Ecology and Evolution Flashcards
physiological ecology
the study of an organism’s physiological response to its environment
Life history strategy: r-strategist
R-strategists “live” near the line of exponential growth r; often live in unstable environments; evolved to develop as many offspring as possible, ensuring that at least a few will survive their harsh environment; offspring are often small in size; do not depend on parents for long, they grow and start reproducing on their own quickly
Life history strategy: k-strategist
near the carrying capacity k on the population growth curve; under stable environment conditions; focusing their energy on generating a few, healthy, complex offspring that can receive ample care so that they go on to survive till adulthood;
Life history strategy
how organisms divide their resources into survival, growth, reproduction and parental care
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 than beneficial, and will therefore tend to drift to fixation in populations
pseudoreplication
The use of inferential statistics to test for treatment effects with data from experiments where either treatment are not replicated (though samples may be) or replicates are not statistically independent.
types of pseudoreplication
simple, sacrificial, and temporal
simple pseudoreplication
samples are grouped together in a way that creates nonrandom differences between groups that don’t include ‘treatment effects. For example, two separate plots where all experimental organisms are in one plot, and all control are in the other
sacrificial pseudoreplication
data is pooled prior to statistical analyses or 2+ samples taken from each unit treated as independent replicates
temporal pseudoreplication
samples aren’t taken from experimental units (like in simple pseudoreplication) but sequentially, creating nonrandom differences between grouped samples
why non-native species behave differently in systems they’ve invaded compared to their native systems? theories/ideas
novel weapons hypothesis, enemy release hypothesis, propagule pressure, biotic resistance
enemy release hypothesis
invasive species are less impacted by enemies (e.g., herbivores) than native species, because in the new geographical location, the invasives species are freed from the parasites, pathogens, and predators that kept their growth in check in their native environment. For example: zebra mussels in North America. Fish and especially waterbirds in their native habitat in Eurasia keep them in check, but the organisms in North America did not coevolve with zebra mussels, and do not consume them at a high enough rate to control their population growth. Argument against: not all non-native organisms become invasive.
novel weapons hypothesis
some invasive species may be successful due to “unique allelopathic, defense, or antimicrobial biochemistry to which naïve native species are not adapted” (He, et al., 2009). Callaway and Ridenour, 2004 (proposed this hypothesis) suggest that “some exotics transform from native weaklings to invasive bullies by exuding biochemicals that are highly inhibitory [allelopathic] to plants or soil microbes in invaded communities, but relatively ineffective against natural neighbors that may have adapted over time. Example: some species were outcompeted by diffuse knapweed in its non native range compared to its home range, did experiments and found some chemical in knapweed roots that inhibited species not found in home range much more than those from home range (evolved tolerance). Argument against: little evidence.
propagule pressure
composite measure of the number of individuals of a species released into a region to which they are not native. It incorporates estimates of the absolute number of individuals involved in any one release event (propagule size) and the number of discrete release events (propagule number). Propagule pressure can be defined as the quality, quantity, and frequency of invading organisms (Groom, 2006). Propagule pressure is a key element to why some introduced species persist while others do not (Lockwood, 2005). Species introduced in large quantities and consistent quantities prove more likely to survive, whereas species introduced in small numbers with only a few release events are more likely to go extinct (Lockwood, 2005). Example: cheatgrass produces a lot of seeds, and also goes to seed a lot earlier than native plants, so it has a high propagule pressure.
biotic resistance hypothesis
Charles Elton (1958) predicts that species-rich native communities limit the niche space available to other species, and thus more diverse communities have greater biotic resistance to incoming non-native species. Example: non-native plant occurrence was negatively related to native plant richness across all community types and ecoregions, although the strength of biotic resistance varied across different ecological, anthropogenic and climatic contexts (Beaury, et al. 2020).
biodiversity
Biological diversity refers to the global variety of species and ecosystems and the ecological processes of which they are part, covering three components: genetic, species and ecosystem diversity
Latitudinal diversity gradient
The gradient involves high species’ numbers near the equator (at low latitudes) and lower numbers of species at high latitudes. Lack of consensus about why, but some likely theories are: increased solar energy increases net primary productivity; more stable and tolerable climate at lower latitudes, allows organisms to use their energy for reproduction instead of thermoregulation (ecological regulation hypothesis); effective evolutionary time - habitats with a long undisturbed evolutionary history will have greater diversity than habitats exposed to disturbances in evolutionary history, tropical conservation hypothesis states that higher latitudes have the capacity to have higher diversity but are younger and thus have not had the time to build higher diversity levels such as those found in lower latitudes; diversification rate hypothesis postulates that species rich clades diversify more rapidly
drivers of biodiversity
Latitudinal diversity gradient (+), niche filling (+), climate change (-), gene flow (+)
importance of biodiversity
maintain healthy ecosystems; decrease invasive species invasions; safety net when a species is lost, others can fill its role; high genetic diversity means higher ability to adapt to new environmental conditions
drivers of genetic diversity
mutation, novel recombination, and gene flow
genetic recombination
the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent
evolutionary significant unit
a population of organisms that is considered distinct for purposes of conservation; often a species; often include: current geographic separation, genetic differentiation at neutral markers among related ESUs caused by past restriction of gene flow, or locally adapted phenotypic traits caused by differences in selection.
