Classification, phylogeny, and systematics

Question 1

How were organisms classified before Darwin?

Answer 1

Kinds, types, ideals (Scala naturae), similarities, characteristic features

Question 2

How were organisms classified after Darwin?

Answer 2

Shared ancestry, phylogeny, adaptations

Question 3

How do we know all life originated from a single common ancestor?

Answer 3

DNA evidence, all life has DNA, suggesting it originated before domain Bacteria spilt off

Question 4

What is LUCA?

Answer 4

Last universal common ancestor

Question 5

How is Linnean taxonomy hierarchal?

Answer 5

Starts with the most inclusive categories and gets more exclusive

Question 6

What levels of classification did Linneaus have?

Answer 6

Kingdom, phylum, subphylum, class, order, family, genus, species

Question 7

How many levels of classification do we have now?

Answer 7

35-37

Question 8

What is systematics?

Answer 8

Study of evolutionary relationships

Question 9

What does systematics do?

Answer 9

Reconstructs patterns of relationships between species, who shares common ancestors and builds classifications based on the patterns. It tries to establish phylogenies

Question 10

Who was Willi Hennig? What did he do?

Answer 10

Developed the idea of phylogenetic systematics

Question 11

What 3 things were important when creating a phylogeny according to Willi Hennig?

Answer 11

Genealogical relationships, synapomorphies, and the taxonomy needs to be logically consistent with what is believed to be the pattern of historical relationship

Question 12

What is the difference between an ancestral and derived character state?

Answer 12

An ancestral character state was found in the ancestor, so is more primitive. Derived states are not seen in the ancestor

Question 13

What is a pleisiomorphy?

Answer 13

An ancestral character state

Question 14

What is a symplesiomorphy?

Answer 14

A shared ancestral character state

Question 15

What is an apomorphy?

Answer 15

A derived character state

Question 16

What is a synapomorphy?

Answer 16

A shared derived character state

Question 17

Between pleisiomorphies, sympleisiomorphies, apomorphies, and synapomorphies, which one is most important for systematics?

Answer 17

Synapomorphies

Question 18

What is the difference between a character and a character state?

Answer 18

A character is the characteristic of an organism with variable features. A character state is alternate conditions of a feature, like something present or absent

Question 19

What characters are examined when determining phylogenies?

Answer 19

Characters that reveal evolutionary relationships without being too common

Question 20

Why do we want a character to have two character states when determining phylogenies?

Answer 20

Much easier to plug into a computer as 0 and 1

Question 21

What is homology?

Answer 21

Similarities because of shared ancestry, doesn’t need to have the same function

Question 22

What is analogy?

Answer 22

Similarities because of similar function and not common ancestry

Question 23

What is convergent evolution? Is it homology or analogy?

Answer 23

Organisms from different ancestries converged onto similar habitats and developed similar traits as a result. It is analogy

Question 24

What is parallelism?

Answer 24

Independent evolution of a similar structure in related groups, but that trait was not passed down from the most recent common ancestor

Question 25

What is a monophyletic group?

Answer 25

Taxon/group that includes the most recent common ancestor and all its descendants

Question 26

What is a polyphyletic group?

Answer 26

Taxon/group that includes members from two or more ancestors

Question 27

Which of the original 5 kingdoms was a polyphyletic group?

Answer 27

Protista

Question 28

What is a paraphyletic group?

Answer 28

Taxon/group that includes the most recent common ancestor but not all of its descendants

Question 29

What is an evolutionary tree? What is on the x and y axises ?

Answer 29

Plots time on the y-axis and genetic divergence on the x-axis

Question 30

What is the difference between an evolutionary tree and a phylogenetic tree/cladogram?

Answer 30

Evolutionary trees recognize paraphyletic groups, while phylogenetic trees only recognize monophyletic groups

Question 31

What is the operational taxonomic unit?

Answer 31

The taxonomic level of sampling used in a study that is selected by the researcher

Question 32

What is a clade?

Answer 32

A group of 2 or more taxa that includes the most recent common ancestor and all its descendants

Question 33

What is a node?

