EXAM 1

What are the sources of data evolutionary biologists use to test hypothesis?

1. Fossil record

2. Behavioral Data (ex: grooming behavior)

3. Morphological (ex: wing patterns/colors)

4. Embryological (ex: magnetic resonance)

5. Molecular genetics (ex: DNA sequence)

What are the 3 Applications of Evolution?

1. Artificial selection developed food we eat and therefore changed our bodies

2. Development of disease and therefore pharmacy/drugs (antibiotic resistance)

3. Phylogenetic Trees for hypothesis (scientific and math models explain the past)

Empirical Research

• Testing ideas/hypothesis/theories using real world experience

• Observation versus manipulation

Descent with Modification

• evolution of how species change over time

• populations have variations in traits

• differences in traits result in differences in reproduction

• populations will resemble the most successful individuals of the previous generation

Anthropogenic evolution

• evolutionary change due to humans

Anthropocene Era

• “recent age of man”

• 1950s on

Uniformitarianism

• slow processes over long time produce large results (ex: erosion producing canyon)

Theories

• 8ngerstandings form ovservation, experiements, reflection, using tests

Hierarchical patterns of similarity

• species cluster due to similarity at hierarchical diversity levels

Carl Linnaeus (1707-1778)

• developed hierarchical classification of nature

• Viewed species as an ideal form, created and unchanging (‘type specimen’)

• Young Earth (approximately 6000 years old)

James Hutton and Charles Lyell

• founded modern geology field by developing uniformitarianism

Mary Anning

• fossil purveyor and paleontologist

• in communique with several geologists including Lyell

• her remarkably detailed and accurate depictions of fossilized remains contributed to the growing acceptance of extinction

Lamarckism

• new traits are result of new environmental pressure

• as organisms use a trait, they build that trait

• offspring then inherit the changed trait and continue to build on it

Natural Selection

• describes the circumstances under which a population changes over time

• survival of fittest

Criteria of modern theory of natural selection

1. variation- genes can differ in DNA sequence (alleles)

2. Heritability- genetic information (DNA) can be passed from parents to offspring

3. Differential reproduction- some alleles are spread more in a population, because the traits they code for are selectively advantageous

Why is heritability a requirement for natural selection?

• without it, evolution can not ensure that adaptations are maintained in population

• must be correlation for causation!

Why can’t organisms ever be perfectly adapted to their environment?

Environment is always changing!

Adaptation

• trait that increases fitness of organism

• change thorugh heritability

Acclimation

• process of adjusting physiology and behavior to maintain homeostasis under prevailing conditions

• change through exposure

• Individuals acclimate while populations adapt!

What are the 4 types of selection?

1. directional

2. stabilizing

3. disruptive

4. Balancing

directional selection

Stabilizing selection

Disruptive selection

Balancing selection

Phylogeny

• model/hypothesis of branching relationships of lineages as they give rise to multiple descendant lineages (AKA evolutionary ancestry)

Branches v.s. Nodes of phylogenetic tree

• branches=lineages evolving through time

• nodes=points in time when lineages diverge (ex: speciation events in a taxon tree)

Cladogram

• show branching order (does not include length of time which is how its different from phylogeny)

Clade

• collection of branches and nodes including common ancestor and all of its descendants

• Monophyletic

• Phylogeny=nested hierarchy of clades

Clade v.s Taxon

• different bc all phylogenies are hypothesis and therefore subject to change

Non-monophyletic groups

• do NOT contain all descendants of most recent common ancestor

• ex: prokaryotes and fish

Apomorphy

• derived trait

Synapomorphy

• derived characteristics shared by all members of the clade

• unites monophyletic groups

• homologous characteristics

Plesiomorphy

• ancestral trait

Symplesiomorphy

• ancestral traits occurring before MRCA

• found in paraphyletic groups

Homoplasy

• similar traits because of similar environmental pressures

• can unite polyphyletic groups

• Analogous characterstics

Parsimony/most parsimonious model

• Ockham’s Razor

• fewest evolutionary changes is often correct

Outgroup

• lineage that split off prior to common ancestor of ingroup

Homologous v.s Analogous Characters

• Homo-shared b/c inherited from CA

• Ana- shared b/c of similar environments that selected for similar characters (convergent evolution)

Types of Fossils

• Preserved remains-compressions, casts/molds, petrified/mineralized, amber

• Trace fossils- coprolites, trackways, burrows, nests, gastroliths

• Index fossils- help estimate time, widely distributed and easily recognizable

3 Biases in the Fossil Record

1. Habitat-marine organisms dominate but make up only 10% of living species

2. Taxonomic- organisms with hard parts dominant without DNA

3. Temporal- old fossils are very rare

Relative Dating

• Deeper fossils=older

• used to match distant locations

Absolute Dating

Background Extinction

• normal rate at which species go extinct

• species typically go extinct after 1-10 my of existence

• extinction rate < speciation rate

Mass Extinction

• extinction rate > speciation rate

• 60%+ of all species go extinct within a relatively short (<3 million years) geologic time

