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Evolution > Exam 2 > Flashcards

Exam 2 Flashcards

1
Q

phenotypic plasticity

A

single genotype can lead to multiple different phenotypes depending on the environment

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2
Q

developmental plasticity

A

fixed, often irreversible, happens during early development

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3
Q

acute plasticity

A

short term, reversible

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4
Q

genotype norm of reaction

A

a curve that relates the contribution of environmental variation to observed phenotypic variation

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5
Q

three types of phenotypic distribution

A

continuous variation, polymorphism/polyphenism, canalization

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6
Q

polymorphism/polyphenism

A

discontinuous genetic variation resulting in the occurrence of several different forms or types of individuals among the members of a single species. opposite of genetic fixation

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7
Q

canalization

A

fixed trait, same phenotype regardless of environmental variation

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8
Q

four major types of phenotypic plasticity

A

shifts in phenology, acclimation/acclimatization, polyphenism, transgenerational plasticity

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9
Q

phenology

A

timing of life history events, such as flowering time or clutch laying

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10
Q

acclimation

A

physical adjustment to a controlled change in one specific environmental variable, occurs in a lab

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11
Q

acclimatization

A

physical adjustment to changes in multiple environmental variables in nature

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12
Q

transgenerational plasticity

A

initiated in past generations, but has consequences in current and future generations, such as maternal effects and epigenetic inheritance. Often genetic, but driven by environmental effects

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13
Q

maternal effects

A

phenotype of the offspring is influenced by the environment experienced by the mother (and thus her phenotype)

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14
Q

proximate drivers of phenotypic plasticity

A

gene expression and allelic sensitivity

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15
Q

gene expression (relative to phenotypic plasticity)

A

upregulation or downregulation by transcription factors of specific genes in response to environmental stimuli, often through the action of regulatory genes

can influence allelic sensitivity, and can be heritable

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16
Q

allelic sensitivity

A

the downstream product (protein or messenger RNA) of a particular allele responds directly to environmental stimuli. For example: in response to an environmental change, a protein changes its binding site to no longer allow binding

Not as important as gene expression. Allelic sensitivity is rare because homeostasis is good.

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17
Q

why aren’t all traits plastic?

A

plasticity has costs

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18
Q

3 costs of phenotypic plasticity

A

It costs energy to synthesize new proteins, to break down those proteins when they are not needed, and to maintain the cellular machinery that detects environmental stimuli.

Trade-offs whereby plasticity in a particular trait increases survival but reduces fecundity, or vice versa

The plastic response might “misfire” in response to the wrong environmental cue.

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19
Q

under what conditions should developmental plasticity be expected?

A

non-mobile organisms, environmental variation that is high, predictable, and occurs within the lifespan of the organism

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20
Q

under what conditions should acute plasticity be expected?

A

unpredictable changes and stable environments

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21
Q

climatic variability hypothesis

A

thermal tolerance (climate niche) correlates with latitude

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22
Q

is behavior considered plasticity?

A

we don’t know

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23
Q

behavioral drive

A

Behavioral flexibility leads to the exploitation of new niches and faster evolutionary diversification

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24
Q

behavioral inertia

A

Behavioral flexibility causes individuals to track their niche and “hide” from selection, reducing evolutionary diversification. Example: behavioral thermoregulation - changing micro-environment (dark rocks, shade, etc.)

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25
Q

how to determine if behavioral inertia?

A

track ancestral niche

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26
Q

three ways plasticity enhances or reduces evolution?

A
  1. Plasticity can reduce rates of genetic change through a process analogous to behavioral inertia
  2. Plasticity can (indirectly) enhance rates of genetic change by reducing mortality and increasing population sizes—leading to a greater chance for beneficial mutations to arise
  3. Plasticity can enhance genetic change by exposing cryptic genetic variation that is then acted on by selection via the processes of genetic accommodation and genetic assimilation
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27
Q

genetic accommodation

A

Any adaptive change in the environmental
regulation of a phenotype, can be positive or negative

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28
Q

genetic assimilation

A

The complete loss of plasticity through genetic canalization, is a subtype of genetic accommodation

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29
Q

An organism evolves extreme behavioral flexibility to deal with a variable and unpredictable environment. Is that organism now more or less likely to evolve other forms of plasticity such as high acclimation capacity?

