Final Exam Flashcards
(180 cards)
1
Q
neutralist-selectionist controversy
A
a debate about the relative importance of drift and selection in molecular evolution
2
Q
Is sequence evolution primarily driven by selection or drift?
A
there is no right answer to this question
3
Q
neutral theory
A
neutral mutations that fix by drift vastly outnumber beneficial mutations that rise to fixation by natural selection
formulated in 1966
4
Q
neutral theory (observations and inference)
A
the vast majority of base substitutions are neutral
observation: comparisons across species show that amino acid substitutions happen very frequently and very regularly
inference: the rate of molecular evolution is inconsistent with selection being the primary driving force
–> sub. due to selection should happen in bursts
5
Q
would deleterious mutations contribute to evolutionary divergence?
A
No because selection would remove the deleterious mutations
beneficial mutations fix by selection!
6
Q
negative (purifying) selection
A
selection against deleterious mutations
6
Q
nearly neutral theory
A
drift is stronger in small populations
the effective population size (Ne) influences the fraction of mutations that evolve neutrally (fixed or lost by drift)
–> therefore, as Ne decreases, more and more mutations will behave neutrally
7
Q
positive selection
A
selection favoring beneficial mutations
8
Q
Why do neutral substitutions accumulate more rapidly than non-neutral substitutions?
A
Most non-neutral mutations are under negative selection
9
Q
Which is more likely to be neutral: synonymous or nonsynonymous sub. ?
A
synonymous –> accumulate faster than non-synonymous substitutions
genes with critical functions have low rates of nonsynonymous substitutions
ex: histones are critical for DNA replication, so negative selection will be super high to prevent deleterious alleles from forming
10
Q
because most non-neutral mutations are under negative selection, does that mean positive selection doesn’t come into play here?
A
No! In some species, a large fraction of amino acid substitutions are driven by positive selection
11
Q
tests for natural selection at the molecular level
A
dN/dS, McDonald-Kreitman test, selective sweep
12
Q
test for natural selection: sequence divergence between species
A
dN/dS
13
Q
test for natural selection: diversity and divergence
A
McDonald-Kreitman
14
Q
test for natural selection: sequence diversity (polymorphism) within species
A
selective sweep
15
Q
dN/dS
A
the rate of nonsynonymous substitutions divided by the rate of synonymous substitutions
16
Q
Which value indicates that a gene is evolving under positive selection
A
dN/dS > 1 (positive selection)
dN/dS < 1 (negative selection)
dN/dS = 1 (neutral)
limitation: it is rare for a gene to be under such strong positive selection that dN/dS > 1 –> this test is very conservative for selection
17
Q
McDonald-Kreitman (MK) test
A
compare dN/dS to the ratio of non-synonymous to synonymous polymorphisms within species
–> If a site is evolving neutrally, the two ratios will be the same (dN/dS = pN/pS)
–> If a site is under positive selection, there will be more nonsynonymous substitutions than nonsynonymous polymorphisms (dN/dS > pN/pS)
18
Q
selective sweep
A
the reduction in genetic variation at sites linked to a beneficial (adaptive) mutation as a result of selection
19
Q
example of lactose tolerance
A
Lactase enzyme is expressed in young mammals, but usually not in adults
Each horizontal line represents the length of the run of homozygosity in one individual
In individuals with the new lactase allele, there is a region of reduced genetic diversity centered on the lactase locus. This means that the data is consistent with a selective sweep favoring the new lactose tolerance allele
19
Q
What types of loci tend to be under strong positive selection?
A
Loci involved in arms race
- between pathogens and their hosts
- in reproductive conflict (sperm competition and egg-sperm interactions)
Loci involved in adaptation to a new environment
- recently duplicated genes that have attained new functions
- loci that are adaptive after a major environmental change
20
Q
Does adaptation occur from new mutations or standing genetic variation?
A
Both!
New mutation: environment changes first, then adaptive mutation arises
standing genetic variation: adaptive mutation arises first, then environment changes
21
Q
example of melanic allele from the melanic peppered moths
A
the melanic allele arose around the time of the industrial revolution
–> adaptation from new mutation
21
Q
example of light fur allele from mice
A
light fur allele arose after the formation of the Nebraska Sand Hills
–> adaptation from new mutation
22
New mutations or standing genetic variation: Test
If multiple lineages convergently evolved a trait, test whether the mutation arose in a common ancestor or independently in each lineage
Independently in each lineage: new mutation
In the common ancestor: standing genetic variation
23
New mutations or standing genetic variation: Adaptation from new mutation
If multiple lineages convergently evolved a trait, test whether the mutation arose in a common ancestor or independently in each lineage
Same gene, but different amino acid substitutions in each species
--> adaptation from new mutation
24
Adaptation from standing genetic variation
If multiple lineages convergently evolved a trait, test whether the mutation arose in a common ancestor or independently in each lineage
Same amino acid substitutions at the Eda locus in all freshwater populations
--> adaptation from standing genetic variation
25
Phylogenetic tree (phylogeny)
A visual representation of the evolutionary history of a set of species
represents a hypothesis about the history of descent with modification from a common ancestor that produced a set of species
tips: extant species
nodes: branch points; common ancestors
phylogenies are bifurcating
26
Polytomy
Unresolved evolutionary relationship
27
Monophyletic group
An ancestor and all of its descendants
28
How to read a phylogeny (IMPORTANT)
lineages that share MORE RECENT COMMON ANCESTORS are considered more closely related
--> nodes can rotate, and it doesn't impact the inferences you draw from a phylogeny
what's important is the sequence of branching events
29
do the example with the cats from the slides!
good job :D
30
How do we infer phylogenetic relationships?
