Biology 2


Parsimony
(selection of trees)


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


Maximum Likelihood
(selection of trees)


Molecules


Monopyletic


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


Paraphyletic


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


Polyphyletic


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


Protobionts


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)


Prokaryotes

2 Domains: Bacteria & Archaea

Features:


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)


Autotrophs


Obtain food w/o eating other organisms

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


Heterotrophs


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


Bacteria-Proteobacteria


Gram Neg. ex: E. Coli, Salmonella


Bacteria-Chlamydias


Gram neg., No PG


Bacteria-Spirochetes


Helical ex: syphilis, lime disease


Bacteria-Gram +


Ex: leprasy, lime disease


Bacteria-Cyanobacteria


Photoautotrophs


Archaea


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