Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Evolutionary Biology > Exam 1 > Flashcards

Exam 1 Flashcards

You may prefer our related Brainscape-certified flashcards:
AP® Biology flashcards Biology 101 flashcards
1
Q

How many people infected by HIV worldwide?

A

~76 Million

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

How does HIV spread?

A

Through bodily fluids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is HIV?

A

Intracellular parasite

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Cells vulnerable to HIV?

A

Macrophage cells, effector helper T cells, memory helper T cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What does HIV latch on to on the outside of the cells?

A

CD4 and CCR5 Receptors

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Why is HIV difficult to treat?

A

Hard to find drugs that interrupt the viral life cycle but not the host cell’s life cycle

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

How does the body respond to HIV infection?

A

Destroys virion in bloodstream, kills infected T cells and macrophages

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is AIDS?

A

Acquired Immune Deficiency Syndrome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

When does AIDS occur after infection?

A

~10 years

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

How does HIV cause AIDS?

A

The immune system begins to collapse and can no longer fend off a number of opportunistic viruses, bacteria, and fungi

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is AZT?

A

Reverse transcriptase inhibitor that prevents HIV from reproducing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

How does AZT work?

A

It inserts itself (azidothymidine) in thymidine’s place in growing DNA strand, stops transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Why doesn’t AZT effect our own transcriptase?

A

Our cells are more selective and will not choose the AZT in place of T

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Why does AZT fail in the long run?

A

Natural mutations in HIV that are more selective (don’t pick AZT over T) will increase in abundance as all of the ones that AZT worked on die out

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Coreceptor Inhibitors

A

Block HIV from attaching to cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Entry/Fusion Inhibitors

A

Bar entry into host cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

RT Inhibitors

A

Inhibit reverse transcriptase by mimicking normal building blocks of DNA or interfere with bonding site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Integrase Inhibitors

A

Block viral DNA incorporation into host DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Protease Inhibitors

A

Block the enzyme that cleaves precursor proteins to allow maturation of virions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

HAART Cocktails

A

Highly Active Anti-Retroviral Therapy (mix of many drugs)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What did HIV evolve from?

A

SIV (simian Immunodeficiency Virus)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

HIV-1

A

The most prevalent and pathogenic type of HIV virus, came from chimps

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

HIV-2

A

Found primarily in West Africa and less virulent, came from sooty mangabeys

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

HIV-1 Group M

A

Major/Main
9 Subtypes
Global (95%)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

HIV-1 Group N

A

Non-M, Non-O
< 20 cases
Cameroon only

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

HIV-1 Group O

A

Outlier
High diversity
West-Central Africa

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

HIV-1 Group P

A

Pending
One case
Found in gorillas

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Virulence

A

Severity or harmfulness of a disease
Caused by reproduction rate of a virus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Transmission Rate Hypothesis

A

If transmission of sexually transmitted diseases is frequent, virulent viruses are naturally selected. If transmission is low, less virulent strains are selected. Cost/benefit ratio for the virus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Relationship between HIV virulence and sexual practices

A

Increase in safe sex decreases virulence, no change in practices keep virulence the same

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Delta32 Mutation

A

Has 32-base pair deletion so CCR5 coreceptor does not present itself on surface of host T-cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Special Creation

A

Earth 6,000-10,000 years old
Species independently created
Species do not change

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Descent with Modification

A

Species change over time
New life forms derive from old life forms
Earth 4.5 billion years old

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Microevolution

A

Species change over time

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Speciation

A

Lineages split and diverge

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

Macroevolution

A

New life forms derive from older forms

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

Common Ancestry

A

All life forms are related

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Discovery of Charles Darwin

A

Natural selection, the mechanism of evolution (NOT evolution itself)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Hutton Hypothesis

A

Proposed geological change because of Earth’s hot core

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Lamarck Hypothesis

A

Species evolve through use and disuse, and those change are heritable

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

Paul Kammerer Experiment

A

Inheritance of acquired traits in midwife toads when forced back into water

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

Darwin’s Biogeographic Discoveries

A

Plants and animals more similar based on location rather than biome type

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

Darwin’s Geology Discoveries

A

Fossils of seashells in mountains
More recent the fossils, more similar to extant organisms