Shared derived characters: Traits shared by an ancestor and all of its descendants
--> We used to use physical traits, but now most phylogenies are built with genomic data
31
Most phylogenies today are built with genomic data
Each nucleotide (or amino acid) is a trait
there are only four possible character states, so convergence (independent evolution of the same base in different lineages) is common
--> Solution: use MANY MANY base pairs (many genes or the entire genome)
32
Rapidly and slowly evolving genes
Rapidly evolving genes are used to resolve relationships among closely related lineages
Slowly evolving genes are used to resolve relationships among distantly related lineages
33
What is a species?
Species consist of interbreeding populations that evolve independently of other populations
"I was much struck how entirely vague and arbitrary is the distinction between species and varieties" - Darwin
34
Biological species concept
species are groups of actually or potentially interbreeding populations that are reproductively isolated from other groups
--> Widely used! captures reproductive isolation
35
limitations of biological species concept
can be difficult to apply. ex: if nearby populations do not actually come in contact, are they reproductively isolated? cannot be applied to extinct lineages. irrelevant in asexuals
36
morphospecies concept
species are defined based on morphological characteristics
strength: applicable to extinct lineages
37
how do species form?
speciation
ex: darwin's finches in the galapagos islands
ex: cichlid fish in african rift lakes
ex: anolis lizards in the Caribbean
37
phylogenetic species concept
the smallest monophyletic group of common ancestry; a group that is diagnosably distinct from others, with a pattern of ancestry and descent
strength: applicable to extinct lineages; asexuals
38
Speciation
a three-stage process
1) populations become reproductively isolated
2) evolution occurs independently in the two new populations. different alleles and traits fix in each population (experiencing selection and drift independently)
3) eventually, so many differences accumulate that when the two groups come back into secondary contact, they can no longer produce viable offspring (function as 2 separate species)
39
allopatric speciation
speciation when populations become geographically isolated
there is no gene flow connecting the populations, so they are reproductively isolated
selection and drift act on them independently
big geographic barriers --> grand canyon and northside/southside squirrel
small geographic barriers--> benthic (swim at the bottom of lake) and limnetic stickleback (swim near the top of lake)
39
allopatric speciation vs. sympatric speciation
allopatric speciation: populations are geographically separated (ex: ocean, canyon)
sympatric speciation: populations are not geographically separated
40
Would you expect allopatric or sympatric speciation to be more common?
Allopatric speciation is more common --> the 2 species literally cannot interact with each other
41
allopatric speciation with snapping shrimp and the isthmus of panama
hypothesis: the rise of the Panama Isthmus drove speciation between Pacific and Caribbean populations of snapping shrimp
in each species pair, one sister species is found on either side of the Panama Isthmus
allopatric speciation: the land bridge separated populations that then evolved into separate species
42
Testing allopatric speciation
Populations that are separated for a longer period of time should be more reproductively isolated (therefore becoming more genetically distinct)
two populations are reproductively isolated if they do not mate or produce viable, fertile offspring
43
Allopatric speciation: Axes of graph + look at graph of drosophila species in slides
x-axis: genetic distance (D) --> proxy for how long two species have been separated
y-axis: reproductive isolation
44
Key takeaways: Ring species
- Adjacent populations can interbreed
- Populations at opposite ends of the chain cannot interbreed (allopatrically separated by mountain)
- Speciation is a process — it isn't binary or non-binary
- Continuum of relatedness (there can be variation among species and they can still be related)
45
Reversal of speciation (allopatric speciation)
If the barrier is removed early enough in the speciation process, speciation will reverse
--> the two incipient species will collapse back to a single species
46
example of reversal speciation
lake pollution reverses speciation!
