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.

Lecture 1: What is Evolution?

This course, Biology 336, explores four major big picture problems 
1. How does evolution happen

2. What has evolution produced. What happens to what it has produced?

3. How is it studied?

4. How is it relevant to Human Society? 

Today, however, we explore: 

•  Evolution is... 
• Introduction to evolution: evidence for evolution
• Course structure and organization 
• Instruction for the coming week\

• Preview of the next class 

Curiously, we start class first with the discussion of the blue whale.

A. The Blue Whale

Blue whales are remarkable for a few reasons. 

1. They are enormous, reaching lengths of 30 m
2. Newborn blue whales are 7 m in length and weight 2700 kg. They also consume 400 L of milk a day in the first few weeks 
3. They are mammals... that live in the ocean
4. There are about 12 000 remaining, dispersed in all the world's oceans 
5. This represents 5% of the historic population, before the whaling industry collapsed numbers. 

Blue whales represent one of only 90 species of Cetaceans, which include mostly marine mammals such as whales, dolphins and porpoises. They are, however, descendents of terrestrial animals. 

The blue whales themselves are part of a group of whales known as the Baleen whale. These whales take up a large volume of water, then squeeze it out across their baleen (which acts as a sieve) trapping everything else inside. They mostly eat krill. 

Fun fact: despite their size, blue whales can't swallow anything larger than the size of a basketball. So says my professor. We're safe.

So begins the discussion. How did these massive, beautiful animals evolve from the terrestrial environment to an exclusively aquatic one? 

B. What is Evolution? 

This is where we had a class activity where everyone rights down their definition of Evolution and an example. The professor then picked one randomly to talk about. The key points (or the only notes I managed to take of it)

• Despite most people's emphasis of natural selection as the driving force of evolution, it is not the only form of evolution. There are other means by which evolution happens, sometimes, a means which does not improve fitness, but just happens by chance (e.g. an avalanche that kills 90% of a population). 
• Change does  not have to mean acquiring a new characteristic
• Other means of evolution may be sexual selection, chance events etc. 

 "Descent with modification" - Darwin's definition (recall that Darwin lived in a time where genetic underlyings of evolution was not well understood)

"Change in frequency of an allele (trait) in a population over successive generations" - a more genetics focused definition 

"Any change in the inherited traits of a population that occur from one generation to the next" - our textbook's definition 

So in short, there are three key elements: 

1. Heritable elements 

2. Multiple generations 

3. Change

Evolution vs. Natural Selection  

Although the two get mixed up fairly often, natural selection is only one of the mechanisms of evolutionary change, in which a favored trait (which increases both chances survival and reproduction) increase in frequency over generations. 

C. Evidence for Evolution 

There are three "types" of evidence for evolution 

1. Evidence of Change through time

a. observing Change Through time

We went through a very classic study here.

Geotaxis experiment in Drosophila (fruit flies)

This study uses fruit flies. Starting with 500 males, we start the flies off on a maze. For each intersection, the flies have a choice of going up or down and continuing their way. And once they choose, they choose up or down again at the next intersection. And the next. This goes on until they reach the end of the maze, where food sits inside 12 vials. The maze is set up such that the entire apparatus is in the shape of a pyramid tipped on its side, so there are flies that have decided to go up up and up again (ending up in the top vials) and those that chose down more (ending up in the bottom vials). 

The scientists next took 50 flies from the topmost vial(s) and mated them with random females. The offspring were again used in the maze study and the cycle starts again. This was done for 30 generations. 

The results? The thirtieth generation of fruit flies were found to fly, on average, 4.25 vials higher than the control thirtieth generation of flies. Since this is not a learned behavior, the scientists inferred that this is an example of evolution, where the inherited change is a response to gravity, where fruit flies were more likely to respond to gravity by going up. 

b. Presence of Vestigial Traits

Modern day whales have vestigial hip bones where the hind limbs would've been. 

A vestigial trait is something that no longer functions or only partially functions, or that functions differently in related groups. 

E.g. Hind limbs of whales, wings of ostriches and, interestingly enough, goosebumps. 

c. Extinction

Indicates that the flora and fauna of a region/whole planet has changed. 

d. Transitional forms

Going back to our example of whales, ambulocetus, an animal that existed 50 - 80 mya, is one of the transitional forms of modern day whales. This animal had forelimbs and hindlimbs for both walking and swimming. 

2. Evidence of Common Ancestry

a. Phylogenetic tree 

Phylogenetic Tree of Whales

Connect groups recognized based on one sort of evidence (e.g. morphology) into a hypothesis of descent. This hypothesis can then be tested with other evidence, such as DNA. 

  

 b. Homology 

Homology of Tetrapod limbs 

Shared similarity due to common ancestry. 

E.g. the number and arrangement of bones in forelimbs of tetrapods (four-legged) 

The amino acid code, which is almost universal to every organism, including microorganisms. 

3. Evidence for action of natural selection: in nature

This is where we looked at a study on seed dispersal in plants, more details later. 

The pappus is the furry end, and is used for dispersal. If the pappus is very large, then the seed (actually a fruit) will be air-borne more easily and will therefore float away further from the parent plant. The scientists thought through this. If a dandelion (or a related species with similar dispersal mechanisms, I'll just call them dandelions) were to be living on the mainland, dispersal as far away as possible will usually be advantageous. However, if the dandelion existed on an island, such that dispersal too far away could land the seed in water, then this would not be a good thing! Therefore, they hypothesized that the dandelions on the mainland should, over many generations, evolve larger pappuses to disperse further whereas island ones will generally be smaller. 

They then compared the dispersal ability of mainland and island dandelions in first generation and 10 generation flowers, and found that over multiple generation, the pappus of mainland flowers are indeed larger than the island flowers.