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EVE2 > Eve Final > Flashcards

Eve Final Flashcards

1
Q

Codon bias influenced by

A

-mutational bias and genetic drift
Natural selection
Gene expression
Translational efficiency

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2
Q

Codon bias

A

No random usage of synonymous codons to encode a given amino acid
(Different codons that correspond to the same amino acid appear at different frequencies in the genome)

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3
Q

Codon bias example

A

Mutations from G to A and from C to T are TWICE AS COMMON
(Tends to favor accumulation of codons with A and T bases)

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4
Q

Natural selection as a cause of mutation bias

A

translation of highly expressed genes is most efficient when their codons correspond to transfer RNA that are common; so selection favors these codons

Can also favor codons that produce messages that are less prone to translation errors

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5
Q

Codon bias driven by selection

A

tends to be stronger in genes that are highly expressed and in species with very large population sizes such as free living microbes

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6
Q

Codon bias and population size

A

Species with smaller population sizes drift, overwhelms, whatever selection actions anonymous mutations, and codon bias is very weak or absent
STRONGER IN LARGE POP

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7
Q

Synonymous mutations weakly selected, in LARGER POP…

A

Selection MORE IMPORTANT; Ns»>1
SMALLER POP MORE INFLUENCED BY DRIFT

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8
Q

Male driven evolution

A

male germ line mutation rate is higher than the female germ line mutation rate, the Y chromosome is exposed to a more hostile mutation environment so its going to incur more mutations per generation

Y chromosome evolves very very fast

mutation rate. Is 3 x greater

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9
Q

Nonsynonymous sites are more

A

Clock-like than synonymous sites

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10
Q

dN

A

Non synonymous site

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11
Q

Expected dN/dS for a “typical” gene

A

<1

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12
Q

Expected dN/dS for a gene coding for an unconstrained protein

A

=1

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13
Q

Recurrent directional selection

A

dN/dS >1

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14
Q

What requires dN/dS»1

A

Very conservative test for adaptive evolution, as large numbers of selective fixations

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15
Q

Directional selection and evolution rate

A

Very rapid evolution

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16
Q

What does a smaller dN/dS ratio suggest

A

rates of protein evolution are slowed down by functional constraint

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17
Q

Recurrent directional selection ratio; dN/dS&raquo_space;1

A

Very RARE
have to have a lot of amino acid changes going through under selection
Very frequent adaptive evolution has been acting on it

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18
Q

BIG dN/dS tells…

A

evolving adaptively - potentially its biology is changing

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19
Q

Examples of genes dN/dS >1

A
  1. Vertebrate immune system
  2. Viral coat proteins, other pathogens
  3. Reproduction related genes
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20
Q

More powerful way of detecting adaptive protein divergence (compared to dN/dS) ?

A

McDonald-Kreitman (MK) test

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21
Q

McDonald Kreitman test

A

Under the null hypothesis (neutral evolution), polymorphism and divergence result from genetic drift

Rapidly evolving proteins should also show high levels of protein polymorphism within species

Polymorphic and fixed a.a variants are compared to polymorphic and fixed synonymous variants

Can only detect recurrent adaptive fixations and can only reject if there are sufficient numbers of variants in a gene

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22
Q

A protein under very LOW FUNCTIONAL CONSTRAINT should show a lot of

A

Protein polymorphism

diverging very quickly between species

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23
Q

Gene under STRONG CONSTRAINT

A

should show very little polymorphism at amino acid level and show be evolving very slowly at the protein level between species

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24
Q

polymorphism is

A

positively correlated with recombination

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25
Q

stronger selection/lower recombination

A

larger hitchhiking effects

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26
Q

hitchhiking effect

A

as the copies of the beneficial mutation spreads to higher frequency, the neutral variance linked to them hitchhike to higher frequency
mutation becomes fixed, genetic variation is eliminated in the region nearby

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27
Q

Hitchhiking: Regions further from beneficial mutation

A

Regions of the chromosome further from the beneficial mutation retain variation because recombination joints together chromosomes that carry the beneficial mutation with chromosomes that carry neutral variants

polymorphism remains at regions farther away on the chromosome
this is a telltale sign used by geneticist to find evidence of recent adaptation

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28
Q

background selection

A

rather than the spread of beneficial mutants having this effect on the genome, its the removal of deleterious mutations that have this effect on the genome
Introduce mutation but selection removes that chromosomal region out
(basically reducing effective population size of chromosomes)

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29
Q

rapid spread of beneficial allele to intermediate frequency

A

generates long regions of linkage disequilibrium

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30
Q

evolution of human skin pigmentation

A

indirect result of selection on thermoregulation
- selection for hair loss
- COMPENSATORY selection for skin pigmentation

