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ENVS 212 > Lecture 3: Phylogeny, Tree of Life, Taxonomy and Systematics > Flashcards

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

1
Q

Taxonomy

A

the science of describing, naming, and classifying organisms

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2
Q

Taxon (plural = taxa)

A

a unit of taxonomic classification

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3
Q

Systematics

A

the study of biological diversity and the evolutionary relationships among organisms

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4
Q

What types of hypotheses can be tested with systematics?

A

Hypotheses about which groups have descended from a common ancestor

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5
Q

Extinct

A

no longer present

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6
Q

Extant

A

taxa that exist today

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7
Q

Phylogeny

A

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

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8
Q

What is used to depict phylogenies?

A

Phylogenetic trees

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9
Q

Phylogenetic hierarchy

A

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

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10
Q

3 Domain System

A

Eukayra (multicellular eukaryotes)

Bacteria (prokaryotes)

Archaea (single celled prokaryotes)

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11
Q

Who introduced binomial nomenclature?

A

Carl Linnaeus

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12
Q

What are the two parts of binomial nomenclature?

A

Genus and species

Ex: Megacephala virginica

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13
Q

What do the tips of a phylogenetic tree represent?

A

Taxa

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14
Q

Root

A

Common ancestor of all taxa

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15
Q

Node

A

A branchpoint in a tree

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16
Q

Clade

A

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

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17
Q

Common ancestor

A

Ancestor shared by 2+ individuals

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18
Q

Monophyletic group

A

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

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19
Q

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

A

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

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20
Q

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

A

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

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21
Q

Paraphyletic group

A

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

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22
Q

Polyphyletic group

A

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

23
Q

Character

A

A particular trait of interest

24
Q

Homologous characters

A

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

25
Q

Character state

A

A given character can have many different character states

Ex: 5 digits on forelimb, one digit on forelimb

26
Q

Ingroup

A

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

27
Q

Outgroup

A

A group of taxon that is related to the ingroup

28
Q

Steps

A

The number of inferred changes in character state on a tree

29
Q

Most parsimonious tree

A

The tree with the shortest number of steps/changes

30
Q

Plesiomorphy

A

Ancestral character state

31
Q

Symplesiomorphy

A

Shared ancestral characters, not phylogenetically informative

32
Q

Apomorphy

A

Derived character state

33
Q

Synapomorphy

A

Shared derived character, most useful for inferring phylogenetic relationships

34
Q

Autapomorphy

A

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

35
Q

Occam’s razor, related to Parsimony

A

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

36
Q

Topology

A

Pattern of branching

37
Q

Two methods for dealing with long branches

A

Maximum Likelihood and Bayesian

38
Q

Maximum Likelihood

A

Calculate the likelihood of observing the data

39
Q

Bayesian

A

Maximizes the probability of observing a tree

40
Q

Maximum likelihood vs Bayesian

A

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

41
Q

Long branch attraction

A

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

42
Q

Gene tree

A

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

43
Q

What are orthologous genes?

A

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

44
Q

What are paralogous genes?

A

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

45
Q

Which of the following is more closely related:

  • orthologous loci in different species
  • paralogous loci within the same species
A

Orthologous loci in different species

46
Q

What is an example of an ancestral character state

A

Opposable vs non-opposable foot/thumb

47
Q

What can the Molecular Clock be used for

A

To calibrate evolutionary trees to absolute time

48
Q

Homology

A

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

49
Q

Homoplasy

A

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

50
Q

Convergent evolution (convergence)

A

Organisms independently evolve similar traits

51
Q

Parallel evolution (parallelism)

A

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

52
Q

Evolutionary reversal

A

Return from an advanced to a more primitive character

53
Q

Does branch length impact patterns of evolutionary decent?

A

no it is the same regardless of branch length

54
Q

Does rotating branches change relationships on a phylogenetic tree?

A

no

ENVS 212 (10 decks)

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