Pros and cons of conserving ecological and evolutionary processes, rather than preserving of specific phenotypic variants - Moritz (1999)
Can still help individual species, but focusing more on overall eco and evo processes until extinction rates begin to decline; gene flow (via connecting fragmented habitats) helps populations, especially small ones; increase genetic diversity; certain phenotypic variants may be well suited for their current environment, but if they don’t have sufficient underlying genetic diversity, they will not be able to adapt to environmental changes; however, may lose certain species that are needed, like keystone species, if they aren’t given enough individual attention
Types of direct interactions
competition, predation, parasitism, mutualism (not all)
Two forms of indirect interactions
interaction chains and interaction modifications
interaction chains (indirect interactions)
occurs when one species affects the abundance of a second species, which has an impact on a third species. For example, if a population of wolves increases predation on a population of deer, this could lead to an increase in a clover population, because there would be a decrease in consumption by the deer
interaction modifications (indirect interactions)
when the effect is on something other than abundance, such as behavior. Using a similar example, if a population of wolves influences a population of deer to shift their herd movements to avoid contact with the wolves (a change in behavior), this could lead to an increase in the clover population where the deer previously ranged
9 types of indirect interactions
–Keystone predation (one of most important)
–Apparent competition (one of most important)
Trophic cascades (also called tri-trophic interactions)
Exploitation competition
Indirect mutualism
Indirect commensalism
Habitat facilitation
Indirect defense (newly identified by Menge, 1995)
Apparent predation (newly identified by Menge, 1995)
keystone predation
occurs when a predator removes a prey species, leading to an increase in abundance of that prey’s competitor species. For example, if a wolf population caused the local extinction of a moose population, the deer population could increase, as the deer and moose compete for resources. Most common indirect interaction, according to Menge 1995
apparent competition
an increase in one species leading to the decrease in a second species due to an increase in a shared predator species. For example, an increase in a deer population leading to an increase in a wolf population could lead to a decrease in a moose population, as the wolves consume both deer and moose. In Menge’s research (1995), apparent competition was the second most common type of indirect effect
How important are indirect interactions, compared to direct interactions?
Debatable - Schoener (1993) determined in one study system that indirect interactions were responsible for about 25% of community changes, while Menge (1995) determined in a different study system that indirect interactions were responsible for 40-50% of the community changes. In fact, Menge went far enough to say that we can predict about half of the changes in a community structure can be attributed to indirect interactions. Of course, both direct and indirect interactions can be difficult to quantify, but especially indirect interactions. It is also very likely that, as in most ecological questions, the amount of impact from indirect interactions is context dependent. However, we can be certain that indirect interactions matter a great deal, possibly just as much as direct interactions, and thus cannot be overlooked
Less important/common types of indirect interactions
Trophic cascades are an increase in plant abundance due to predators controlling herbivore populations. Exploitation competition is the reduction in one predator population due to a reduction in its’ prey species, caused by consumption by a different predator species. Indirect mutualism is the mutual positive interaction of two predators consuming the competitors of each other’s prey. Indirect commensalism is similar to indirect mutualism, except that one of the predators is more of a generalist, and also consumes the other predator’s prey in addition to consuming the competitor of its prey. Habitat facilitation occurs when one species interacting with another species improves the habitat of a third species. Indirect defense occurs when competition between two species causes a reduction in one of them, which leads to a reduction in a third species that preys on one of the competing species. Alternatively, indirect defense also includes when an increase in a prey species causes an increase in a predator species, which leads to a decrease in a species also preyed upon by that predator. Apparent predation occurs when a non-prey species has an indirect positive effect on a consumer species, or a predator species has a negative effect on a non-prey species.
ecological hypotheses about propagule pressure
The ecological hypothesis between propagule pressure and invasion is the idea that invasive species will try to enter a new environment and fill an empty niche to gain ground within this new environment (empty niche hypothesis). After it has been established, it will then disperse out and begin invading surrounding areas thus increasing the propagule pressure. To combat this, endemic species will have biotic resistances to invasive species usually stemming from low niche vacancy and high local diversity (limiting similarity hypothesis).
metapopulation
“population of populations;” a group of spatially separated populations of the same species which have gene flow, or at least the possibility of gene flow between them.
What are the factors that characterize metapopulations, and what conditions need to be satisfied in order for metapopulations to persist?
balance between local colonizations and extinctions; suitable habitat patches (even unoccupied ones); replacement condition (colonizations must be greater than extinctions); large and well-connected networks of populations; habitat patches close enough for migration to occur
Describe what data you would collect to test whether populations in a fragmented habitat were behaving as a metapopulation.
Genetic samples; Track migration events; Survey landscape to identify habitat patches; Spatial data to determine connectivity of patches; Incidence function model (IFM) to model metapopulation dynamics
Example of metapopulation
Glanville fritillary butterfly in Finland (Hanski, 2011), highly fragmented heterogeneous environment in the Åland Islands in Finland. 4,000 small, dry meadows. Small local populations with small effective population sizes because most are siblings, which are prone to local extinction, and compensated for by the establishment of new populations by dispersing butterflies, and the metapopulation has persisted in a balance between stochastic local extinctions and recolonizations. Entire metapopulation has remained relatively stable over the past 20 years.
Why are small populations more likely to go extinct?
Genetic drift; Environmental stochastic events; Inbreeding depression; deleterious alleles rising to fixation; Genetic hetero- and homozygosity; Gene flow (lack of)
Factors that limit geographic ranges of species
Environmental conditions; lack of resources; organisms unable to adapt to all conditions at once; ability to disperse/migrate; gene flow knocking off adaptive peak
Batesian mimicry (dishonest signal)
phenomenon in which members of a palatable species or a group of such species, gain protection from predation by resembling or mimicking the defensive signaling of an unpalatable or defended species or of a group of defended species.
The problem with reliability, or honest vs dishonest signals
Signals may be honest, conveying information which usefully increases the fitness of the receiver, or dishonest. An individual can cheat by giving a dishonest signal, which might briefly benefit that signaller, at the risk of undermining the signalling system for the whole population. With sexual selection, the cheater may have a slight increase in fitness by deceiving their mate and reproducing, but if they are not actually very fit and their signal is dishonest, it will decrease the fitness of their population. In a non-sexual selection situation, such as batesian mimicry, eventually the dishonest signals may swamp out the honest signals, and the signal itself will lose meaning, thus rendering them useless.
density-dependent population regulation examples
Examples: limited resources and competition (-); attract more predation (-); diseases/parasites (-); emigration (-); Allee effect = better mate finding, environmental conditioning, and group defense against predators (+). These effects tend to regulate the population around the carrying capacity.
density-independent population regulation
Example: environmental and stochastic events, such as natural disasters, severe weather, and pollution (-). Density-dependent limiting factors, density-independent limiting factors alone can’t keep a population at constant levels. That’s because their strength doesn’t depend on the size of the population, so they don’t make a “correction” when the population size gets too large. Instead, they may lead to erratic, abrupt shifts in population size. Small populations may be at risk of getting wiped out by sporadic, density-independent events
What are the factors that appear to be most important in regulating wild populations?
context-dependent. In most cases, density-dependent factors are more common/important. However, density-independent regulation can be more important in certain populations, such as coral reefs dying due to ocean acidification.
population regulation
the ecological processes (biotic and abiotic factors) by which the growth of populations is limited due to the effects on birth and death rates.