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31
Q

theory for evolution of lighter skin

A

selection for vitamin D related traits at high latitudes
more pigment protecting against folate depletion at low latitudes carries a cost and is unnecessary at higher latitudes

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32
Q

light skin alleles evolution

A

significant amount of lighter pigmentation seems to have evolved independently in groups of European and Asians

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33
Q

eye color: before or after

A

eye color might have evolved before pigmentation

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34
Q

Species: BSC

A

groups of actually or potentially interbreeding populations, which are reproductively isolated from other such groups
GENE FLOW (reproductive isolation) is focus

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35
Q

cryptic species

A

isolated but with little phenotypic differentiation

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36
Q

problems with BSC

A

asexuals
extinct groups
gene flow between “good” species
breeding experiments impractical

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37
Q

phylogenetic species concept

A

two populations are species if they are different in MORPHOLOGY, DNA

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38
Q

species are often

A

reproductively isolated AND phenotypically diverged

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39
Q

speciation is the

A

evolution of reproductive isolation or the absence of gene flow between two populations is required for them to no longer exchange genes with each other

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40
Q

mechanisms of reproductive isolation

A

pre zygotic
post zygotic

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41
Q

premating barriers

A

features that impede transfer of gametes to members of other species

potential mates do not meet
potential mates meet but do not mate

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42
Q

postmating

A

mating occurs, but zygotes are not formed

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43
Q

postzygotic barriers

A

hybrids are formed but have reduced fitness

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44
Q

extrinsic

A

hybrids have low fitness for ENVIRONMENTAL reasons
not well adapted
cant obtain mates

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45
Q

intrinsic

A

low hybrid fitness is independent of environmental incompatibility

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46
Q

Haldane’s Rule

A

when hybrid breakdown is differentially expressed in the two sexes, the HETEROgametic sex is usually affected more severely

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47
Q

which appears first; sterility or inviability

A

hybrid sterility often appears before hybrid inviability

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48
Q
A
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49
Q

Most common mode of speciation

A

Allopathic speciation

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50
Q

Allopatric speciation

A

Two populations have to become geographically separated to eventually evolve these reproductive isolating mechanisms

Might be able to reproduce if they come back together; depends how diverged they are

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51
Q

Allopatric divergence

A

populations that are more geographically distant from one another have accumulated more genetic differences from each other
More reproductively isolated they are
The more geographically different the population are the less likely they are to meet

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52
Q

Strength of sexual isolation is correlated with

A

Geographic distance

53
Q

Are sister species sympatric

A

Rarely sympatric

54
Q

Is speciation likely to occur on small islands

A

Less likely to occur on small islands

Taxa in which gene flow is high, such as bats have speciated only on very large islands while taxa in which gene flow is very limited such a snails have speciated on small islands’

speciation is more likely to occur on larger islands, and in species with restricted gene flow

55
Q

How is gene flow influenced by isolating mechanisms

A

Play a role in RESTRICTING GENE FLOW
Come back together= Secondary contact

56
Q

Interaction after secondary contact

A

newly formed species can then coexist as distinct populations if they are selfish sufficiently reproductively isolated

57
Q

Dobzhansky Muller Model

A

model posits that genetic incompatibilities between diverging populations, arising from mutations at different loci, can lead to reduced fitness or reproductive isolation in hybrids upon secondary contact. These incompatibilities contribute to the process of speciation by creating barriers to gene flow between populations

58
Q

Dobzhansky-Muller incompatibilities

A

refer to the negative genetic interactions that occur between genes from different populations that have diverged from a common ancestor, leading to reduced fitness or reproductive isolation in hybrids.

arise due to the accumulation of mutations in isolated populations and can contribute to the process of speciation by creating barriers to gene flow.

59
Q

Incompatibilities are effect of what

A

Incidental effect of DIRECTIONAL SELECTION

60
Q

Isolation evolution rate

A

Rate is greater than rate of genetic drift
Males are completely sterile- suggests that isolating mechanisms evolve very, very fast

there hasn’t been enough time for genetic drift to lead to any significant genetic differences between the three species yet they are strongly isolated from each other

61
Q

What do clades that have strong sexual selection show

A

Tend to be more species rich

62
Q

Why might speciation rates be higher in some groups than in others

A

Dispersal and opportunities for allopatry
Variation in mating systems or the intensity of selection

63
Q

Assortative mating

A

Pattern of mating where individuals with similar phenotypic or genotypic traits preferentially mate with each other