--> benthic (bottm of the lake) and limnetic (open water) stickleback species in Enos Lake on Vancouver Island
agricultural pollution in the 1980s erased ecological differences between the top and bottom of the lake --> by 2000, benthic and limnetic sticklebacks were indistinguishable
47
sympatric speciation
speciation in the same geographic area, without a physical barrier to gene flow
sympatric speciation requires assortative mating to generate reproductive isolation
48
assortative mating
a tendency to mate with other individuals with the same genotype or phenotype
49
sympatric speciation in apple maggot flies
apple maggot flies lay their eggs in both apples and hawthorne flies within the same area, but apples and hawthornes are around 3-4 weeks in different months of the year
50
Mechanisms of reproductive isolation
prezygotic (before fertilization) and postzygotic (after fertilization)
prezygotic: ecological, temporal, behavioral, mechanical (two species cannot mate --> chihuahua + Great Dane)
postzygotic: hybrid inviability (offpsring cannot survive)
hybrid sterility (offspring survive but they are sterile)
ex: zedonk (donkeys and zebras)
51
temporal isolation (prezygotic barrier)
different species breed at different times during the year, season, or day (more likely to mate with its own breed)
ex: frog example in the slides
52
behavioral isolation (prezygotic barrier)
mating displays and species-specific signals are very important barriers between closely related species
53
Cost of mating with the wrong species
mating with the wrong species is a costly mistake
--> during secondary contact, individuals from recently species can interbreed (hybridize)
- if hybrids have low fitness, individuals that avoid mating with the wrong species will have the highest fitness
reinforcement: natural selection favors the evolution of prezygotic barriers (mechanisms that prevent hybridization)
54
Reinforcement
Natural selection favors the evolution of prezygotic barriers (mechanisms that prevent hybridization)
55
Would you expect to find stronger prezygotic barriers in allopatric or sympatric populations?
Prezygotic barriers should be stronger in zones of sympatry than in allopatry. This is because natural selection has favored the evolution of mechanisms that prevent mating with the wrong species
--> allopatric species do not have to worry about mating with the wrong species because the wrong species won't be there!
56
D. yakuba and D. santomea example
D. yakuba females from the sympatric area laid fewer eggs after mating with a D. santomea male than did females from allopatric areas
--> consistent with the hypothesis that prezygotic barriers have evolved in this species
57
Which evolutionary forces can cause speciation?
Natural selection, genetic drift, mutation, and gene flow
--> natural selection is thought to be the most important
57
Genetic distance + allopatric/sympatric speciation
In allopatry, prezygotic isolation increases with genetic distance
--> as genes differ more and more, prezygotic mechanisms will become more pronounced
In sympatric populations, even very close relatives have very high prezygotic isolation
58
Ecological speciation (natural selection)
adaptation to different environments can lead to physical, behavioral, or temporal isolation
selection eliminates hybrid offspring because they are poorly adapted to both parental environments
natural selection favors the evolution of prezygotic barriers, which drives the speciation process to completion (reinforcement)
59
Reinforcement
Natural selection favors the evolution of prezygotic barriers, which drives the speciation process to completion
60
Ecological speciation in the lab
flies adapted to different diets quickly evolved reproductive isolation
speciation was driven by NATURAL SELECTION; flies in different vials of the same food could still mate just fine
reproduction is more affected by mating flies across food sources as opposed to mating flies from different populations
61
mutation affecting speciation
polyploidization (whole-genome duplication) can cause instant sympatric speciation
--> matings between tetraploids (4N) and diploids (2N) are sterile because they produce triploid (3N) offspring, and the chromosomes of triploids fail to segregate properly at meiosis
62
genetic drift affecting speciation
two loci, A and B interact epistatically
different alleles fix by chance at each locus in two diverging populations
hybrids are inviable because they inherit an incompatible allelic combination (a and b)
63
gene flow affecting speciation
Hybridization (gene flow) can create new species
--> wheat and sunflowers are hybrids
64
regulatory genes
Regulatory genes are those genes that code for proteins or factors that control the expression of structural genes
64
evolutionary developmental biology (evo-devo)
developmental biology is the study of the processes by which can organism grows from zygote to reproductive adult
--> evo-devo is the study of how changes in developmental trajectories contribute to evolution
Genotype ---> (development + environment) ---> phenotype
65
hypothesis for evo-devo: regulatory genes
relatively modest changes in regulatory genes could have profound impacts on development, and hence evolution
66
regulatory evolution
a change in where or when a gene is expressed
influences the timing of developmental events and how different tissues develop
regulatory evolution is central to evo-devo
67
allometry
different parts /organs / tissues grow at different rates
68
heterochrony
change in the rate or timing of developmental processes
--> falls under "when" a gene is expressed
69
neoteny (paedomorphosis)
retention of juvenile features in adulthood
although some juveniles and adults differ phenotypically, sometimes dramatically
ex: axolotls are salamanders that retain many juvenile traits, including gills, as adults
ex: adult humans retain many features of juvenile primates
--> compared to other primates, human brains have an extended period of high neuronal plasticity
70
Homeotic gene
gene that induces the formation of particular structures in animals and plants
--> provides positional information in multicellular embryos
--> homeotic genes are transcription factors: they regulate the expression of other genes
71
hox genes
hox genes are important for body patterning in invertebrates and verterbrates
changing where hox genes are expressed can cause huge morphological changes
--> they are master regulators: they determine what body parts go where
--> when hox genes are mutated, appendages appear in the wrong places
homeotic genes in plants: control floral patterning in plants "ABCDE model"
72
ortholog
genes in DIFFERENT species derived from a common ancestor
73
paralog
genes WITHIN a species that arise via gene duplication
74
developmental constraints
pleiotropy: the same gene affects the development of multiple traits
tradeoff: the development of one trait trades off with another
75
developmental constraints: beetle
horns are located on different body segments in different dung beetle species
--> horn size trades of with other body parts produced on the same segment
ex: large horn = small antenna and eye size
76
using experimental evolution to test the strength of a developmental constraint (butterfly example)
* look in slides
experimentally evolved butterflies with large-small or small-large combinations
--> successfully broke the developmental constraint in just 10 generations (weak developmental constraint)
could not evolve butterflies with more black in one eyespot and more gold in the other (A strong constraint, because it is difficult to escape (i.e., experimental evolution didn’t manage to independently change the amount of black or gold in eyespots 4 and 6).