Is density-dependent population regulation a “law” of ecology?
No, according to Turchin 2001; Always fluctuations, cannot be reliably predicted always (affected by factors like abiotic); May never even reach carrying capacity - Not always due to a limited resource, can be due to competition, predation, etc. Turchin considered some other ideas in population ecology to be laws, however, such as the law of exponential growth, which is logically very similar to certain laws of physics (Newton’s law of inertia, for example, is almost a direct analogue of exponential growth).
Lotka-Volterra equations
a pair of first-order nonlinear differential equations, frequently used to describe the dynamics of biological systems in which two species interact, one as a predator and the other as prey
context-dependent species interactions
when the sign (positive or negative effect) or magnitude (weak or strong effect) of an interaction changes, depending on the biotic or abiotic context
context-dependent species interactions
when the sign (positive or negative effect) or magnitude (weak or strong effect) of an interaction changes, depending on the biotic or abiotic context
context dependence of predation
The sign of this interaction is generally positive for the predator, and negative for the prey, and is the least likely of the three interaction types to be context-dependent, which is intuitive, as predation almost always benefits the predator and hurts the prey. According to Chamberlain, context-dependence in sign can occur when predation has no effect on prey in one context, and a negative effect on prey in another context. Predation can also cause a positive effect on the prey’s competitors, so it can be a positive interaction on the species level, rather than the individual level. Magnitude is context-dependent for predation, but was not significantly different between the three interaction types (Chamberlain, 2014). Predation varied the least overall of the three interaction types.
context dependence of competition
These interactions tend to have a negative impact on both, due to a reduction in resources, but can also have a neutral impact on one organism and a negative impact on the other. Relative to predation and mutualism, competition was more likely than predation to change sign, but less likely than mutualism. Again, context-dependency in magnitude was not significantly different between the three interaction types.
context dependence of mutualism
the sign is most likely to be context-dependent in mutualism interactions. According to Chamberlain, this is likely because mutualisms have weaker interaction strengths on average, leading to greater variation. Mutualisms also have more complicated energy transfers than antagonistic interactions like predation and competition; the exchange of resources comes with both costs and benefits for each party. This leaves a lot of room for variation, especially in different contexts.
What factors drive the variable outcomes of interactions? (context dependence)
the type of interaction heavily influences how context-dependent that interaction is. Other factors include abiotic factors, spatial gradients, temporal gradients, and third-party involvement. Abiotic gradients include environmental variation, such as soil type, precipitation, and temperature. The influence of spatial gradients was measured by including studies done across different geographical sites. The influence of temporal gradients was measured by including studies with data recorded at different points across time. The influence of third-party involvement was measured by considering differences when there was a presence or absence of third-party species. Each of these factors has at least a small influence on how context-dependent interactions are. For example, abiotic gradients had the largest effect on predation relative to competition and mutualism. (Chamberlain, 2014). As another example, while still having a small influence, third-party interactions had the least effect on any of the interaction types compared to the other factors. Though not included in Chamberlain’s meta-analysis, species abundance and relative frequencies are also likely to influence context-dependence of interactions.
What are the broader consequences or implications of context-dependent outcomes in species interactions?
variation in interaction outcomes can affect population growth and community structures, such as food webs and overall stability. Furthermore, it is important to consider how context-dependent an interaction is in order to fully understand the interaction. The likelihood of an interaction to change sign or magnitude from one context to another is crucial to know. If an interaction is context-dependent, then any results about the outcomes of that interaction cannot necessarily be trusted if it is only studied in a limited context. Therefore, context-dependence must be considered when designing a research project and interpreting the results.
Origin of species-level diversity
Biological diversification is regulated through a combination of availability of niche space and developmental constraints. Rapid diversification within a lineage, also called radiation, can occur when niche space suddenly becomes available, due to emergence of new niches or extirpation of niche occupants.
Maintenance of species-level diversity
Competitive exclusion (two species cannot coexist on one limiting resource) & limiting similarity (there is a minimum niche difference between two competing species that allows them to coexist); Niche partitioning (natural selection (through competition and limited resources) drives competing species to occupy slightly different niche space); Sexual preference and pre and post-reproductive barriers (reinforce speciation and prevent hybridization); Dispersal and recruitment limitation (Some species may fail to reach or establish in all possible sites where niche conditions are favorable simply due to stochasticity in dispersal and recruitment. Thus, the perfectly adapted species may fail to inhabit niches at some sites, and competitive exclusion can be infinitely delayed)
Distribution of species-level diversity
latitudinal diversity gradient, geographic barriers, environmental gradients
island biogeography
ecological and evolutionary processes that regulate species richness in isolated areas, such as islands by balancing the gain and loss of species
island biogeography
ecological and evolutionary processes that regulate species richness in isolated areas, such as islands by balancing the gain and loss of species
How distance of the island from the mainland and the size of the island interact with colonization and extinction rates to predict species richness
when there is an addition of the number of species on an island, the island’s immigration rate of new species will decrease while the extinction rate of resident species will increase. MacArthur and Wilson thus assume that there will be an equilibrial point where the immigration rate equals the extinction rate. They further hypothesize that an increase in island size will lower extinction curves while a decrease in distance between the island and the source region will raise immigration curves. Since the intersection of immigration and extinction rate curves determines the species number, the authors predict that larger islands will have more species than smaller islands (assuming these islands are comparably isolated) and isolated islands will have fewer species than islands more proximal to source regions (assuming these islands are equally large)
top-down process
a higher trophic level influences the community structure of a lower trophic level through predation
bottom-up process
a lower trophic level in the biological network affects the community structure of higher trophic levels by means of resource restriction
relative importance of top-down vs bottom-up processes?
