Evolutionary Forces I - Key Terms (Skin Color, Selection, Drift, Phylogeny, Speciation, Physiology)
UV Radiation and Skin Color
Topic: Evolution of human skin color and its connection to UV radiation.
Part 1: Is there a connection between UV radiation and skin color?
UV radiation varies by latitude; highest UV intensity at low latitudes.
Skin color varies with latitude; darkest skin colors at low latitudes.
Part 2: What was the selective pressure?
A selective pressure is any reason that makes certain phenotypes have a survival benefit or disadvantage.
At equatorial latitudes, people with dark skin have an advantage because eumelanin (brown/black pigment) absorbs UV radiation and protects folate circulating in the blood.
Folate is important for healthy embryonic development and sperm production.
Practical implication: Dark skin protects folate from UV destruction, which is crucial for reproduction and development in high-UV environments.
Skin Color as a Polygenic Trait
Polygenic trait: a phenotype determined by alleles at more than one gene.
Skin color involves 6 primary genes, but as many as 169 genes may be involved.
An example shown: variation expected if skin color were controlled by 3 genes with two alleles each.
Negative and Positive Selection
Negative selection (purifying selection): constantly sorts variation from mutations, removing unfit variants.
Positive selection: increases rare variants that improve fitness; not always the focus of a study, which may instead emphasize the increase of beneficial variants.
Relationship: Negative and positive selection are not truly separable; they are different focal points of the same process.
Example sources: Nature Scitable on negative selection; studies often discuss positive selection when focusing on advantageous variants.
Vitamin D and Folate Trade-Off
High UV radiation leads to less vitamin D production and more folate destruction; low UV has the opposite effects.
Trade-off: Selection for lighter skin at higher latitudes to allow more vitamin D production; selection for darker skin at equatorial latitudes to protect folate.
Outcomes:
Selection for light skin to increase vitamin D production in low-UV environments.
Selection for dark skin to protect folate in high-UV environments.
Health implications mentioned: Vitamin D deficiency can lead to rickets; folate-related neural tube defects.
Evolutionary Forces: Types of Natural Selection, Genetic Drift, and Gene Flow
Learning goals overview: identify types of natural selection from allele frequency distributions; understand genetic drift due to random fluctuations; relate population size to drift; compare natural selection, drift, and gene flow; understand frequency-dependent selection.
Types of Natural Selection
Definitions: Evolution = change in allele frequencies across generations; types determine how phenotypes change over time.
Types:
Directional selection
Stabilizing selection
Disruptive selection
Frequency-dependent selection (positive and negative)
How Phenotype Distributions Change Under Different Selections
Disruptive selection: distribution shifts toward extremes; average phenotype is selected against.
Example context: variation in beak sizes or feeding strategies that favor extreme traits.
Directional selection: distribution shifts toward one extreme (mean increases or decreases).
Stabilizing selection: average trait value is maintained; extreme values are selected against.
Frequency-dependent selection: fitness depends on how common/rare a phenotype is.
Positive frequency-dependent: common phenotypes have higher fitness.
Negative frequency-dependent: rare phenotypes have higher fitness; maintains variation.
Positive and Negative Frequency-Dependent Selection: Examples
Positive frequency-dependent selection:
Heliconius butterflies: multiple morphs are toxic; common morphs are more readily avoided by predators, whereas rare morphs may be eaten more until predation learning catches up.
Link: common phenotypes gain a fitness advantage as predators learn to avoid them.
Negative frequency-dependent selection:
Grove snails and song thrushes: common shell types are eaten more often; rare shell types gain a fitness advantage; maintains variation over time.
Takeaway: Frequency dependence can maintain polymorphisms in populations.
Natural Selection Example: Hornbills and Pigmentation
Scenario: Southern yellow-tailed hornbills in Kalahari Desert; males possess pigmented feathers; richer pigment increases attractivity but also can increase heat load.
With climate change (warmer temperatures), the pattern of selection may shift with respect to pigment amount in males (less pigment may be favored if overheating reduces survival).
Natural Selection Example 2: Fantail Warblers and Parasitic Weavers
Fantail Warblers vs parasitic weavers: thicker feathers were beneficial against parasitism, but climate change shifts selection toward different feather thickness due to energy costs.
This illustrates how environmental changes can alter the direction or strength of selection on a trait like feather thickness.
Type of Natural Selection: Practice Questions (from slides)
Examples provided as interactive Wooclap questions (directional vs stabilizing vs disruptive) to test understanding of which type of selection applies to given scenarios.