A

less likely, because it would be very costly for an organism to have both extreme behavioral flexibility AND high acclimation capacity, especially considering they really only need one or the other. Behavioral flexibility would allow the organism to avoid the stresses of the environmental changes (example, by relocating to a different microclimate, or exploiting a new niche entirely) while high acclimation capacity would allow the organism to adapt to the environmental changes without avoiding it. It cannot use both strategies at the same time, so it would not be worth the cost of maintaining both.

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30
Q

Can genetic assimilation occur with standing genetic variation only or does the process require new mutations?

A

genetic assimilation can occur with standing genetic variation, the trait already exists, even though it arises by plasticity in response to the environment. Assimilation just fixes it, so it is no longer plastic.

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31
Q

Under what conditions would you expect plasticity to be non-adaptive?

A

more likely to be non-adaptive in novel environmental stress, such as environmental conditions that are outside of the range of environments they have experienced before and impose a particular challenge to the organism’s homeostasis. Anthropogenic contaminants, such as herbicides, are novel stressors that are not present in the evolutionary history of most species.

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32
Q

cryptic genetic variation

A

build up of genes expressed in new environment, giving rise to novel phenotypes, which selection can then act on

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33
Q

how might plastic responses to environmental variation influence the process of natural selection?

A

reduce: genotype can “hide” under plastic phenotypes
enhance: indirectly, more individuals to act on
enhance: cryptic genetic variation arising in new environments leads to new phenotypes
enhance: genetic assimilation/canalization

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34
Q

role of plasticity in macroevolution?

A

genetic assimilation leads to reproductive isolation leads to speciation or adaptive radiation, especially if canalized trait has anything to do with mating choice, habitat choice, or reproduction

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35
Q

how might plasticity influence genetic variation, genetic architecture, and molecular evolution?

A

genetic variation: plasticity can both decrease (hide genes) and increase genetic variation (cryptic genetic variation)

genetic architecture: plasticity can influence the expression of the gene itself or the regulators of the gene

molecular evolution: when loci don’t affect the trait until its in a novel environment, then it affects the phenotype, leading to a relaxation of selection, allowing mutations to accumulate, can end up with a surprise product

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36
Q

*do we need a theory of forms?

A

?

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37
Q

describe the guppy experiment

A

field experiment to manipulate agents of selection, guppies with predators in lower elevation, guppies without predators in higher elevation, showed phenotypic differences such as color, fin size, behavior (shyness, schooling), life history (growth rate, clutch size). Reciprocal transplants were done and trait evolution was tracked

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38
Q

describe anole experiments

A

introduced brown anoles on islands, and curly-tailed lizards to half of the islands, which influenced their behavior (more shy) and eventually limb length (shorter)

anoles on islands with different vegetation in Panama Canal, limb length in offspring evolved in one generation (some plasticity, but mostly evolutionary change), showing rapid evolution - also an example of behavioral drive

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39
Q

scientist who explored link between genotype and environment, experimented on field mice

A

Hopi Hoekstra

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40
Q

if evolution can be this rapid, what are the implications?

A

speciation can occur more quickly, macro and micro-evolution should not be considered so separate, climate change and conservation (evolution is relevant to conservation)

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41
Q

eco-evolutionary dynamics

A

how ecology and evolution influence each other, and are tightly linked on time scales, heritable variation among individuals in a population can be as or more important than traditional ecological drivers of population dynamics (e.g. predation, competition, climate)

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42
Q

dynamics

A

feedback between levels (genes, phenotypes, populations, communities, ecosystems)

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43
Q

evolutionary rescue

A

occurs when occurs when a population recovers from environmental change due to increases in the frequencies of advantageous alleles (independent of gene flow). AKA The recovery and persistence of a population through natural selection acting on heritable variation

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44
Q

contemporary evolution

A

the study of evolution on shorter timescales than originally thought, often dealing with research in climate change, habitat loss, etc.

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45
Q

how has contemporary evolution influenced invasion biology?

A

evidence is mounting that rapid evolution may be a key to the success of invasive species, even when extreme bottlenecks occur

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46
Q

how has contemporary evolution influenced ecosystem ecology?