77
convergent evolution and the underlying developmental mechanisms
convergent evolution: different lineages independently evolve the same trait
parallel evolution: convergent evolution via the same developmental mechanism
78
Red-wing butterfly example (H. melpomene and H. erato)
H. melpomene and H. erato independently evolved red coloration via the same hometic gene: optix
--> example of parallel evolution
79
c4 photosynthesis key takeaways
Is convergence by parallelism or not?
--> anatomically different (not parallel)
Intermediate forms
--> exadaptation (each intermediate step performs a different ecological function)
--> another ex: evolution of feathers for wings (originally evolved for insulation --> then flight)
80
macroevolution
large-scale evolutionary change (major morphological transitions over long timescales)
speciation and extinction
looking at the scale of an entire phylogeny
81
the tree of life
animals, plants, and fungi represent less than 10% of the genomic diversity on earth
82
transitional forms
if the hypothesis of descent with modification is correct, then the fossil record should contain transitional forms
--> species with traits typical of ancestral populations and novel traits seen later in descendants
ex: archaopteryx --> a transitional form between dinosaurs and modern birds
83
tiktaalik
a transitional form between fish and tetrapods
[Tiktaalik] is a fish with fins, but fins that flexed and extended like arms and hands. It has a tetrapod-like ribs, a mobile neck and wrist
84
5% of a wing problem
feathers originally evolved for insulation, and they were later co-opted for flight
example of exaptation
85
exaptation
a trait that originally evolved to perform one function, and was later co-opted for another (C4 photosynthesis, feathered wings)
86
Transitional forms exist—but they're rare. Why?
1) Evolution is gradual. Transitional forms are rare because the fossil record is incomplete (phyletic gradualism)
2) Evolution is characterized by morphological change during speciation, followed by long periods of stasis
--> transitional forms are rare because they're around for a geological blink of an eye (punctuated equilbrium)
87
Phyletic gradualism
Evolution is gradual. Transitional forms are rare because the fossil record is incomplete
88
punctuated equilbrium
evolution is characterized by morphological change during speciation (occurs quickly), followed by long periods of stasis
--> transitional forms are rare because they're around for a geological blink of an eye
--> horizontal lines represent morphological change
--> vertical lines represent stasis
89
axes for phyletic gradualism and punctuated equilbrium
x-axis: morphology
y-axis: time
90
adaptive radiation
diversification of a single common ancestor into many species adapted to different ecological niches
strong evidence for the importance of natural selection in speciation and rapid evolutionary change
91
beetle phylogenetic tree
switching to a new host is associated with a burst of speciation (adaptive radiation)
diversification within this species is parallel with occupying a new ecological niche
92
stasis
"Living fossil": a clade with little or no morphological change over a long period of time
93
What mode of selection could lead to stasis?
Stabilizing selection. It favors individuals with trait values near the population mean, so it prevents change in the trait over time.
94
morphological stasis ≠ equal genetic stasis
organisms that are "static" could either have little or lots of morphological (genetic?) evolution
95
what predicts background extinction?
geographic range size, dispersal distance
ex: if something were to happen to rats in Hawaii, rats around the world would be okay
96
Which would be more likely to go extinct: a species with long-distance dispersal or short-distance dispersal?
Short-distance dispersal: More vulnerable to local environmental changes
97
Who is our common ancestor?
We are an African great ape!
Shared derived traits of apes:
- large brains
- no tail
- straighter posture
- increased flexibility of hips, ankles, wrist, and thumb
- changes in the structure and use of the arm and shoulder
the most recent common ancestor of humans, chimpanzees, and bonobos lived 5-7 million years ago
98
how genetically different are we from other great apes?
humans and chimps are distinguished by about 35 million SNPs, 5 million indels, and some chromosomal rearrangements
--> 30% of our proteins are identical to the homologous protein in chimps
--> for the remaining 70%, the typical difference is two amino acid substitutions
99
branch lengths
branch lengths represent the genetic distance between species
--> longer branch = more change since the last common ancestor
--> more genetically similar pairs will have shorter branches
100
some genetic differences between humans and chimps
gene loss
--> olfactory, taste and other chemoreceptors
---> immune response
gene gain
--> duplication of the gene SRGAP2, which encodes a protein that extends brain development and allows nerve cells to develop more dendrites
positive selection
- sensory perception
- immune response
- tumor suppression
- spermatogenesis
- language (biggest one)
101
hominins
extinct species that are more closely related to us than chimpanzees
--> many hominin species
--> many existed at the same time
--> homo sapiens only survived
102
the origin of our species
- all were bipedal
- some lived in the same place at the same time
103
does human evolution represent the progressive evolution of a single lineage or an evolutionary radiation?
evolutionary radiation
--> throughout most of the last 4 million years, multiple hominin species coexisted at the same time
--> humans are the lone survivor
104
homo ergaster
some homo ergaster individuals left Africa about 1.8 million years ago and spread across Asia and Europe
105
When and where did modern humans arise?
