Biology 2

(selection of trees)

The tree that is the simplest explanation of relationships is the tree adopted.

Maximum Likelihood
(selection of trees)



A group that includes the ancestrial species and ALL of its descendents


A group that consists of an ancestrial species, and some, but not all of the descendents


A grouping of several species that lack a common ancester.

Early Earth

4.6 billion years ago

Molten Planet

First Rocks

3.8 billion years ago

1. Abiotic synthesis of organic molecules2. Synthesis of polymers3. Protobionts4. First Genetic Material

Abiotic (non-living) Synthesis of Organic Molecules = Abiogenesis

-1920's Oparin-Haldane Hypothesis

-1953 Stanley Miller & Harold Urey

Oparin-Haldane Hypothesis

Reducing atmosphere + lightening/UV light = organic molecules

Stanley Miller & Harold Urey

-created early earth's atmosphere (CH4 NH4 H2O H2S)-when they added lightening--->produced small organic molecules-this hypothesis was controversial since some support the idea that early earth was not very reducing & made up mainly of CO2 & N2 gas

Synthesis of Polymers

-replication by dripping solutions of amino acids on hot sand, clay or rock


Abiotic groups of molecules surrounded by a membrane

ex: Liposomes = lipids + H2O -"replicate"

First Genetic Material

-Probably RNA, not DNA

Fossil Record - Provides the history of life

1. Relative Dating

2. Absolute Dating

Relative Dating

Certain rock layers above/below others w/ certain fossils give us a sequence of events

Absolute Dating

Determination of how old something is in calendar years

-based on decay of radioactive isotopes-each radioactive isotope has half-life
ex: C-14 half life: 5,730 years

First Fossils

Stromatolites = Bacterial Mats 3.5 bya-cyanobacteria

2.7-2.2 Billion years Ago

O2 levels begin to creep up-banded-iron formations

2.1 Billion years ago

First Eukaryotes-endosymbiont origin of mitochondria & plastids-mitochondria = aerobic heterotrophic prokaryote-plastid = photosynthetic prokaryote-serial endosymbiosis

Serial Endosymbiosis

1. Mitochondria endosymbiosis likely occured first -Found in all plants and animals
2. Plastids - only found in plants -Likely occured after mitochondrial endosymbiotic event

Evidence for Endosymbiosis

1. Mitochondria & plastids have their own DNA

2. Membranes of both are similar to those seen in prokaryotes

1.5 Billion years ago

First Multicellularity-small in size, limited in distribution-likely evolved independently several times-not much advancement after this point for a long time

570-550 Million years ago

Larger, soft bodied organisms

Cambrian Explosion

~542 million years ago-first hard-shelled organisms-in first 20 million years most of the major animal phyla we know of originated (exceptions: Porifera-sponges & Chidaria-jellyfish)Reasons for this:1. O2 levels2. Predator-prey relationships

Archaean (Eon)

4.6 bya - 2.5 bya

Proterozoic (Eons)

2.5 bya - 542 mya

Phanerozoic (Eons)

542 mya - Present

Paleozoic Era

542 mya - 251 mya (age of invertebrates)

Mesozoic Era

251 mya - 65 mya (age of reptiles)

Cenozoic Era

65 mya - Present (age of mamals)

Major Events that Shaped Diversity During Phanerozoic

1. Plate techtonics2. Mass Extinctions & Explosive Diversifications

Plate Techtonics

-continents moving around via plate techtonics-come together, break apart, come together, etc.-create mountains, oceans, volcanoes, earthquakes
ex: Pangea

Pangea (250 mya)

-a single, large super continent -reduced coastline-higher gene flow possible-more of the continental land mass is drier (more inland area)-ocean currents change

Mass Extinctions & Explosive Diversifications

End Permian Extinction

-(251 mya) *largest extinction in Earths history *90% of all species go extinct

Mass Extinctions & Explosive Diversifications

End Cretaceous K-T Extinction

-65 mya *asteroid impact in the Yucatan Peninsula (Alvarez, 1980) *wiping out dinosaurs (except birds)


2 Domains: Bacteria & Archaea


1. Smaller than Eukaryotes (1-5um)2. Generally single celled3. 3 common shapes (cocci, bacillus, spiral)4. Cell wall present a) Bacteria-primarily PG b) Archaea-mainly polysaccharides & protein, no PG5. Many cell walls covered by a capsule (sticky outer layer that helps organism adhere to substrates6. About half can move in a direction (flagella)7. Generally lack internal membrane bound structures8. No nucleus9. Reproduce via binary fission10. Many have plasmids (smaller rings of DNA)


Obtain food w/o eating other organisms

A) Photoautotrophs-light, CO2B) Chemoautotrophs-inorganic chemicals, CO2


Obtain food by eating other organisms

A) Photoheterotrophs-light, organic compoundsB) Chemoautotrophs-organic compounds

Oxygen Metabolism

Obligate Aerobes

Use and need O2 for cellular respiration

Oxygen Metabolism

Facultative Aerobes

Use O2 if present, but can also use fermentation

Oxygen Metabolism

Obligate Anaerobes

Poisoned by O2, only fermentation or other chemical energy used

Nitrogen Metabolism

Various types of Nitrogen used


Gram Neg. ex: E. Coli, Salmonella


Gram neg., No PG


Helical ex: syphilis, lime disease

Bacteria-Gram +

Ex: leprasy, lime disease




Live in extreme environments

Thermophiles-hot environmentsHalophiles-Salty environmentsMethanogens-use CO2 and generate methane

Archaea-Synampomorphies shared w/ Eukarya

1. Lack PG in cell walls2. Several kinds of RNA Polymerase3. Introns present in DNA4. Histones present (proteins associated w/ chromatin)5. Use Methionine as initiator amino acid for protein synthesis6. Growth not inhibited by antibiotics