A

recent work has shown that evolution can affect nutrient and energy flow through ecosystems, among other processes

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47
Q

how can we reconcile the observation that evolution can be extremely rapid with the observation of stasis in the fossil record?

A

evolution does not necessarily cause clear morphological change, can also be cryptic evolution, sampling issue/snapshots not necessarily realistic, could be multiple reasons

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48
Q

does the persistence and stability of ecological communities depend on evolution? Or is evolution trivial?

A

negative feedback of evolution creates stability/persistence

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49
Q

if evolution can be extremely rapid, why do we find large amounts of genetic variation in wild populations?

A

the magnitude and direction of selection is not consistent, gene flow, mutations

50
Q

does contemporary evolution represent a paradigm shift in biology?

A

these ideas have been around, but not applied. however, it does change the way we think about the relationship between ecology and evolution

51
Q

what is the relationship between contemporary evolution and the maintenance or erosion of genetic variation within populations?

A

increase: hybridization rescuing genetic variation, increase: temporal and spatial fluctuation changing selection (metapopulations), increase: old/ancient alleles re-emerging after being neutral when environment conditions reoccur and allowing selection to act on it, decrease: selection reduces variation

52
Q

do you think it would be useful to consider contemporary evolution or eco-eco dynamics in your own research?

A

yes - bees are heavily affected by habitat loss, diseases, habitat loss, and more, which are all things that could drive rapid evolution. It will be important to consider how these populations may quickly adapt. It’s important to consider how these evolutionary trends may then influence the community structures.

53
Q

differences between micro and macroevolution

A

timescale and process vs pattern

54
Q

microevolution

A

Shorter-term; changing allele frequencies
within species or populations

55
Q

macroevolution

A

Longer-term; evolution above the level of
species—evolution of clades

56
Q

punctuated equilibrium

A

Eldridge and Gould’s definition of macroevolution: long periods of stasis punctuated by rapid cladogenesis, or the evolution of new clades (what we actually see occurring). Helps explain why we see discontinuities in the fossil record—big gaps between the “morphological space”occupied by clades that have existed at different times over Earth’s history

57
Q

phyletic gradualism

A

idea that evolutionary change proceeds smoothly at similar rates over time

58
Q

anagenesis

A

evolutionary change within clades

59
Q

according to Darwin, what could explain the gaps between extant clades?

A

driven by interspecific competition, the species on the edges persist (the most different do the best) and keep diverging. Most closely related species compete with each other, so there is most cost for similarity. Drift and random extinction events can also contribute.

60
Q

speciation

A

study of how reproductive isolation evolves, not really when and how new species form

61
Q

sympatric speciation

A

the generation of two or more species from a common ancestor, in the absence of geographic isolation between descendants. Controversial and rarely demonstrated to occur in nature (although it may be more common in plants)

62
Q

polyploidy

A

heritable condition of possessing more than two complete sets of chromosomes, can cause instant reproductive isolation

63
Q

mechanisms of sympatric speciation

A

polyploidy, disruptive selection (intermediate forms have low fitness) - need strong selection, any gene flow counteracts

64
Q

allopatric speciation

A

the generation of two or more species from a common ancestor, facilitated by complete geographic isolation between descendants, and often aided by reinforcement upon secondary contact

65
Q

secondary contact reinforcement

A

hybrids are low-fitness, mating traits coevolve to discourage interbreeding - example: birds and frogs with divergent calling traits

66
Q

character displacement

A

interspecific competition leads to phenotypes farther apart being favored decrease competition

67
Q

speciation by hybridization

A

hybrids have higher fitness (and are therefore better competitors) than parental populations, leading to the extinction of the parents. Here, two species lead to one, but a new species has been created nonetheless

68
Q

incipient species

A

diverged species

69
Q

adaptive radiation

A

speciation occurring much faster than is typical in the fossil record

70
Q

example of sympatric speciation

A

African cichlids

71
Q

conditions that favor adaptive radiation

A
  1. Sudden opening of a new suite of ecological niches.
  2. The evolution of novel traits that permit the exploitation of previously existing, but empty, niches.
  3. The presence of strong selection leading to phenotypic and genetic divergence across niches
72
Q

ecological speciation

A

divergent selection causes the accumulation of pre- and post-zygotic barriers to successful mating between closely related populations or species

73
Q

driver of adaptive radiation

A

ecological speciation

74
Q

does genetic drift play an important role in shaping macroevolutionary patterns?