Multiregional hypothesis:
- homo sapiens evolved from archaic humans concurrently in Europe, Africa, Asia, and Oceania
- gene flow was frequent enough to prevent populations in different places from evolving into separate species
replacement hypothesis:
H. sapiens evolved only in Africa
- some individuals then migrated to Europe, Asia, and Oceania (and eventually the Americas)
- the H. sapiens who left Africa replaced archaic humans
106
does evidence support the multiregional hypothesis or replacement hypothesis?
replacement hypothesis
107
replacement hypothesis prediction #1
all modern humans are more closely related to each other than to any archaic hominin
108
replacement hypothesis prediction #2
African human populations contain more genetic diversity than non-African human populations
--> serial founder effects (bottlenecks)
--> human populations in sub-saharan africa contain tons of genetic diversity
--> human populations far from sub-saharan africa contain much less genetic diversity
--> the most recent common ancestor of all modern humans lived ~ 171,000 years ago
--> the most recent common ancestor of non-Africans lived ~50,000 years ago
all modern humans are extremely closely related
109
how do you detect gene flow from an archaic human species?
present-day human genomes
--> present-day humans are the largest repository of archaic human DNA
dr. priya moorjani found neanderthal and denisovan ancestry in 2,700 south asian genomes
110
genomic deserts
regions of the genome where no present-day humans have neanderthal or denisovan alleles
there are also regions of the genome that are enriched for neanderthal or denisovan alleles
111
When did gene flow between Neanderthals and modern humans take place?
larger tracts of neanderthal ancestry = more recent gene flow
--> as time passes, neanderthal segments get broken up into smaller and smaller fragments by recombination
112
studying local adaptation in humans—what to figure out?
- the phenotype (s) that selection is acting upon
- the genomic region (s) under selection
- the external conditions driving selection
...entirely via observational studies, not experiments
113
What is the strongest evidence for local adaptation in humans?
Strongest evidence
- Adaptation to environments that severely challenge survival
- convergent evolution in different populations
114
understanding recent human evolution and understanding functional variation in the human genome
any two people are ~99.9% genetically identical
--> but there's still a ton of standing genetic variation in human populations
--> 80 million variable sites
--> structural variants: duplications, copy number variants, deletions, insertions, inversions
- single-nucleotide polymorphisms
most of it is likely neutral, but some may be functional. why do functional polymorphisms exist? what do they do?
115
Lactase persistence
cattle were domesticated ~7,500 - 9,000 tears ago in North Africa and the Middle East
--> hypothesis: This caused strong selection favoring the ability to digest milk in adulthood
--> this occurred independently in african and eurasian populations
116
did lactase persistence (the ability to digest lactose as an adult) evolve via a change to a protein-coding sequence or a regulatory region?
A regulatory region. This is an example of heterochrony: a change in the timing of a developmental event
117
Why is convergence strong evidence for adaptive evolution?
Convergence is a similar but evolutionarily independent response to a common environmental problem. It is strong evidence for natural selection, because convergence is unlikely to evolve via random processes (drift, mutation)
118
Genetics of lactase persistence: Graphs
look at the slides!!!
119
is lactase persistence in european and african populations an example of parallel evolution?
Yes. European and African populations evolved lactase persistence via SNPs in the same gene
120
Are the lactase persistence SNPs synonymous or non-synonymous substitutions?
Synonymous. They’re located in introns, so they don’t change the resulting protein
This is an example of how synonymous substitutions can affect phenotype: they can affect gene regulation
121
Do the lactase persistence alleles increase lactase expression?
Yes! The african and eurasian alleles increase lactase expression in vitro
122
"Low prevalence of lactase persistence in neolithic south-west europe"
Consistent with the idea that before lactose-producing cows came to Europe, lactase persistence was rare
lactase persistence is an example of convergence at phenotype, parallel evolution, under natural selection
123
what does the lactase persistence allele show evidence of?
Selective sweep in both European and African populations
--> evidence that selection drove this allele to fixation
124
adaptive introgression
One person gains an allele through gene flow but then increases in frequency due to selection
125
adaptation to high elevation
andean altiplano, tibetan plateau, ethiopian highlands
adaptive high-altitude allele was introduced to Tibetan populations by gene flow from the ancestors of present-day Sherpas
--> then increased in frequency due to selection
identified one of the same genes that Tibetans had in Andeans, but identified completely different genes in Ethiopian Highlanders --> therefore, the adaptation to high altitude in Tibet and Ethiopia is not an example of parallel evolution
126
Is adaptation to high altitude in Tibet and Ethiopia an example of parallel evolution?
No. Tibetans and Ethiopians evolved adaptations to high altitude via different genetic mechanisms
127
which signatures of selection are easier to detect?