Genetic Drift: Random Allele Frequency Change
Genetic drift: allele frequencies change by chance due to random sampling across generations; not driven by adaptation.
Occurs in all finite populations; its effects are stronger in small populations.
Consequences: harmful alleles may increase by chance; advantageous alleles may be lost; can cause large shifts in small populations.
Sampling error: probability differences when drawing a sample from a population; larger samples reduce sampling error.
Bottleneck Effect
Bottleneck: a drastic reduction in population size for at least one generation, amplifying genetic drift.
Example: Northern elephant seals experienced a severe bottleneck; surviving population shows different allele frequencies and reduced genetic diversity.
Founder Effect
Founder effect: loss of genetic variation when a new colony forms from a small number of individuals.
Example: The Amish population in Lancaster County, PA originated from about 200 German immigrants; high homozygosity for rare recessive alleles.
Disease example: Ellis-van Creveld syndrome is more frequent in the Old Order Amish due to founder effects.
Gene Flow (Migration)
Gene flow: transfer of genetic material (alleles) between populations.
Can introduce new alleles or change existing allele frequencies; often constrains local adaptation and reduces genetic divergence between populations.
Factors affecting gene flow:
Habitat fragmentation
Species mobility (e.g., birds can travel long distances; seeds/pollen move in plants; fish have limited movement)
Location (islands reduce exchange)
Corridors can facilitate movement in fragmented habitats
Example: Galápagos marine iguanas illustrate limited gene flow and geographic isolation.
Phylogeny and Classification
Tree of life: three domains; phylogeny is the evolutionary history of relationships among organisms.
Reading a phylogenetic tree: root (common ancestor), nodes (splits), clades (monophyletic groups).
Taxon vs clade: a taxon is any named group; a clade is a group consisting of an ancestor and all its descendants.
Significance: homologous vs analogous traits underpin tree construction; only homologous traits are reliable for inferring ancestry.
Homologous vs Analogous Traits; Convergent Evolution
Homologous traits: shared due to common ancestry; may not look similar.
Example: arm bones in tetrapods deriving from a common ancestor.
Analogous traits: similar due to convergent evolution; not due to common ancestry.
Example: wings of birds and bats; both used for flight but evolved separately; wings are analogous, not homologous in origin.
Homoplasy (an analogous trait) is when similar traits arise independently.
Ancestral vs Derived Traits; Clades
Ancestral trait: present in the ancestor of a group.
Derived trait: present in a descendant and differs from the ancestral trait.
Shared derived traits define clades.
Practice questions on ancestral vs derived traits are provided in slides.
Species and Speciation Concepts
Species concepts:
Morphological species concept: based on look-alike and unique physical traits.
Lineage/Phylogenetic species concept: species as branches on the tree of life; can apply to asexual organisms.
Biological species concept: groups that actually or potentially interbreed and are reproductively isolated from other such groups; not applicable to asexuals.
Speciation: one species splits into two; involves isolation and genetic divergence; allopatric vs sympatric speciation.
Prezygotic barriers: barriers before fertilization that prevent mating or fertilization.
Habitat isolation, temporal isolation, behavioral isolation, mechanical isolation, gametic isolation.
Postzygotic barriers: barriers after fertilization that reduce viability or fertility of hybrids (hybrid inviability, hybrid infertility, hybrid breakdown).
Allopatric Speciation and Vicariance/Dispersal
Allopatric speciation occurs when populations are geographically separated.
Dispersal: individuals move to a new area.
Vicariance: a habitat is physically split.
Vicariance vs dispersal can be inferred from data; examples include Amazon trumpeters dataset with vicariance/dispersal hypotheses and their support metrics.
Allopatric speciation is thought to be dominant in sexually reproducing organisms.
Sympatric Speciation and Polyploidy
Sympatric speciation occurs without geographic barriers; populations diverge in the same area.
Polyploidy can drive sympatric speciation:
Autopolyploidy: extra chromosome set within the same species; offspring often cannot mate with parent due to chromosome mismatch.
Allopolyploidy: combining chromosomes from two different species to form a viable polyploid; e.g., hexaploid bread wheat.
Prezygotic and Postzygotic Barriers: Examples
Prezygotic barriers:
Habitat isolation, temporal isolation, behavioral isolation, mechanical isolation, gametic isolation.
Postzygotic barriers:
Hybrid inviability, hybrid infertility (e.g., mules), hybrid breakdown (F2 inviability).