Context dependent, and very difficult to accurately measure; different temporal scales; data is often not collected at the appropriate scale (Hunter, 1997)
evidence that climate change is occurring?
global temperature increases - 1 degree celsius surface temps since late 1800s, and 0.3 degrees celsius ocean temps since 1969 (Levitus, 2017) - current warming is occurring roughly 10 times faster than the average rate of warming after an ice age; ice cores showing history of temperatures; melting glaciers and ice sheets; satellites show us that snow cover is decreasing; sea levels rising - 20 cm in the past century; extreme weather events are increasing in frequency and intensity; ocean acidification has increased by 30%
evidence that climate change is human caused?
“Since systematic scientific assessments began in the 1970s, the influence of human activity on the warming of the climate system has evolved from theory to established fact.” (IPCC); increasing greenhouse gases, especially carbon dioxide from the burning of fossil fuels (transportation, industrial/factories) as well as deforestation (which reduces CO2 sinks), but also methane (landfills, agriculture, and natural gas leaks), nitrous oxide (agriculture/fossil fuels/burning vegetation), and chlorofluorocarbons (refrigerants, solvents). These greenhouse gases trap the heat within the atmosphere, preventing it from dispersing at the rate it normally would.
Describe some of the effects of climate change on species distributions, community composition, and ecosystem function
extreme weather events/natural disasters (drought, wildfire, hurricane) increases species through ecosystems losses in a stochastic way, as well as changing community composition (shifting alpine bumble bee communities toward species who are better suited for warmer temperatures - Scharnhorst, et al, 2023) (plant communities in most ecoregions in North, Central and South America have experienced thermophilization over the past four decades - Feeley, 2020) and ecosystem function (kelp forests provide food and shelter for animals in the community, but also provide ecosystem services for humans, such as carbon sequestering, reduce the force of storm-driven tides and surges and act like a trash fence to help retain nearshore sand, preventing erosion, but are declining due to increased ocean temperatures and acidification - Smale, 2019); range shifts (a meta-analysis of 764 species (mostly arthropods) found an average rate of poleward migration of 16.9 km/decade - Chen et al 2011); phenology mismatches
How could climate change influence evolutionary processes?
Evolutionary adaptation can be rapid and potentially help species counter stressful conditions or realize ecological opportunities arising from climate change; natural selection - changing or increasing selective pressures; gene flow - increasing or decreasing as species shift ranges; genetic drift - if populations become smaller or isolated due to die-offs or dispersal, would affect them more
paleontological example of climate change influencing evolutionary processes
(Simoes, 2022) time tree for the early evolution of reptiles and their closest relatives to reconstruct how the Permian-Triassic climatic crises shaped their long-term evolutionary trajectory. By combining rates of phenotypic evolution, mode of selection, body size, and global temperature data, we reveal an intimate association between reptile evolutionary dynamics and climate change in the deep past. We show that the origin and phenotypic radiation of reptiles was not solely driven by ecological opportunity following the end-Permian extinction as previously thought but also the result of multiple adaptive responses to climatic shifts spanning 57 million years. a strongly directional evolutionary regime by archelosaurs at the end of the Permian is associated with an adaptive response to those fast climatic shifts. ombined with ecological opportunity arising from the demise of several groups of early synapsids after the EGE and PTE (13, 14, 17, 18), climate change–driven adaptive evolution resulted in the rapid diversification of the vast diversity of reptile morphotypes that came to characterize worldwide ecosystems later on during the Triassic. Smaller body sizes favored (smaller area-volume ratios make them better capable of heat exchange with the surrounding environment). accelerated rates of morphological evolution among large-bodied archosauromorph reptiles, invasion of the marine realm by ichthyosauromorphs and sauropterygians, as well as maintenance of a small-bodied morphotype in lepidosauromorphs.
contemporary example of climate change influencing evolutionary processes
Brassica rapa blooms nearly 2 days earlier than pre-drought plants in response to a multi-year drought caused by climate change (Franks, 2007). One of the best examples of plant evolutionary response to an extreme climatic event comes from a resurrection study of the annual field mustard Brassica rapa [42,60]. The investigators collected a large sample of seeds from two California populations in 1997, after several wet years, and again in 2004 after several years of severe spring drought. They then grew population samples of genotypes collected in 1997 and in 2004 together in a common garden. The 2004 genotypes flowered significantly earlier in the common garden than the 1997 genotypes. Experimental water manipulations showed that early drought onset strongly selected for earlier flowering, evidence that the observed evolutionary change was adaptive. These B. rapa populations also display a genomic signature of temporal drought adaptation [42]. A genome-wide scan for Fst outlier-loci found 855 genes with significant temporal differentiation in allele frequencies between the 1997 and 2004 samples. Many had annotations suggesting involvement in flowering time and drought response. However, only 11 genes exhibited parallel shifts in allele frequencies in both populations. Thus, rapid adaptation to drought in the two populations appears to have occurred along largely independent trajectories.
How do the characteristics of species affect their ability to thrive versus decline in the face of anthropogenic change?
life history strategies; behavior; propensity to disperse/migrate; plasticity; genetic diversity
genetic architecture
physical genetic basis of phenotypes, such as where genes are located, how they are linked, etc.; underlying genetic basis for a phenotypic trait and it’s variation
behavioral drive
when behavior exposes an organism to novel experiences or environments and thus to novel selection pressures, which in turn trigger a cascade of evolutionary changes in morphology, physiology, or ecology; example - sexual selection, in which changes in mate-choice behaviors drive the rapid evolution and diversification of bizarre male ornaments (Lande 1981)
behavioral inertia
when behavior dulls the impact of natural selection because the organism is changing its behavior to avoid the selective force; example - lizards thermoregulating by moving to shade or sun, dulling or avoiding the selective pressure of temperatures - lizards across different environments had very similar internal temperatures (Bogert 1949, 1959)
What characteristics of communities influence their susceptibility to invasion by non-native species?