Hard selective sweeps and adaptive introgression (look at image in slides)
hard selective sweep --> loss of all genetic diversity
--> not only do you get the new adaptive allele but also the mutations that come with it
adaptive introgression --> gain of the gene through gene flow at first and then natural selection fixates it
128
which signatures of selection are harder to detect?
soft selective sweeps and polygenic adaptation
soft selective sweep --> reduction of genetic diversity is much more subtle
--> if natural selection selects for both beneficial alleles, some people will have 1 over the other
129
How can organisms respond to human-altered environments?
They can move (poleward, to greater depths, upslope)
They can acclimate
They can go extinct :(
They can adapt
130
Acclimation
Plastic (not evolved) physiological changes that allow organisms to tolerate environmental change
example: if a plant grows in crappy vs. good soil --> its the environment that affects the state of the plant
131
background extinction
extinction that is happening all the time --> affects one or a few taxa at a time
132
mass extinction
a rapid global extinction even that affects a broad range of organisms. associated with environmental catastrophes
133
cumulative vs background extinction rate
current extinction rates (cumulative) are much higher than background levels
134
Mass Extinction: The Big 5
Global in extent, involves a broad range of taxa
--> associated with environmental catastrophes
ex: permian-triassic
--> likely cause: massive volcanic eruptions
ex: cretaceous-paleogene
--> likely cause: metor
135
A sixth mass extinction?
Only about 1,100 species have gone extinct since 1600 (that we know about)
But if all threatened species go extinct, we will be halfway to the benchmark for a mass extinction event
75% is the threshold for mass extinction
136
Barnosky et al. 2011
If [the current rate] continues unabated, amphibian, bird and mammal extinction would reach Big Five magnitudes in 240 to 540 years
points the paper makes:
1) question we can bring data to
2) we are in the fast lane towards this endpoint
3) most current extinction loss due to habitat loss
137
"evolution of life in urban environments" recitation reading
thus, the phenomenon of global urbanization represents an unintended but highly replicated global study of experimental evolution
--> potential for convergent adaptation to save environmental pressure
138
"Parallel selection on thermal physiology facilitates repeated adaptation of city lizards to urban heat islands" Shane C. Campbell-Staton and Dr. Kristin Winchell
lizards collected from urban areas have higher heat tolerance than lizards collected from forests
--> not enough information to say whether its acclimation or adaptation (with the first graph)
139
testing for a genetic basis of thermal tolerance (lizard paper)
in 3 of the 4 cities, genetic differences between urban and forest lizards localize to the same region of the genome
arginyl-transfer RNA synthetase catalyzes protein biosynthesis
--> prevents the aggregation of misfolded proteins, which occurs under environmental stress and damages cells
--> lizards with the urban allele had higher thermal tolerance (data not shown) --> adaptation, not just acclimation
140
Is this parallel evolution? (thermal tolerance in urban anoles in different Puerto Rican cities)
Yes. Urban lizards are more closely related to nearby forest lizards than to urban lizards in other cities. They independently evolved thermal tolerance via the same mechanism
141
"Adaptive changes in sexual signaling in response to urbanization"
Túngara frog
--> they exist in both forest and urban settings. bats are rate in cities, and cities are loud!
--> therefore, more urban frogs will produce more chucks than forest forest frogs
The environment is noisier, and the risk of attracting a bat predator is lower
142
"Limited potential for adaptation to climate change in a broadly distributed marine crustacean" Dr. Morgan Kelly
Habitat for copepods: tide pools
--> huge change in temperature each day
--> southern populations have the highest thermal tolerance (baja, mexico and s. cali vs. n. cali and oregon)
experimental evolution: can copepods evolve higher thermal tolerance?
--> in this experiment, the thermal tolerance after selection is no different from the control lines --> this means that southern copepod populations failed to evolve higher thermal tolerance
143
Why did southern copepod populations fail to evolve higher thermal tolerance?
Southern copepod populations have reached their thermal limit. There is no longer genetic variation in thermal tolerance in the south.
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the limits of adaptation
genetic variation is required for evolution
adaptation via new mutation is slow --> in most species, rapid adaptation most likely requires standing genetic variation (existing HERITABLE variation)
--> THINK OF BREEDER'S EQUATION!!
--> R = h^2S
species with small population sizes and long generation times are especially vulnerable
145
strengths and limitations of dN/dS
strength: straightforward to calculate; only requires one sequence per species
limitation: too conservative to detect positive selection in some cases
146
strengths and limitations of McDonald-Kreitman
strength: more powerful test for positive selection than dN/dS
limitation: requires significantly more data (multiple sequences per species from multiple species)
147
Why does negative selection not reduce genetic diversity at or near the site of a harmful mutation?
If the red star mutation is deleterious, selection will remove it from the population. Selection will also eliminate linked neutral mutations that occur in the same individual. However, this affects only a tiny fraction of mutations that are segregating in the population.
Most neutral mutations are on other genetic backgrounds, so they remain in the population after selection removes the individual with the deleterious allele. As a result, selection does not affect genetic diversity in the region of the genome where the harmful mutation arose.
148
What is the key difference between adaptation from new mutation and adaptation from standing genetic variation? What are the two approaches used to discriminate between these hypotheses?