64
Q

Reinforcement

A

Isolation is DIRECT result of SELECTION ON TRAITS PROMOTING ASSORTATIVE MATING (non-heterozygote)

65
Q

Factors working against reinforcement

A

Gene flow into hybrid zone
Alleles increasing Assortative mating may have deleterious pleiotropic effects outside hybrid zone
Alleles favoring Assortative mating may not be strongly genetically associated with alleles reducing hybrid fitness

66
Q

Reinforcement applies where

A

There’s at least some gene flow occurring

67
Q

Opposing forces in contact zone

A

Selection and gene flow

68
Q

Gene flow tends to

A

Homogenize the population (reducing genetic differentiation and increasing genetic similarity)

69
Q

What happens if selection wins

A

Reinforcement occurring; lead to completion of speciation event

70
Q

Data required to support reinforcement

A

Hybridization occurs in nature
Hybrids have reduced (but non-zero) fitness
Assortative mating is stronger in contact zone

71
Q

Character displacement

A

A pattern; occur in species pairs that are completely isolated ( not experiencing reinforcement)

72
Q

Sympatric drosophila species pairs tendency to show isolation

A

Strong tendency to show greater isolation at lower genetic distances compared to allopatric species pairs

Evolved much stronger pre mating/pre zygotic isolation

73
Q

Sympatric speciation

A

Prob rare
Unlikely due to no impediment to gene flow
“Magic traits” that influence ecological and reproductive isolation make speciation more likely
Many supposed examples might just be rapid evolution in allopatry with range expansion leading to current sympatric speciation
Allopatric speciation is STRONG NULL hypothesis

74
Q

Sympatric speciation

A

two populations can become different species without ever experiencing allopatry
so their ranges remain overlapping the entire time and somehow they still evolve reproductive isolation from eachother

75
Q

POSSIBLE example of sympatric speciation

A

African cichlid radiatons in lakes Malawi, tanganyika and Victoria

76
Q

Best examples of sympatric speciation

A

Due to culturally driven reproductive isolation

77
Q

Strong sexual selection very likely to

A

Lead to higher rates of speciation than those with NO SEXUAL SELECTION

78
Q

How do changes of ploidy affect speciation

A

changes of ploidy often lead to instantaneous isolation or speciation
for example, if you cross two diploids and you get a tetraploid, then this offspring is now isolated from each of the different diploid species completely

79
Q

Haldane’s Rule explanations

A
  1. Faster X evolution
  2. X-A incompatibilities that are recessive are EXPOSED in the heterogametic sex
80
Q

Why do phylogenetics

A

Basic description of nature
Often interesting from an organismal perspective
Detecting evolutionary patterns

81
Q

Taxa

A

Anything from individuals to “higher” levels such as genera, phyla, etc

82
Q

Characters

A

Anything measured from DNA sequences to highly complex traits

83
Q

Sequence alignment between two or more species

A

A hypothesis about nucleotide homology

84
Q

Phenetics

A

Organisms that are more similar share a more recent common ancestor compared to organisms that are LESS SIMILAR

85
Q

Cladistics

A

Branching patterns can be reconstructed based on shared derived character states, known as synapomorphies

86
Q

Premise

A

Only one true tree of life; shared derived character state can only be explained by virtue of inheritance through a common ancestor

87
Q

“Ancestral” character state can ALSO result from

A

Reversal to the ancestral state in a lineage

88
Q

Outgroup method

A

Assumes state in the outgroup represents ancestral state, which may not be true if there has been considerable evolution in an outgroup

89
Q

Fossil record usage

A

Poor fossil record may cause incorrect inferences
Not applicable on all taxa or characters

90
Q

Developmental biology may be used to

A

Infer ancestral/derived states
Derived states may appear LATER in development than ancestral states

91
Q

Homoplasious characters

A

Can lead to conflicting patterns (due to parallel and convergent evolution)

92
Q

Rapid radiations

A

Rapid speciation events
Internal branches very short
Shared derived character states are just not there to provide the info you need to have confidence about which species are more closely related to which other species

93
Q

What are slow evolving molecules used for

A

Used to resolve deep evolutionary history
Want to have as FEW parallel convergent changes as possible

94
Q

What are rapidly evolving molecules used for

A

Used to resolve recent history
Reconstruct very short time scale evolution

95
Q

Incomplete lineage sorting (ILS) in recently separated populations may result in

A

DISAGREEMENT between gene trees and species trees

Influenced by amount of ancestral variation and the timescale of separation

96
Q

Incomplete lineage sorting

A

occurs when ancestral genetic variation is not sorted into distinct lineages within a population before speciation events

97
Q

Comparative method

A

Search for general patterns of evolution
Correlated evolution of particular traits
Temporal patterns of trait evolution

98
Q

Independent contrasts

A

if we have two traits that we measure in species A and B and they DIFFER in these two traits

those differences must have evolved since that ancestor

the evolution between A and B differ from evolution in C and D

99
Q

a tree and two different traits that are evolving

how strong is case that this trait is correlated with evolution of this other trait

A

LOOK FOR: how many independent times did this trait evolve on the tree
When that trait evolved, did the other one evolve at the same time ??