A

genetic drift doesn’t really result in dramatic changes on a macroevolutionary scale. Selection plays a more dominant role, leading to genetic variation.

75
Q

anole lizards and ecological speciation

A

geographically isolated, drift causes divergence even without selection, pre-zygotic and post-zygotic barriers prevent future offspring

76
Q

is the concept of speciation relevant to asexually reproducing (haploid) organisms? Do “speciation” processes, if they occur in haploids, work in the same way as they do with sexually-reproducing organisms?

A

no real answer, but important to consider different perspectives, like microbes. biological species concept not relevant to asexually reproducing organisms like microbes

77
Q

does most speciation occur within adaptive radiations? In other words,
do we need adaptive radiation to get cladogenesis?

A

don’t need adaptive radiation for cladogenesis, however, adaptive radiation is probably really important. cladogenesis = new branch, species level and up. adaptive radiation requires a higher-than-background level of speciation

78
Q

what is the role of sexual selection in speciation?

A

sexual selection can cause reproductive isolation by mate preference for certain secondary sexual characteristics, which leads to reproductive incompatibility aka prezygotic isolation

79
Q

what 5 forces drive evolution of the genome?

A

mutation, recombination, genetic drift, selection, intragenomic conflict (gene-level selection)

80
Q

5 types of mutations

A

point mutations (single nucleotide polymorphisms), duplications, insertions, deletions, inversions

81
Q

mutation transitions vs transversions

A

transitions: A-G or C-T, tranversions: A-C or G-T

82
Q

are transitions or transversions more common?

A

transitions

83
Q

recombination

A

genetic exchange between chromosomes or genomes, can occur both within and between species

84
Q

genetic hitchhiking

A

increase in frequency of an allele due to it’s physical linkage with a different allele that is under selection

85
Q

how does recombination influence genomic evolution?

A

reduces linkage, counteracts genetic hitchhiking

86
Q

intragenomic conflict (gene-level selection)

A

gene level selection, sometimes (but not always) at expense of organism-level fitness—selfish genetic elements (e.g.
transposons)

87
Q

introgression

A

the transfer of genetic material from one species into the gene pool of another by the repeated backcrossing of an interspecific hybrid with one of its parent species

88
Q

homologous genes

A

genes shared from common ancestor, but can have differences due to divergence

89
Q

substitution rates

A

rate of point mutations that occur over time - example: number of differences in homologous sequences between clades, are variable across the genome

90
Q

why do substitution rates vary across the genome?

A

some sections of genes are under selection to remain the same because they are crucial

91
Q

C-value Paradox

A

surprisingly low correspondence between the “complexity” of an organism and its genome size - for example, trees, salamanders, and specific protists have large genomes, while viruses have small genomes because they can co-opt the genomes of other organisms

92
Q

c-value

A

amount of DNA contained within haploid nucleus (in picograms)

93
Q

what type of genes make up the majority of the genome in many species?

A

non-coding, repetitive genetic elements

94
Q

why are there non-coding segments of genes?

A

introns from transposable elements, vestigial sections

95
Q

transposable elements (transposons)

A

a type of repetitive genetic element that self-replicates and can proliferate in the genome and may have no (or little) effect on organism-level fitness

96
Q

gene duplication

A

A gene gets copied and inserted into another place in the genome, eventually mutates to serve a new or modified function (or lose function completely to become a pseudogene). Can happen by
several mechanisms, including retrotransposition

97
Q

retrotransposition

A

mRNA is translated back to DNA and inserted back into the genome

98
Q

hemoglobin origin

A

gene duplication, leading to redundant sequence becoming mutated/modified until it had a different function

99
Q

why do redundant genes accumulate mutations?

A

losing function in redundant genes is not selected against

100
Q

chimeric genes

A

duplication, deletion, or incomplete retrotransposition combines two different coding sequences into a novel sequence

101
Q

de novo gene birth

A

mutation(s) in non-coding, presumably “junk” DNA give rise to a new, functioning gene.