The difference involves when the adaptive mutation appears, relative to the environmental change that favors it. Two ways to discriminate between these hypotheses:
1. Date the origin of the adaptive mutation, relative to the change in the environment.
2. If multiple lineages convergently evolved the trait, determine whether they inherited the adaptive mutation from their common ancestor (standing genetic variation) or whether it independently arose in each lineage (new mutation).
149
Why is reproductive isolation central to the biological species concept?
Reproductive isolation restricts or eliminates gene flow between populations. This is important because gene flow is a homogenizing evolutionary force. In the absence of gene flow between the two populations, they evolve independently and eventually may accumulate enough differences that they can no longer produce viable offspring.
150
Determine whether prezygotic or postzygotic isolating mechanism: Sperm from one species is chemically incompatible with the egg of another, so even when they mate, FERTILIZATION does not take place.
prezygotic (mechanical — differences in the gametes leads to failure of copulation)
151
Why doe reinforcement require a pre-exisiting mechanism of post-zygotic isolation?
Natural selection will only favor the evolution of pezygotic barriers if there's a fitness cost to making a hybrid, i.e., if hybrids have lower fitness than non-hybrid offspring. By definition, postzygotic isolation means that hybrids have low fitness (e.g. they're sterile / infertile)
152
Difference between regulatory evolution and coding sequence evolution?
Regulatory evolution changes when/where a gene is expressed, but it doesn't change the structure of the protein. Coding sequence evolution usually changes the structure of a protein.
153
List the examples from lecture of how changes in where or when a gene is expressed can cause major morphological changes.
Where: Hox genes in flies, floral development in plants
When: Neoteny in axolotls and human brains
154
Parallel evolution is a subset of convergent evolution. Explain the difference between these two concepts.
Convergent evolution is when different populations/species independently evolve the same trait in response to a similar environment (i.e., in response to the same agent of selection). Some cases of convergent evolution are parallel, meaning that the genetic basis of the convergent trait is the same in different populations / species.
Not all convergent evolution is parallelism, but all parallel evolution is convergence
155
How does the concept of exaptation account for the evolution of very complex traits?
An exaptation is a trait that originally evolved for one reason and was later co-opted for another. Feathers are an example: they are hypothesized to have originally evolved as insulation, and later were co-opted to build a wing.
This resolves the "5% of a wing problem": how could something like a wing evolve, if an incomplete wing doesn't work for flight? The answer is that it originally evolved for a reason other than flight.
156
Humans and chimps differ at roughly 1% of the base pairs in our genome. A major area of ongoing research is which of these differences is functional, i.e., what makes us human and them chimps.
According to the neutral theory of molecular evolution, would you expect most of the differences between humans and chimps to have been fixed by drift, positive selection, or negative selection? Explain.
Neutral theory predicts that most differences would have fixed by drift rather than by positive selection. Negative selection does not contribute to sequence divergence between species, because it removes new mutations from a population.
157
According to the multiregional hypothesis, answer the following:
1) Where did H. sapiens evolve?
2) Where (In what geographic region) is genetic diversity in modern humans the highest?
3) Relationship between H. sapiens and other ancient Homo species
1) Independently in Africa, Europe, and Asia with lots of gene flow between H. sapiens populations in different regions
2) Approximately equal amounts of genetic diversity in all regions
3) In each geographic region, H. sapiens's closest relative is the ancient Homo species that previously inhabited that region
158
Did lactase persistence evolve via a change in the expression or function of the lactase gene?
Via a change in gene expression. Both European and African populations had substitutions in introns, not in coding sequence. This is consistent with the resulting phenotype: lactase persistence involves the expression of lactase during a life stage where it is usually not expressed. It does not involve a change in the function of the enzyme.
159
According to the replacement hypothesis, answer the following:
1) Where did H. sapiens evolve?
2) Where (In what geographic region) is genetic diversity in modern humans the highest?
3) Relationship between H. sapiens and other ancient Homo species
1) We evolved from in Africa, and some H. sapiens individuals then left Africa and migrated around the world.
2) Greatest genetic diversity in Africa (founder neck events)
3) All H. sapiens are more closely related to each other than to any other ancient Homo species
160
What is a major challenge of studying adaptation in humans, relative to an organism like Drosophila or mice? Why is convergent adaptation especially useful for researchers studying humans?
Manipulative experiments are usually not possible in humans. For example, you can't perform common garden or reciprocal transplant experiments to test adaptive hypotheses (for obvious reasons).
This means that researchers studying human adaptation rely on replicated natural experiments, like when human populations in different parts of the world independently adapt to the same environment (convergence).
161
Most traits are polygenic, yet there are few examples of polygenic adaptation in humans. Instead, most examples of the genomic basis of adaptation focus on traits with a simple genetic basis, like the lactase persistence example that we covered in lecture. Why?
When a trait is highly polygenic, the effect of each locus on phenotype is small, and selection on each locus is weak. This is because an individual's phenotypic value is determined by the small contributions of alleles at hundreds/thousands of loci.
Selection on the phenotype is distributed across all the loci that contributes to it, so selection on each locus is very weak. This results in soft selective sweeps (a small reduction in genetic variation at each locus), which are much harder to detect in genomic data than hard sweeps.
