Exam 1 Flashcards
Human Evolution and Cultural Adaptations:
Timeline:
- 300,000 years ago: Emergence of modern Homo sapiens (oldest transitional modern human found in Morocco)
- For hundreds of thousands of years: Limited to lithic (stone) technology
- ~30,000 years ago: Major advancements begin with domestication
- ~12,000 years ago: Emergence of agriculture
- Industrial Revolution: Dramatic changes in human health
Human Life Expectancy:
- Myth: People in the past were not all dead by 30
- Evidence from ancient documents, artworks, and studies of extant traditional peoples
- Characteristic human lifespan evolved:
- High mortality in infancy
- Sharp decrease and constant mortality till about 40 years
- Mortality rises to peak at about 70 years
- Most individuals remain healthy through their 60s or beyond
Changes in Human Population Size & Technology:
- Exponential increase in population size correlates with technological advancements
- Key events: Agriculture, Mathematics, Rise of Civilizations, Industrial Revolution
Factors Contributing to Increased Life Expectancy:
- Advances in nutrition
- Infection control and treatment
- Trauma care
- Maternity and neonatal services
Challenges with Increased Life Expectancy:
* Rise in diseases like cardiovascular disease, cancer, and mental disorders
* Aging process: DNA packaging changes (e.g., Werner syndrome)
Mismatch: Human Expectation & Evolution:
- Evolution is concerned with species propagation in a particular environment
- Evolutionary success ≠ long, healthy life
- Fitness defined as successful passing of genes to the next generation
Theory of aging
- Cells are not getting packaged correctly as you age
Niche Construction:
- Humans as niche constructors through technology
- Environmental modifications can have positive and negative consequences on human health
- Niche construction is the process by which organisms alter their environment, which can have a significant impact on their ecosystems and evolution.
What is Disease?:
- Lactose Intolerance Example:
* Inuit: 99% meat diet
* Lactase enzyme production in small intestine
* Mutations in silencer region allow gene expression in some populations (helps breakdown enzyme to help tolerate lactose)
* Lactose tolerance may have posed a reproductive advantage in pastoral societies (societies that use lot of dairy) - Types of Lactose-related Conditions:
* Adult Hypolactasia: Normal from evolutionary standpoint for non-dairy consuming populations
* Congenital Hypolactasia (baby cannot digest mother’s milk): Fatal condition 500+ years ago, now treatable. (temporal problem because this is not as big of a problem with modern culture) - Mismatch Theory:
* Understanding disease by comparing evolutionary history to current environment (a disease in one environment might not be a disease in another) - Plasticity:
* Physiological/Epigenetic adaptations to environmental changes
* Example: Water flea developing horn in presence of predators
* Disease occurs when plasticity limit is exceeded
Phenotypic Plasticity: Phenotypic plasticity isthe ability of an organism to express different phenotypes in response to environmental changes. (ex : water flea)
If we didn’t have culture we would have to rely on plasticity, which demonstrates the necessity of culture
Human-Induced Environmental Change:
- Dramatic changes, especially since Industrial Revolution
- Question: What is the extent of human plasticity to these new environments?
Psychiatric Disorders and Mismatched Environments:
- Humans evolved for limited social interactions
- In the past: Approximately 150 total lifetime social interactions
- Modern environment: Vastly increased social interactions
- This mismatch may contribute to psychiatric disorders
Human Variation:
- Different populations experienced distinct evolutionary pressures
- Globalization leading to genetic admixture between populations
- Special abilities in populations due to evolutionary history (e.g., Inuit enhanced digestion of omega fatty acids)
- Adaptations can become vulnerabilities in different environments
Genetic admixture isthe process of gene flow between two or more genetically distinct populations, resulting in mixed ancestry.
