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Chapter: Three-Five: Variation
Fundamentals of Evolutionary Change
Heritability
Inheritance: Variation is passed down from one generation to the next, allowing for traits to be inherited and potentially modified over time.
Variability must be heritable
ie: For populations to evolve by natural selection, favorable new variations have to be passed to offspring intact and remain discrete,that the genetic variations (or traits) remain distinct and do not blend into a uniform mix over generations; this ensures that specific advantageous traits can be consistently expressed in subsequent generations, thereby enhancing the overall adaptability of the population in response to environmental pressures.
Phenotypes may mix, but not genotypes
Variation
Variations among individuals is the raw material for evolution
Sources of Variation: Change in DNA sequence =mutation
if the change is in a protein-coding region, then a new
“allele” is created
Nature of Variation: In order to be evolutionarily relevant:
new variation must be in a germ (reproductive) cell
that germ cell must be very very lucky in several
respects:
become part of the next generation (most do not)
remain viable
contribute to the following generation
Selection Requires Variation: Evolutionary change depends on the availability of variation to select from.
Ex: Variability can be seen in different species, such as distinct patterns on blacktip sharks, various fly species, and turtle shells.
Human Variability: Humans have less variability compared to other species, making it easier for us to recognize differences.
Ex: One possibility is that humans are more variable. Another possibility, however, is that we just pay more attention to the variation among people. Data show that, compared to other animals, the variation in height among humans is actually rather modest. Whether we notice it or not, variation among individuals is ubiquitous.
Types of variation
Environmental Variation: differences due to exposure to different environmental conditions
Arises when external factors influence how much protein is made from particular genes or how the proteins work. When individual experience different environments, they make different amounts of proteins or show differences in protein function.
This variation is generally not heritable
Some variations are environmentally induced, but many are genetic
Genetic variation: variable phenotype depending on which combination of
alleles are inherited from parents
parents produce 2 x 2 = 4 alleles
each offspring inherits only 2
Genotype-Environment Interaction: Refers to how different genotypes respond to environmental conditions, showing different phenotypes.
his variation is heritable
Ie. : is a concept that shows how an individual's genetic makeup influences their sensitivity to environmental factors. In other words, your genes can affect how you respond to things like diet, stress, climate, or toxins, which is why people with the same environmental exposure can experience different outcomes. This interaction helps explain the complexity of traits like height, mental health, disease susceptibility, and many other characteristics.
Remember:
Genetic: A parent with the Pp genotype (purple flowers) and a parent with pp genotype (white flowers) can produce offspring with either Pp (purple) or pp (white) genotypes. The color is genetically determined and heritable.
Phenotypic: The color of a flower can be affected by environmental factors like sunlight. If a flower is exposed to too much shade, it may not express its full color potential, resulting in a lighter or different color. This is a phenotypic variation influenced by the environment.
Genetic Basis of Traits
Role of Proteins: Proteins determine the characteristics of cells and tissues; diverse proteins result in different kinds of cell types (e.g., red blood cells, muscle cells).
Proteins define everything that an organism is:
– proteins define cells →define tissues→define tissue systems→systems define organisms.
Coding Sequence Variability
Genes have variations called alleles: Within a population, the same gene can have slightly different versions (alleles). These alleles code for proteins with small differences in their amino acid sequences.
Slightly different amino acid sequences = slightly different protein shapes: Proteins are made of amino acids, and small changes in the sequence can alter how the protein folds, leading to differences in its shape.
Different shapes = different properties: When the shape of a protein changes, it can affect how it works. For example, it might bind to other molecules more strongly or weakly, or work faster or slower.
Protein differences = phenotype differences: Since proteins play key roles in how an organism looks and functions, these slight changes in protein shape can lead to small differences in traits, like hair color, height, or resistance to a disease.
Most differences are minor: These variations usually cause only small changes in traits. This is because most proteins are still able to do their job even if their shape is slightly different. Only in some cases do these changes lead to significant differences
DNA and RNA Connection: Proteins are coded by genes in DNA, which are transcribed to RNA.
