Exam 2 Flashcards
phenotypic plasticity
single genotype can lead to multiple different phenotypes depending on the environment
developmental plasticity
fixed, often irreversible, happens during early development
acute plasticity
short term, reversible
genotype norm of reaction
a curve that relates the contribution of environmental variation to observed phenotypic variation
three types of phenotypic distribution
continuous variation, polymorphism/polyphenism, canalization
polymorphism/polyphenism
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
canalization
fixed trait, same phenotype regardless of environmental variation
four major types of phenotypic plasticity
shifts in phenology, acclimation/acclimatization, polyphenism, transgenerational plasticity
phenology
timing of life history events, such as flowering time or clutch laying
acclimation
physical adjustment to a controlled change in one specific environmental variable, occurs in a lab
acclimatization
physical adjustment to changes in multiple environmental variables in nature
transgenerational plasticity
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
maternal effects
phenotype of the offspring is influenced by the environment experienced by the mother (and thus her phenotype)
proximate drivers of phenotypic plasticity
gene expression and allelic sensitivity
gene expression (relative to phenotypic plasticity)
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
allelic sensitivity
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.
why aren’t all traits plastic?
plasticity has costs
3 costs of phenotypic plasticity
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.
under what conditions should developmental plasticity be expected?
non-mobile organisms, environmental variation that is high, predictable, and occurs within the lifespan of the organism
under what conditions should acute plasticity be expected?
unpredictable changes and stable environments
climatic variability hypothesis
thermal tolerance (climate niche) correlates with latitude
is behavior considered plasticity?
we don’t know
behavioral drive
Behavioral flexibility leads to the exploitation of new niches and faster evolutionary diversification
behavioral inertia
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.)
how to determine if behavioral inertia?
track ancestral niche
three ways plasticity enhances or reduces evolution?
- Plasticity can reduce rates of genetic change through a process analogous to behavioral inertia
- 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
- 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
genetic accommodation
Any adaptive change in the environmental
regulation of a phenotype, can be positive or negative
genetic assimilation
The complete loss of plasticity through genetic canalization, is a subtype of genetic accommodation
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?
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.
Can genetic assimilation occur with standing genetic variation only or does the process require new mutations?
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.
Under what conditions would you expect plasticity to be non-adaptive?
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.
cryptic genetic variation
build up of genes expressed in new environment, giving rise to novel phenotypes, which selection can then act on
how might plastic responses to environmental variation influence the process of natural selection?
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
role of plasticity in macroevolution?
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
how might plasticity influence genetic variation, genetic architecture, and molecular evolution?
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
*do we need a theory of forms?
?
describe the guppy experiment
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
describe anole experiments
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
scientist who explored link between genotype and environment, experimented on field mice
Hopi Hoekstra
if evolution can be this rapid, what are the implications?
speciation can occur more quickly, macro and micro-evolution should not be considered so separate, climate change and conservation (evolution is relevant to conservation)
eco-evolutionary dynamics
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)
dynamics
feedback between levels (genes, phenotypes, populations, communities, ecosystems)
evolutionary rescue
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
contemporary evolution
the study of evolution on shorter timescales than originally thought, often dealing with research in climate change, habitat loss, etc.
how has contemporary evolution influenced invasion biology?
evidence is mounting that rapid evolution may be a key to the success of invasive species, even when extreme bottlenecks occur
how has contemporary evolution influenced ecosystem ecology?
recent work has shown that evolution can affect nutrient and energy flow through ecosystems, among other processes
how can we reconcile the observation that evolution can be extremely rapid with the observation of stasis in the fossil record?
evolution does not necessarily cause clear morphological change, can also be cryptic evolution, sampling issue/snapshots not necessarily realistic, could be multiple reasons
does the persistence and stability of ecological communities depend on evolution? Or is evolution trivial?
negative feedback of evolution creates stability/persistence
if evolution can be extremely rapid, why do we find large amounts of genetic variation in wild populations?
the magnitude and direction of selection is not consistent, gene flow, mutations
does contemporary evolution represent a paradigm shift in biology?
these ideas have been around, but not applied. however, it does change the way we think about the relationship between ecology and evolution
what is the relationship between contemporary evolution and the maintenance or erosion of genetic variation within populations?
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
do you think it would be useful to consider contemporary evolution or eco-eco dynamics in your own research?
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.
differences between micro and macroevolution
timescale and process vs pattern
microevolution
Shorter-term; changing allele frequencies
within species or populations
macroevolution
Longer-term; evolution above the level of
species—evolution of clades
punctuated equilibrium
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
phyletic gradualism
idea that evolutionary change proceeds smoothly at similar rates over time
anagenesis
evolutionary change within clades
according to Darwin, what could explain the gaps between extant clades?