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

Uniformitarianism

A

Earth has been undergoing the same natural processes since the beginning

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

Most important observations made in the Galapagos Islands

A

Animals on island most similar to those on mainland South America
Islands have different environment, organisms also differed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

Works by Darwin

A

Origin of Species
Descent of Man

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

Evidence for Evolution

A

Selective breeding (species not immutable)
Vestigial structures
Homology
Fossil record

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

Vestigial Structures

A

Structure in an organism that has lost all or most of its original function in the course of evolution

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

Homologous Structures

A

Structures that are inherited from a common ancestor but may have different functions (ex. forelimb of mammals)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

Analogous Structures (Homoplasy)

A

Structures similar in appearance and function but details of structure differ and not derived from common ancestor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

Convergent Evolution

A

When. two or more unrelated lineages. acquire the same biological trait because of selection for a shared ecological niche

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

Functional Genes

A

Exons
Introns
Promoters

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

Processed Pseudogenes

A

Missing introns and promoters (non-functional)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

What causes processed pseudogenes?

A

Reverse transcription of mRNA into DNA and put randomly at another locus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

Law of Succession

A

States that extinct specie are ancestors of living species

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

Transitional Forms

A

Organisms that usually show a blend of traits that you would expect at intermediate stages of evolution (can be alive or in fossil record)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

Example of living transitional form

A

Amphibious Mudskipper compared to aquatic and terrestrial relatives

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

Example of fossil transitional form

A

Archaeopteryx (Dino with modern flight feathers)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

What does the universal genetic code support?

A

Evidence we all descend from a common ancestor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

Universal Genetic Code

A

With only minor exceptions, all organisms studied to date use the same nucleotide triplicates or codons to specify the same amino acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

Who first proposed continental drift?

A

Alfred Wegener
Said the continental shelves fit together like a puzzle (plate tectonics)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
62
Q

How was Earth concluded to be very old?

A

Early geologists measured rates of erosion, then also used relative dating

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
63
Q

Marie Tharp

A

Combined datât from ship surroundings and undersea earthquakes to make map of seafloor (confirmed plate tectonics)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
64
Q

Marie Curie

A

Discovered radioactivity
Lead to radiometric dating

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

Radiometric Dating

A

Absolute dating of rocks measuring decay of radioactive isotopes into its daughter isotopes using known half-life rates

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
66
Q

Half-life

A

Length of time for 50% of an isotope to decay

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
67
Q

Age of Earth

A

4.54 ± 0.05 billion years

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
68
Q

Age of Life

A

~3.7 billion years

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

Darwin’s Four Postulates

A

Variation between individuals within a population
Some variation is passed on to offspring
More young are born than can survive
Survival and reproduction are not random

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

Who else independently developed a theory of natural selection?

A

Alfred Russel Wallace

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
71
Q

fw2.2 gene

A

Protein made during early fruit development to repress cell division (ex. tomatoes)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
72
Q

Darwinian Fitness

A

The ability of an individual to survive and reproduce in its environment

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
73
Q

Darwinian Fitness Example

A

Beach mice of Alabama/Florida

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
74
Q

Where did Peter and Rosemary Grant study finches?

A

Galapagos Islands, isla Daphne Major
Most isolated island because of distance from other islands

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
75
Q

How did the Grants test for postulate 1?

A

Was beak depth variable? Yes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
76
Q

How did the Grants test for postulate 2?

A

Is the variation in be beak depth heritable? Yes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
77
Q

Why is measuring heritability difficult?

A

Misidentified paternity
Nest parasitism (birds)
Maternal effects
Shared environments

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
78
Q

BMP4

A

Bone morphogenic protein 4
Associated with deep beaks

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
79
Q

How did the Grants test for postulate 3?

A

Testing for excess offspring
89% die before reproduction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
80
Q

How did the Grants test for postulate 4?

A

Was survival nonrandom (due to beak depth)? Finches with deepest beaks survived more during drought

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
81
Q

Why were deep finch beaks favorable after drought?

A

Only birds with deep, narrow beaks could crack the fruit of one of the one plant that could produce fruit

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
82
Q

What does natural selection act on?

A

Individuals and EXISTING phenotypes (can’t make new ones)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
83
Q

Where does evolution occur?

A

Populations and allele frequencies

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
84
Q

Where is the evidence of natural selection seen?