• “Big 5” Mass extinction events are best studied

Primary Extinction

• extinction of species whereas secondary extinction is the extinction of a species because of its dependency on another, now extinct species

Secondary extinction

• only occurs if another essential species goes extinct

Extinction Cascade

• enough primary extinctions in ecosystem cause community to collapse

• more diverse ecosystems are more resilient to collapse

• Mass extinction-worldwide extinction cascade

5 Big Mass Extinctions

1. End Ordovician

2. Late Devonian

3. Permian Triassic

4. Triassic-Jurassic

5. K-Pg Mass Extinction

End Ordovician Mass Extinction

• 445 MYA

• only plants and insects made it to land

• 60-70% of all species went extinct

• Massive glaciation=new climate patterns (glaciation dropped sea levels and changes in ocean circulation deprived depths of oxygen)

• brief “ice age” straight into rapid warming period=environmental stress

Late Devonian Mass Extinction

• 370 MYA

• 75% species extinct

• Volcanism=gases and atmosphere change

• led to brief cooling then rapid global warming

• increased weathering of rocks oversupplied nutrients to shallow water and oxygen dropped

Permian Triassic Extinction

• 252 MYA

• AKA “Great Dying”, > 90% species extinct

• Volcanism released CO2 and Sulfur dioxide

• temp increase and acidified ocean, methane hydrates from warming of ocean depleted oxygen and warmed planet

Triassic-Jurassic Extinction

• 201 MYA

• 70-80% extinct

• massive volcanism, ect.

K-Pg Mass Extinction

• 66 MYA

• 75% extinct

• Asteroid impact vaporized rock, released CO2 and heat

• climate change ensued

What causes mass extinction?

• extraordinary and sudden environmental changes

What causes Background extinction?

• poor adaptation, specialization, environment change, new competitors, and predators

4 Ways to Survive Mass Extinction

1. Be able to go dormant

2. Have wide geographic range (marine bivalve genera w/wide geographic ranges were less likely to become extinct)

3. Small with many offspring

4. Have luck!

Whats the equation for the molecular clock?

What are the assumptions of molecular clocks?

1. Constant mutation rate-different genes can have different rates but mutation rate needs to be constant

2. Mutations are neutral-beneficial mutations “accelerate” mol. clock and high constraint slows it down

3. Homologous genes- same gene in different species, same as phylogenies

Adaptive Theory v.s Neutral Theory

• today we balance adaptive molecular evolution and neutral molecular evolution

• reductionist/reductionism= adaptive theory of evolution (same as Darwins)

What other considerations must be made with the molecular clock?

• choosing right DNA segment (present in all samples and not under selection)

• Calibration (initial # of changes, fossil data, geographic data, known sampling data)

• Uncertainty

What is a common use of molecular clocks?

• questionable infections to estimate timing and origin of infection

• ex: tripoli six

HWE

• null model

• no mutations

• no selection

• no migration

• random mating

• infinite population size

• No evolution!

Does Mendelian Inheritance alone cause a change in genotype/allele frequencies? Is Mendelian Inheritance an evolutionary force?

• No! B/c its a null model :)

When is a population considered to be in HWE?

• genotype frequencies are p² , 2pq, and q²

• genotype frequencies are NOT changing over time

• Never assume a pop is in HWE!!

Absolute fitness (W)

• number of offspring per individual over lifetime

• 0→ infinite

• =1, then individuals replace themselves

Relative Fitness (w)

• fitness relative to highest fitness genotype

• 0→1

• =(absolute fitness)/(AF of most fit phenotype)

• lets us calculate allele frequency after selection

Strength of Selection (s)

• difference in fitness between one genotype and another

Mean Population Fitness

• weighted average of all fitnesses

Single locus v.s many loci for variation in traits?

• single=2 alleles=discontinuous variation

• many=continuous variation

Polygenic traits

• many loci influencing the same trait

• # phenotypes=2n+1, n=# of loci

What equation describes variance?

Epistatic Genetic Variation (Vi)

• variation due to interactions among loci

Dominance genetic variation (Vd)

• variation due to dominance relationships among alleles

Additive genetic variance (Va)

• variation due to additive effects of alleles

• many polygenic traits assume Vg=Va

How is heritability calculated?

Variance

• measures how much variation exists in population around the mean value

• same mean but different variances

Narrow sense heritability

Breeder’s Equation