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.
speciation
study of how reproductive isolation evolves, not really when and how new species form
sympatric speciation
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)
polyploidy
heritable condition of possessing more than two complete sets of chromosomes, can cause instant reproductive isolation
mechanisms of sympatric speciation
polyploidy, disruptive selection (intermediate forms have low fitness) - need strong selection, any gene flow counteracts
allopatric speciation
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
secondary contact reinforcement
hybrids are low-fitness, mating traits coevolve to discourage interbreeding - example: birds and frogs with divergent calling traits
character displacement
interspecific competition leads to phenotypes farther apart being favored decrease competition
speciation by hybridization
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
incipient species
diverged species
adaptive radiation
speciation occurring much faster than is typical in the fossil record
example of sympatric speciation
African cichlids
conditions that favor adaptive radiation
- Sudden opening of a new suite of ecological niches.
- The evolution of novel traits that permit the exploitation of previously existing, but empty, niches.
- The presence of strong selection leading to phenotypic and genetic divergence across niches
ecological speciation
divergent selection causes the accumulation of pre- and post-zygotic barriers to successful mating between closely related populations or species
driver of adaptive radiation
ecological speciation
does genetic drift play an important role in shaping macroevolutionary patterns?
genetic drift doesn’t really result in dramatic changes on a macroevolutionary scale. Selection plays a more dominant role, leading to genetic variation.
anole lizards and ecological speciation
geographically isolated, drift causes divergence even without selection, pre-zygotic and post-zygotic barriers prevent future offspring
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?
no real answer, but important to consider different perspectives, like microbes. biological species concept not relevant to asexually reproducing organisms like microbes
does most speciation occur within adaptive radiations? In other words,
do we need adaptive radiation to get cladogenesis?
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
what is the role of sexual selection in speciation?
sexual selection can cause reproductive isolation by mate preference for certain secondary sexual characteristics, which leads to reproductive incompatibility aka prezygotic isolation
what 5 forces drive evolution of the genome?
mutation, recombination, genetic drift, selection, intragenomic conflict (gene-level selection)
5 types of mutations
point mutations (single nucleotide polymorphisms), duplications, insertions, deletions, inversions
mutation transitions vs transversions
transitions: A-G or C-T, tranversions: A-C or G-T
are transitions or transversions more common?
transitions
recombination
genetic exchange between chromosomes or genomes, can occur both within and between species
genetic hitchhiking
increase in frequency of an allele due to it’s physical linkage with a different allele that is under selection
how does recombination influence genomic evolution?
reduces linkage, counteracts genetic hitchhiking
intragenomic conflict (gene-level selection)
gene level selection, sometimes (but not always) at expense of organism-level fitness—selfish genetic elements (e.g.
transposons)
introgression
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
homologous genes
genes shared from common ancestor, but can have differences due to divergence
substitution rates
rate of point mutations that occur over time - example: number of differences in homologous sequences between clades, are variable across the genome
why do substitution rates vary across the genome?
some sections of genes are under selection to remain the same because they are crucial
C-value Paradox
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
c-value
amount of DNA contained within haploid nucleus (in picograms)
what type of genes make up the majority of the genome in many species?
non-coding, repetitive genetic elements
why are there non-coding segments of genes?
introns from transposable elements, vestigial sections
transposable elements (transposons)
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
gene duplication
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
retrotransposition
mRNA is translated back to DNA and inserted back into the genome
hemoglobin origin
gene duplication, leading to redundant sequence becoming mutated/modified until it had a different function
why do redundant genes accumulate mutations?
losing function in redundant genes is not selected against
chimeric genes
duplication, deletion, or incomplete retrotransposition combines two different coding sequences into a novel sequence
de novo gene birth
mutation(s) in non-coding, presumably “junk” DNA give rise to a new, functioning gene.
selectionist hypotheses
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
positive selection
selection acting to increase the frequency of beneficial mutations
purifying/negative selection
selection acting to decrease the frequency of deleterious mutations
neutralist hypotheses
differences in sequence variation between clades is primarily due to mutations that do not strongly affect organism-level fitness (such as genetic drift)
molecular clock
use of mutation rate to determine the timing of divergence between clades
scientist who proposed neutral theory
Motoo Kimura, 1968
neutral theory
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
Substitution rate in regions of the genome with little functional constraint?
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)
paradox of variation
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)
relatively high levels of genetic variation in
natural populations was (and still is) seen as evidence in support of or against the neutral theory?
support
how can we know whether variation in a gene’s sequence has been driven by selection or drift?
dN/dS ratio
dN/dS ratio
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).
which of the following cases do you think you would find for most protein-coding regions: positive selection, negative/purifying selection, or neutral evolution?
purifying selection - impact function and fitness
which of the following cases do you think you would find for most redundant regions: positive selection, negative/purifying selection, or neutral evolution?
positive selection
Would we expect natural selection and sexual selection to leave different signatures in the genome?
if you only see signs (such as non-synonymous positive selection) in the sex chromosomes, this is a signature of sexual selection.
Would there be a selective benefit for the evolution of increased chromosome number?
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)
Does the neutral theory of molecular evolution suggest that phenotypic variation between species is mostly neutral as well?
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.
Is the neutral theory of molecular evolution dead? why or why not?
*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.
compare natural selection and sexual selection
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.
