Human Genetics and Evolution
Lecture 18: Human Genetics
Challenges in Genetics Study
Longer Generation Time: It takes many years to observe inheritance patterns, making genetic studies lengthy.
Ethical Limits: Conducting controlled crosses for studies on humans is not ethically permissible.
Low Birth Rates: Human populations have lower birth rates compared to other organisms, complicating genetic studies.
Fewer Offspring Per Family: Families often have fewer offspring, limiting sample sizes for genetic analysis.
Tools Used in Genetics
DNA Sequencing Analysis: A method used for assessing the sequence of nucleotide bases in DNA, critical for understanding genetic information.
Pedigree: A diagram that shows the occurrence and appearance of phenotypes in several generations of a family, useful for tracking inheritance.
Inheritance Patterns
Autosomal Dominant:
Traits appear in every generation.
An affected individual usually has one affected parent.
Autosomal Recessive:
Traits may skip generations, with unaffected parents potentially being carriers.
X-Linked Recessive:
Mothers pass the trait to sons; generally affects more males than females.
Chromosomal Mutations
Definition: Changes in the structure of chromosomes, as opposed to changes in the number of chromosomes.
Types of Structural Changes:
Insertion (Duplication): An additional copy of a chromosome segment is created.
Deletion: A segment of the chromosome is lost.
Inversion: A segment of a chromosome flips its orientation.
Translation: A segment breaks off and attaches to another chromosome.
Changes in Chromosome Number
Also referred to as Aneuploidy.
Causes: Often due to nondisjunction during Meiosis I at Anaphase I.
Types of Aneuploidy:
Monosomy (2n-1): Missing one chromosome.
Trisomy (2n+1): Presence of an extra chromosome.
Monoploidy: A haploid set of chromosomes.
Lecture 19: Intro to Evolution
Carolus Linnaeus:
A naturalist who developed a hierarchical classification system, illustrating patterns of similarity among organisms and supporting evolutionary theories.
Geological Contributions to Evolutionary Theory:
Gradualism (James Hutton):
Proposed that the Earth undergoes small, continuous changes over time, akin to gradual erosion.
Uniformitarianism (Charles Lyell):
Postulated that processes shaping the Earth today are the same as those that occurred in the past, suggesting an ancient Earth, allowing time for evolutionary processes.
Jean-Baptiste Lamarck:
An early naturalist who proposed evolutionary change based on individual organisms.
Two Main Ideas:
Use and Disuse: Traits that are used frequently become enhanced, while those not used diminish.
Inheritance of Acquired Traits: Changes an individual acquires in its lifetime can be passed to its offspring.
Charles Darwin's Theory of Evolution:
Shifted focus from individuals to populations as principal units of evolution.
Descent with Modification:
Each generation represents modified descendants of previous ones, leading to diversity over time.
Four Observations of Natural Selection:
Overproduction: More offspring are produced than can survive in the environment.
Unequal Survival and Reproduction: Some individuals reproduce more successfully than others due to variations in traits.
Heritable Phenotypic Variation: Individuals in a population exhibit differences in traits that can be inherited.
Non-Random Survival and Reproduction: The ability to survive and reproduce is affected by phenotypic traits, with better-adapted individuals leaving more offspring.
Competition:
Results from overproduction and unequal survival; influenced by Thomas Malthus’s observations on resource scarcity as a driving force for competition.
Competition is a cause of evolutionary change; unlimited resources would reduce competition while still allowing for unequal reproduction.
Natural Selection:
Beneficial traits increase in frequency while non-beneficial traits diminish.
Causes non-random changes in allele frequencies over time driven by competition.
Mutations serve as the only source of new alleles in populations.
Natural selection acts on observable traits influenced by the environment, such as size and speed.
Fitness:
Defined as an organism's ability to survive and reproduce successfully.
Measured by:
Reproductive success: The number of offspring contributing to the gene pool of the next generation.
Individuals with higher fitness produce more offspring and pass on advantageous alleles more frequently.
Lecture 20: Population Genetics
Evolution Definition:
Changes in allele frequencies in populations over time.
