1. Label the groupings depicted on the phylogenies below with the correct term: monophyletic, paraphyletic, or polyphyletic.

4. As defined above, is a crown group monophyletic? Is a stem group monophyletic? It is sometimes useful to think in terms of stem groups and crown groups because it helps us to place extinct taxa in their appropriate evolutionary context without having to "force" them into a box (e.g., bird-like reptiles do not have to be classified as birds, per se). And so, when we discuss extinct taxa in this course, we will sometimes refer to them as being part of a stem group.

What are the criteria for five kingdom system of classification?

Describe the parts of a phylogeny, and interpret it (e.g., identify a given taxon's sister taxon, and correctly identify the order of diversification events)

2. Draw the branches for the next phylogenetic tree using the matrix below and then map the traits like you did in the last example. Sharks and relatives Ray-finned fishes Amphibians Primates → Rodents and rabbits → Crocodiles and relatives Dinosaurs and birds Vertebrae? Bony YES YES YES YES YES YES YES skeleton? Sharks and Relatives Ray Finned Fishes Amphibians Primates Rodents and Rabbits Crocodiles and Relatives Dinosaurs and Birds no no YES no YES YES YES YES YES YES YES Four limbs? no no no YES YES YES YES YES YES YES Amniotic egg? Hair? no no no YES no 2 2 2 2 2 YES no no no no no YES YES Two post-orbital fenestrae? 1. Name the outgroup of this tree 2. Name a pair of sister taxa 3. Are there any polytomies on this tree? 4. Name a derived trait for primates and rodents: 5. Name 4 ancestral traits for primates and rodents: Vertebrae, Bony Skeleton, Four Limbs, Amniotic Eqa

The “kingdom” concept is considered out-of-date but most continue to use it in a revised manner. What are the traditional Linnaean taxonomic categories: Kingdom, phylum, ____________, ___________, ____________, _______________, species. When the traditional Linnaean taxonomic categories are not used, people can say “clade” or “taxon” for any genetic group.

Why would it be nice to have classification reflect phylogeny accurately that is, to only name monophyletic groups

8. Evolutionary biologists can estimate when major clades probably diverged from each other using molecular clocks. How do they know when these splits happened? 9. Describe how evolutionary reversal and horizontal gene transfer make it more difficult to create an accurate phylogenetic tree

2. Examine the phylogeny below, which is the phylogeny for all extant species from a genus of birds, constructed using nuclear sequences (the numbers simply label the species). 2 3 Clade A 5 6 Clade B 1 7 (a) Give two explanations for why there are more species in clade A compared to B (i.e. I want general explanations for why some clades have more species than others 4.