A

The NEXT generation, its a backwards looking process (not predicting for the future)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
85
Q

Artificial Selection Experiment

A

Selection for highest oil content in corn, over 60 years went from 4-6% to 20% oil

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
86
Q

How did pandas get as “thumb” if natural selection can’t make new structures?

A

Elongated wrist bone grew to serve as a sort of thumb (natural selection used what was already there)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
87
Q

Is natural selection perfect?

A

No, it makes organisms good enough for survival

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
88
Q

Darwin’s 3 Problems

A
  1. Did not know how variability was created (mutations)
  2. Did not know how traits were inherited (alleles)
  3. Earth thought to be 15-20 million years old and two young for mutation (radioactive isotopes proved older)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
89
Q

How did Darwin understand variability?

A

Thought there was set variability and it would all eventually be used up

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
90
Q

How did Darwin understand traits?

A

Thought individual traits would be lost eventually by merging with other traits

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
91
Q

The Modern Synthesis

A

The fusion of genetics with evolutionary biology

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
92
Q

Modern Synthesis Postulate 1

A

Individuals within a population are variable because of mutations making new alleles and recombination of those alleles

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
93
Q

Modern Synthesis Postulate 2

A

Individuals pass their alleles onto their offspring

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
94
Q

Modern Synthesis Postulate 3

A

In most generations, more offspring produced than can survive

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
95
Q

Modern Synthesis Postulate 4

A

Individuals that survive and reproduce the most are those with alleles and allelic combinations that best adapt them to their environment

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
96
Q

Is natural selection the only cause of evolution?

A

No, just means of adaptive evolution

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
97
Q

Scopes Monkey Trial

A

Tennessee schoolteacher John Scopes was arrested for teaching the theory of evolution despite a state law banning it

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
98
Q

When did the US protest teaching evolution by law?

A

1967

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
99
Q

When was “Creation Science” (creationism) banned being taught in public schools?

A

1987

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
100
Q

Why was creationism given the title creation science?

A

So it would look less religious and be taught alongside evolution

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
101
Q

What did creationism morph into?

A

Intelligent Design Theory

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
102
Q

Argument by William Paley

A

Like a watch, which you would assume was made by an intelligent organisms, the vertebrate eye must be the same

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
103
Q

Darwin rebuttal to Paley

A

Vertebrate eyes must have arisen from simpler eye
Proof of simpler eyes in living organisms

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
104
Q

How does science differ from creationism?

A

Creationism does not use evidence to test its claims, does not allow evidence to alter beliefs, and does not grow in capacity to explain the natural world

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
105
Q

Hypothesis

A

A proposition

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
106
Q

Scientific Fact

A

A hypothesis that has become so well supported by evidence that we feel safe in acting as if it were true

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
107
Q

Scientific Theory

A

A mature, interconnected body of statements, based on reasoning and evidence, that explains a wide variety of observations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
108
Q

Is evolution untestable?

A

No, you can test the 4 postulates of evolution
Can test predictions based on evolution

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
109
Q

How has entropy been compared to evolution?

A

Since organisms evolve to be more complex, they are going against the idea of entropy

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
110
Q

Why does evolution NOT break the second law of thermodynamics?

A

Entropy only applies to CLOSED systems which Earth is not, also organisms don’t always evolve to be more complex

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
111
Q

Example of organisms evolving to be less complex

A

Snakes losing their legs

112
Q

Entropy

A

A measure of disorder or randomness

113
Q

Significance of butterfly. species in genus Hedylepta?

A

Genus to native Hawaii, but 2 species have mouthparts which only allow them to eat bananas (which were only introduced to Hawaii 1000 years ago) -> proof of species evolution

114
Q

How old was Earth originally thought to be based on combustion?

A

15-20 million years old

115
Q

Is the sun combustion or nuclear fusion?

A

Nuclear fusion

116
Q

Epigenetics

A

The environment can influence the way genes are expressed

117
Q

Examples of observed evolution

A

HIV
Daphne Major finches
London Underground vs Above Ground mosquitoes

118
Q

Systematics

A

Study of biological diversity and evolutionary relationship of organisms

119
Q

The two field of Systematics

A

Study of biological diversity and evolutionary relationship of organisms

120
Q

Taxonomy

A

The science of naming taxa and placing them into groups

121
Q

Taxon

A

Species, genus, or kingdom, etc

122
Q

Is taxonomy absolute?