Mechanisms of Evolution:
Mutations:
Random changes in DNA sequences; the primary source of new alleles, increasing genetic variation.
Non-Random Mating:
Changes genotypic frequencies through processes such as interbreeding, increasing homozygosity and decreasing genetic variation.
Genetic Drift:
Random changes in allele frequencies, predominantly affecting small populations; can lead to allele loss by chance, causing genetic variation to decline.
Types of Genetic Drift:
Bottleneck Effect: Occurs when a large population rapidly shrinks due to an event, leaving a random sample of alleles.
Founder Effect: A small group leaves a large population, resulting in a new population with a different allele frequency due to random sampling.
Gene Flow:
Movement of alleles between populations, leading to increased similarity over time; can either increase or decrease genetic variation based on the population receiving new alleles.
Natural Selection:
A non-random change in allele frequencies where individuals with higher fitness leave more offspring; favorable traits increase in frequency while less adaptive traits decrease.
Hardy-Weinberg Equilibrium:
A principle describing populations that are not evolving, requiring:
Absence of natural selection, mutations, and gene flow.
Large population size.
Random mating.
Equations:
Allele frequency: P + Q = 1
Where P = frequency of dominant allele and Q = frequency of recessive allele.
Genotype frequency: P^2 + 2PQ + Q^2 = 1
Where P^2 = frequency of homozygous dominant, 2PQ = frequency of heterozygous, and Q^2 = frequency of homozygous recessive.
Lecture 21: Speciation
Speciation Definition:
Occurs when populations can no longer interbreed to produce viable offspring; physical separation alone does not suffice.
Biological Species Concept:
Defines species as groups that can interbreed in nature and produce viable offspring, requiring reproductive compatibility.
Applicable to extant, sexually reproducing organisms but presents challenges for:
Asexual organisms.
Extinct species.
Microbes and viruses, which complicate evaluations of reproductive isolation.
Reproductive Isolation:
A central concept of speciation preventing species from interbreeding, maintaining distinct gene pools.
Prezygotic Barriers:
Prevent formation of zygotes, categorized by interaction level from least to most effective:
Habitat Isolation: Different habitats restrict encounters.
Temporal Isolation: Species breed at different times.
Mechanical Isolation: Morphological differences hinder mating attempts.
Gametic Isolation: Sperm and egg biochemistry incompatibility prevents fertilization.
Postzygotic Barriers:
Zygote forms but maintains separate gene pool:
Reduced Hybrid Viability: Hybrids develop improperly and have poor survival.
Reduced Hybrid Fertility: Healthy hybrids cannot reproduce.
Hybrid Breakdown: F1 hybrids are viable and fertile, but F2s are not.
Morphological Species Concept:
Defines species based on physical traits, applicable to living and extinct organisms.
Challenges include:
Determining which traits are significant.
Defining species boundaries.
Ecological Species Concept:
Defines species by their ecological niche, resource use, and roles in ecosystems.
Limitations include:
Multiple niches per species complicate identification.
Defining boundaries can be difficult.
Types of Speciation:
Allopatric Speciation:
Occurs due to geographic barriers halting gene flow.
Key Steps:
Geographic separation of populations.
Halted gene flow.
Divergent mutations, selection, and drift occur.
Genetic differences accumulate.
Reproductive isolation evolves, forming new species.
Sympatric Speciation:
Occurs without physical barriers, often due to behavioral or ecological factors leading to reduced gene flow.
Examples include sexual selection favoring specific traits, habitat differentiation, and polyploidy which instantly creates reproductive isolation.
Lecture 22: Phylogenetics
Lineage Hierarchy:
Systematic classification order from broad to specific:
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Parts of Phylogenetic Tree:
Node:
A branch point representing a divergence event; indicates a most recent common ancestor (MRCA) to descendant lineages.
Polytomy:
A node with more than two branches indicating uncertainty in the branching order of lineages.
Sister Taxa:
Groups that are each other’s closest relatives, sharing an immediate common ancestor.
Root:
The MRCA of all taxa in the tree.
Basal Taxon:
The lineage that diverged earliest from all other taxa, appearing near the root.