Chromosomes: Genes in organisms are embedded in long DNA molecules called chromosomes. A typical chromosome carries numerous genes.
Humans have 46 chromosomes (23 pairs): one from each parent, leading to genetic diversity.
Haploid: is a single set of chromosomes, which in humans is represented by the gametes (sperm and egg cells) that contain 23 chromosomes each.
Prokaryotes have a single haploid state and reproduce asexually.
Mitosis: Is a process of cell division that results in two genetically identical daughter cells, each with the same number of chromosomes as the original cell.
Meiosis: is a specialized type of cell division that reduces the chromosome number by half, resulting in four genetically diverse gametes, each containing 23 chromosomes.
Alleles
Alleles: These are different versions of the same gene. Variants of a gene can lead to different phenotypes (e.g., blue, brown, and green eyes). Typically, multiple alleles exist for most traits.
: DNA → Gene → Alleles → Protein.
Minor Differences Between Alleles: The differences between alleles are often minor—they usually involve only a small change in the DNA sequence. These changes can occur in one or a few bases (the building blocks of DNA). Even though these changes are small, they can lead to differences in the proteins produced by the gene, but the proteins are still usually functional. They work in the body, but they might function in slightly different ways depending on the allele.
How Do Alleles Arise? Mutations in the DNA sequence are the primary source of new alleles. These mutations can occur spontaneously during DNA replication or be induced by environmental factors such as radiation and chemicals. Over time, these mutations can accumulate and lead to genetic variation within a population.
Ex: if a "T" base changes to a "C" base, that could create a new allele of a gene.
Two Alleles vs. Many Alleles:
For simplicity, genetic examples often focus on two alleles for a gene (e.g., A and a).
One allele may be dominant (expressed even if only one copy is present) and the other may be recessive (only expressed if two copies are present). However, in reality, most genes have more than two alleles within a population. This creates more genetic diversity.
Ex: blood type is controlled by multiple alleles: A, B, and O
Rarely Only One Allele
In rare cases, a population might have only one allele for a particular gene, meaning there’s no variation for that gene within the population. This is unusual because genetic variation usually occurs within populations, and mutations often create new alleles.
Mutations
Mutations: Changes in nucleotide sequences that create new alleles; can be beneficial or harmful.
Occur due to errors during DNA replication or environmental factors (e.g., radiation, chemicals).
Mutations are chance events, so the generation of variation in a population is random.
Types of Mutations:
silent—most common type
Even lethal mutations (which cause non-viable organisms) are considered "silent" because they don't produce observable phenotypes in surviving individuals.
deleterious—common
allele with lower fitness than the population mean, meaning the organism is less likely to survive or reproduce compared to others in the population.
usually removed from the population eventually
not to be confused with lethal, as they may still allow survival but with reduced success.
neutral—rare
allele that is different but with the same fitness as
population mean
either silent, or different but equal phenotype
may evolve by genetic drift,a random process that can change allele frequencies in a population.
beneficial (advantageous)—extremely rare
organism with fitness higher than the population mean
usually increase in frequency by natural selection
Mutations are rare so this is the rarest form of an already
rare event
However…
Neutral cannot be selected for or against because they have no impact on fitness.They may persist or change in frequency due to genetic drift.
Deleterious have reduced fitness, therefore phenotypes resulting from beneficial
Beneficial mutations increase in frequency. Thus, average fitness increases over time
Maintenance of DNA Sequences:
Mutations are extremely rare
repair mechanisms correct 99.9% of all damage
Mutation rates are surprisingly similar across a wide range of taxon
From mammals to E.coli ~ 1 base per 109 nucleotides per
copying event (generation)
Occasional changes to DNA sequences benefit a species over the long-term
but individual survival requires genetic stability
Evolution has led to repair systems that allow just the
“right” number of mutations to escape detection
“Right” in the sense that enough mutations occur to drive evolutionary change and allow species to adapt.
