Lecture 3: Phylogeny, Tree of Life, Taxonomy and Systematics

Question 1

Taxonomy

Answer 1

the science of describing, naming, and classifying organisms

Question 2

Taxon (plural = taxa)

Answer 2

a unit of taxonomic classification

Question 3

Systematics

Answer 3

the study of biological diversity and the evolutionary relationships among organisms

Question 4

What types of hypotheses can be tested with systematics?

Answer 4

Hypotheses about which groups have descended from a common ancestor

Question 5

Extinct

Answer 5

no longer present

Question 6

Extant

Answer 6

taxa that exist today

Question 7

Phylogeny

Answer 7

the history of descent of a group of taxa from their common ancestors

Question 8

What is used to depict phylogenies?

Answer 8

Phylogenetic trees

Question 9

Phylogenetic hierarchy

Answer 9

Kingdom, Phylum, Class, Order, Family, Genus, Species
(King Philip Came Over For Good Soup)

Question 10

3 Domain System

Answer 10

Eukayra (multicellular eukaryotes)

Bacteria (prokaryotes)

Archaea (single celled prokaryotes)

Question 11

Who introduced binomial nomenclature?

Answer 11

Carl Linnaeus

Question 12

What are the two parts of binomial nomenclature?

Answer 12

Genus and species

Ex: Megacephala virginica

Question 13

What do the tips of a phylogenetic tree represent?

Answer 13

Taxa

Question 14

Root

Answer 14

Common ancestor of all taxa

Question 15

Node

Answer 15

A branchpoint in a tree

Question 16

Clade

Answer 16

A group of two or more taxa that includes both their common ancestor and all their descendents

Question 17

Common ancestor

Answer 17

Ancestor shared by 2+ individuals

Question 18

Monophyletic group

Answer 18

A clade. A group that includes all of the descendents of a common ancestor

Question 19

What is a trick to see if a group is monophyletic?

Answer 19

Rotate the node and see if the taxa stay in the same box

Question 20

How can you tell which species are closely related on a phylogenetic tree?

Answer 20

Species that share a more recent common ancestor are more closely related

Question 21

Paraphyletic group

Answer 21

A group that includes some, but not all descendants of a common ancestor

Question 22

Polyphyletic group

Answer 22

A group that consists of members of multiple lineages but does not consist of the most recent common ancestor and all of its descendents

Question 23

Character

Answer 23

A particular trait of interest

Question 24

Homologous characters

Answer 24

Characters that a given set of organisms have inherited from their common ancestor

Question 25

Character state

Answer 25

A given character can have many different character states Ex: 5 digits on forelimb, one digit on forelimb

Question 26

Ingroup

Answer 26

The group of interest, usually assumed to be monophyletic with respect to an outgroup

Question 27

Outgroup

Answer 27

A group of taxon that is related to the ingroup

Question 28

Steps

Answer 28

The number of inferred changes in character state on a tree

Question 29

Most parsimonious tree

Answer 29

The tree with the shortest number of steps/changes

Question 30

Plesiomorphy

Answer 30

Ancestral character state

Question 31

Symplesiomorphy

Answer 31

Shared ancestral characters, not phylogenetically informative

Question 32

Apomorphy

Answer 32

Derived character state

Question 33

Synapomorphy

Answer 33

Shared derived character, most useful for inferring phylogenetic relationships

Question 34

Autapomorphy

Answer 34

Unique derived character state, not useful for inferring relationships, but helpful for identification of species

Question 35

Occam's razor, related to Parsimony

Answer 35

Among competing hypotheses, the one with the fewest assumptions should be selected

Question 36

Topology

Answer 36

Pattern of branching

Question 37

Two methods for dealing with long branches

Answer 37

Maximum Likelihood and Bayesian

Question 38

Maximum Likelihood

Answer 38

Calculate the likelihood of observing the data

Question 39

Bayesian

Answer 39

Maximizes the probability of observing a tree

Question 40

Maximum likelihood vs Bayesian

Answer 40

ML calculates likelihood of observing a possible tree, Bayesian provides probability of multiple trees

Question 41

Long branch attraction

Answer 41

Just by chance, two long branches will have the same change at some nucleotide positions. These branches are attracted to each other in a parsimony analysis

Question 42

Gene tree

Answer 42

A phylogeny of alleles/genes for a specified stretch of DNA

Question 43

What are orthologous genes?

Answer 43

Genes that descended from the same locus in their most recent ancestor (a1 and a2, b1 and b2)

Question 44

What are paralogous genes?

Answer 44

Genes that arise via ancestral gene duplication (a1 and b1, a2 and b2)

Question 45

Which of the following is more closely related: - orthologous loci in different species - paralogous loci within the same species

Answer 45

Orthologous loci in different species

Question 46

What is an example of an ancestral character state

Answer 46

Opposable vs non-opposable foot/thumb

Question 47

What can the Molecular Clock be used for

Answer 47

To calibrate evolutionary trees to absolute time

Question 48

Homology

Answer 48

Features inherited from common ancestors. Ex: birds, bats, mice, and crocodiles all have four limbs

Question 49

Homoplasy

Answer 49

Independent evolution of a character or character state on a phylogenetic tree

Question 50

Convergent evolution (convergence)

Answer 50

Organisms independently evolve similar traits

Question 51

Parallel evolution (parallelism)

Answer 51

Two species that have descended from the same ancestor remain similar over time

Question 52

Evolutionary reversal

Answer 52

Return from an advanced to a more primitive character

Question 53

Does branch length impact patterns of evolutionary decent?

Answer 53

no it is the same regardless of branch length

Question 54

Does rotating branches change relationships on a phylogenetic tree?

Answer 54

no