Types of Groups in Phylogenetics:
Monophyletic Group:
Comprises one common ancestor and all its descendants, also called a clade.
Paraphyletic Group:
Includes a common ancestor and some, but not all, descendants, excluding at least one lineage.
Polyphyletic Group:
Group assembled based on shared traits that were not inherited from a common ancestor, lacking a linking common ancestor.
Outgroup:
Taxon that is least closely related to the study group, helping to establish the root of the tree.
Similar Traits Across Species:
Homologous Traits:
Similarity due to common ancestry, exhibiting divergent evolution; same origin but differing function (e.g., human arm and bat wing).
Analogous Traits:
Similar traits arising from similar environmental pressures, evolving separately (convergent evolution); different origins but similar functions (e.g., bird wings vs. insect wings).
Synapomorphies:
Shared derived traits indicative of clades.
Plesiomorphies:
Shared ancestral traits.
Lecture 23: Population Genetics
Population Definition:
Comprised of members of the same species living in a specific area at the same time.
Population Density:
Calculated as the number of individuals per area or volume.
Key Variables:
b: Per capita birth rate.
m: Per capita mortality rate.
B: Total number of births.
M: Total number of deaths.
r: Population growth rate.
N: Population size.
K: Carrying capacity of the environment.
Population Growth Trends:
Growing Population:
Indicators include b > m, B > D, r > 0, and N < K.
Shrinking Population:
Marks include b < m, B < D, r < 0, and N > K.
Growth Models and Curves:
Exponential Growth:
Represents population growth to its maximum without resource limitations.
Logistic Growth:
Population growth that gradually levels off as it approaches carrying capacity (K) due to limited resources.
Type I Survivorship Curve:
High parental care, with most individuals surviving to old age (e.g., humans).
Type II Survivorship Curve:
Moderate mortality risk throughout life.
Type III Survivorship Curve:
High juvenile mortality with few surviving to adulthood.
Life History Strategies:
Interparous Species:
Display multiple reproductive events; must be K-selected.
Semelparous Species:
Exhibit a single large reproductive event; often die after reproduction and must be r-selected.
R-Selected Species:
Characterized by numerous offspring, rapid reproduction, minimal parental care, and substantial juvenile mortality.
K-Selected Species:
Exhibit few offspring, slow reproduction with high parental care, and lower juvenile mortality, often in stable environments (e.g., humans, elephants).
Lecture 24: Community Ecology
Community Ecology Definition:
The interactions of different populations of species living together in the same ecosystem.
Types of Species Interactions:
Competition (-/-):
Both species harm each other.
Predator Adaptations vs. Prey Adaptations:
Predator Adaptations: Claws, fangs for hunting.
Prey Adaptations:
Physical Defenses: Shells, spines, and quills.
Cryptic Coloration: Blend into surroundings for concealment.
Aposematic Coloration: Bright colors as warnings (warning coloration).
Mimicry: Two forms:
Batesian Mimicry: Non-toxic species mimic toxic ones.
Müllerian Mimicry: Both species are toxic, reinforcing avoidance by predators.
Symbiosis:
Long-term interactions between species, including:
Mutualism (+/+): Both species benefit.
Parasitism (+/-): One benefits, and the other is harmed.
Commensalism (+/0): One benefits without affecting the other.
Co-Evolution:
Two species exert selective pressures on each other, leading to mutual evolutionary changes.
Competitive Exclusion Principle:
When two species compete for the exact resource, one will outcompete the other, preventing both from occupying the same niche.
Succession Types:
Primary Succession: Initiates in an area without existing soil (e.g., post-volcano).
Secondary Succession: Occurs in an area where soil remains post-disturbance (e.g., after fires or floods).
Lecture 25: Ecosystem Ecology
Ecosystem Definition:
Comprises all biotic (living) and abiotic (non-living) components of the environment, encompassing organisms, energy, nutrients, water, and light.
Energy Production in Ecosystems:
Source of Energy: The sun.
Producers (Autotrophs): Organisms performing photosynthesis; convert light energy to chemical energy.
Primary Production: The amount of energy captured and stored by producers, dictating overall ecosystem energy availability.