Most harmful mutations are repaired or prevented to ensure the survival and health of individuals.
This balance is a result of natural selection optimizing the efficiency of DNA repair systems over millions of years
Repair systems are not perfect—and that’s intentional. They allow a small number of mutations to escape detection, striking a balance between stability and variability.
Silent Mutations: Most mutations do not significantly alter phenotype and may not affect protein function. Most mutations are “silent”.
Mutation is in non-coding region
Much of the genome consists of non-coding regions that do not directly code for proteins (e.g., introns, regulatory sequences).
Mutations in these regions often have no effect because they don’t alter the proteins produced by the gene.
Example: A mutation in an intron is usually spliced out before the protein is made.
In coding region but no amino acid substitution
Codons in the genetic code are often redundant—multiple codons can specify the same amino acid.
A mutation that changes one codon to another synonymous codon does not alter the amino acid sequence of the protein.
Ex: Both GAA and GAG code for the amino acid glutamic acid. A mutation changing GAA to GAG has no effect on the protein.
Amino acid change but no loss of function
Some mutations result in a different amino acid being incorporated into the protein, but this change doesn’t affect the protein’s function significantly.
This happens if:
The new amino acid has similar chemical properties to the original.
The change occurs in a non-critical part of the protein.
The protein structure is flexible enough to tolerate the change.
Ex: Changing alanine to valine might not affect the protein if the site is not essential for its activity.
lethal loss of function = non-viable organism thus nothing
to observe
Some mutations cause a loss of function in essential genes, leading to a non-viable organism. These mutations often go unnoticed because the organism does not survive to be observed.
Ex: A mutation that prevents a vital protein from being made can lead to early embryonic death.
Mutations causes:
Damage: Caused by external factors; must be repaired to avoid becoming permanent mutations.
Many events can damage DNA:
thermal fluctuations (extremely common)
metabolic “accidents” (unintended oxidation)
rearrangements caused by radiation
UV, X-ray, etc.
environmental toxins (mutagens, carcinogens)
These are quite frequent events
Duplication: Amplification of specific gene sequences during replication.
Gene duplication accounts for a substantial fraction of the genomic variation among individuals and, thus, the raw material for evolution. Recent estimates suggest that more of the genome is affected by copy number variation than by differences derived from point mutations
During replication– accidental copying of the same sequence more
then once during replication—replication “slips”
During meiotic crossing over– “misalignment”
One chromosome experiences a deletion the other experiences a duplication. Thus one of the resulting chromosomes now has twocopies of one of the alleles involved in the crossover
Ex
Normal Crossover:
Chromosome 1: A - B - C - D - E
Chromosome 2: A - B - c - d - E
After proper alignment and crossover:
Chromosome 1: A - B - c - d - E
Chromosome 2: A - B - C - D - E
Misaligned Crossover:
Chromosome 1: A - B - C - D - E
Chromosome 2: A - B - c - d - E
Misalignment results in:
Chromosome 1: A - B - D - E (Deletion of C)
Chromosome 2: A - B - C - C - D - E (Duplication of C)
Substitution mutations…
can hinder: the organism if they result in a missense or nonsense mutation that leads to a malfunctioning protein or a loss of function.
can be beneficial: be silent or if they lead to a protein that is better suited to the environment
Horizontal Transfers:
In contrast to vertical transfer, horizontal transfer allows for the acquisition of new genetic material for one or both of the involved cells, enriching genetic diversity across populations. The main methods of horizontal transfer include
Transformation: the uptake of free DNA from the environment by a cell.
Transduction: the transfer of genetic material between bacteria via bacteriophages.
When a bacteriophage infects a bacterial cell, it can inadvertently package part of the host's DNA into a new viral particle, which can then be transferred to another bacterium during subsequent infections.
Conjugation: the direct transfer of DNA between two bacteria through a physical connection.