Human Variation (continued):
- Example of adaptation and potential vulnerability: The Inuit
- Arctic Inuit consume 99% of their calories from meat
- Adaptation: Enhanced digestion and utilization of Omega Fatty Acids
- Potential vulnerability: If exposed to a Western Diet, this adaptation may leave them more susceptible to disease
Timeline of Human Adaptation:
- 100,000+ years: Adaptation to different natural environments
- 10,000 years ago: Agriculture & Domestication, adaptation to new diets
- 250 years ago to present: Dramatic environmental change
Key Question:
Can humans adapt genetically to the dramatic environmental changes of the past 250 years, or will the limits of plasticity and human variation lead to disease?
Diversity of Life
- Tree of Life concept introduced
- Tropical rainforest: Over 1000 different tree species in an area the size of 15 city blocks
- Panamanian rainforest: One tree species can yield 945 different beetle species
- Africa’s Lake Malawi: Over 500 fish species belonging to a single genus
- Scientists have identified ~2,000,000 species
- Current species diversity is only a minuscule fraction when considering all extinct species on Earth
Evolutionary Theory and Adaptation
- Explains diversification of life and adaptation to environment (only partially)
- Adaptation (evolutionary sense):
- Effect on fitness: Ability to survive & reproduce with viable offspring
- Does NOT mean matching to environment
Mechanisms of Evolution
Charles Darwin’s Concept
- Evolution: “Descent with Modification”
Key Mechanisms
- Genetic Changes
- Individual Variation within the Species
- Differential Reproductive Success (A situation in which some individuals leave more offspring in the next generation than do others, often due to traits that confer advantages in survival and/or reproduction.)
- Variation is Heritable
Natural Selection Process
- Bears with successful mating traits increase that trait in the population over time
- Population frequency changes over time
- Definition: Change in inherited traits of a population through successive generations
- Traits passed on include:
- Tangible traits (e.g., butterfly wing patterns, crocodile scales)
- Anonymous traits (e.g., DNA nucleotide sequences)
- Evolutionary inheritance focuses on transfer of genetic sequences
- Evolution occurs when genetic sequences change and are inherited across generations
Individual vs. Population Evolution
- Individuals do not evolve (sort of) - only in the context of population evolution
- Individual evolution argument - Our cells are evolving through every replication
- Populations evolve via changes passed on to successive generations
- Illustrated with “Generation 1” and “Generation 2” concept
Importance of Variation
- Without variation, populations would stay the same over time
- Darwin recognized variation as the motor of evolution
- Evolution would not exist without variation
Source of Variation
Genetic Code Mutation
- Mutation must occur in gametes for evolution
- Not in somatic cells (skin cells, liver cells)
Sexual Reproduction and Recombination
- DNA recombination during meiosis
- Maternal and paternal copies combine
- Exchange of genetic code from both copies
- Creates new combinations of genes
- Maximizes genetic diversity in offspring
- Occurs during prophase I of meiosis
- Homologous chromosomes swap DNA segments (crossing over)
Importance of Variation
- Not all variation is important for deterministic evolution
- Most variants are neutral (no effect on phenotype)
- New variation passed to next generation through mutation and recombination
Definitions
- Phenotype: Observable trait or characteristic of an organism
- Can refer to complex traits, adaptations, and behavior
- Genotype: Genetic code at various levels
- Genome level
- Chromosome level
- Gene level
- Single nucleotide level
Evolution vs. Natural Selection
- Not equivalent terms
- Natural selection is one force driving evolutionary change
- Other mechanisms can be equally important
- Trait changes not always result of selective processes
- Neutral theory of molecular evolution: Many genetic differences between species are selectively neutral
Constraints on Variation
- Small population size limits variation for adapting to changing environments
- Variation highly constrained in vital genome areas
- Variation in coding and regulatory areas can cause disease
- Deleterious gene (allele) categories can depend on environment
- Can vary by simple medical classification
Natural Selection
Darwin’s Theory
- Based on fitness-enhancing traits
- Traits that improve survival or reproductive success more likely to be passed on
