"Informal" time periods during which Earth has existed

• Phanerozoic = current eon
• precambrian = collection of the 3 prior eons (Hadean, Archean, Proterozoic)

Made of 3 eons:

• Hadean
• Archaen
• Proterozoic.

Major events:

• Origin and Radiation of of Eukaryotes
• First simple multicellular organisms
• Origin and Radiation of Prokaryotes (photosynthesis --> O2 in atmosphere)

• Started ~4.6 Ga (Earth's formation)
• ended ~3.8 Ga (billions of years ago)
• Includes impact which created the moon.
• Hella CO2 in atmosphere.
• No life yet.

• Began ~3.8 Ga
• ended at 2.5 Ga (billions of years ago)
• Likely includes the original development of life
• Not a lot known about it.
• Bacterial (and even simpler) fossils found only.

• Began 2500 Ma
• Ended 542 Ma
• Atmosphere was Oxygenated
• Eukaryotes formed
• soft-bodied multicellular organisms formed (e.g. sponges).

• From 542 Ma to now.
• Current Eon.
• Consists of 3 Eras
  • Paleozoic
  • Mesozoic
  • Cenozoic

• Began 542 Ma (first era of current phanerozoic eon)
• Ended 251 Ma
• Cambrian Explosion happened near beginning.
• Permian Extinction marked the end.

• happened ~530 Ma over the course of many millions of years
• near beginning of Paleozoic Era
• Rapid appearance of most major Phyla
• First vertebrates
  • Fish
  • amphibians
  • reptiles.
• Invasion of land
  • plants
    • Fern Forests (before gymnosperms and angiosperms)
    • First gymnosperms
  • insects [w/ exoskeletons]
•  Supported by fossil evidence in 3 fossil deposits
  • Duoshanto Fossils
    • Southern China
    • 580-570 Ma
    • microscopic fossils (sponges, embryos)
    • likely all filter feeders
  • Eidacaran Fossils
    • Southern Australia
    • 560-540 Ma
    • sponges, jellies, combjellies, burrows, tracks
    • No hard shells, limbs, or heads w/ feeding appendages
  • Burgess Shale Fossils
    • British Columbia
    • 525-515
    • Abundant sponges, jellies, combjellies
    • Eyes, mouths, limbs, shells, feeding appendages
    • Almost every modern phyla present

• Circa 248 Ma, end of Paleozoic
• Largest of all mass extinctions 
• 90-95% of all marine taxa lost
• Big losers: pelycosaurs, trilobites, placoderms 
• 2 potential causes
  • Rapid climate shift
  • massive volcanic eruptions due to plate tectonics in the formation of Pangea.

• first Dinosaurs
• gymnosperms radiate
• dinosaurs radiate
• first angiosperms(flowering plants)
• Ended with the Cretaceous Extinction

• 65 Ma
• 85% of species lost
• Big losers: dinosaurs & marine reptiles
• Unaffected: mammals, birds, amphibians, crocodiles, lizards, snakes
• Likely caused by big meteor impact in Yucatan

• 65.5 Ma until RIGHT NOW!
• Began with Cretaceous Extinction
• radiation of flowering plants/insects/mammals.
• Appearance of hominids [only significant cuz they turned into us].

• Support for idea that species change through time:
  • Fossils: The fossil record has transitional forms
  • Vestigial traits: Useless trait
  • Observations on natural populations: They change through time
  • Extinct species: Species have gone extinct
• Support for idea that species share common ancestors:
  • Biogeography
  • Homologous traits (anatomical, embryological, molecular)

Hardy-Weinberg equation

What is it used for?

What are the assumptions?

• Measuring for changes in allele frequency
• Assumptions:
  • No natural selection
  • No genetic drift
  • No gene flow
  • No mutation
  • Random mating
• The frequency of all alleles in a population sum to 1. If the frequency of all alleles in a generation is known, and this population is not evolving, then you can predict the frequency of alleles in the next generation.

• Directional selection
• Stabilizing selection
• Disruptive selection
• Sexual selection

• Natural selection driven by environment due to random chance (sampling error)
• Founder effect (new population forms from old population) vs genetic bottleneck (population has hella deaths, continues). Both result in loss of genetic variation
• 3 key aspects of genetic drift
  • Random with respect to fitness
  • Most pronounced in small populations
  • Can lead to lost/fixed alleles

• Maintains less fit alleles in population
• Two types:
  • Heterozygote advantage: sometimes heterzygotes have higher fitness than homozygote (homo-recessives get Sickle cell anemia, heterozygotes have resistance to malaria)
  • Negative frequency selection: Rare individuals have higher fitness.  Becomes not rare.

• The movement of alleles from one population to another. Equalizes allele frequency between the two.
• Effects on genetic diversity for donor & recipient populations:
  • decreased in donor
  • increased in recipient.

• Breeding with relatives
• Does not alter allele frequency in gene pool, but does alter genotype frequencies (homozygote frequency increases)
• Inbreeding depression = homozygous genotypes lowering fitness.

• Formation of new species from ancestral species.
• Two components:
  • Genetic isolation: two populations of 1 species are isolated → new specie(s)
  • Genetic divergence: one species becomes 2 different species

• Reproductively isolated.
• Purely based off of ability to breed and produce viable offspring.
• Disadvantages: can't apply to fossils, or asexual organisms, or geographically isolated pops

• Based on differences in morphology/phenotypes.
• Advantages: works with fossils and asexual organisms
• Disadvantages: hella subjective: sometimes striaght up misleading

• Based on ancestral analysis
• Advantages: widely applicable, strong theoretical foundation. Hella truth.
• Disadvantages: No thorough phylogenies available.