Evolution of Genes and Genomes
Mutations and recombination:
Mutations create new alleles; the only source of new genetic variation.
Recombination creates new combinations of existing alleles; allele frequencies remain the same in the population (no new alleles).
Gene duplication and genome evolution:
Gene duplications can lead to new functions (neofunctionalization), partitioning of functions (subfunctionalization), or redundant retention.
Pseudogenes are nonfunctional copies; de novo genes arise from non-coding DNA.
Antifreeze proteins in fish: antifreeze traits can evolve from duplications or de novo changes; Antarctic icefish antifreeze proteins evolved from a duplicated digestive gene family.
Horizontal (lateral) gene transfer: transformation, conjugation, transduction, endosymbiosis (mitochondria and chloroplasts).
Signatures of Evolution in DNA Sequence
Synonymous (S) vs nonsynonymous (N) substitutions:
N/S = 1: neutral replacement; no fitness effect.
N/S > 1: positive selection; amino acid changes favored.
N/S < 1: purifying (negative) selection; amino acid changes selected against.
Implications: helps identify genes under different selective pressures.
Molecular Clock
Concept: DNA/protein sequences evolve at relatively constant rates; divergence time is proportional to sequence differences.
Calibration: must be anchored to independent data (fossils, known divergence times, biogeographic dates).
Uses: dating infections (e.g., HIV-1 origin estimates), dating divergence times in phylogenies.
Genes, Genome Size, and Duplication
Genome size varies widely among eukaryotes; not tightly correlated with organismal complexity.
Gene number varies less than genome size; many organisms share similar numbers of genes, but genome sizes differ due to noncoding DNA and transposable elements.
Gene duplication as a major source of novelty:
Outcomes: nonfunctionalization (pseudogene), neofunctionalization (new function), subfunctionalization (partitioning of function), retention of original function in both copies.
De Novo genes: new genes arising from noncoding DNA.
Notothenioids Icefish Case Study (Making of the Fittest; Transcripts 289–291)
Icefish (Notothenioids) live in extremely cold Antarctic waters and lack hemoglobin and red blood cells in some species.
Icefish blood is dilute; they can absorb enough oxygen through scaleless skin to survive without hemoglobin.
The antifreeze proteins in Antarctic icefish evolved to prevent ice crystallization in body fluids; icefish exhibit unique antifreeze genes that arose via gene duplication followed by functional divergence.
Origins of antifreeze proteins: in Antarctic icefish and Arctic cod, antifreeze proteins originated via duplication or de novo formation; some antifreeze genes resemble preexisting genes and were modified to gain a new function.
The narrative emphasizes that evolution often borrows from existing genes and tinkers with them; sometimes loses ancestral functions (e.g., loss of hemoglobin in icefish) when new strategies provide adequate survival advantage.
Surface Area to Volume Ratio, Temperature Regulation, and Homeostasis
SA/V ratio: smaller or thinner objects have higher SA:V; larger or thicker objects have lower SA:V.
Implications: exchange of gases and heat is diffusion-limited; SA/V influences metabolic rate and heat exchange.
Evolutionary solutions: various anatomical adaptations modify SA/V to optimize exchange (e.g., flat leaves vs spines in cacti).
Homeostasis: regulation of a stable internal state in the face of environmental changes; includes negative feedback and positive feedback.
Negative feedback: opposes the trend to return to a set point (e.g., mammalian temperature regulation).
Positive feedback: reinforces the current trend to accelerate a process (e.g., blood clotting).
Temperature Regulation in Organisms
Endotherms: rely on metabolic energy to regulate body temperature (mammals and birds).
Ectotherms: rely on external energy sources to regulate body temperature (reptiles, many fish, invertebrates).
Heterotherms: alternate between endothermic and ectothermic strategies depending on conditions (e.g., hibernation).
Comparative examples: lizard vs mouse metabolic rates; thermoneutral zones; countercurrent heat exchange in limbs.
Behavioral regulation: ectotherms regulate body temperature via behavior (e.g., basking, seeking shade).
Gas Exchange and the Respiratory System
Gas exchange is driven by diffusion according to Fick's law: Q = rac{D A}{L} (P1 - P2) where Q is the rate of gas exchange, D is the diffusion coefficient, A is surface area, L is diffusion path length, and P1, P2 are partial pressures.