- Example: Breeding for desirable traits (e.g., sociability in dogs)
Complexity of Traits
- Simple traits: Few genes control phenotype, little environmental interference
- Complex traits: Many genes, gene interactions, vulnerable to environment
- Example: King Frederick William of Prussia’s attempt to breed an army of giants
- Result: Average-sized army with reduced heights compared to parents
- Example: King Frederick William of Prussia’s attempt to breed an army of giants
Key Points
- Ecology is an agent of selection
- Acts on traits linked to differential fitness (reproductive success)
- Natural Selection Does NOT equal “Survival of the Fittest” (Herbert Spencer’s misinterpretation - also assumed evolution is directional)
- Evolution is not directional or progressing toward an ultimate goal
- Not “going somewhere” - just describes changes in inherited traits over time
- Increases in biological complexity not necessarily “progress”
- Left-hand wall to complexity: Simplest organism can only become more complex or stay the same
- Terms like “reverse evolution” and “devolution” are nonsensical
Speed of Selection
- Varies based on complexity, environment, and genetic constraints
- Can take many generations (e.g., lactase persistence trait - thousands of years)
- Can be rapid with pathogens
- Example: European rabbits in Australia
- 1859: 12 pairs introduced
- 1900: Population increased to hundreds of millions
- 1950: Myxoma virus introduced (the gave mosquitoes that are known to bite the bunnies to give the bunnies the virus - virus shuts off immune system)
- First epidemic: 99.8% mortality
- Second season: 90% mortality
- Third outbreak: 40-60% mortality
- Resistance increased: Less than 50% deaths after 7 years
- Depended on inheritance of genetic immunity
- Example: European rabbits in Australia
Detecting Natural Selection
- J.B.S. Haldane’s “malaria hypothesis” (1940s)
- Red blood cell disorders (sickle-cell anemia, thalassemias) prominent in malaria-endemic regions
- A.C. Allison’s confirmation:
- Sickle-cell mutation (HBB gene) limited to Africa, correlated with malaria endemicity
- Sickle-cell trait carriers resistant to malaria
- First example of human adaptation through natural selection
- Helps identify biological mechanisms of disease resistance
- Shows how pathogens evolve to remain threats
- Human Genome Project (2001) and population sequencing (2007) allowed detection of selection signals across the genome
Richard Dawkin
- theory is gene is the most important entity there is
- Natural Selection Favors the Gene
- The Selfish Gene, published in 1976, established Professor Richard Dawkins as a leading figure in evolutionary theory and popularised the idea that replicating genes are the central force behind evolution, not individual organisms or species.
- Gene doesn’t care about the organisms, it cares about propagating itself as a gene
- it’s not about the fitness about the species
- Evolutionary Theory: This refers to the understanding of how species change over time through natural selection, mutation, and other mechanisms.
- Richard Dawkins (20th Century): Dawkins, a British evolutionary biologist, is well known for emphasizing the role of genes in evolution. His book The Selfish Gene (1976) argues that natural selection favors genes that best promote their own replication.
- Natural Selection Favors the Gene: According to Dawkins, it’s the gene, rather than the individual or species, that is the principal unit of selection. Genes that are successful in ensuring their own survival get passed on to future generations.
- Agent of Evolution is the Gene Itself: Genes drive evolutionary changes. Traits that confer advantages (or disadvantages) to an organism’s phenotype (physical characteristics) affect how likely it is that the genes will be passed on in a particular environment.
- Gene Propagation: Dawkins argues that genes essentially “care” about their own survival. This is metaphorical, meaning that genes persist if they help organisms survive and reproduce, even at the expense of the individual or species.
The Genomic Reality vs. The Selfish Gene
- Michael Eisen, an evolutionary biologist, critiques the gene-centric view of evolution.
- He describes it as an “artefact of history,” arising from convenience rather than accuracy.
- The emphasis on genes in evolution grew because they were easier to identify and study.
- This historical focus does not necessarily reflect the true importance of genes in evolutionary processes.
- Eisen warns against confusing ease of study with actual significance in shaping evolution.