A

No, taxonomy is always changing as new data is discovered

123
Q

Where do the formal rules of taxonomy come from?

A

International Union of Zoological Nomenclature

124
Q

Who was the father of modern classification system (binomial nomenclature)?

A

Carolus Linnaeus

125
Q

Taxonomic levels from highest to lowest

A

Kingdom, Phylum, Class, Order, Family, Genus, Species

126
Q

What levels of classification are in binomial nomenclature?

A

Genus species

127
Q

How are taxonomic groups formed?

A

Based on evolutionary history regardless of outwards similarity

128
Q

How did scientists used to form taxonomic groups?

A

Based on similarity of appearance

129
Q

What makes grouping organisms into taxonomic groups difficult?

A

Convergence/Homoplasies

130
Q

Phylogeny

A

Hypothesis of evolutionary relationships

131
Q

Phylogenetic Tree

A

Graphical summary of evolutionary history

132
Q

Is phylogeny absolute?

A

No, it is only an estimate

133
Q

Law of Parsimony

A

The simplest explanation is most likely to be true

134
Q

Occam’s Razor

A

Law of Parsimony
Trying to minimize homoplasy in a data set

135
Q

Who came up with Occam’s Razor?

A

William of Ockham

136
Q

Homology

A

Evolutionary relationships should only be reconstructed from traits that are similar because they are derived from a common ancestor

137
Q

Synapomorphy

A

Shared derived characters of all members of a group

138
Q

What is used to decide where branches should be on a phylogeny?

A

Synapomorphies

139
Q

Can common ancestors ever be living?

A

NO! Even the most ancient-like animals that are typically the outgrip are still not technically the same species as the ancestor placed at where that branch splits

140
Q

Autapomorphy

A

Unique derived trait

141
Q

Can autapomorphies be used for estimating relatedness?

A

No, they are basically useless

142
Q

Pleisiomorphy

A

Any ancestral or primitive character
Shared among members of a clade, but significantly older than that group’s common ancestor

143
Q

What is a pleisiomorphy also know as?

A

Sympleisiomorphy

144
Q

Homoplasy

A

A similar (analogous) structure or molecular sequence that has evolved independently in two species

145
Q

What creates homoplasies?

A

Convergent evolution

146
Q

Does homoplasy come from common ancestry?

A

No

147
Q

What traits are uninformative?

A

Autapomorphies

148
Q

Uniformative

A

Not very useful or helpful info

149
Q

What kind of characters does homoplasy choose?

A

Characters that evolve slowly relative to the age of taxa

150
Q

Maximum parsimony method

A

Minimizes total amount of evolutionary change in a tree

151
Q

Evolutionary Reversal

A

When a lineage evolves toward one of its ancestral traits, effectively losing a more recently evolved trait

152
Q

What are the most common types of traits?

A

Synapomorphies

153
Q

Assumptions of characters for phylogenetic analysis

A

Homology
Character states have genetic basis
Characters are independent
Characters evolution reflects organismal phylogeny

154
Q

Examples of phylogenetic characters

A

DNA sequence
Presence/Absence of skeletal elements
Mode of embryonic development

155
Q

Pros of grouping taxon with morphological traits

A

Well established characters
Loss of material
Less expensive
Examine many “genes” at once
Can use fossils
Can look at more individuals more often

156
Q

Pros of grouping taxon with molecular traits

A

Huge number of characters
Closer to real genetic basis
Better models of how characters evolve
More amenable to certain analyses

157
Q

3 Principles of Cladistics

A
  1. Any group of organisms is related by descent from a common ancestor
  2. There is a bifurcating pattern of cladogenesis
  3. Change in characteristics occurs in lineage over time
158
Q

Cladistic methods of phylogenetic

A

Techniques that identify monophyletic groups based on synapomorphies and direction of change through time

159
Q

Most commonly used cladistic method

A

Outgroup method

160
Q

Outgroup

A

A closely related taxon that is used to represent the ancestor

161
Q

What does the outgrip in a phylogenetic tree tell ups?

A

Which characters are derived and which are ancestral

162
Q

Clade

A

Monophyletic group (they mean the exact same thing)

163
Q

When are all synapomorphies congruent?