100
Q

Bipedalism is a

A

Key event in hominid history
- reduced galloping speed and tree-climbing ability
- greatly increased efficiency of walking
- humans unusual in ability to run for long periods of time
- climate cooling and drying in Africa, leading to pressure to forage more widely might have been the agent of selection

101
Q

Bipedal how long ago

A

7 mya

102
Q

Deviation from the expected relationship of brain versus body size

A

Massively deviated

103
Q

Common ancestor with H. Sapiens

A

800,000 years ago

104
Q

Protein overlap and chimps, Neanderthals, and humans

A

Several proteins at which chimp and Neanderthal are identical, and human is DIFFERENT

105
Q

Non-African chromosomes have more…

A

Neanderthal ancestry than African chromosomes

106
Q

Who were the Denisovans

A

Archaic hominin group from Denisova Cave in Siberia
Sister to Neanderthal

107
Q

Diseases and Humans

A

Múltiple diseases have jumped to human in RECENT past (malaria, tuberculosis)
Agriculture led to HIGH POPULATION DENSITIES and close interaction with domestic animals

108
Q

Origin of alleles contributing to RECENT HUMAN ADAPTATION

A

Some alleles have their origin in introversion event from ANCIENT hominins (ESPA1 and high altitude adaptation)
Pigmentation alleles and alleles associated with w diet (Inuits)

109
Q

Human health effects due to mismatch between our ancestral biology and our recent environment?

A

Like w wisdom teeth
- skulls of pre-industrial farmers exhibit lots of dental problems
- skulls of ANCIENT HUNTER GATHERERS have FEW dental problems
SO COMMON?
- were chewing a lot more
-jaw bones aren’t as big now

110
Q

Possible effects of agriculture and the rise of cities

A

HIGH POPULATION DENSITIES led to infectious disease such as measles, mumps, influenza, smallpox
Some infectious diseases jumped from domesticated animals to humans

111
Q

Do modern lifestyles increase BREAST CANCER risk?

A

Women are not always pregnant or lactating now so we have MORE menstrual cycles which means more cell division

112
Q

Hygiene hypothesis

A

Cleaner environment leads to lower rates of childhood infection
Sometimes hace adult immune systems that OVERREACT

113
Q

Old friends hypothesis

A

In the absence of ancestral pathogens, our immune systems don’t even develop properly
Also lead to OVERREACTION

114
Q

Genes involved in oncogenisis

A

About 1% of genes in the genome

115
Q

Which cells produce cancer

A

Mutations in stem cells

116
Q

Cancer is produced by competition among

A

Clonal lineages generated by somatic mutations

117
Q

Renal cell carcinoma; evolutionary divergence poses PROBLEMS for THERAPY

A

Primary tumor on kidney sent metastases into the lung and chest wall
Therapies sent to treat primary would miss variation in the mestastes

118
Q

Gene duplications often result in

A

Unequal crossing over

119
Q

Human phenotypes associated with copy number variants

A

Parkinson’s, autism, color blindness

120
Q

Orthologous

A

Genes that diverged from common ancestral gene by phylogenetic splitting

121
Q

Paralogous

A

Loci in the same species or different species that descended from different duplicate genes in ancestral species
A1 and b2

122
Q

Potential case of adaptive variation related to gene dosage in humans

A

Amylase

123
Q

Subfunctionalization

A

A gene performs two functions at once, duplication and divergence occurs, and now on copy performs one function and one performs the other function

124
Q

Neofunctionalization

A

One gene performs one function, duplication and divergence occurs, one gene KEEPS performing ancestral function, and other gene is free to get NEW FUNCTION

125
Q

Gene duplications can give us…

A

Can lead to novel traits!

126
Q

Approach for detecting HGT

A

Phylogenetic discordance

127
Q

Amount of genes in unicellular organisms

A

Seem to have the least amount of

128
Q

New genes

A

One could arise in non genic DNA and it becomes transcribed and favored somehow

Maybe spread under directional selection

EVE2 (3 decks)

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