Viruses
procaryotic and eukaryotic
Acquisition of environmental DNA
almost exclusively prokaryotic
Sexual reproduction
primarily eucaryotic
occasionally prokaryotic
Vertical transfer :
Vertical transfer is defined as the direct transfer of genetic materials from parent to offspring. This process typically involves replication of the parent organism's DNA and division into daughter cells. In prokaryotes, this is often accomplished through binary fission, where DNA is replicated and distributed evenly to two new cells. Vertical transfer does not introduce new genetic material into a population but may result in genetic variations through replication errors or mutations that arise during DNA synthesis. These mutations can potentially affect the offspring's fitness and adaptability.
parent to offspring
no “new” genetic material
Genetic (Protein-Based) Variation
Examples: Taste
Humans show different variation when it comes to the perception of taste
caused by different protein receptors on cells of the tongue—products of coding regions. Different proteins bind different “chemicals”.
PTC and TAS variants
involves the genetic basis for the ability to taste phenylthiocarbamide (PTC), a chemical compound that some people can taste while others cannot. This ability is linked to a gene called TAS2R38, which encodes a protein that binds to PTC and helps transmit a taste signal to the brain
PTC does not naturally occur in food
How it works: The TAS2R38 gene produces a receptor that is sensitive to the presence of PTC, triggering a cascade of signals that inform the brain about the taste, resulting in a perception of bitterness for those who possess the tasting variant. Individuals who lack the tasting variant of the TAS2R38 gene do not experience this bitterness, highlighting the genetic diversity in taste perception among humans.
There are two versions of the gene for TAS; the TAS protein is variable
Taster (T) alleles: The variant of the TAS protein binds PTC very tightly—delivers a strong signal (+) [PAV ]
Non-taster (NT) alleles: the other variant, does not bind to the compound so no signal (-) [AVI]
Difference between them is just three amino acids
out of 333 total
Humans inherit two copies of the TAS gene
– one from mother, one from father
Three genotypes possible
– (+/+) , (+/-) , (-/-) (in textbook (+) =PAV, (-) =AVI)
Three phenotypes possible
– strong taste, moderate taste, no taste at all
Best one is (+/-): because it demonstrates a balanced expression of traits, allowing for a diverse range of phenotypic outcomes.
Evolution Lesson
Heritable Variation in the TAS2R38 Gene: meaning the ability to taste bitter compounds like PTC and certain chemicals in green vegetables is passed down from parents to offspring (heritable). This (variation) leads to different versions (alleles) of the gene, which can result in different abilities to taste bitterness.
Selection on the TAS2R38 Gene: Selection refers to the process by which certain traits become more or less common in a population due to their effects on survival or reproduction. In this case, the TAS2R38 gene could be subject to selection based on its effects on food preferences, which might influence health outcomes.
Green Vegetables and Bitter Taste:Some people (especially those with the (+/+) or (+/-) genotypes) find green vegetables like broccoli bitter because these vegetables contain compounds (like glucosinolates) that bind to the TAS2R38 protein, triggering a bitter taste. People with the (-/-) genotype, who are non-tasters, are less sensitive to this bitterness and are, therefore, more likely to enjoy eating green vegetables.
Are (-/-) Individuals Healthier?: (-/-) individuals, who enjoy green vegetables more, may consume them more regularly, which could provide them with health benefits.On the other hand, (+/+) individuals who find these vegetables bitter may avoid them, potentially missing out on these health benefits.
However, it's not as simple as saying that (-/-) individuals are definitively healthier. The relationship between the TAS2R38 gene and health outcomes is complex and depends on many other factors, such as overall diet, lifestyle, and genetic predispositions to other conditions.
Additionally, research suggests that while (-/-) individuals may have a preference for certain vegetables, their overall health can also be influenced by factors such as physical activity levels, socio-economic status, and access to diverse food options, making it essential to consider the broader context when evaluating health outcomes.
Why Does the (+) Allele Exist?:
Balancing Selection: The presence of the (+) allele, which makes individuals more sensitive to bitter tastes, might be explained by balancing selection. This is a type of selection where different alleles are maintained in the population because they each offer some advantage in different environments or situations.