Disturbance ; Decrease in resources ; Increase in resources; Lack of biotic resistance; Lack of natural enemies; Difference in propagule availability between native and invasive species
What characteristics of non-native species facilitate their ability to become established in novel environments and become invasive?
Generalist; Rapid reproduction; Rapid growth; Rapid dispersal; Lack of natural predators
adaptive evolution
change in gene frequencies/alleles over time that increases fitness
non-adaptive evolution
deleterious or neutral mutations; genetic drift; gene flow; neutral theory
What are some of the constraints that limit the responses of wild populations to natural selection?
Genetic and epigenetic constraints, such as genetic variation or the genetic architecture; heritability; Mutations can be deleterious; Correlated traits can constrain - if one trait increases fitness and the other decreases fitness - genetic hitchhiking; Genetic drift is random (small population size, bottleneck effects); High rates of gene flow, dilutes the local adaptive effect (gene swamping); Traits have limits to adaptation, physiological/morphological/energetic constraints, trade-offs; Ecological constraints
population bottleneck
a sharp reduction in the size of a population due to environmental events or human activities; a limited number of randomly selected individuals create a founding population, resulting in genetic drift.
natural selection
differential survival and reproduction of individuals due to differences in phenotype
What is the evidence for natural selection in the wild, and how variable is it in terms of direction and intensity
Earliest evidence for natural selection (Darwin, Wallace), evidence all around us = differential reproduction rates based on traits; incredibly variable in direction and intensity, based on environmental conditions and other selective pressures, which often change
How do we measure natural selection in wild populations?
measuring phenotypic traits and estimating relative fitness (approximated by survival, reproductive output, mating success), longitudinal studies; look for correlations between traits and fitness; Directional selection (positive or negative) can be detected when the mean phenotype changes; Nonlinear selection (disruptive or stabilizing) can be detected when the variance of the phenotypic distribution changes; Genomic revolution allows us to measure selection on the genome
Classic example of measuring natural selection in the wild
Logan, 2014 - measured survival as a function of the thermal sensitivity of sprint speed in two populations of anoles lizards, a reference population and an experimental population that was transplanted to a warmer and more variable environment, which resulted in strong directional selection on thermal performance traits (sprint speed at different temperatures). These same traits were not under selection in a reference population studied in a less thermally stressful environment. Our results indicate that climate change can exert strong natural selection on tropical ectotherms, despite their ability to thermoregulate behaviorally. To the extent that thermal performance traits are heritable, populations may be capable of rapid adaptation to anthropogenic warming.
example of a recent molecular approach to measuring natural selection in the wild
genomic analysis of killifish, geographically separate and independent populations of which have adapted recently to severe pollution (see the Perspective by Tobler and Culumber). Sequencing multiple sensitive and resistant populations revealed signals of selective sweeps for variants that may confer tolerance to toxins, some of which were shared between resistant populations. Thus, high genetic diversity in killifish seems to allow selection to act on existing variation, driving rapid adaptation to selective forces such as pollution - Reid, 2016
effects of selection, random genetic drift and gene flow on genetic diversity within populations
Selection decreases diversity; Genetic drift decreases diversity (especially smaller populations); Gene flow increases diversity; they work together to create populations that are ever-changing yet in equilibrium, Migration-selection balance
effects of selection, random genetic drift and gene flow on genetic diversity among populations
Metapopulations and gene flow; Selection will be different between populations if environment is different; Speciation (like allopatric)
stabilizing selection
a type of natural selection in which genetic diversity decreases as the population stabilizes on a particular trait value
example of stabilizing selection
human birth weight: infants with low birth weight will be weak and experience health problems, while large babies will have problems passing through the birth canal. Babies with average birth weight are more likely to survive than a baby that is too small or too large.
bird clutch size: too many eggs results in babies that are undernourished and weak, while too few reduces the amount of genetic material passed on (decreasing fitness), especially if some of the offspring perish
directional selection
a mode of natural selection in which a single phenotype is favored, causing the allele frequency to continuously shift in one direction
example of directional selection
The drought, and resulting increase in seed size and strength, put a directional selection the finches. Birds with small beaks were no longer able to eat, while birds with large beaks could survive on the large, tough seeds. This directional selection caused the resulting population of finches to have a much larger average beak size than the population before the drought.
peppered moths - originally light colored, progressively evolved to become darker as industrial revolution in England caused more soot, so they could blend in with their new background colors and survive better
disruptive selection
(or diversifying selection) a mode of natural selection in which extreme values for a trait are favored over intermediate values
example of disruptive selection
plumage color in male lazuli buntings. feather brightness of males varies, ranging from brown to bright blue. Females choose to mate with males that have the best territories. Dull yearlings were tolerated by adult males, which allowed them to settle nearby in high-quality habitat and obtain mates. The brightest colored yearling males were the most aggressive of the yearlings, and able to hold their own when fighting with adults for good territory, thus able to obtain good territory and mates. Meanwhile, yearling males with intermediate plumage are attacked by adults but not aggressive enough to win the conflicts, and therefore fail to obtain good territories and mates. (Greene, 2000)
Most important discoveries since Darwin
Mendelian inheritance; discovery of the double-helix DNA structure (Watson, Crick, and Franklin); neutral theory (Motoo Kimora); population genetics (Dobzhansky); eco-evo dynamics; plasticity
mendelian genetics
Blended inheritance shown to not be the case; Alleles, dominant and recessive alleles, why offspring can look more like one parent over another; Traits can disappear for a generation & reappear because they are recessive; Before, no explanation for how genetic material passed down
double-helix DNA structure
Understand the way DNA constructs itself; Helped understand how DNA replicates, how potential mistakes arise during replication/recombination, etc.; Mistakes in DNA replication, etc, led to Neutral Theory; double helix structure revealed how genetic information is stored, copied, and transmitted between generations. This discovery paved the way for understanding the molecular mechanisms underlying genetic variation and evolution, ultimately leading to the development of molecular biology, biotechnology, and genomics.
