1. Review…

2. Terms associated with phylogenetic trees
Tips represent terminal taxa (or genes) of a lineage, usually extant
(a.k.a. leaf, or terminal node or just a terminal) A B C D E
A, B, C, D, E: can be a strain, a population, a species, etc. Anything that forms a closely-related unit.
A clade is a group of taxa that includes a common ancestor and ALL of its descendants. These are nested within one another.
Like reading a family tree
The ancestor of all of the descendants (such as extant species or groups) is at the bottom.
As you move towards the tips, you move forward in time

3. Terms associated with phylogenetic trees
Nodes represent branching or splitting points on a tree; may represent extinct or hypothetical ancestor(s) A B C D E
1. Each node on a tree is an ancestor. The branches descending from each ancestor (in the direction away from the root) lead to its descendants.
2. Each ancestral node can be rotated. This places the descendants on different parts of the printed page, but does not change their relationships to one another.
3. All descendants of a particular ancestor are more closely related to one another than they are to any other taxa on the tree, no matter where they happen to be placed on the printed page.
What has happened where the lines split?
Speciation! These are the nodes, and they represent common ancestors.
Which is the common ancestor of A and B? Of B and C? Of D and A?

4. Terms associated with phylogenetic treesB C D E
“Root” refers to the node at the ‘base’ of the tree; represents the common ancestor of all descendant taxa in the tree.
Time
Note: some trees have no ‘root’, to be discussed later

5. Terms associated with phylogenetic trees
Branches are the parts of a tree that connect the node or the nodes to the tips (aka internodes, edges) A B C D E a c b
Note: branches such as a, b, and c are sometimes referred to as ‘internal branches’

6. Terms associated with phylogenetic treesB C D E
Topology of a tree refers to the overall pattern of connectedness of the nodes and termimal taxa
The pattern of branching (i.e., the topology) is what matters here. Branch lengths are irrelevant--they are simply drawn in whatever way makes the tree look most tidy. (Unless it’s a phylogram, where branch lengths are meaningful and usually indicate the estimated length of time since divergence.)

7. Monophyletic group
A proper clade. Includes a common ancestor and ALL descendants.
Outgroup – species closely related to monophyletic group, but not part of it A B C D E F

8. Paraphyletic Group
Includes a common ancestor and only SOME descendants. (e.g. great apes – doesn’t include humans, others?) A B C D E F

9. Polyphyletic Group
A group that share a common trait, but the trait is an analogy (which means?) e.g., birds of prey, marine mammals, others? A B C D E F

10. How do we figure out the evolutionary relationships among organisms?
We rely on shared, derived characters
Shared = shared, found in multiple related groups/species
Derived = new, non-ancestral
Characters = heritable traits of an organism (e.g., morphology, physiology, biochemistry, behavior, developmental pattern, chromosome features, gene sequences, etc.)
So, groups of organisms that share more of these characters by common ancestry are likely to be more closely related

11. Clarification
Ancestral/derived are terms that have to be used relatively.
For example, when comparing reptiles, dinosaurs, birds, and mammals, body hair is a derived feature for mammals. However, when discussing mice, rats, dogs, and people, body hair is ancestral (the most recent common ancestor of all four groups had body hair).

12. Homology, Analogy, and Cladistics
Homologies are characteristics that are alike because of common descent
Analogies, or homoplasies, are characteristics that are alike in form or function (probably due to similar selective pressures), but do not share a common ancestry (evolved independently). This is known as convergence.
Give your favorite example to illustrate convergence. Succulents in multiple continents, gliding rodents, whatever.

13. Cladistics
A cladogram is a graphical representation of the relatedness of species (their phylogeny) based on the number of characteristics from common ancestors that they share (can be morphology, behavior, genes, etc.)
One axis is time, with the top (or right) being the present and the bottom (or left) being earlier.
Nodes are the splitting points. Represent the most recent common ancestor of two or more taxa.
The more homologies, the more closely related.

14. Parsimony
Parsimony – the fewest number of evolutionary changes is the most likely explanation. For example, you don’t want to have feathers evolve 317 times in your phylogeny if you can help it. The idea that feathers evolved only once is more parsimonious.
However, if you have a whole bunch of traits on which to base your cladogram, it might be simpler for one trait to evolve independently multiple times. This trait is an analogy.

15. Synapomorphy
Trait found in two or more taxa that is present in their most recent common ancestor but is missing in more distant ancestors.
Allows for biologists to recognize clades (What else is a clade known as?)

16. Fossil record
Fossil – physical evidence of organisms that lived in the past
Form when the organism is buried and preserved
Provide information about what the organisms looked like and where they lived
Critical to understanding the history of life, yet biased

17. Limitations of the fossil record
Habitat bias
Taxonomic and tissue bias
Temporal bias
Abundance bias
Habitat loss: organisms that live in areas where sediments are actively being deposited- including beaches, mudflats, and swamps- are much more likely to form fossils than are organisms that live in other habitats.
Taxonomic and tissue bias :slow decay is almost always essential to fossilization, so organisms with hard parts such as bones or shells are most likely to leave fossil evidence. Tissues and cartilage are more predisposed to decay and not fossilize.
Temporal bias: Recent fossils are much more common than ancient fossils. This causes a temporal bias in the fossil record.
Abundance bias: Organisms that are abundant, widespread, and/or present on Earth for long periods of time leave evidence much more often than do species that are rare, local, or ephemeral.

18. Paleozoic era: origin and initial diversification of the animals, land plants, and fungi, as well as the appearance of land animals.
Mesozoic era: In terrestrial environments of the Mesozoic, gymnosperms were the most dominant plants and dinosaurs were the most dominant vertebrates.
Cenozoic era: On land, angiosperms were the most dominant plants and mammals were the largest vertebrates. First appearance of humans in Quarternary period. Page 514 for more info.

19. Adaptive radiation
Speciation events and morphological change occur rapidly
A single lineage diversifies into a wide variety of ecological roles
Instances when species originate and rapidly diversify
Periods when species go extinct rapidly

20. Adaptive radiation
When a species produces many descendent species that
live in a wide diversity of habitats and
use a wide array of resources
Adaptive radiations occur through these mechanisms:
Ecological opportunity; e.g., by the colonization of a new habitat that offers resources and lacks competitors
Morphological innovations; e.g., feathers, any structure that allows individuals to exploit resources more efficiently or in a new way

21. Mass Extinctions
Rapid extinction of a large number of lineages scattered throughout the tree of life; e.g.; at least 60% of the species are wiped out within one million years
Have occurred repeatedly throughout history, at least 5 times
Environmental catastrophes that rapidly eliminate most of the species
‘Prune’ the tree of life; marked the end of several prominent lineages and the rise of new branches
Can take ecosystems approx. 15 mil years to recover their diversity