• Based on environmental context where each species occupies a unique niche.
• Advantages: avoids problems with morphologically similar species and asexual ones
• Disadvantages: difficult to characterize niche in sufficient detail.

• prezygotic: caused by disruptions that make them never fuck, no zygote formed
  • temporal: the populations are not present at the same time (often seasonal)
  • spatial: physically not close to each other
  • behavioral: not attracted to one another
• postzygotic: zygote is formed, but cannot produce viable offspring or does not survive because of genetic incompatibility.

• Allopatric speciation: there is geographic isolation
• Sympatric speciation: There is not geographic isolation.

• there is geographic isolation
• Dispersal/colonization: they go away from each other
• Vicariance: shit naturally forms between them separating them

• Flowering plant
• Produce seeds
• Differences from gymnosperms
  • flowers
  • endosperm within seeds
  • fruits that contain the seeds
  • Not vascular.

• There is not geographic isolation
• Mechanisms
  • spatial/temporal/behavioral isolation
  • polyploidy

• type of spermatophyte (seed-bearing) plant
• type of vascular plant
• unenclosed seeds (unlike angiosperms, whose seeds are enclosed during pollination)
• e.g. conifers

• Can be formed when isolated populations reconnect after being apart
• Hybrids may have different fitness than parents.

• if hybrid fitness lower than either parent, we can predict narrow hybrid zones
• if hybrid fitness higher fitness than both parents, then new species is created
• if hybrid fitness higher than one parent, it can lead to extinction of worst parent.

• Gradualism: when change occurs gradually over long periods of time continuously. One would predict transitional forms
• Punctuated equilibrium: change occurs in short bursts with long periods of little change. One would predict new species to occur rapidly
• Fossil data supports punctuated equilibrium, molecular data supports gradualism, both seem to occur.

• Genes that regulate development along an axis,
• Can be specific to body regions
• Gene duplication mutations produce more Hox genes
• Turned on/off by their own regulatory genes
• Mutations can occur in hox genes or their regulatory genes.

• Gremlin in chicken vs duck feet: Gremlin gene results in webbed feet in ducks.
• Ubx in arthropod appendages: A mutation in the ubx gene causes a reduction in legs in the abdomen creating the insect body plan
• Hox d11 expression in fish vs mice: Have the same genes that form limb buds in embryos (which go on to form limbs/fins), but mice genes express this gene for longer (results in leg).
• Paedomorphosis: When adults retain juvenile characteristics, can lead to new body plan.
• Allometric growth: The same genes have differences in growth rates. e.g. human & chimp skull.

Eyes in animals (Pax6 gene in mice vs eyeless gene in flies). Made eyes grow on flies (sometimes in weird places) using the Pax6 gene. Eyeless and Pax6 genes are orthologs (have common ancestor gene, meaning the eye trait is homologous).

• Paralog: gene copies within the same species that sometimes result in different or similar traits
• Orthologs: Genes in separate species that share common ancestors

Origin of Life

(Abiogenesis = life arising from inorganic matter)

1. Formation of Primordial Soup
   • 3 theories
     • Reducing atmosphere: organic molecules created in rich atmosphere
     • Extraterrestrial: we came from outerspace / asteroids / ET
     • Deep sea vent: organic molecules formed near deep sea hydrothermal vents (prolly)
2. Formation of Organic Polymers
   • Clay surfaces served as templates for first RNA to form
3. Formation of protobionts
   • boundary, polymers inside, enzymatic action, and replication
4. Chemical selection
   • Natural selection, but chemicals
   • New protobionts w/ enhanced enzymatic or replicating abilities are favored
   • RNA served for both info-storage & catalyst
5. RNA world --> DNA World
   • Separated info storage and catalyst role
   • DNA more stable
   • Protein better catalyst

• Branches: populations through time
• Nodes: Forks where ancestors split into two or more descendants
• Tips: Extinct/Extant (mutually exclusive) species
• Root: The common ancestor
• Taxon: a group of organisms
• Outgroup: The taxon that diverged prior to the most ancient node of a tree.
• Ingroup: The defined group
• Sister taxa: Groups that occupy adjacent branches linked by a node.
• Polytomy: AKA Star Phylogeny, more than two groups emerge from one node.

• Monophyletic: An ancestor and all of its descendants
• Polyphyletic: Groups who's members' last common ancestor is not a member of the group
• Paraphyletic: Group with common ancestor, but only some descendants

• Appears in phylogenies as polytomies (aka star phylogenies).
• Driven by 3 potential mechanisms:
  • Colonization events: Unoccupied habitat is colonized. Hella resources
  • Morphological innovation: A new trait allows new resources to be exploited
  • Mass extinctions: Allows surviving species to exploit leftover resources no longer exploited

• Habitat bias: Organisms in sandy/muddy/sediment rich habitats are more likely to fossilize
• Taxonomic bias: Organisms with hard parts are more likely to leave fossils
• Temporal bias: The older organisms are the less likely they are to have fossils left
• Abundance bias: The more abundant an organism is the more likely it is to have hella fossils

• Organically preserved: Insects in amber (sappy substance), pollen
• Compressed: Compressed, organic material turns into carbon rich films
• Casts: Original remains completely gone, but imprint remains
• Permineralized: Minerals fill empty spaces in dead organisms. Similar to petrification where the minerals completely replace the organism. (but in this class they basically the same cuz teacher is like wtf they're the same wtf)

• Way of estimating the time speciation occurred in the past based on known genetic mutation rates.
• Most mutations are neutral, and these neutral mutations are tracked
• Limitations:
  • Generation times aren't always equal
  • Mutations are affected by selection
  • Species' specific differences in mutation rates
  • Solution: independent calibrate each species' clock