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BIOL 108 Lecture > Topic 4: Systematics and Phylogeny > Flashcards

Topic 4: Systematics and Phylogeny Flashcards

1
Q

what is “evolutionary taxonomy”?

A

using Linnaean classification in the context of evolution

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2
Q

why does “evolutionary taxonomy” not work?

A
  • it is practically impossible to find the common ancestor
  • in this system you were meant to find the direct exact ancestor rather than just relationships between species
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3
Q

what is meant by the term “systematics”?

A

-discipline focussed on classifying organisms based on evolutionary relationships among organisms (assign classification)

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4
Q

what is meant by the term “phylogenetics”?

A
  • field of systematics focused on evolutionary relationships among organisms
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5
Q

why does the Linnaean classification struggle for adaptation? (2 reasons)

A
  • there are not enough ranks to accommodate every taxon (number of ranks is limited)
  • ranks on phylogeny may not be comparable
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6
Q

what is the key part of Linnaean classification that is still used?

A
  • binomial nomenclatures
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7
Q

what are the four key principles to finding relationships in cladistic (phylogenetics)?

A
  1. evolutionary relationships are represented in a tree with diverging branches
  2. super specific taxa are groups of closely related species
  3. to build tree species are grouped based on shared derived features
  4. direct ancestors are never specified, always treated as hypothetical
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8
Q

what is a phylogenetic tree? what is another name for this?

A
  • an evolutionary hypothesis of a group of biologically related taxa
  • also called a phylogeny
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9
Q

what is meant by the term “root” in relation to phylogenetic trees?

A

base of phylogeny

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10
Q

what is meant by the term “tips” in relation to phylogenetic trees?

A

terminals of phylogeny

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11
Q

what is meant by the term “node” in relation to phylogenetic trees?

A
  • also called the branch point
  • the point that the branches meet, representing the hypothetical last common ancestor and the divergence of two taxa
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12
Q

what is meant by the term “specification” in relation to phylogenetic trees?

A
  • the divergence of two taxa from their common ancestor
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13
Q

what is meant by the term “internal node” in relation to phylogenetic trees?

A

connection between nodes

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14
Q

what is meant by the term “external node” in relation to phylogenetic trees?

A

connection between node and tip

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15
Q

what is meant by the term “branch/clade” in relation to phylogenetic trees?

A

lines connecting nodes, roots and tips

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16
Q

what is meant by the term “ingroup” in relation to phylogenetic trees?

A

the group under study

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17
Q

what is meant by the term “outgroup” in relation to phylogenetic trees?

A

any group outside of the clade of interest

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18
Q

what is meant by the term “sister taxa” in relation to phylogenetic trees?

A

two closest branches from a node

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19
Q

what is meant by the term “basal taxa” in relation to phylogenetic trees?

A

lineages that diverge relatively early

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20
Q

what is meant by the term “derived taxa” in relation to phylogenetic trees?

A

lineages that diverge relatively late

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21
Q

what is meant by the term “dichotomy” in relation to phylogenetic trees?

A

only 2 branches diverge from the common ancestor

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22
Q

what is meant by the term “polytomy” in relation to phylogenetic trees?

A

more than two branches diverge from a common ancestor

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23
Q

what are the two types of polytomy?

A
  • soft polytomy
  • hard polytomy
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24
Q

what is meant by the term “soft polytomy” in relation to phylogenetic trees? what are the implications related to this term?