neutral theory
most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to random genetic drift of mutant alleles that are selectively neutral; Non-adaptive evolution - synonymous base pair substitution
population genetics
Connection between evolution & genetics - genetics is the thing that evolution/natural selection is acting upon; Mutation gives rise to genetic variation - very important for natural selection to act upon (Dobzhansky)
Eco-evo dynamics
reciprocal effects that ecology and evolution have on each other. The effects of ecology on evolutionary processes are commonly observed in studies, but the realization that evolutionary changes can be rapid led to the emergence of eco-evolutionary dynamics; Merging the fields of biogeography, ecology, evolution; Evolution & ecology happen on the same timescale, evolution affects ecology, ecology affects evolution; important enough that some consider it a paradigm shift
plasticity
the ability of individual genotypes to produce different phenotypes when exposed to different environmental conditions (Pigliucci); not all phenotypic variation is due to genotypic variation
Pangenesis
Darwin’s theory to explain variation between individuals in a species; gemmules = seeds of cells, produced by all organs, and if enough came together from the parent -> baby. If the offspring resembled one parent more strongly than the other, it is because that parent had more or stronger gemmules; We now know about gametes and DNA, and variation that happens between individuals of a species or even between siblings because of underlying genetic variation, and recombination of genes leading to varying offspring; Darwin also believed that gemmules could be altered throughout life, and these changes could be passed onto offspring, similar to Lamarckism.
We know now that DNA is behind heredity, and changes are not generally picked up during a lifetime and passed on… although, epigenetics? And mutations?
adaptive landscape
a way to visualize mean fitness of a population, with peaks being the highest points of fitness (local peaks and global peak) and valleys being the lowest
shifting balance theory
Sewall Wright (1932), populations can peak shift (skip over valleys) by genetic drift, and natural selection will carry the population up to the new peak; This new superiorly adapted subpopulation may then expand its range and outcompete or interbreed with other subpopulations, causing the spread of new adaptations and movement of the global population toward the new fitness peak.
current utility of shifting balance theory in evolutionary biology
This theory is a good theoretical framework for understanding how gene flow may influence evolution at the population level; likely not a very realistic for nature, however, as the adaptive landscape is more likely an adaptive “seascape,” and is constantly changing with different selective pressures
Spandrels of San Marco and evolution
Spandrels are part of a cathedrals structure, but don’t actually serve any structural purpose for holding up the building, they are just a design choice. In 1979, Stephen Jay Gould and Richard Lewontin published a paper about the Spandrels that compared them to the idea that not all evolution is adaptive. When we first see the spandrels, we might assume they are there for a necessary purpose, just like there was a trend for a long time for evolutionary scientists to assume all traits were adaptive, and evolved for a necessary purpose. However, that is not the case. Traits can also be neutral (or even maladaptive through hitchhiking, inversions, novel recombination, and mutations), and can occur via mutations and genetic drift. These traits can also occur as a by-product of adaptive evolution. Traits can become adaptive after developing (exaptation) such as bird feathers originally developing for warmth, but becoming adapted for flight.
Spandrels of San Marco examples
human eye color, neutral genes
modern synthesis
Using mendelian genetics to explain darwinian natural selection in a joint mathematical framework; combined the ideas of natural selection, Mendelian genetics, and population genetics; related the broad-scale macroevolution seen by palaeontologists to the small-scale microevolution of local populations
Theodosius Dobzhansky and modern synthesis
evolution based on genetics; one of the first to work on population genetics with natural populations; using fruit flies, he found evidence for a wide range of genetic variation within species; theorized that neutral mutations cause genetic variation and can lead to speciation; wrote Genetics and the Origin of Species (1937)
RA Fisher and modern synthesis
Wrote “The Correlation Between Relatives on the Supposition of Mendelian Inheritance” - This book demonstrated how a number of discrete genetic loci could cause continuous variation. This gave backing to the idea that Mendelian genetics is in line with evolution by natural selection
JBS Haldane and modern synthesis
peppered moths = real-world examples of natural selection; natural selection can occur faster than previously thought;
Sewall Wright and modern synthesis
effects of inbreeding on small, isolated populations and genetic drift; combinations of genes that interacted as complexes; adaptive landscape concept
Julian Huxley and modern synthesis
wrote Evolution: The Modern Synthesis (1942); examples of natural selection and genetics; made modern synthesis more popular; summarized what was known about genetic evolution
Three species concepts
biological sc, morphological sc, and phylogenetic sc
biological species concept
defines a species as organisms that are reproductively isolated, and can interbreed and produce viable and fertile offspring. This is the most well-known species concept, proposed by Ernst Mayr in 1942. This concept does not require knowledge of evolutionary history, and can be easy to apply in situations when it is clear if individuals in a group are breeding or not. However, this is difficult or impossible to apply in field observations, when there is no control over breeding. It is also difficult to apply to species that have complicated or infrequent reproductive behavior. It also does not apply to asexual organisms, fossil species, geographically isolated species, or freely hybridizing species
morphological species concept
the smallest possible group of organisms that share defined morphological characteristics (Regan, 1925). Unlike the BSC, the MSC can be used for asexual organisms and fossil species. This species concept is particularly common for use with fossil organisms, in fact. Like the BSC, though, it does not require knowledge of evolutionary history. Unfortunately, this species concept can be misleading, due to different species sharing traits, such as through convergent evolution. This concept is often used when other concepts are not applicable, or in combination with other concepts.
phylogenetic species concept
the smallest possible group descending from a common ancestor, defined by cladistic methods and phylogenetic history (Nixon and Wheeler, 1990). Based on this concept, species can be identified by unique derived traits. This species concept is useful for understanding the history of trait development and evolutionary relationships of a species. However, unlike the BSC and MSC, it does require knowledge of a species’ evolution and phylogenetics, which is not always possible. It could also lead to more divisions between species than necessary, due to intraspecific variation.