A

When no convergence or reversal occurs

164
Q

Node (on a genetic tree)

A

Represent EXTINCT taxa and bifurcating branching points

165
Q

What does it means when you rotate a branch about the node of a tree?

A

As long as it does not change the relationships, it will still represent the same tree

166
Q

Cladogram vs Phylogram

A

Cladogram- branch lengths have no meaning
Phylogram- branch lengths are proportional to change

167
Q

What does cladogram branch length mean?

A

Represent the amount of changes that have been undergone

168
Q

Polytomy

A

A branch point form which more than two descendant groups emerge

169
Q

Why is there polygamy in some trees?

A

It occurs when the evolutionary relationship between 3 or more species is not fully understood and so is left unresolved

170
Q

Monophyletic Group

A

All members are believed to stem from a single common ancestor, and the group includes this common ancestor

171
Q

Paraphyletic Group

A

Group that is monophyletic except that some descendants of the common ancestor have been left out

172
Q

Polyphyletic Group

A

Consisting of unrelated lineages, each more closely related to other lineages not placed in the taxon

173
Q

What is more common, paraphyly or polyphyly?

A

Paraphyly

174
Q

What is more troublesome, paraphyly or polyphyly?

A

Polyphyly (again, complicates finding monophyletic groups to classify species)

175
Q

Order of whales and dolphins

A

Cetacea

176
Q

Synapomorphy of Cetacea

A

loss of posterior limbs

177
Q

What order are whales closely related to?

A

Artiodactyla (even toed ungulates) which includes pigs, camels, cattle, and hippos

178
Q

What does new molecular research suggest about where hippos belong in phylogenetic trees?

A

Hippos more mostly related to Cetacea than previously thought (based on genetics)
Clade of cetaceans with hippos more likely than clade with all artiodactyls and cetaceans

179
Q

Why are homoplasies hard to identify in molecular phylogeny?

A

Only 4 bases (ATCG)

180
Q

Why were hippos previously believed to not be as closely related to whales?

A

Whales lack the astragalus, which all artiodactyls have

181
Q

Astragalus

A

Ankle joint bone

182
Q

What morphological data suggested that whales may be artiodactyls?

A

While modern whales don’t have an astragalus, extinct whales with legs had features of astragalus similar o artiodactyls

183
Q

How do scientists evaluate the statistical confidence in a tree?

A

Bootstrapping

184
Q

Bootstrap values

A

Percentages of the number of times the same branch arose after repeated sampling

185
Q

When percent of bootstrap support is needed to indicate the correct relationship in a tree?

A

Over 70%

186
Q

Reconstruction methods for trees besides parsimony

A

UPGMA
Neighbor Joining
Maximum Likelihood
Bayesian Analysis

187
Q

UPGMA

A

Unweighted pair-group method using arithmetic averages

188
Q

Neighbor Joining

A

A distance method for reconstructing phylogenies; identifies the tree topology with the shortest possible branch lengths using ALL characters (homoplasy, synapomorphies, autapomorphies, etc)

189
Q

Maximum Likelihood

A

Assumes a particular probabilistic model of sequence evolution and then calculates for each tree the probability of the data given the tree P(data|tree)

190
Q

What characters does the maximum likelihood method use?

A

Synapomoprhies
Autapomorphies
Invariant Sites
ALL DATA

191
Q

What does the maximum likelihood calculate?

A

The likelihood statistic, which helps estimate the topology of the tree

192
Q

Distance reconstruction methods for trees

A

Uses differences (distances) among genetic character states to group taxa
NOT a cladistic method
Typically very fast and easy to estimate trees

193
Q

Why aren’t distance methods considered cladistic?

A

They do not look for synapomorphies, just overall similarity
Prone to error when many homoplasies present

194
Q

Topology

A

Shape of phylogenetic trees

195
Q

How accurate are maximum likelihood methods?/

A

VERY accurate, among the most accurate methods

196
Q

Is maximum likelihood a quick process or a long process?