Answer 33

A branch point in a cladogram

Question 34

What is a branch?

Answer 34

Represents a lineage, the relationship between taxa and their descent and ancestry

Question 35

What is topology?

Answer 35

The branching pattern of the tree

Question 36

What is the branch length?

Answer 36

The number of changes in characters that occurred on the branch

Question 37

What is the root?

Answer 37

The common ancestor of all OTUs on the cladogram

Question 38

What is a sister group?

Answer 38

Two clades that split off from a single lineage

Question 39

What is the terminal node?

Answer 39

The terminal taxa at the end of the cladogram

Question 40

What is an internal node?

Answer 40

A branch point that represents a common ancestor

Question 41

How can we use phylogenetic trees to get an idea of the rate of evolution?

Answer 41

Look at the branch length, how many characters have changed since diverging off from the common ancestor

Question 42

If two species that diverged off from the same ancestor evolve at different rates, are they still sister groups?

Answer 42

Yes, because they branched off from the same ancestor

Question 43

How do we know when a species is evolving fast or slow?

Answer 43

More character changes means faster evolution

Question 44

What are homoplasies? What are the two types?

Answer 44

Shared features that aren't homologies. Evolutionary reversals and convergences

Question 45

What is an evolutionary reversal?

Answer 45

The reversion of a character state from derived back to ancestral

Question 46

What is convergence?

Answer 46

Independent origin of apomorphies in 2 or more taxa

Question 47

What is parsimony?

Answer 47

The tree with the fewest evolutionary changes is the best one

Question 48

Why the shortest phylogenetic tree the most likely and best tree?

Answer 48

It minimizes the number of hypotheses required to explain it

Question 49

What is an outgroup?

Answer 49

A group that is a close relative to the group of interest that isn't being studied itself

Question 50

What is the ingroup?

Answer 50

What is being studied

Question 51

Why is an outgroup useful when building a phylogenetic tree?

Answer 51

It indicates the direction of evolutionary change and which character states are primitive and derived

Question 52

What makes the best outgroup?

Answer 52

The sister group to the ingroup

Question 53

What is phylogenetic tree rooting?

Answer 53

Defining the position of the hypothetical ancestor of the groups on that phylogenetic tree

Question 54

What information does an unrooted tree not tell us?

Answer 54

The direction of evolution

Question 55

What is midpoint rooting?

Answer 55

The root is in the middle of the two most distantly related species

Question 56

What is outgroup rooting?

Answer 56

The root is placed so the outgroup is the first to diverge off, shows time-directed evolutionary history

Question 57

What are the steps for creating a cladogram with maximum parsimony?

Answer 57

1. select ingroup species 2. select one or more outgroup species 3. Determine the polarity of many different characters in the outgroup and all the ingroup species (pleisiomorphic or apomorphic) 4. Draw unrooted trees with all species that plot the changes in all characters 5. Choose the most parsimonious tree 6. Root the tree between the outgroup and the ingroup

Question 58

What is a gene tree?

Answer 58

A branching diagram of the history of a DNA sequence - haplotypes. A phylogenetic tree of genetic information

Question 59

Why are haplotypes (DNA sequences) more similar among organisms in the same region?

Answer 59

Being in the same region increases interbreeding, and less likely to interbreed with other populations

Question 60

What are pseudogenes? Are they affected by natural selection?

Answer 60

Sections of DNA that don't encode anything. They aren't affected by natural selection

Question 61

What is a molecular clock?

Answer 61

An estimation of the time at which a lineage diverged

Question 62

What regions of the DNA do molecular clocks examine?

Answer 62

Non coding DNA. It isn't affected by natural selection, so it probably has a clock-like rate of change

Question 63

Why does the rate of change of a DNA sequence remain relatively constant?

Answer 63

Changes in non coding regions and silent mutations don't show up in the phenotype and aren't affected by natural selection, so they accumulate at a stochastic rate

Question 64

Why doesn't the rate of change of a DNA sequence always remain constant?

Answer 64

Rates are different from one taxonomic group to another, and molecular clocks are estimates only