Factors that increase gas exchange:
Increase surface area (A)
Increase partial pressure gradient (P1 - P2)
Decrease diffusion distance (L)
Gas exchange in water vs air:
Air has higher O2 partial pressures, lower density and viscosity, and is easier to diffuse through than water.
Water has lower O2 concentration and is more challenging to extract O2 from; aquatic animals often have specialized lungs or gills to maximize diffusion.
Fish gills use countercurrent flow to maximize O2 uptake; gill lamellae increase surface area and minimize diffusion distance.
In humans, the respiratory system includes nasal cavity, pharynx, trachea, bronchi, bronchioles, and alveoli where gas exchange occurs.
The ventilation/perfusion (V/Q) ratio measures respiratory efficiency: ventilation (airflow) vs perfusion (blood flow).
Oxygen transport and exchange:
Hemoglobin binds O2; the O2 dissociation curve shows Hb saturation as a function of PO2.
Bohr effect: lower pH (higher CO2) reduces Hb affinity for O2, promoting O2 release in tissues with high metabolic demand.
CO2 transport in blood involves bicarbonate formation via carbonic anhydrase and can bind to hemoglobin (carbaminohemoglobin).
Evolving respiratory strategies: diffusion constraints, countercurrent vs concurrent flow, and adaptations in endotherms vs ectotherms.
The Oxygen Dissociation Curve and the Bohr Effect
Oxygen dissociation curve: Hb-O2 saturation vs PO2; left shift indicates higher Hb affinity; right shift indicates lower affinity.
Factors shifting the curve to the left (higher affinity): lower temperature, higher pH, lower CO2, and reduced 2,3-BPG (in mammals).
Bohr effect (pH influence): in tissues with high CO2, pH decreases, Hb affinity for O2 decreases, promoting delivery of O2 to tissues.
The Making of the Fittest: Antifreeze Proteins and Evolution of Notothenioids
Antarctic icefish notothenioids evolved antifreeze proteins that prevent ice crystallization in body fluids, enabling life in near-freezing waters.
Origins: antifreeze genes originated from duplicated/de novo changes of existing genes; icefish later lost hemoglobin in many species, relying on other mechanisms for oxygen transport.
The broader lesson: evolution repurposes existing genetic material, sometimes discarding ancestral functions when new strategies offer greater fitness in changing environments.
Additional Notes on Learning Assessments and Practice
Throughout the slides, interactive questions (Wooclap) were used to test understanding of natural selection types, allele frequencies, and phylogeny concepts.
Recitation and problem sets are part of the course evaluation in addition to the final exam.
Quick Reference: Key Terms and Concepts
Allele frequency: proportion of a given allele in a population.
Polygenic trait: trait controlled by multiple genes.
Folate: essential B vitamin important for embryonic development and reproduction.
Vitamin D: nutrient synthesized with UV exposure; deficiency can lead to rickets.
Eumelanin vs pheomelanin: brown/black vs red/yellow pigments in skin.
Positive/negative selection: differential survival or reproduction leading to shifts in allele frequencies.
Genetic drift: random changes in allele frequencies, especially in small populations.
Bottleneck and founder effects: drastic reduction or new population formation that alters allele frequencies.
Gene flow: movement of alleles between populations.
Phylogeny: evolutionary history relationships among organisms.
Clade/monophyletic group: an ancestor and all its descendants.
Homologous vs analogous traits: homologous = due to common ancestry; analogous = similar due to convergent evolution.
Allopatric vs sympatric speciation: geographic isolation vs reproductive isolation without geographic barriers.
Polyploidy: multiple sets of chromosomes; autopolyploidy vs allopolyploidy.
Synonymous vs nonsynonymous substitutions: silent vs amino acid-changing mutations; used to infer selection.
Molecular clock: constant rate of genetic change used to estimate divergence times.
Gene duplication, neofunctionalization, subfunctionalization, pseudogenes, de novo genes.
Horizontal gene transfer: movement of genes between non-related organisms (transformation, conjugation, transduction, endosymbiosis).
SA/V ratio: surface area to volume ratio; affects diffusion and exchange.
Countercurrent exchange: maintains a gradient for efficient gas exchange (e.g., fish gills).
Hemoglobin and O2 dissociation curve: describes how Hb picks up/releases O2; Bohr effect modulates this with pH/CO2.
Notothenioids icefish: case study of extreme adaptation with antifreeze proteins and variable reliance on hemoglobin.
ventilation
negative or purifying is less than 1
third letter codon does not change anything. but changing other amino acids will