.

- Surviving strain is often the strain with the most antigenic mutations

Phylogeny of hemagglutinin (H) genes

- H genes have jumped across flu strains

- Pigs can host both bird and human strains

- H3 likely moved from birds to humans

Origin of pandemic flu strains

1. Two strains infecting the same host (human, pig) can allow RNA strands to recombine

2. This could create a new strain unrecognizable to hosts

3. Rapid virus spread (pandemic) can result

Evidence that antibiotics select for resistance

- Antibiotic resistance of bacteria in Iceland when use of penicillin was reduced

-Pattern implies that resistance is costly for bacteria

-From a pop perspective, minimize the use of antibiotics

Virulence

The harm done by a pathogen to the host

Coincidental virulence evolution

Accidental byproduct of selection for other traits

Short-sighted virulence evolution

Traits that enhance within host fitness may produce harmful side-effects (polio in nerve tissue is never transmitted)

Tradeoff virulence hypothesis

Natural selection favors strains that optimally balance the costs and benefits of harming the host

Virulence is higher in...

1. Vectorborne (malaria) vs directly transmitted pathogens (colds & flus)

2. Waterborne vs directly transmitted digestive / diarrhea-causing bacteria

What do vectors and water allow?

Disease transmission even from sick hosts

What are the "diseases of civilization"

Heart disease, strokes, cancer, myopia, and breast cancer. Diets and exercises have changed over the last 10,000 years

What does evolutionary psychology assert?

Human behavior is fundamentally shaped by natural selection, and the ultimate goal is to increase fitness

Why is evolutionary psychology limiting

Not ethically possible to do experiments to make strong conclusions

How much of animal genomes is unexpressed DNA

Around 10%, which is a lot. Viruses and prokaryotes have a little

What are mobile genetic elements, aka genetic parasites?

They contain only the sequence required to move. They are selfish, as duplication increases fitness.

Variation in mobile element content

Most of the unexpressed DNA in animals is from mobile elements. They aren't expressed but can alter transcription rates.

Alu elements

The most abundant transposable elements in primates. Humans have 500k copies but they are short

What is the primary source of new genes?

Duplication of existing genes

Segmental duplication

Duplication of stretches of chromosomes with many genes, single genes, or pieces of genes.

How does segmental duplication occur

From unequal crossing over during meiosis or by mobile element activity

Judicious use of antibiotics

The best defense against antibiotic-resistant bacteria is to avoid letting bacterial populations evolve resistance in the first place

What adaptation allowed icefishes to

dominate and speciate in ridiculously cold

Antarctic waters?

Antifreeze glycoproteins (

Heat shock proteins (HSPs)

Under periods of cellular stress, like high temperature, hsp genes are highly expressed to help cells deal with the stress

Anagenesis

Lineage changes, produces a new form

Cladogenesis

A lineage splits, producing new forms

Hybridization

Lineages combine, producing new forms

Three-step model of speciation

Isolation, divergence, secondary contact

Isolation in speciation

Gene flow is disrupted

Divergence in speciation

Genetic differences accumulate

Secondary contact in speciation

Populations re-establish contact and hybridize, outcomes vary

Mechanisms of isolation

Physical, dispersal & colonization, and vicariance

Allopatric speciation

Speciation initiated by physical/geographic isolation

Vicariance

The physical splitting of a habitat. (Pangaea or natural disasters)

Divergence

The accumulation of differences in genetics and phenotypes between isolated groups

Mechanisms of divergence

Adaptation to different habitats and assortative mating

Assortative mating

The type of mating that occurs when an organism selects a mating partner that resembles itself genotypically and/or phenotypically

Three possible outcomes of secondary contact

No speciation, very low fitness (postzygotic isolation), and reinforcement. Depends on relative fitness of hybrids

Postzygotic isolation

Hybridization that produces individuals with very low fitness. Often occurs due to genetic incompatibilites.

Reinforcement

When second contact occurs and populations evolve new traits to keep them separate.

Requirements of life

Ability to store and transmit information (genotype), ability to express stored info (phenotype), and ability for adaptive evolution.

Ribozymes

30-1000 ribonucleotides, single strand (folds like a protein), active site, and often forms and breaks phosphoester bonds.

Ribosomes are a "holdover" from the RNA world

- They translate info from proteins.

- They are highly conserved across taxa

- They consist of both proteins and RNA

- They require RNA adaptors (tRNA) to function

Four issues earliest replicator needed to solve

1. Going from simple inorganics -> larger molecules

2. Reactions must be favorable and have an energy source

3. Self-assembly of molecules into polymers such as RNA or polypeptides

4. Protection of biomolecules from harsh environments

How did simple inorganics -> larger molecules?

Possible from meteorites that often contain amino acids. However, both stereoisomers are usually present (they are not likely derived from living organisms)

Panspermia hypothesis

If microbes exist on other planets, could they have seeded Earth?

Radiation poses a problem (cold and vacuum aren't problematic)

Oparin-Haldane model: primordial soup

Reactions must be favorable and have an energy source

Methane + ammonia + H2 + energy = amino acids

Self-assembly of molecules into polymers

Clay may facilitate the 2nd step of the Oparin-Haldane model

Activated nucleotides join together on clay substrate

Minimum age of life, from fossil evidence

About 3.7 billion years. Better fossil evidence at 3.4 bya. Excellent fossils 1-2 bya.