162
A major area of current debate is whether human activities are causing a mass extinction. The number of species that have gone extinct as a result of human activity is nowhere near the 75% threshold for mass extinction. Despite this, many researchers in this area believe that human activities are likely to drive a mass extinction. Why?
Most mass extinctions have taken place over a much longer period of time (tens or hundreds or thousands of years). At the current rate of extinctions (number of extinctions per year), we are on track to reach mass extinction in only 500 years, which is a fraction of the time past mass extinctions have taken.
163
In their review on urban evolution, Johnson and Munshi-South write "Thus, the phenomenon of global urbanization represents an unintended but highly replicated global study of experimental evolution." What do they mean by this?
All cities share several similar features, and are different from surrounding rural areas. This means that all cities impose similar selective pressures on urban populations, so the populations in each city can be thought of as an experimental replicate, akin to different vials of Drosophila or different test tubes of microbes.
164
What is adaptive evolution, and how do you prove it?
Trait has evolved because of a fitness advantage
To prove adaptive evolution, you need the following:
- A trait increases fitness in a specific environment
- The trait arose due to natural selection, not random processes like drift
- The trait is heritable, meaning that changes persist across generations
165
In the Johnson et. South paper, how was parallel evolution studied? Was there adaptation?
Observing patterns across many cities, specifically exploring HCN in white clovers across urban cities. When looking for changes, significant clines showed selective pressures that were probably due to environmental differences, such as temperature.
--> does not prove adaptation (could be acclimation), but it suggests selection is present
166
The study found evidence of both parallel and non-parallel evolutionary responses to urbanization. What does this tell us about the balance between shared selective pressures and local environmental variation in shaping evolution?
Parallel adaptive evolution is most likely when populations experience similar environmental selective pressures on the same genes or phenotypes. Selective pressures in a similar urban environment evoke similar evolutionary responses.
Environmental pressures have a stronger effect on adaptation than predation pressures. When shared selective pressures are stronger --> parallel evolution takes place
When local environmental variation is stronger --> non-parallel evolution takes place
166
Why is adaptive evolution harder to prove than nonadaptive evolution?
Negating a theory is easier because you carry the burden of finding one exception to disprove the hypothesis.
Adaptive evolution, driven by natural selection, is generally harder to prove than non-adaptive evolution due to the influence of other evolutionary forces and the difficulty of definitively attributing specific changes to selection alone
167
How do the differing conclusions of Miller and Weisberg reshape how we understand resistance to evolution in the U.S.?
Some resistance factors include religion and upbringing: a lot of knowledge comes from what is being taught within families during childhood and early schooling.
The US also seems to have politicised the topic of evolution, which has added to the resistance to evolution. This, in part, is due to the fact that political parties are deeply tied to religion, or has used religion in the past to gain support.
“The conservative wing of the Republican Party has adopted creationism as a part of a platform designed to consolidate their support in southern and Midwestern states—the “red” states.” - Miller
168
Given Weisberg’s finding that knowledge predicts acceptance, what kinds of changes would you propose for science curricula or informal education to improve public understanding of evolution?
- Early education on evolution
- Elementary school in science classes
- Narratively through museum exhibits and
games
- Using non-human examples to illustrate the
progression of evolution
- Using real-world examples to illustrate the
significance of evolution
- Removing as much misconceptions as
possible about evolution in the media →
stricter news coverage (difficulties are large)
- Including religion into the discussion about evolution
169
What do the graphs in Weisberg et al. tell us about how knowledge interacts with religious or political identity?
The more liberal the higher the acceptance of evolution
The more religious the lower the acceptance of evolution
Overall: The graphs explain how knowledge of evolution predicts acceptance, and has a direct relationship to religion and political beliefs. This relationship across different groups, suggesting that there is an education divide when it comes to acceptance, even in very polarized contexts.
170
How did the integration of evolution into political ideologies shape the content and purpose of evolution education in China?
In China, Darwinian theory was interpreted through a political lens to serve national and ideological ends.
Late Qing and Republican Era promoted nationalism by creating slogans like “survival of the fittest” ideologic mantras symbolizing national strength and survival
171
Why was a theory riddled with capitalistic undertones (“survival of the fittest”) able to spread easily in communist China yet not gain wide acceptance in capitalistic USA?
Even though survival of the fittest sounds capitalistic, the theory of evolution fundamentally contradicts creationism ideologies, which were/are very prevalent in the predominantly Christian United States.
The idea of evolution and associating such with the image of China can also help spread evolutionary beliefs due to the patriotism and nation’s pride essentially being shared and supported by the entirety of the nation in communism.
172
Specifically, does religion/politics hamper evolutionary knowledge? Are there any aspects of such that could perpetuate its spread?
Based on the Miller paper, religious literalism in US protestant fundamentalism is the strongest predictor of rejecting evolution.
Political ideologies that emphasize science for national advancement such as China can spread evolutionary ideas, however sometimes at the cost of distorting scientific nuance.
China’s social norms would accelerate the spread of information as opposed to the United States, based on the communist versus capitalist way of thinking (especially components like group selection)
China: community-driven for others
United States: free thinking for yourself