Ex: while (+) individuals might avoid bitter-tasting vegetables, they might also be more sensitive to toxic substances that have a bitter taste, potentially providing a survival advantage in environments where bitter compounds are linked to harmful toxins.
Ex: (+) allele could therefore confer a protective advantage against certain toxins, while (-/-) individuals may benefit from eating more green vegetables due to their ability to tolerate bitterness.
Ex: Environmental Factors: In different environments or historical contexts, the benefits of being a taster (with the (+) allele) might have outweighed the disadvantages. For instance, if people were more exposed to toxic plants or foods, being a taster could have helped them avoid harmful substances.
Recap
Vegetables contain many toxins in addition to beneficial nutrients
defense against predation by herbivores
many of these toxins carry a bitter flavor
A “healthy” diet requires balancing nutritional intake with toxin avoidance
(+/-) would favor this balance and may have been the
most “fit” genotype when early humans were experimenting with possible new plant food sources
the (+) allele would prevent eating highly toxic plants
the (–) allele would allow one to tolerate plants with just a
little toxin but otherwise beneficial
Importance of Genetic Variation
Survival of Species: Genetic variation is crucial for a species' adaptability in changing environments.
Most variable trait values are the result of variation in the structure of proteins
Protein structures that convey higher “fitness” will automatically become more common in a population over time
Protein structures leading to decreased fitness will become less common may even disappear over time
Evolutionary Trade-offs: Phenotypes often show trade-offs, where certain traits may enhance fitness in one environment but hinder it in another.
Fitness often involves tradeoffs
The balance of alleles like PTC sensitivity in humans affects dietary preferences and fitness
No Single Protein Defines Fitness:
Fitness refers to an organism's ability to survive and reproduce, passing its genes to the next generation. While proteins play a crucial role in biological functions, no single protein determines an organism's overall fitness. Instead, fitness depends on the interaction of many proteins and traits within the organism.
Ex. A protein that helps detect bitter toxins might increase fitness in one environment but have little or no effect in another.
Slight Differences in Fitness:
Many proteins are variable, meaning there are slightly different versions of them (due to genetic variation).These differences might lead to small changes in how the protein functions, which can result in slight differences in fitness.
Ex: One version of a protein might work a little faster or more efficiently than another, giving a slight advantage. In some cases, the differences might not matter much in terms of survival or reproduction.
Fitness Depends on the Environment:
The environment plays a critical role in determining fitness because it affects how useful or detrimental a particular protein (or trait) is.
Ex: A protein that helps tolerate cold temperatures might improve fitness in a cold climate but provide no advantage in a warm climate.
Ex: Similarly, a protein that helps digest a particular food might be advantageous if that food is abundant but irrelevant if it’s not available
The Environment is Not Static:
Environments change over time, which means the traits or proteins that were advantageous in one setting might become less useful—or even harmful—in another.
Ex: A mutation that provides resistance to a disease might increase fitness while the disease is present but provide no benefit (or even a cost) once the disease is eradicated.
Remember:This dynamic nature of the environment ensures that fitness is not a fixed quality; it is always changing in response to new environmental pressures.
Environmental Variation, Plasticity, and Developmental Stages
Environmental Variation:
Most components of the environment are variable–different organisms may respond differently to the same environmental exposure
sun tan vs sun burn
strength increase as a result of training
these are not permanent changes; rather, they represent temporary adaptations that can fluctuate based on ongoing exposure and individual resilience.
Phenotypic Plasticity: Some organisms can develop different forms based on environmental conditions during early development but retain these forms for life (e.g., color of moths based on tree background).
involves some component of the environment modifying early gene expression
Plasticity can be fast or slow depending on the context
Fast plasticity involves quick changes in response to environmental cues (e.g., color change in animals or rapid brain adaptation during learning).
Slow plasticity involves gradual changes over time (e.g., bone density adjustment, long-term brain recovery)hormonal regulation of growth factors that influence development.