- Genes can drive evolutionary change, but a gene-centered model is only one way to explain it.
- Other significant evolutionary dynamics challenge the single-gene model.
- The gene-centered model may obscure other drivers of evolution, such as:
- Cultural transmission of knowledge and behavior in social species (e.g., bees, humans) that allows adaptation without genetic changes.
- Culture-gene evolution, where culture and genes co-evolve, each influencing the other, rather than culture being subordinate to genes.
Epigenetics
- Epigenetic changes present another challenge to the selfish-gene model.
- These changes, such as DNA methylation and modifications to chemical wrappings around DNA, can alter gene expression without changing the DNA sequence.
- Epigenetic changes can allow heritable traits to be passed down through several generations without altering the actual genes.
- Gene function can be remodulated without altering the genetic code.
- Genes can be shut down or activated in response to environmental factors.
- This modulation allows organisms to adapt without permanent genetic changes.
- Examples
- Grasshopper vs. Locust - both are same species
- Locusts are dangerous to humans and can consume a lot of biomaterial in little time
- Grasshoppers mind their own business , don’t eat as much
- Locusts are grasshoppers in swarming mode - grasshoppers turn into locusts if they are crowded as nymphs
- Phenotypic plasticity where organisms exhibit different phenotypes (observable traits) based on external factors rather than genetic changes
Gene Expression, Chromatin Structure, and Epigenetics: The Regulation of Cellular Identity and Disease
- Eukaryotic cell-cell differences are determined by the expression of different sets of genes.
- An undifferentiated fertilized egg differs from a skin cell, neuron, or muscle cell due to differences in gene expression.
- Cancer cells act differently from normal cells because they express different genes.
- Microarray analysis can help scientists detect gene expression differences for cancer diagnosis and treatment selection.
- In eukaryotes, the default state of gene expression is “off” due to chromatin structure.
- Chromatin is a complex of DNA and histone proteins found in the nucleus.
- Histones are highly conserved proteins crucial for eukaryotic survival.
- Genes tightly bound with histones are “off.”
- The histone code, including modifications of histones’ positively charged amino acids, helps regulate gene expression.
- DNA methylation works with histone modifications to silence gene expression.
- Small noncoding RNAs like RNAi also contribute to forming “silent” chromatin.
- Acetylation of histone tails reduces DNA-histone interaction, making DNA more open.
- Chromatin remodeling complexes, using ATP, repackage DNA into more open configurations.
- Cells can maintain the same histone code and DNA methylation patterns through many divisions.
- Epigenetics involves the persistence of these patterns without reliance on base pairing.
- Epigenetic changes are linked to many human diseases.
- DNA can’t be read when its tightly packed into nucleosomes
- one mechanism of epigenetics is that it changes how DNA is packed so it effects how it is read
- Our choices on what we put in out body (ex. nutrition, smoking) can lead to epigenetic change over time leading to disease
Q: What determines eukaryotic cell-cell differences, and how does this relate to cancer and cell specialization?
A: - Eukaryotic cell-cell differences are determined by the expression of different sets of genes.
An undifferentiated fertilized egg differs from specialized cells (like skin cells, neurons, or muscle cells) due to differences in gene expression.
Cancer cells act differently from normal cells because they express different genes.
Microarray analysis can help scientists detect gene expression differences for cancer diagnosis and treatment selection.
Q: Describe the structure of chromatin and its role in gene expression.
A: - Chromatin is a complex of DNA and histone proteins found in the nucleus.
In eukaryotes, the default state of gene expression is “off” due to chromatin structure.
Histones are highly conserved proteins crucial for eukaryotic survival.
Genes tightly bound with histones are “off.”
DNA can’t be read when it’s tightly packed into nucleosomes.
Q: What is the histone code, and how does it relate to gene expression?
A: - The histone code includes modifications of histones’ positively charged amino acids and helps regulate gene expression.
Acetylation of histone tails reduces DNA-histone interaction, making DNA more open.