A
  • represented uncertainty about which of the taxa arising from the node are most closely related to each other
  • implications –> more data, observation and experiments
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25
what is meant by the term "hard polytomy" in relation to phylogenetic trees? what are the implications related to this term?
- represents a hypothesis that more than two taxa arose from the same common ancestor - implications --> an evolutionary event is likely taking place (natural phenomenon)
26
is it more common for a phylogeny to be rooted or not rooted?
- most are rooted
27
what does a branch/clade represent?
- an ancestor and all of its descendants after divergence from a node
28
what can happen to branches/clades to aid in analysis and interpretations?
- can be collapsed or expanded
29
how are branches/clades often organized?
- as nested heirarchy (like Russian nesting dolls)
30
what is meant by the term "topology" in relation to phylogenetic trees?
- branching pattern
31
what are the names of the two types of phylogenies?
- phylograms - cladograms
32
what are the key features of phylograms?
- include measures of time (lengths of the lines) - depicts hypotheses of evolutionary history - fossil is required for calibration
33
what are the key features of cladograms?
- only hypothesis on the relative relationships among taxa
34
what are monophyly / monophyletic groups? give an example.
- clade that includes the most recent common ancestor and all of its descendants - e.g. all mammals
35
what is the only valid classification in phylogenetic systematics?
- monophyly or monophyletic group
36
what are paraphyletic groups? give an example.
- group that includes most recent common ancestors and some of its descendants - e.g. non-avian dinosaurs
37
which groups were accepted in "evolutionary taxonomy"?
- monophyletic - paraphyletic
38
what are the two sources of information used to build phylogenies?
- morphological data - molecular data
39
what is morphological data?
- anatomical features - qualitative (colour, shape) - quantitive (length) - measurements taken with rigorous procedures - widely used in fossils
40
what is molecular data?
- genomic (DNA sequence) - protein structure
41
what are morphological and molecular data used for?
- both used to construct characters with multiple states (traits) (which can be used to make phylogenies)
42
how are organisms grouped in phylogenies?
shared traits (which should represent information on evolutionary history)
43
what does the term "character" mean?
heritable feature of a given organism (anatomical, physiological or molecular)
44
what are the different types of characters possible?
- anatomical - physiological - molecular
45
what does the term "character state" mean? give some details about this term.
- specific condition or state of the character - largely related to character - observable condition of the character - a character can have two or more states
46
what does the term "homology" mean? give some details about this term.
- character traits that evolved from common ancestral structure --> similar due to shared ancestry among taxa, superficial appearance may not display the similarity (comparing limbs)
47
homology is identified through similarities in what? (4 types and give an example)
- topology (e.g. where humerus is relative to other arm bones) - detailed morphology (e.g. humeral head is convex) - neural innervation (e.g. diaphragm innervated by the phrenic nerve) - embryonic development (e.g. process of cell growth and differentiations that form the eyes)
48
simple definition of homology.
- character traits that evolved from a common ancestral structure
49
what does the term "apomorphy" mean?
moving away from ancestors
50
what does the term "synapomorphy" mean? give an example.
a derived feature shared by more than two taxa and their last common ancestor (e.g. shell of turtles)
51
what does the term "autapomorphy" mean?
a derived feature found only in one taxa (meaning a species)
52
what does the term "symplesiomorphy" mean? give an example.
an ancestral (not primitive) feature shared by at least some members of a taxonomic group (e.g.) fur covering the body of most mammals
53
what does it mean that synapomorphy and symplesiomorphy are context dependant?
character can be synapomorphy on one phylogeny, and symplesiomorphy on another with a different scope
54
what does the term "uninformative characteristic" mean?
do not really tell you anything because they are too generalized
55
what does the term "analogy" mean?
character traits that independently evolved from convergence evolution
56
why do we not use analogy traits to build phylogenies?
because they do no have any information about shared ancestry
57
what is the order of change in character states, meaning the number values that represent the change from ancestral to derived?
'0'-->'1'
58
what is the order of change in character states, meaning the number values that represent the change from derived to ancestral?
'1'-->'0'
59
what is the idea of maximal parsimony?
that the simplest hypothesis consistent with the facts is the one most likely to be correct
60
what is the more specific meaning of parsimony in cladistics?
of all possible cladograms for a set of taxa, the one that implies the fewest evolutionary changes (from '0'-->'1') is considered most likely
61
what are the methods used to choose phylogenies?
- maximal parsimony - maximum likelihood - bayesian inference
62
what a key problem faced with phylogenies?
distinguishing between ancestral/basal and derived character state can be difficult
63
what are solutions to this key problem?
- embryonic development - fossil evidence
64
what are the key features or characteristics of embryonic development studies?
- more general (basal) characters appear earlier in the embryo than more special (derived) characters - von Baer's law
65
what are the exceptions to von Baer's law (the one surrounding embryonic development)?
- ancestral traits do not always appear in embryonic development - metamorphosis can occur
66
what are the key features or characteristics of fossil evidence studies?
- indisputable existence of taxa in time long ago, traits demonstrated by fossil taxa that are relatively early in Earth's history are likely ancestral
67
what are the key point to keep in mind when discussing fossil evidence?
- fossil record is incomplete - molecular data is very rare in fossils
68
why are phylogenetic trees only a hypothesis?
a lot of subjective steps that lead to the creation of these trees, which is why it is only a hypothesis
69
due to phylogenetic trees being only a hypothesis what are some key things we must keep in mind?
- never take a phylogeny as the true evolutionary relationship - different source of information can generate distinct phylogeny - phylogenies are always subjected for improvement (new fossils or sequence)
70
what do phylogenetic trees depict?
- patterns of evolutionary history, not overall similarity

BIOL 108 Lecture (9 decks)

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