How might an evolutionary biologist, ecologist, and conservation biologist differ in their use of the species concept?
Which species concept is the most useful depends heavily on the questions being asked. Evolutionary biologists, ecologists, and conservation biologists would likely use different species concepts, depending on what they are studying. For example, if an evolutionary biologist would like to study the phylogenetic relationships of a species, the phylogenetic species concept is likely most helpful. If a conservation biologist wants to preserve an endangered species, and needs to know which organisms can be introduced to increase gene flow for genetic rescue, the biological species concept is likely most useful. If an ecologist is studying an ancient community and only has fossil samples with degraded DNA from a species, the morphological species concept is likely most useful.
Which species concept do you find most useful?
The species concept I would find most valuable also depends on the question I am asking. One of my research topics involves predicting which of my study species may respond better to climate change than others. In this example, the phylogenetic species concept would likely be the most valuable. Some species will have traits that make them more well-suited or adaptable for climate change conditions, and the phylogenetic species concept would allow me to explore the evolutionary development of those traits. It would also allow me to explore which species are closely related to the well-adapted species, possibly leading to predictions that the closely related species may also have higher fitness in response to climate change.
most common modes of speciation
allopatric, peripatric, parapatric, and sympatric
allopatric speciation
occurs when biological populations become geographically isolated from each other to an extent that prevents or interferes with gene flow
peripatric speciation
a new species is formed from an isolated peripheral population. Since peripatric speciation resembles allopatric speciation, in that populations are isolated and prevented from exchanging genes, it can often be difficult to distinguish between them; in peripatric speciation, one group is much smaller than the other. Unique characteristics of the smaller groups are passed on to future generations of the group, making those traits more common among that group and distinguishing it from the others.
parapatric speciation
two subpopulations of a species evolve reproductive isolation from one another while continuing to exchange genes; when a species is spread out over a large geographic area, but only reproduces with local species, resulting in the development of a new species
sympatric speciation
occurs when there are no physical barriers preventing any members of a species from mating with another, and all members are in close proximity to one another. evolution of a new species from a surviving ancestral species while both continue to inhabit the same geographic region; apple and hawthorn maggot flies; polyploidy; two cichlid species in Nicaraguan lake, though overall very similar, do have slight differences in appearance, and they cannot interbreed (Barluenga, 2006)
What are the most interesting current questions in the area of speciation research?
how sympatric speciation occurs; speciation in response to climate change; what is a species?;
Evidence for origin and diversification of bees
genetic data, morphological features, phylogenetics,
origin and diversification of bees
Bees arose from within a group of carnivorous hunting wasps in the mid-Cretaceous period, around the same time that flowering plants began spreading; pollinivory was an important step, but the rapid diversification of bees is better explained by a later development when bees shifted from being specialists narrowly focused on a few host-plant species to generalists that fed on many host plants; Broadening of plant diets opened up new and unexploited ecological niches (Murray, 2018)
phylogenies
trees that depict evolutionary relationships between species, including their ancestry and common ancestry, divergence times, and relative branching order
how are phylogenies constructed?
constructed from various types of data, including morphological data (such as physical features of organisms), molecular data (such as DNA and protein sequences), and paleontological data (such as fossil evidence); construction of phylogenies involves the use of various algorithms and statistical models to infer evolutionary relationships based on the data available. The most commonly used algorithms for constructing phylogenies include maximum parsimony, maximum likelihood, and Bayesian inference.
how are phylogenies useful?
understand the evolutionary history and relationships among species. This information can be used to infer the distribution of traits and adaptations among species, and to make predictions about their evolutionary histories.
How can phylogenies be used to avoid pseudoreplication?
In comparative studies, it is often assumed that species that are closely related have a more recent common ancestor, and therefore, share more recent evolutionary history, genes, and environments. This non-independence of species can lead to problems of pseudoreplication if not accounted for, because it can result in correlations that are not meaningful. By incorporating a phylogeny into the analysis, researchers can correct for non-independence by modeling evolutionary relationships among species, and thereby obtain more accurate estimates of evolutionary processes.
phylogenetic signal
the tendency of closely related species to resemble each other more than a species picked at random from a phylogenetic tree (Blomberg and Garland 2002)
Coevolution and competition
Individuals compete for the same resources (food, females, places to breed, etc.). However, resources are limited. Thus, one of the species needs to change their “preferred resource” in order for the two species to be maintained. Ex: beak morphology in Galapagos finches.
coevolution and predation
Evolutionary arms race ⇒ Predators hunt and kill prey, this way diminishing prey’s population. However, some preys always survive and these are the ones that will have a higher fitness. Thus, this will ultimately change the phenotype of preys, that will be more able to escape predation. ⇒ Only predators that are able to hunt and kill are the ones to survive and reproduce ⇒ same logic.; example: rough skinned newt and common garter snake - newts produce toxins to deter predators, snakes develop resistance to toxin, newts become more toxic, snakes become more resistant, and so on
coevolution and mutualism
coevolution occurs when it is obligatory mutualism ⇒ both species rely on each other to survive ⇒ yucca plants and yucca moths
Why is genetic variation important?
more material for adaptation/natural selection to act on; prevent detrimental effects from low genetic diversity like deleterious alleles rising to fixation; less detrimental effects from genetic drift
What form of genetic diversity is most important for retaining evolutionary potential and why?
heterozygosity = more genetic diversity; more broad-sense heritability means more phenotypic variation and heritability;
What factors influence the spatial distribution of genetic variation?
geographic barriers; population density, breeding system (how they reproduce, and also things like sexual selection/what drives who mates with who), and environmental heterogeneity; gene flow and ability to disperse/migrate; distribution of individuals; habitat degradation and fragmentation (Pometti, 2018)
population size equation
N = B + I - D - E; B=Births, I=Immigration, D=Deaths, E=Emigration;
effective population size
a specific subset of the census population size. While influenced by the same processes as the census population size, the genetic effective population size, or effective population size for short, only refers to individuals who are fertile and have reached a sexually mature age. In other words, individuals which comprise the effective population are the ones which are capable of increasing the census population size through reproduction.