Water Fleas:
Genetically identical individuals (clones) no genetic variation between them
When conditions are auspicious, they reproduce by cloning, switching to sexual reproduction only when conditions deteriorate. Also useful is that certain environmental cues trigger changes in their morphology, physiology, and behavior
Exposed to two different environmental conditions
1 ) midges and Kairomone present
2 ) midges and kairomone are not present
Group 1 develops armor
inducible defense: a strategy employed by organisms, such as the midges, to develop protective traits in response to environmental cues, such as the presence of kairomones.
Group 2 does not
phenotypic variability tied to environmental
variability—Plasticity
What if not all water fleas respond to midge
kairomone the same way?
Genetic Variation: Some water fleas may have genetic differences that affect their sensitivity to kairomones.
For example:
Some fleas may respond strongly by developing defensive traits (e.g., spines or thicker carapaces).
Others may have a weaker or no response, either because they lack the necessary receptors or because their physiology prioritizes other traits.
The genes provide the "blueprint" for flea, but the kairomone acts as the "on switch” to synthesize
certain proteins, and armor is built. So that is why this new armor is not heritable, as this change was done by the environment; the environment can't change the genetic code.
Also because of…
natural selection: If midges are a consistent and significant predator, fleas that respond strongly to kairomones (e.g., by developing defenses) might have higher survival rates. Over time, this could lead to an increase in the frequency of genes associated with a strong kairomone response.
trade off : Defensive traits (e.g., spines) often come with a cost, such as slower growth or reduced reproduction. In environments with fewer predators, fleas that don’t respond to kairomones might have an advantage because they avoid these costs.
Ecological Implications:
Predator-Prey Dynamics:Non-responsive fleas might be more vulnerable to predation, while responsive ones survive better, influencing the population structure and predator-prey interactions.
Population-Level Defense: If only a portion of the population responds to kairomones, the population may still experience reduced predation overall, as predators might focus on less-defended individuals.
Leopard gecko:
Temperature-Dependent Sex Determination: Some species, like the leopard gecko, have sex determined by incubation temperature due to protein shape changes influenced by heat.
Sex determination is tied to environmental variation but there is apparently a genetic component also
Phenotypes Vs Genotypes
Genotype:
The genotype refers to the genetic makeup of an organism—the specific set of genes and alleles it inherits from its parents.
It is the internal genetic code that provides the instructions for an organism’s development and traits.
Ex: The gene that codes for eye color in humans is part of the genotype. A person may have two alleles for eye color: one for brown eyes (B) and one for blue eyes (b).
Inheritance: Passed from parents to offspring through reproduction.
Changes through: mutations, recombination, gene flow, and natural selection can all lead to variations in traits among individuals in a population.
control:Controlled by genetic information encoded in DNA.
Phenotype:
The phenotype refers to the observable characteristics or traits of an organism, which result from the interaction between its genotype and the environment.
The phenotype reflects the combination of alleles in the genotype, and whether a trait appears dominant or recessive depends on the alleles involved.
Offspring do not inherit phenotypic expressions directly, ie, from their parents, but rather the underlying genotypes that can influence the expression of traits in varying environments.
Ex. If people bulk up by lifting weights, their offspring are not more powerful. If giraffes stretch for leaves, it has no consequence for the reach of their offspring.
Recap
It includes things like physical appearance, behavior, biochemical properties, and how an organism responds to environmental factors.
Ex: A person with the genotype Bb (brown and blue eye color alleles) will have brown eyes as the dominant brown allele (B) is expressed in the phenotype.
Inheritance: Affected by genotype, but also influenced by environmental factors.
Changes through: Changes can happen through natural selection, mutations, and environmental factors. These changes affect how an organism looks, behaves, or survives in its environment.
Control: Affected by both genetic factors (genotype) and environmental influences (e.g., nutrition, climate).
Together they…
The genotype provides the potential for certain traits to develop, but the phenotype is the actual expression of those traits in the organism.
The phenotype is not only influenced by the genotype but also by environmental factors, such as diet, climate, and experiences.
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