Lecture 2: The Phylogenetic Tree and Tree of Life

Learning Objectives for today

1. Be able to use the key terms to describe a phylogenetic tree
2. Identify the closest relative of a taxon on a phylogenetic tree 
3. Define "fossil" and, in general terms, describe how they form 
4. Discuss and evaluate the types of information contained and missing in the fossil record 
5. Define LUCA and phylogenetic event horizon and explain how the two terms relate to one another
6. Describe historical and recent efforts to understand pre-biotic chemical reactions
7. Describe the self-replicating molecules that could have preceded cellular life 
8. Explain how protocells could be compartmentalized both with, and without, membranes 

We didn't get to go over all the learning objectives and Dr. Whitton herself said that they are prone to change. I am so exhausted today. Six courses can be tough... I didn't realize almost every one of my classes had a tutorial (aka external class time) associated with them, which really sucks x.x. Note to self, get your butt in bed at 12 am pronto and stay there. And please stop skipping dinner kthxbai! 

What we DID go over in class today

1. Introduction to Tree Thinking

Depicts the levels of generations from
individual to phylogeny

a. How we use Phylogenies (and a little bit about how we get phylogenies)

• Phylogenies/Phylogenetic Trees: a visual representation of a hypothesis of the evolutionary history of populations, taxa (e.g. species, genera) or genes. 
• Key points: a phylogeny is a hypothesis of the evolutionary history of a bunch of stuff... 

What are phylogenies used for? 

• Inferring evolutionary history 
• Character evolution (understanding how a trait evolved, once or more than once) - e.g. did fur evolve in mammals once or more than once?
• Biodiversity discovery (e.g. mapping the entire tree of life and seeing where a "new' species may fit and finding new lineages)
• DNA barcoding (don't really get it...)
• Biodiversity characterization (don't really get it either... something about larvae and matching them to their adult stages, and all other lifestages)

b. Tree terminology using examples (refer to glossary on the last page) 

Branch: segment that separates two nodes in a phylogenetic tree. Represents the time or character change that separates two nodes or a node and a tip

Node (or internode): Point where a lineage splits, representing ancestral populations or species 

Tip (terminal node): taxa included in a phylogenetic tree that are depicted at the ends of branches

Root: Common lineage from which all species indicated on the tree derive. In a rooted tree, the root is placed between the outgroup(s) and the ingroup

Taxon (Plural taxa): a named group of organisms; a taxonomic unit (examples include a species, a genus, a family, etc.

Note we don't need to know the definitions, but when given a questions, know what it is referring to and how to use the words in context on a test. 

The above trees represent a cladogram: a phylogeny where the length of branches arbitrary. (can be recognized by all the tips lining up). 

We can just as likely we presented with a 

phylogram: branch lengths are proportional to time (or to the number of character that change along their lengths. 

Sister Group: the two groups derived from a single node. By definition, sister groups are the same age

Remember, sister groups are relative to which node we are referring to. 

C. How trees are drawn

I don't believe we've actually gone through this yet. we'll see how it goes. but in the meantime, we'll skip this one

d. interpreting relationships and reading trees 

taxonomic groups are not always Monophyletic (all the descendants of a common ancestor) 

they may be paraphyletic: includes some but not all descendents of a common ancestor

The mammals and amphibian are monophyletic. The reptilia (does not include birds) and fishes are not.

2. The Origins of Life and The Tree of Life

the yellow portion is LUCA (last universal common ancestor)
thought to be the ancestor to all life on Earth (< sounds like something out
of a mecha anime...)

a Features of the Three Domains

Bacteria

• Single celled (no nucleus or oranelles)
• In wide range of habitats, wide range of lifestyles (predators, autotrouphs, parasites)
• Cell membranes have pedidoglycan

Archaea

• Single celled (nucleus or organelles; some lineages lost to varying degrees)
• Many occur in extreme environments including thermal vents, saline habitats and hot springs 
• can get energy from variety of sources (sugar, ammonia and even hydrogen gas)

Eukarya

• Most lineages are single celled. Some multicellular groups 

And that's all we covered for lecture 2.