102
Q

selectionist hypotheses

A

differences in sequence variation between clades is primarily due to selection acting to increase the frequency of beneficial mutations (positive selection) and
decrease the frequency of deleterious mutations (purifying, or negative, selection). Loss or gain of neutral mutations is seen as due primarily to their physical linkage with loci under positive or
purifying selection

103
Q

positive selection

A

selection acting to increase the frequency of beneficial mutations

104
Q

purifying/negative selection

A

selection acting to decrease the frequency of deleterious mutations

105
Q

neutralist hypotheses

A

differences in sequence variation between clades is primarily due to mutations that do not strongly affect organism-level fitness (such as genetic drift)

106
Q

molecular clock

A

use of mutation rate to determine the timing of divergence between clades

107
Q

scientist who proposed neutral theory

A

Motoo Kimura, 1968

108
Q

neutral theory

A

most sequence variation within and among clades is driven by genetic drift acting on selectively neutral mutations, most mutations are deleterious and therefore are rapidly removed by selection, most non-deleterious mutations are neutral rather that beneficial, and will therefore tend to drift to fixation in populations

109
Q

Substitution rate in regions of the genome with little functional constraint?

A

should be higher. for example, substitution rate is much higher in regions
that are non-coding , regions that produce proteins with unimportant or minor biochemical functions, or in the third position of a codon (which are redundant and do not result in amino acid substitution)

110
Q

paradox of variation

A

levels of genetic diversity are only weakly correlated with population size, and is seen as strong evidence against the neutral theory (more individuals should lead to more opportunities for neutral mutations)

111
Q

relatively high levels of genetic variation in
natural populations was (and still is) seen as evidence in support of or against the neutral theory?

A

support

112
Q

how can we know whether variation in a gene’s sequence has been driven by selection or drift?

A

dN/dS ratio

113
Q

dN/dS ratio

A

the ratio of non-synonymous to synonymous mutations in protein coding sequences.
If dN/dS > 1, positive selection (non synonymous actually affect protein).
If dN/dS < 1, negative (purifying) selection (non-synon are selected against).
If dN/dS = 1, neutral evolution (not affecting fitness).

114
Q

which of the following cases do you think you would find for most protein-coding regions: positive selection, negative/purifying selection, or neutral evolution?

A

purifying selection - impact function and fitness

115
Q

which of the following cases do you think you would find for most redundant regions: positive selection, negative/purifying selection, or neutral evolution?

A

positive selection

116
Q

Would we expect natural selection and sexual selection to leave different signatures in the genome?

A

if you only see signs (such as non-synonymous positive selection) in the sex chromosomes, this is a signature of sexual selection.

117
Q

Would there be a selective benefit for the evolution of increased chromosome number?

A

more opportunity for de novo genes and thus novel traits, and redundancy (which can act as a backup in case one of the genes gets messed up)

118
Q

Does the neutral theory of molecular evolution suggest that phenotypic variation between species is mostly neutral as well?

A

no. neutral theory is about the whole genome, not just coding sequences. most of the genome is not coding, but rather introns or redundant. a lot of changes are in these sequences, and thus are neutral, and don’t affect the phenotype. a lot of traits are also plastic and controlled by multiple genes. ultimately, phenotypic variation is driven by natural selection.

119
Q

Is the neutral theory of molecular evolution dead? why or why not?

A

*not dead, but difficult to quantify how much variation is driven by selection or neutral processes. The neutral theory does not claim that selection doesn’t exist, though, just that variation is driven by neutral mutations that rise to fixation via genetic drift, as the majority of the genome is non-coding. However, Kern and Hahn have fair points about linkage and selection affecting nearby loci, which means selection can drive variation in non-coding sequences. If neutral theory was fully accurate, recombination rates and polymorphism should not be correlated, because recombination doesn’t affect neutral mutations.

120
Q

compare natural selection and sexual selection

A

sexual selection acts on fecundity/reproductive success, while natural selection acts on survival. fecundity may occasionally counteract survival (example: birds of paradise). while it can result in different patterns, the fundamental process is the same.

Evolution (2 decks)

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