Phylogeny

Question 1

Define phylogeny

Answer 1

The evolutionary history and relationships among groups of organisms. It describes the patterns of descent from a common ancestor.

Question 2

What is taxonomy?

Answer 2

A branch of biology concerned with the classification, naming, and identification of living organisms.

Question 3

What is the binomial system?

Answer 3

Founded by Linnaeus. Scientific naming system for an organsism, consisting of 2 parts: the genus and the species.

Question 4

What are the taxonomic groups?

Answer 4

Domain, kingdom, phylum, class, order, family, genus, and species

Question 5

What is the taxonomic unit?

Answer 5

A taxon

Question 6

What is a phylogenetic tree?

Answer 6

Represents a hypothesis about evolutionary relationships, and shows patterns of descent

Question 7

What does each branch point of a phylogenetic tree represent?

Answer 7

The divergence of 2 evolutionary lineages from a common ancestor

Question 8

What are sister taxa?

Answer 8

Groups that share an immediate common ancestor that is not shared by any other group

Question 9

What is cladistics?

Answer 9

Groups organisms by common ancestry

Question 10

What is a clade?

Answer 10

A group of species that includes an ancestral species and all its descendants

Question 11

What is a monophyletic group?

Answer 11

A valid clade; a group of organisms that includes a single common ancestor and all of its descendants.

Question 12

What is a paraphyletic group?

Answer 12

Includes a common ancestor and some, but not all, of its descendants.

Question 13

What is a polyphyletic group?

Answer 13

Includes organisms from multiple evolutionary lineages that do not share a recent common ancestor.

Question 14

Define character

Answer 14

A heritable feature or observable property of an organism that can vary among individuals or species.

Question 15

Define trait/character state

Answer 15

A specific form or variant of a character.

Question 16

Define homology

Answer 16

Homology is similarity in the structure, physiology, or development of different species of organisms based upon their descent from a common evolutionary ancestor. Homologous characters are inherited from a common ancestor.

Question 17

Define analogy

Answer 17

Analogy is similarity in the function or superficial appearance of structures in different species that do not share a recent common ancestor. Analogous characters have multiple, independent evolutionary origins.

Question 18

What is convergent evolution?

Answer 18

Occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages.

Question 19

Define morphological characters

Answer 19

Morphological characters are the physical traits and structures of an organism that can be observed and used to describe, identify, and classify it. These characters relate to the form and structure (morphology) of the organism, both externally and internally.

Question 20

How can homology be distinguished from analogy?

Answer 20

By comparing fossil evidence and the degree of complexity

Question 21

What evidence suggests 2 organisms are homologous?

Answer 21

1. If many elements in 2 complex structures are similar
2. If the genes in 2 organisms share many portions of nucleotide sequence

Question 22

Define synapomorphy

Answer 22

Shared, derived character:
A derived state shared by two or more lineages, which was present in their common ancestor, and is not found in other organisms.

Question 23

Define symplesiomorphy

Answer 23

Shared, ancestral character:
An ancestral state shared by two or more lineages, which was present in their common ancestor, but is not found in all of its descendants.

Question 24

Define homoplasy

Answer 24

Convergent character (analogy):
A state shared by two or more lineages which is not due to common ancestry. Convergent evolution, or parallelism.

Question 25

What group do synapomorphies diagnose?

Answer 25

Monophyletic groups

Question 26

What group do symplesiomorphies diagnose?

Answer 26

Paraphyletic groups

Question 27

What group do convergent characters diagnose?

Answer 27

Polyphyletic groups

Question 28

What are the assumptions when using character based methods to build a phylogenetic tree?

Answer 28

1. A character found in both the outgroup and ingroup is ancestral. 2. Each derived character arose only once in the ingroup. 3. A character that only occurs in a subset of the ingroup arose in the lineage leading to those members

Question 29

What is maximum parsimony?

Answer 29

Assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely.

Question 30

What is maximum likelihood?

Answer 30

Based on probability rules about how DNA changes over time and assumes a tree can be found that reflects the most likely sequence of evolutionary events.

Question 31

What is a molecular clock?

Answer 31

Converts measures of genetic distance between sequences into estimates of the time at which the lineages diverged.

Question 32

What does the molecular clock estimate for homologous genes?

Answer 32

In homologous genes, nucleotide substitutions are assumed to be proportional to the time since they last shared a common ancestor.

Question 33

What does the molecular clock estimate for paralogous genes?

Answer 33

In paralogous genes, nucleotide substitutions are proportional to the time since the genes became duplicated.

Question 34

Do all individual genes evolve at the same "clocklike" rate?

Answer 34

No, individual genes vary in how clocklike they are. Some genes accumulate mutations more regularly than others.

Question 35

Under what condition is the rate of molecular change in genes and proteins expected to be regular, like a clock?

Answer 35

If most of the evolutionary change in genes and proteins has no effect on fitness.

Question 36

What factors can cause differences in the molecular clock rate for different genes?

Answer 36

Differences in clock rate for different genes are a function of: 1. The importance of the gene. 2. How critical the specific amino acid is to protein function.

Question 37

What evolutionary force can cause irregularities in the molecular clock?

Answer 37

Irregularities in the molecular clock can result from natural selection, where some DNA changes are favored over others, leading to faster or slower rates of substitution than expected under neutrality.

Question 38

What is a limitation regarding the accuracy of molecular clock estimates for very old evolutionary events?

Answer 38

Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty. This is because calibration points for the clock become less reliable further back in time.