The phylogeny of all living things

Small subunit ribosomal RNA: Highly conservative and useful for deep phylogeny

Horizontal gene transfer lesson

Use multiple genes to build phylogenies

Why is the tree of life so complicated and not tree-like?

Horizontal gene transfer

Fossilization and types of fossils

- Amber & freezing

- Permineralization & replacement

- Natural molds & casts

- Trace fossils

Ediacarian Biota

Represents the first assemblage of macroscopic fossils. Run-up to the more diverse Cambrian fauna.

The early animal radiations: Cambrian Explosion

The Burgess Shale Fauna reveals a massive variety of large, bilateral animals

What caused the Cambrian Explosion?

The extinction of the Ediacaran fauna and an increase in atmospheric oxygen

The fish-tetrapod transition

New fossils illuminate the origin of tetrapods in the Devonian era. Key bones in modern tetrapods can be recognized in transitional fossils

The dinosaur-bird transition

Origin of feathers predates the evolution of flight

The origin of mammals

Bones in lower jaw were incorporated into the middle ear of modern animals

Morphological diversity measured by what?

Occupancy of morphospace and periods/eras of natural history

Mass and background extinction

Constant, low rate of extinction side from 5 rare and large events

Evidence for the Cretaceous-paleogene extinction

- Iridium at the boundary

- Shocked quartz grains

- Microtektites

- A huge impact crater off the coast of Yucatan

Poisson Process

A process in which events occur continuously and independently at a constant average rate

Permian-Triassic extinction

Massive volcanic activity in Russia may have caused climate change that led to this event. Domination of terrestrial communities by the mammal-like reptile may reflect climatic instability during and after the event

Is the 6th mass extinction event underway?

Extinction follow in the footsteps of human dispersal around the world. The role of humans is especially clear in the case of New Zealand Moas.

Macroevolution: punctuated equilibrium and the importance of stasis

Early caricatures stressed a distinction between punctuated vs. constant change. However, recent data compilation and analysis indicate that substantial evolutionary change is punctuated but very rare.

Macroevolution: Why does stasis occur?

Stasis is not due to a lack of genetic variation.

Evolution above species level: traits that affect extinction rate

Attributes of whole species and genera, such as geographic range, may influence extinction rate. For example, marine taxa with planktonic larvae experience lower extinction rates.

Adaptive radiation

Rapid morphological diversification and occupancy of diverse ecological space. Can occur on a remote island following colonization, suggesting that ecological opportunity is the driver

Fossil & molecular divergence timing

Time-calibration of trees relies on fossil checkpoints and the clock-like regularity of molecular divergence.

What varies from branch to branch on time-calibrated trees?

Rates of morphological divergence

Was the Cambrian explosion really explosive?

Cambrian taxa may have originated much earlier than their appearance in the fossil record. Meaning it may be less explosive than fossils show

Did the end-of-Cretaceous mass extinction release mammals?

Time-calibrated trees indicate that many mammals originated and diversified long before

Altruism

Actor pays, recipient benefits

Altruism in nature

Cooperative and selfish behavior are common. Spiteful behavior is rare.

Coefficient of relatedness (r)

r = Probability that two alleles in 2 individuals are identical by descent. Similar to the inbreeding coefficient F (which measures whether 2 alleles within an individual are IBD)

Hamilton's rule

An allele for altruistic behavior will spread it Br > C.

B = benefit to the recipient

C = Cost to actors

r = coefficient of relatedness

Inclusive fitness

Direct fitness (actor's personal reproductive success) + Indirect fitness (change in relative's fitness due to actor's actions)

Kin selection

Selection for traits that increase indirect fitness

Parent-offspring conflict

Occurs when offspring favor their own well-being over parents' well-being

Siblicide, abortion, and infanticide

Fitness includes the number of young AND the survival of young. Therefore, it can be adaptive to reduce brood size during food shortages and overproduction of offspring.

Eusocial species traits

Overlap between parent and offspring generations.

Cooperative brood care

Specialized castes of non-reproductive individuals

Eusociality is an extreme form of altruism seen in...

Ants, bees & wasps. Termites, snapping shrimp & naked mole rats.

Haplodiploidy in Hymenoptera (ants, bees, and wasps)

Sisters are more closely related to each other than to their own daughters (if they could make daughters).

The haplodiploidy hypothesis states that female bees/ants should favor the production of sisters rather than their own offspring.

Haplodiploidy

To calculate r, the coefficient of relatedness:

- Follow paths from actor to recipient

- Tally proportion of genes shared

- Multiply to get r

What is a "Darwinian demon"?

Begin reproducing soon after birth, live forever, and produce an unlimited number of offspring

Why can't "darwinian demons" exist?

Trade-offs. Mainly between growth and reproduction. One must be prioritized.

Diversity in reproductive strategies

Some species reproduce once, and others many times.

Some species produce one-two eggs, and others millions.

Semelparous

Reproduce and die

Iteroparous

Reproduce multiple times

Life history

Pattern of energy allocation to growth vs. reproduction. Fundamental tradeoff between growth and reproduction

What does natural selection favor?

Growth vs reproduction rates that yield the highest total fitness.

Senescence

Late-life decline in fertility and survival