Chromatin remodeling complexes, using ATP, repackage DNA into more open configurations.
DNA methylation works with histone modifications to silence gene expression.
Small noncoding RNAs like RNAi also contribute to forming “silent” chromatin.
Q: What is epigenetics, and how does it persist through cell divisions?
A: - Epigenetics involves the persistence of histone code and DNA methylation patterns without reliance on base pairing.
Cells can maintain the same histone code and DNA methylation patterns through many divisions.
One mechanism of epigenetics is that it changes how DNA is packed, which affects how it is read.
Epigenetic changes are linked to many human diseases.
Q: How can lifestyle choices affect epigenetics and health?
A: - Our choices on what we put in our body (e.g., nutrition, smoking) can lead to epigenetic changes over time.
These epigenetic changes can potentially lead to disease.
Epigenetic modifications can affect gene expression without changing the DNA sequence.
Understanding epigenetics helps explain how environmental factors can influence gene expression and health outcomes.
This knowledge opens up new possibilities for disease prevention and treatment strategies.
Evolution: The Extended Synthesis
- The selfish-gene model faces tension with certain evolutionary phenomena.
- These phenomena, as noted by Gregory Wray in Evolution: The Extended Synthesis, are observable only at the scale of hundreds or thousands of genes.
- This large-scale view has become accessible only in the past decade with advancements in rapid genome sequencing.
- Epistatic or gene-gene interactions are particularly challenging to the selfish-gene model.
- Epistasis refers to the phenomenon where some genes (or their variants) significantly influence the activity and effects of other genes.
- A gene’s effect can vary greatly depending on the combination of other genes present.
- These interactions highlight the complexity of gene behavior beyond the selfish-gene perspective.
- In certain contexts wven simple traits inheritance could be affected
- Epistatic interactions occur in non-linear, non-additive ways, which were beyond the understanding when Dawkins wrote his book.
- Researchers Casey Greene and Jason Moore of Dartmouth have found that epistatic interactions can significantly distort conventional gene-trait relationships.
- In some cases, these interactions can negate a gene’s reliability as a trait carrier.
- Epistasis is not simply about one gene muffling or amplifying another, or about additive effects (e.g., four ‘tall’ genes making you taller than two).
- Multi-gene epistatic interactions can create complex combinations of mutual influence.
- A gene’s contribution to a trait may depend more on its interactions with other genes than on its inherent trait-making power.
- Card Game Analogy
- Epistasis implies that individual genes often have minimal inherent significance, similar to playing cards in poker.
- In poker, the significance of a card, like the two of hearts, depends heavily on the other cards in hand.
- The card’s trait is almost meaningless on its own; its effect relies on the context of the entire hand.
- A card is replicable in that it remains a two of hearts each time it’s dealt.
- For a gene to have the same effect in future generations, it would need to be in the same genetic context as before, much like needing the same cards and betting behavior in poker.
- This scenario is highly unlikely, indicating that the effect of a gene is greatly influenced by its interactions with other genes.
- Genes is not static however like the Ace card is
Q: What challenges does the selfish-gene model face, and how have recent advancements affected our understanding?
A: - The selfish-gene model faces tension with certain evolutionary phenomena.
These phenomena are observable only at the scale of hundreds or thousands of genes.
This large-scale view has become accessible only in the past decade with advancements in rapid genome sequencing.
Epistatic or gene-gene interactions are particularly challenging to the selfish-gene model.
Even simple trait inheritance could be affected in certain contexts.
Q: What is epistasis, and how does it affect gene behavior?
A: - Epistasis refers to the phenomenon where some genes (or their variants) significantly influence the activity and effects of other genes.
A gene’s effect can vary greatly depending on the combination of other genes present.
These interactions highlight the complexity of gene behavior beyond the selfish-gene perspective.
Epistatic interactions occur in non-linear, non-additive ways, which were beyond the understanding when Dawkins wrote his book.
Epistasis is not simply about one gene muffling or amplifying another, or about additive effects.