A

Very computationally intensive
A tree with 100 species may take several months

197
Q

Bayesian Markov Chain Monte Carlo

A

Combine Bayesian statistics with Marcov Chain Monte Carlo algorithms
P(tree|data)

198
Q

Characteristics of ancient fossils related to whales and artiodactyls

A

Whale like ear bones
Artiodactyls like astragalus

199
Q

SINE/LINE

A

Non-coding DNA inserted into genomes (retrotransposons)

200
Q

Molecular Clock

A

Model that uses DNA comparisons to estimate the length of time that two species have been evolving independently

201
Q

What does the molecular clock hypothesize?

A

Molecular change happens at a steady rate
Use known dates to calibrate the molecular clock

202
Q

What is used to calibrate a molecular clock?

A

Fossils or geological events

203
Q

What rate do most taxa progress on molecular clocks?

A

2% sequence divergence per million

204
Q

What genes do molecular clocks use?

A

Mitochondrial genes (because other gene evolve at different rates)

205
Q

Difficulties with molecular clocks

A

Many estimates/assumptions are likely to have a high degree of uncertainty
Many irregularities caused by natural selection and/or evolutionary fluctuations

206
Q

What kind of group is artiodactyla?

A

Not monophyletic
Order Cetacea should be sunk to family level

207
Q

How is phylogeny mapping done?

A

Optimizing all characters on a phylogeny

208
Q

Sources of Variation

A

Genetic
Environmental
Genotype-by-environment interaction

209
Q

Examples of genetic variation in humans

A

Whether phenythiocarbamide (PTC) tastes bitter or not (and overall ability to detect toxins)

210
Q

Gene responsible for bitter flavors in humans

A

TAS2R38

211
Q

What chromosome is TAS2R38 on?

A

7

212
Q

What alleles are involved in the TAS2R38 gene?

A

PAV (encodes proper PTC taste receptor)
AVI (encodes deformed PTC taste receptor)

213
Q

Environmental Variation

A

Traits that are not genetically controlled (not heritable)

214
Q

Phenotypic Plasticity

A

The ability of an organism to change its phenotype in response to changes in the environment

215
Q

Phenotypic plasticity is a form of what kind of variation?

A

Environmental

216
Q

Inducible Defenses

A

Defensive traits produced only in response to the presence of a predator

217
Q

Inducible defenses are considered what kind of variation?

A

Environmental

218
Q

Example of genotype-by-environment interaction in humans

A

Hating cilantro

219
Q

Reaction Norm

A

Phenotypic expression of a single genotype across a range of environments

220
Q

How is genotype-by-environment interaction tested?

A

Testing a phenotype across a range of environments (if there’s no interaction, the phenotype should be the same in all environments)

221
Q

Reaction Norm Graph

A

Steepness of slope indicates amount of plasticity

222
Q

Example of environmental sex determination

A

Sex determination in leopard geckos
Genotype and temperature influence sex (G-by-E interaction)

223
Q

What is the raw material of evolution?

A

Mutations

224
Q

What creates new alleles?

A

Mutations

225
Q

Components of DNA

A

Deoxyribose sugar
Phosphate group
Nitrogenous base

226
Q

How many rings in purines?

A

2

227
Q

How many rings in pyrimidines?

A

1

228
Q

What enzyme helps with DNA replication?

A

DNA polymerase

229
Q

DNA Polymerase

A

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule

230
Q

Point Mutation

A

Gene mutation in which a single base pair in DNA has been changed

231
Q

Order of pathway in protein synthesis

A

DNA -> mRNA -> protein

232
Q

Why don’t all point mutations result in a change of protein?

A

Multiple codons can code for the same amino acid

233
Q

Transition Mutation

A

Change from purine to purine or pyrimidine to pyrimidine

234
Q

Transversion Mutations

A

Change between purine and pyrimidine or vice versa

235
Q

What kind of point mutations are most common?

A

Transition mutations (2x as common as transversions)

236
Q

Exons

A

Expressed sequence of DNA; codes for a protein

237
Q

Introns

A

Noncoding segments of DNA that lie between coding sequences

238
Q

Synonymous Mutation

A

“Silent”
Does not change amino acid sequence

239
Q

Nonsynonomous Mutation

A

“Replacement”
Changes amino acid sequence

240
Q

Frameshift Mutations

A

Mutation that shifts the reading frame of the genetic message by inserting/deleting a nucleotide

241
Q

Nonsense Mutation

A

(Point Mutation) changes a normal codon into a stop codon

242
Q

What causes gene duplications?