What does the ratio Ne/N tell you about population processes?
gives an indication of both a) the population’s life history and b) the population’s potential future trajectory. If the ratio is low, there is only a fraction of individuals that can produce viable offspring. The reason for this can be a complex life history, where individuals reach sexual maturity at a late age, and/or become sterile at an early age. Populations made up of species which focus on a single reproductive event during their lives, may naturally have a low Ne/N ratio, whereas species who reach sexual maturity early and remain fertile throughout most of their lives may have a high Ne/N ratio. The sexual reproduction itself may also be costly or put sexually mature individuals at high risk of predation/death - further reinforcing the importance of life history when considering this ratio.
Hardy-Weinberg Principle
in a large, randomly-mating population, allele frequencies will remain constant from generation to generation in the absence of forces like natural selection and genetic drift (Hardy-Weinberg equilibrium). If there are alleles with frequencies p and q, one generation of random mating will lead to genotype frequencies of p^2, 2pq, and q^2, and thus equilibrium for both the alleles and genotypes.
Assumptions of Hardy-Weinberg
large population; random mating (no sexual selection); no selection, mutation, gene flow, or genetic drift
historical role of Hardy-Weinberg in the field of population genetics
expanded on Mendelian genetics in a key way, and thus was highly influential in the field of population genetics, as it served as a foundation for understanding the influence of evolutionary forces and other factors (such as inbreeding, for example) on allele and gene frequencies (Mayo, 2008). For example, when R.A. Fisher derived correlations between related individuals, and developed the concept of balanced polymorphism, Hardy-Weinberg equilibrium was the basis for those concepts (Mayo, 2008). In 1924, Haldane used the Hardy-Weinberg equilibrium as the basis for all of his work on selection in populations. In the 1920s and 1930s, Fisher, Haldane, Wahlund, Wright, and others determined that non-random mating, like inbreeding, led to departures from the Hardy-Weinberg equilibrium. Ultimately, most genotype frequency analysis methods use the Hardy-Weinberg equilibrium as a reference point.
modern use of Hardy-Weinberg in population genetics
when analyzing DNA for single-nucleotide polymorphisms, each diallelic SNP can be considered to be in Hardy-Weinberg equilibrium, and searching for any deviation from it is considered to be an important first step in genome scans (Mayo, 2008)
quantitative trait locus (QTL) mapping
statistical method that links two types of information—phenotypic data (trait measurements) and genotypic data (usually molecular markers)—in an attempt to explain the genetic basis of variation in complex traits; Helps to determine the location, effect size, number of loci involved in creating a certain phenotype
How are QTL maps made?
need two or more strains of organisms that differ genetically with regard to the trait of interest; need genetic markers with known locations that distinguish between these parental lines. preferably ones that do not affect the trait of interest, such as single nucleotide polymorphisms (SNPs), simple sequence repeats (SSRs, or microsatellites), restriction fragment length polymorphisms (RFLPs), and transposable element positions; the parental strains are crossed, resulting in heterozygous (F1) individuals, and these individuals are then crossed using one of a number of different schemes (Darvasi, 1998). Finally, the phenotypes and genotypes of the derived (F2) population are scored. Markers that are genetically linked to a QTL influencing the trait of interest will segregate more frequently with trait values (large or small egg size in our example), whereas unlinked markers will not show significant association with phenotypes
What have QTLs taught us about the genetic architecture of traits in wild populations?
can tell us which genes control which traits, where they are located, and how complex the genetic architecture underlying a trait is; many genes with small effects generate a large proportion of observed, quantitative traits; Also shown that traits are highly context dependent, with factors being things like environment, sex, and genetic background; Also, also shown that pleiotropic traits are widespread; In looking at all this, we can determine the genetic architecture and even how genes may interact with environments
epigenetics
the study of stable changes in cell function that do not involve alterations in the DNA sequence; caused by modification of gene expression rather than alteration of the genetic code itself.; DNA methylation, histone modification, and regulating proteins that can switch genes off
quantitative trait
traits that are influenced by multiple genes at different loci; more genes = more normal distribution of phenotypes; each gene that contributes to the trait is a quantitive trait locus (QTL)
epigenetic examples
the glucocorticoid receptor (GR) promoter in rat hippocampi is differentially methylated depending on how mothers care for their young (Weaver et al. 2004, 2005). Cross-fostering has demonstrated that variation in maternal care impacts rat pup stress reactivity and coping behavior; isogenic rats that received little care as pups are anxious and neophobic as adults, whereas those that received ample care are bolder and neophilic. More importantly from an epigenetic perspective, these behaviors are correlated with the methylation status of the GR promoter; greater methylation of the GR promoter results in less GR expression and a greater disposition for anxiety
is epigenetics a serious challenge to traditional ecological and evolutionary theory? For and against
Neo-Lamarckism → can offspring inherit from their parents; A movement away from gene-based science?; on the other hand, epigenetics still relies on natural selection; Baldwin effect may now have some backing due to epigenetics
pleiotropy
single gene -> multiple seemingly unrelated traits
QTL and plasticity
plasticity = one gene -> multiple phenotypes depending on environment - QTL mapping can show us that; plasticity can increase phenotypic variation from the same genotype, and also increase fitness by allowing the organisms to adapt to environment cues without different genetic makeup; plasticity can decrease genetic variation; reversible and developmental plasticity; Spatially, developmental plasticity crates irreversible changes among individuals that leads to phenotypic differences between populations that persist across individual lifetimes; Temporally, both developmental and reversible plasticity can influence the variation present in a population over a certain time span - Phenological changes in migration or reproduction - Body size changes according to environment during early growth; can increase population variation by allowing them to exploit new niches and evolve in other traits,