Consumers: Organisms obtaining energy by consuming producers or other organisms.
Energy Transfer Hypothesis:
Energy transfer between trophic levels is inefficient, with the highest trophic levels receiving the least energy.
Energy is lost as heat at each level, making it unavailable for higher levels.
Energy Flow:
Moves in a one-way direction from the sun to producers to consumers; energy is not recycled.
Trophic Levels: Arranged by feeding levels within an ecosystem.
Food Webs: Illustrate pathways of energy flow; arrows denote energy transfer from prey to predator.
Nutrient Cycling:
Unlike energy, nutrients cycle within ecosystems.
Nitrogen Cycle:
Microbial action converts nitrogen into usable forms for living organisms, integrating nitrogen into food webs.
Limiting Factors:
Factors limiting ecosystem productivity include energy availability and nutrient levels (e.g., nitrogen and phosphorus).
In aquatic systems, light often serves as a limiting factor.
Aquatic Biomes:
Rivers and Streams: Freshwater environments characterized by currents.
Lakes:
Eutrophic Lakes: High nutrient levels, low oxygen, and significant organism sedimentation.
Oligotrophic Lakes: Low nutrient levels, high oxygen, and clear water; characterized by thermoclines.
Oceans:
Composed of saltwater, high oxygen, and shaped by wind-driven currents; contain phytoplankton (photosynthetic organisms).
Aquatic Zones:
Benthic Zone: The lowest layer in aquatic ecosystems, deriving energy from detritus.
Photic Zone: Sufficient light for photosynthesis with potential producers present.
Aphotic Zone: Lacks sufficient light for photosynthesis.
Primary Productivity:
Refers to the rate at which biomass is produced.
Measures how quickly producers convert sunlight energy into organic matter.
Lecture 26: Conservation Ecology
Sources of Biodiversity:
Genetic Diversity: Variations of genes/alleles within populations, indicating resilience and adaptability.
Species Diversity: Number and abundance of species within a given area; greater richness denotes higher biodiversity.
Ecosystem Diversity: The variety of ecosystems on Earth, representing the broadest scale of biodiversity.
Benefits of Biodiversity:
Ecosystem Services: Natural processes that sustain life, deriving from biodiversity rather than human activities (e.g., air and water purification, pollination, nutrient cycling).
Human Benefits: Medicine, food sources, fibers, etc.
Genetic Resources: Vital proteins, enzymes, and resistances essential for survival and adaptation.
Loss of Biodiversity:
Local Extinction (Extirpation): Species disappear from specific locations but remain elsewhere.
Global Extinction: Complete disappearance of a species worldwide.
Causes of Loss: Habitat destruction due to agriculture and human development, overharvesting that exceeds population replacement rates, introduced invasive species that outcompete natives, and climate change impacting survival.
Conservation Strategies:
Small Population Approach: Aimed at preventing the extinction vortex.
Extinction Vortex: A cycle where small populations face reduced genetic diversity, intensified genetic drift, resulting in lower fitness and further population decline, likely leading to extinction.
Minimum Viable Population (MVP): The smallest population size necessary to avoid the extinction vortex.
Declining Population: Identifying causes of population decline while still above MVP to address ecological or human factors before reaching critical levels.
Natural Preserves:
Protected areas that promote ecosystem functionality without human intervention.
Keystone Species:
Species whose presence significantly impacts ecosystem diversity; their removal leads to substantial biodiversity loss.
Effects of Climate Change:
Causes: Elevated greenhouse gas levels resulting in higher global temperatures.
Ecosystem-Level Effects: Altered ecosystem structures, biome redistributions, increased frequency and intensity of extreme weather events, heightened wildfires, and disruption of water circulation patterns.
Ocean Acidification: CO2 interaction with water resulting in carbonic acid formation, harming marine ecosystems, leading to coral bleaching.
Physical Impacts: Melting ice, increased flooding, and altered habitats.
Effects on Organisms:
Species range shifts as organisms migrate towards suitable climates (e.g., northward movements).
Trophic shifts as temperature zones shift to subtropical regions, affecting ecosystems.
Disrupted migration patterns; the rate of environmental changes increases annually.