A

Unequal crossing over during meiosis

243
Q

Where do new genes come from?

A

Gene duplication
Retroposition

244
Q

Retroposition

A

Processed mRNA inserted back into genome

245
Q

Gene duplication relating to mutations

A

Creates an extra copy that is free from natural selection and able to accumulate mutations

246
Q

Example of gene duplication in humans

A

Different global gene families
Produced by past gene duplication events that allowed the gene to take on new functions over time

247
Q

Paralogous Genes

A

Genes that duplicated and diverge in a species (like globin in humans) _> may have different functions

248
Q

Orthologous Genes

A

Genes that are homologous and evolved from a common ancestral gene by speciation (like the original globin gene that can also be found in mice)

249
Q

Inversions

A

Segment of DNA is cleaved in two places, the excited segment flips, and re-anneals in the opposite direction

250
Q

Problem with inversions

A

Can disrupt gene linkage
Cannot align properly with homologs (makes dysfunctional gametes)

251
Q

Example of Inversions

A

Fruit flies
5/6 chromosomes are polymorphic for inversions
Inversion frequencies vary along cline

252
Q

Polyploidy

A

Entire extra sets of chromosomes

253
Q

what species most commonly have polyploidy?

A

Plants and rare in animals
Hermaphroditic species that can self-fertilize

254
Q

How can polyploidy lead to speciation?

A

Meiosis error creates diploid gametes
If two diploids fuse, they make tetraploid
If two tetraploids can mate, a new species is created

255
Q

How does triploidy occur?

A

If diploidy gamete fuses with a haploid one

256
Q

How fertile are triploids?

A

Low fertility unless parthenogenetic

257
Q

Why are polyploids so prone to speciation?

A

They have entire chromosomes of genes that are free from natural selection and can undergo mutation

258
Q

Kleptogenesis

A

Female “steals” sperm from the male, used for energy or to stimulate parthenogenesis, but not fertilization, then eject the sperm nucleus

259
Q

Example of triploid species

A

Ambystoma Salamanders
Use reproductive mode of kleptogenesis

260
Q

What causes sickle cell anemia?

A

Single transversion in hemoglobin gene

261
Q

Where is the best data on mutation rates from?

A

Loss-of-function mutations

262
Q

Loss-of-function Mutations

A

Mutation deactivates gene and causes protein not to be made

263
Q

What are loss of function mutations caused by?

A

Point mutations
Insertions
Deletions
Transposable genetic elements

264
Q

What percentage of human gametes carry a phenotypically detectible mutation?

A

10%

265
Q

Why are mutation rates variable?

A

DNA polymerase vary in error rates
Mismatch repair systems vary in effectiveness
Some species have varying mutation rates overall

266
Q

Examples of species with high mutation rate vs low mutation rate

A

High: Viruses
Low: Fruit flies

267
Q

What regions of DNA have more mutations, coding, or noncoding?

A

Noncoding DNA regions (natural selection allows for less errors)

268
Q

What was traditionally believed about allelic variation?

A

Was low within populations
Variation from wild type was rare

269
Q

How do we known that genetic variation within populations is actually very high?

A

Huge advances in methods for directly measuring genetic and genomic diversity

270
Q

How are genotypes determined?

A

For ome loci, examining phenotype
Others, looking directly at proteins or DNA sequences

271
Q

Gel Electrophoresis

A

Applying electric current to samples of DNA and proteins so they migrate to oppositely charged poles, they migrate according to size and mass (different sized alleles go different distances)

272
Q

HIV Infections and CC-CKR-5 gene

A

Encodes for CCr5 surface protein receptor
If homo, dom (+/+) can be infected
If homo rec. (Delta32/Delat32) cannot be infected
If het. (+/Delta32) infected but progress to AIDS slower

273
Q

Mean Heterozygosity

A

Average frequency of heterozygotes across loci in the genotype of the average individual

274
Q

Percent of polymorphic loci

A

Fraction of loci in a population that have multiple alleles

275
Q

Selectionist Theory

A

Natural selection favors allelic diversity

276
Q

Neutral Theory

A

Polymorphic alleles are functionally equivalent so they are not selected against

277
Q

What factors can influence rate of mutation?

A

Environmental:
UV Radiation
Carcinogens

Evolutionary Biology (1 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions